pkgsrc-WIP-changes archive
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index][Old Index]
Finish removing obsolete packages
Module Name: pkgsrc-wip
Committed By: Jason W. Bacon <bacon4000%gmail.com@localhost>
Pushed By: outpaddling
Date: Fri Dec 30 17:38:44 2022 -0600
Changeset: 9ba2eb9a080f0e8749ba286072f2f7da2a9a4e9d
Removed Files:
antlr/DESCR
antlr/PLIST
antlr/TODO
antlr/buildlink3.mk
antlr/distinfo
antlr/files/antlr.sh.in
antlr/patches/patch-configure
antlr/patches/patch-lib__cpp__antlr__ANTLRException.hpp
antlr/patches/patch-lib_cpp_antlr_CharScanner.hpp
armadillo/DESCR
armadillo/PLIST
armadillo/buildlink3.mk
armadillo/distinfo
armadillo/patches/patch-CMakeLists.txt
blasr/DESCR
blasr/PLIST
blasr/TODO
blasr/buildlink3.mk
blasr/distinfo
blasr/patches/patch-Blasr.cpp
blasr_libcpp/DESCR
blasr_libcpp/PLIST
blasr_libcpp/TODO
blasr_libcpp/buildlink3.mk
blasr_libcpp/distinfo
blasr_libcpp/patches/patch-alignment_MappingMetrics.cpp
blasr_libcpp/patches/patch-alignment_datastructures_alignment_FilterCriteria.cpp
blasr_libcpp/patches/patch-alignment_datastructures_alignment_FilterCriteria.hpp
blasr_libcpp/patches/patch-alignment_format_SAMHeaderPrinter.cpp
blasr_libcpp/patches/patch-alignment_ipc_SharedMemoryAllocator.hpp
blasr_libcpp/patches/patch-configure.py
blasr_libcpp/patches/patch-pbdata_reads_HoleXY.hpp
blasr_libcpp/patches/patch-pbdata_utils_SMRTTitle.cpp
bowtie/DESCR
bowtie/PLIST
bowtie/buildlink3.mk
bowtie/distinfo
bowtie/patches/patch-Makefile
bowtie/patches/patch-scripts_test_random__bowtie__tests.sh
cdbfasta/DESCR
cdbfasta/PLIST
cdbfasta/TODO
cdbfasta/buildlink3.mk
cdbfasta/distinfo
cdbfasta/patches/patch-Makefile
cluster-admin/DESCR
cluster-admin/PLIST
cluster-admin/distinfo
daligner/DESCR
daligner/PLIST
daligner/TODO
daligner/buildlink3.mk
daligner/distinfo
dazz_db/DESCR
dazz_db/PLIST
dazz_db/TODO
dazz_db/buildlink3.mk
dazz_db/distinfo
denyhosts/DESCR
denyhosts/PLIST
denyhosts/TODO
denyhosts/distinfo
diffanal/DESCR
diffanal/PLIST
diffanal/distinfo
dlpoly-classic/DESCR
dlpoly-classic/PLIST
dlpoly-classic/distinfo
dlpoly-classic/patches/patch-build_MakePAR
dlpoly-classic/patches/patch-build_MakeSEQ
gromacs/DESCR
gromacs/PLIST
gromacs/distinfo
gromacs/options.mk
gromacs2018/DESCR
gromacs2018/PLIST
gromacs2018/distinfo
gromacs2018/options.mk
hmmer/DESCR
hmmer/PLIST
hmmer/distinfo
lmod/DESCR
lmod/PLIST
lmod/distinfo
man2html/DESCR
man2html/PLIST
man2html/distinfo
meep-mpi/DESCR
meep-mpi/PLIST
meep-mpi/distinfo
meep-mpi/patches/patch-configure
meep-openmpi/DESCR
meep-openmpi/MESSAGE
meep-openmpi/PLIST
meep-openmpi/distinfo
meep-openmpi/patches/patch-configure
meep-openmpi/patches/patch-configure.ac
meep/DESCR
meep/MESSAGE
meep/PLIST
meep/buildlink3.mk
meep/distinfo
meep/patches/patch-configure
meep/patches/patch-configure.ac
mpb-openmpi/DESCR
mpb-openmpi/PLIST
mpb-openmpi/buildlink3.mk
mpb-openmpi/distinfo
mpb-openmpi/patches/patch-mpb-ctl_Makefile.in
mpb-openmpi/patches/patch-src_util_Makefile.in
mpb-openmpi/patches/patch-src_util_check.c
mpb-openmpi/patches/patch-src_util_check.h
mpb-openmpi/patches/patch-utils_Makefile.in
mpb/DESCR
mpb/PLIST
mpb/buildlink3.mk
mpb/distinfo
mpb/patches/patch-mpb-ctl_Makefile.in
mpb/patches/patch-src_util_Makefile.in
mpb/patches/patch-src_util_check.c
mpb/patches/patch-src_util_check.h
mpb/patches/patch-utils_Makefile.in
multichoose/DESCR
multichoose/PLIST
multichoose/TODO
multichoose/buildlink3.mk
multichoose/distinfo
multichoose/files/Makefile
numactl/DESCR
numactl/PLIST
numactl/TODO
numactl/buildlink3.mk
numactl/distinfo
openmx-openmpi/DESCR
openmx-openmpi/PLIST
openmx-openmpi/distinfo
py-ffc/DESCR
py-ffc/PLIST
py-ffc/buildlink3.mk
py-ffc/distinfo
py-fiat/DESCR
py-fiat/PLIST
py-fiat/buildlink3.mk
py-fiat/distinfo
py-pbfalcon/DESCR
py-pbfalcon/PLIST
py-pbfalcon/TODO
py-pbfalcon/distinfo
py-pbfalcon/patches/patch-src_py_run__support.py
py-pypeflow/DESCR
py-pypeflow/PLIST
py-pypeflow/TODO
py-pypeflow/distinfo
py-snakemake/DESCR
py-snakemake/PLIST
py-snakemake/distinfo
py-ufl/DESCR
py-ufl/PLIST
py-ufl/buildlink3.mk
py-ufl/distinfo
py-viper/DESCR
py-viper/PLIST
py-viper/buildlink3.mk
py-viper/distinfo
python3/DESCR
python3/PLIST
singularity/DESCR
singularity/PLIST
singularity/TODO
singularity/distinfo
singularity/patches/patch-configure.ac
tophat/DESCR
tophat/PLIST
tophat/TODO
tophat/distinfo
tophat/patches/patch-src-bam_merge.cpp
tophat/patches/patch-src-samtools-0.1.18-Makefile
tophat/patches/patch-src_Makefile.in
Log Message:
Finish removing obsolete packages
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=9ba2eb9a080f0e8749ba286072f2f7da2a9a4e9d
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
antlr/DESCR | 4 -
antlr/PLIST | 81 ---
antlr/TODO | 1 -
antlr/buildlink3.mk | 12 -
antlr/distinfo | 8 -
antlr/files/antlr.sh.in | 5 -
antlr/patches/patch-configure | 166 -----
.../patch-lib__cpp__antlr__ANTLRException.hpp | 14 -
antlr/patches/patch-lib_cpp_antlr_CharScanner.hpp | 16 -
armadillo/DESCR | 4 -
armadillo/PLIST | 575 -----------------
armadillo/buildlink3.mk | 17 -
armadillo/distinfo | 6 -
armadillo/patches/patch-CMakeLists.txt | 72 ---
blasr/DESCR | 3 -
blasr/PLIST | 10 -
blasr/TODO | 1 -
blasr/buildlink3.mk | 12 -
blasr/distinfo | 6 -
blasr/patches/patch-Blasr.cpp | 21 -
blasr_libcpp/DESCR | 4 -
blasr_libcpp/PLIST | 290 ---------
blasr_libcpp/TODO | 3 -
blasr_libcpp/buildlink3.mk | 23 -
blasr_libcpp/distinfo | 12 -
.../patches/patch-alignment_MappingMetrics.cpp | 20 -
...ent_datastructures_alignment_FilterCriteria.cpp | 65 --
...ent_datastructures_alignment_FilterCriteria.hpp | 14 -
.../patch-alignment_format_SAMHeaderPrinter.cpp | 26 -
.../patch-alignment_ipc_SharedMemoryAllocator.hpp | 12 -
blasr_libcpp/patches/patch-configure.py | 19 -
blasr_libcpp/patches/patch-pbdata_reads_HoleXY.hpp | 12 -
.../patches/patch-pbdata_utils_SMRTTitle.cpp | 9 -
bowtie/DESCR | 5 -
bowtie/PLIST | 91 ---
bowtie/buildlink3.mk | 12 -
bowtie/distinfo | 7 -
bowtie/patches/patch-Makefile | 18 -
.../patch-scripts_test_random__bowtie__tests.sh | 20 -
cdbfasta/DESCR | 3 -
cdbfasta/PLIST | 3 -
cdbfasta/TODO | 1 -
cdbfasta/buildlink3.mk | 12 -
cdbfasta/distinfo | 6 -
cdbfasta/patches/patch-Makefile | 61 --
cluster-admin/DESCR | 3 -
cluster-admin/PLIST | 119 ----
cluster-admin/distinfo | 5 -
daligner/DESCR | 3 -
daligner/PLIST | 21 -
daligner/TODO | 1 -
daligner/buildlink3.mk | 12 -
daligner/distinfo | 5 -
dazz_db/DESCR | 3 -
dazz_db/PLIST | 17 -
dazz_db/TODO | 1 -
dazz_db/buildlink3.mk | 12 -
dazz_db/distinfo | 5 -
denyhosts/DESCR | 3 -
denyhosts/PLIST | 78 ---
denyhosts/TODO | 1 -
denyhosts/distinfo | 5 -
diffanal/DESCR | 5 -
diffanal/PLIST | 9 -
diffanal/distinfo | 5 -
dlpoly-classic/DESCR | 2 -
dlpoly-classic/PLIST | 3 -
dlpoly-classic/distinfo | 6 -
dlpoly-classic/patches/patch-build_MakePAR | 32 -
dlpoly-classic/patches/patch-build_MakeSEQ | 13 -
gromacs/DESCR | 10 -
gromacs/PLIST | 699 ---------------------
gromacs/distinfo | 5 -
gromacs/options.mk | 28 -
gromacs2018/DESCR | 10 -
gromacs2018/PLIST | 699 ---------------------
gromacs2018/distinfo | 5 -
gromacs2018/options.mk | 28 -
hmmer/DESCR | 7 -
hmmer/PLIST | 38 --
hmmer/distinfo | 5 -
lmod/DESCR | 8 -
lmod/PLIST | 120 ----
lmod/distinfo | 4 -
man2html/DESCR | 1 -
man2html/PLIST | 3 -
man2html/distinfo | 5 -
meep-mpi/DESCR | 0
meep-mpi/PLIST | 10 -
meep-mpi/distinfo | 5 -
meep-mpi/patches/patch-configure | 19 -
meep-openmpi/DESCR | 0
meep-openmpi/MESSAGE | 6 -
meep-openmpi/PLIST | 10 -
meep-openmpi/distinfo | 7 -
meep-openmpi/patches/patch-configure | 13 -
meep-openmpi/patches/patch-configure.ac | 13 -
meep/DESCR | 3 -
meep/MESSAGE | 6 -
meep/PLIST | 10 -
meep/buildlink3.mk | 18 -
meep/distinfo | 7 -
meep/patches/patch-configure | 13 -
meep/patches/patch-configure.ac | 13 -
mpb-openmpi/DESCR | 3 -
mpb-openmpi/PLIST | 5 -
mpb-openmpi/buildlink3.mk | 19 -
mpb-openmpi/distinfo | 10 -
mpb-openmpi/patches/patch-mpb-ctl_Makefile.in | 51 --
mpb-openmpi/patches/patch-src_util_Makefile.in | 13 -
mpb-openmpi/patches/patch-src_util_check.c | 20 -
mpb-openmpi/patches/patch-src_util_check.h | 27 -
mpb-openmpi/patches/patch-utils_Makefile.in | 32 -
mpb/DESCR | 3 -
mpb/PLIST | 8 -
mpb/buildlink3.mk | 19 -
mpb/distinfo | 10 -
mpb/patches/patch-mpb-ctl_Makefile.in | 51 --
mpb/patches/patch-src_util_Makefile.in | 13 -
mpb/patches/patch-src_util_check.c | 20 -
mpb/patches/patch-src_util_check.h | 27 -
mpb/patches/patch-utils_Makefile.in | 32 -
multichoose/DESCR | 4 -
multichoose/PLIST | 8 -
multichoose/TODO | 1 -
multichoose/buildlink3.mk | 13 -
multichoose/distinfo | 5 -
multichoose/files/Makefile | 46 --
numactl/DESCR | 4 -
numactl/PLIST | 17 -
numactl/TODO | 1 -
numactl/buildlink3.mk | 12 -
numactl/distinfo | 5 -
openmx-openmpi/DESCR | 1 -
openmx-openmpi/PLIST | 342 ----------
openmx-openmpi/distinfo | 4 -
py-ffc/DESCR | 2 -
py-ffc/PLIST | 195 ------
py-ffc/buildlink3.mk | 12 -
py-ffc/distinfo | 5 -
py-fiat/DESCR | 2 -
py-fiat/PLIST | 91 ---
py-fiat/buildlink3.mk | 12 -
py-fiat/distinfo | 5 -
py-pbfalcon/DESCR | 3 -
py-pbfalcon/PLIST | 98 ---
py-pbfalcon/TODO | 1 -
py-pbfalcon/distinfo | 6 -
py-pbfalcon/patches/patch-src_py_run__support.py | 14 -
py-pypeflow/DESCR | 3 -
py-pypeflow/PLIST | 22 -
py-pypeflow/TODO | 1 -
py-pypeflow/distinfo | 5 -
py-snakemake/DESCR | 5 -
py-snakemake/PLIST | 143 -----
py-snakemake/distinfo | 5 -
py-ufl/DESCR | 2 -
py-ufl/PLIST | 248 --------
py-ufl/buildlink3.mk | 12 -
py-ufl/distinfo | 5 -
py-viper/DESCR | 2 -
py-viper/PLIST | 43 --
py-viper/buildlink3.mk | 12 -
py-viper/distinfo | 5 -
python3/DESCR | 32 -
python3/PLIST | 3 -
singularity/DESCR | 9 -
singularity/PLIST | 142 -----
singularity/TODO | 4 -
singularity/distinfo | 6 -
singularity/patches/patch-configure.ac | 15 -
tophat/DESCR | 4 -
tophat/PLIST | 29 -
tophat/TODO | 1 -
tophat/distinfo | 8 -
tophat/patches/patch-src-bam_merge.cpp | 10 -
tophat/patches/patch-src-samtools-0.1.18-Makefile | 28 -
tophat/patches/patch-src_Makefile.in | 23 -
178 files changed, 6078 deletions(-)
diffs:
diff --git a/antlr/DESCR b/antlr/DESCR
deleted file mode 100644
index 08dc2a2842..0000000000
--- a/antlr/DESCR
+++ /dev/null
@@ -1,4 +0,0 @@
-ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a
-language tool that provides a framework for constructing recognizers,
-compilers, and translators from grammatical descriptions containing
-C++ or Java actions.
diff --git a/antlr/PLIST b/antlr/PLIST
deleted file mode 100644
index 195825e514..0000000000
--- a/antlr/PLIST
+++ /dev/null
@@ -1,81 +0,0 @@
-@comment $NetBSD$
-bin/antlr
-include/antlr/ANTLRException.hpp
-include/antlr/ANTLRUtil.hpp
-include/antlr/AST.hpp
-include/antlr/ASTArray.hpp
-include/antlr/ASTFactory.hpp
-include/antlr/ASTNULLType.hpp
-include/antlr/ASTPair.hpp
-include/antlr/ASTRefCount.hpp
-include/antlr/BaseAST.hpp
-include/antlr/BitSet.hpp
-include/antlr/CharBuffer.hpp
-include/antlr/CharInputBuffer.hpp
-include/antlr/CharScanner.hpp
-include/antlr/CharStreamException.hpp
-include/antlr/CharStreamIOException.hpp
-include/antlr/CircularQueue.hpp
-include/antlr/CommonAST.hpp
-include/antlr/CommonASTWithHiddenTokens.hpp
-include/antlr/CommonHiddenStreamToken.hpp
-include/antlr/CommonToken.hpp
-include/antlr/IOException.hpp
-include/antlr/InputBuffer.hpp
-include/antlr/LLkParser.hpp
-include/antlr/LexerSharedInputState.hpp
-include/antlr/MismatchedCharException.hpp
-include/antlr/MismatchedTokenException.hpp
-include/antlr/NoViableAltException.hpp
-include/antlr/NoViableAltForCharException.hpp
-include/antlr/Parser.hpp
-include/antlr/ParserSharedInputState.hpp
-include/antlr/RecognitionException.hpp
-include/antlr/RefCount.hpp
-include/antlr/SemanticException.hpp
-include/antlr/String.hpp
-include/antlr/Token.hpp
-include/antlr/TokenBuffer.hpp
-include/antlr/TokenRefCount.hpp
-include/antlr/TokenStream.hpp
-include/antlr/TokenStreamBasicFilter.hpp
-include/antlr/TokenStreamException.hpp
-include/antlr/TokenStreamHiddenTokenFilter.hpp
-include/antlr/TokenStreamIOException.hpp
-include/antlr/TokenStreamRecognitionException.hpp
-include/antlr/TokenStreamRetryException.hpp
-include/antlr/TokenStreamRewriteEngine.hpp
-include/antlr/TokenStreamSelector.hpp
-include/antlr/TokenWithIndex.hpp
-include/antlr/TreeParser.hpp
-include/antlr/TreeParserSharedInputState.hpp
-include/antlr/config.hpp
-lib/libantlr.a
-share/doc/antlr/ANTLRException.gif
-share/doc/antlr/closure.gif
-share/doc/antlr/cpp-runtime.html
-share/doc/antlr/csharp-runtime.html
-share/doc/antlr/err.html
-share/doc/antlr/glossary.html
-share/doc/antlr/hidden.stream.gif
-share/doc/antlr/index.html
-share/doc/antlr/inheritance.html
-share/doc/antlr/j-guru-blue.jpg
-share/doc/antlr/jguru-logo.gif
-share/doc/antlr/lexer.html
-share/doc/antlr/lexer.to.parser.tokens.gif
-share/doc/antlr/logo.gif
-share/doc/antlr/metalang.html
-share/doc/antlr/optional.gif
-share/doc/antlr/options.html
-share/doc/antlr/posclosure.gif
-share/doc/antlr/runtime.html
-share/doc/antlr/sor.html
-share/doc/antlr/stream.perspectives.gif
-share/doc/antlr/stream.selector.gif
-share/doc/antlr/stream.splitter.gif
-share/doc/antlr/streams.html
-share/doc/antlr/subrule.gif
-share/doc/antlr/trees.html
-share/doc/antlr/vocab.html
-share/java/classes/antlr.jar
diff --git a/antlr/TODO b/antlr/TODO
deleted file mode 100644
index b687356e6b..0000000000
--- a/antlr/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test
diff --git a/antlr/buildlink3.mk b/antlr/buildlink3.mk
deleted file mode 100644
index 6bd97c48fa..0000000000
--- a/antlr/buildlink3.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-# $NetBSD$
-
-BUILDLINK_TREE+= antlr
-
-.if !defined(ANTLR_BUILDLINK3_MK)
-ANTLR_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.antlr+= antlr>=2.7.7
-BUILDLINK_PKGSRCDIR.antlr?= ../../wip/antlr
-.endif # ANTLR_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -antlr
diff --git a/antlr/distinfo b/antlr/distinfo
deleted file mode 100644
index 3e5cb49352..0000000000
--- a/antlr/distinfo
+++ /dev/null
@@ -1,8 +0,0 @@
-$NetBSD$
-
-RMD160 (antlr-2.7.7.tar.gz) = 0b7951a28b748e912721fe0f6de4095d9f8da57d
-SHA512 (antlr-2.7.7.tar.gz) = faa72d2ddcba434ef1233e70c1549e63eba67c00793966322e821cf7f015cccb804448cb92d8fbef0429f59928fad65ec954f8ffbda0acbb8e983de0806d349d
-Size (antlr-2.7.7.tar.gz) = 1816180 bytes
-SHA1 (patch-configure) = 41a7e86c32560eef26d0ba54357c5d58d50be63d
-SHA1 (patch-lib__cpp__antlr__ANTLRException.hpp) = 81761161d3cbff6c30675c8eb75daaef26b9751b
-SHA1 (patch-lib_cpp_antlr_CharScanner.hpp) = 845bacc8698fca5252069471f8bf2c1a6384730a
diff --git a/antlr/files/antlr.sh.in b/antlr/files/antlr.sh.in
deleted file mode 100644
index 4dd3b9445d..0000000000
--- a/antlr/files/antlr.sh.in
+++ /dev/null
@@ -1,5 +0,0 @@
-#! /bin/sh
-#
-# $FreeBSD: head/devel/antlr/files/antlr.sh.in 350206 2014-04-05 08:01:26Z pawel $
-
-JAVA_VERSION="%%JAVA_VERSION%%" "%%LOCALBASE%%/bin/java" -classpath "%%JAVAJARDIR%%/antlr.jar" antlr.Tool "$@"
diff --git a/antlr/patches/patch-configure b/antlr/patches/patch-configure
deleted file mode 100644
index 7c79106a8d..0000000000
--- a/antlr/patches/patch-configure
+++ /dev/null
@@ -1,166 +0,0 @@
-$NetBSD$
-
-# Non-portable == in shell script
-
---- configure.orig 2006-11-01 21:37:18.000000000 +0000
-+++ configure
-@@ -2234,7 +2234,7 @@ echo "${ECHO_T}$as_dir/$ac_word$ac_exec_
- fi
- done
- done
-- test "x$as_found" == "x" && {
-+ test "x$as_found" = "x" && {
- echo "$as_me:$LINENO: checking for $ac_word" >&5
- echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
- echo "$as_me:$LINENO: result: no" >&5
-@@ -2299,7 +2299,7 @@ echo "${ECHO_T}$as_dir/$ac_word$ac_exec_
- fi
- done
- done
-- test "x$as_found" == "x" && {
-+ test "x$as_found" = "x" && {
- echo "$as_me:$LINENO: checking for $ac_word" >&5
- echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
- echo "$as_me:$LINENO: result: no" >&5
-@@ -2364,7 +2364,7 @@ echo "${ECHO_T}$as_dir/$ac_word$ac_exec_
- fi
- done
- done
-- test "x$as_found" == "x" && {
-+ test "x$as_found" = "x" && {
- echo "$as_me:$LINENO: checking for $ac_word" >&5
- echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
- echo "$as_me:$LINENO: result: no" >&5
-@@ -2461,7 +2461,7 @@ echo "${ECHO_T}$as_dir/$ac_word$ac_exec_
- fi
- done
- done
-- test "x$as_found" == "x" && {
-+ test "x$as_found" = "x" && {
- echo "$as_me:$LINENO: checking for $ac_word" >&5
- echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
- echo "$as_me:$LINENO: result: no" >&5
-@@ -2486,13 +2486,13 @@ echo "$as_me: error: no suitable value h
-
- ## right now we need to have a GNU make around, other makes are
- ## not supported and likely to fail.
--if test "x${user_make}" == "x" ; then
-+if test "x${user_make}" = "x" ; then
-
- #Search all the common names for GNU make
- ax_gnu_make_list="${MAKE}"
- MAKE=
- for a in . ${ax_gnu_make_list} ; do
-- if test "$a" == "." ; then
-+ if test "$a" = "." ; then
- continue
- fi
- echo "$as_me:$LINENO: checking whether ${a} is GNU make" >&5
-@@ -2508,7 +2508,7 @@ echo "${ECHO_T}no" >&6
- fi
- done
- ## handle search result
-- if test "x${MAKE}" == "x" ; then
-+ if test "x${MAKE}" = "x" ; then
- :
- { { echo "$as_me:$LINENO: error: package requires GNU make" >&5
- echo "$as_me: error: package requires GNU make" >&2;}
-@@ -2641,7 +2641,7 @@ echo "${ECHO_T}$as_dir/$ac_word$ac_exec_
- fi
- done
- done
-- test "x$as_found" == "x" && {
-+ test "x$as_found" = "x" && {
- echo "$as_me:$LINENO: checking for $ac_word" >&5
- echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
- echo "$as_me:$LINENO: result: no" >&5
-@@ -2726,7 +2726,7 @@ echo "${ECHO_T}$as_dir/$ac_word$ac_exec_
- fi
- done
- done
-- test "x$as_found" == "x" && {
-+ test "x$as_found" = "x" && {
- echo "$as_me:$LINENO: checking for $ac_word" >&5
- echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
- echo "$as_me:$LINENO: result: no" >&5
-@@ -2811,7 +2811,7 @@ echo "${ECHO_T}$as_dir/$ac_word$ac_exec_
- fi
- done
- done
-- test "x$as_found" == "x" && {
-+ test "x$as_found" = "x" && {
- echo "$as_me:$LINENO: checking for $ac_word" >&5
- echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
- echo "$as_me:$LINENO: result: no" >&5
-@@ -3036,7 +3036,7 @@ echo "${ECHO_T}$as_dir/$ac_word$ac_exec_
- fi
- done
- done
-- test "x$as_found" == "x" && {
-+ test "x$as_found" = "x" && {
- echo "$as_me:$LINENO: checking for $ac_word" >&5
- echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
- echo "$as_me:$LINENO: result: no" >&5
-@@ -5808,7 +5808,7 @@ echo "${ECHO_T}$as_dir/$ac_word$ac_exec_
- fi
- done
- done
-- test "x$as_found" == "x" && {
-+ test "x$as_found" = "x" && {
- echo "$as_me:$LINENO: checking for $ac_word" >&5
- echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
- echo "$as_me:$LINENO: result: no" >&5
-@@ -5879,7 +5879,7 @@ echo "${ECHO_T}$as_dir/$ac_word$ac_exec_
- fi
- done
- done
-- test "x$as_found" == "x" && {
-+ test "x$as_found" = "x" && {
- echo "$as_me:$LINENO: checking for $ac_word" >&5
- echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
- echo "$as_me:$LINENO: result: no" >&5
-@@ -6122,7 +6122,7 @@ echo "${ECHO_T}$as_dir/$ac_word$ac_exec_
- fi
- done
- done
-- test "x$as_found" == "x" && {
-+ test "x$as_found" = "x" && {
- echo "$as_me:$LINENO: checking for $ac_word" >&5
- echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
- echo "$as_me:$LINENO: result: no" >&5
-@@ -6241,7 +6241,7 @@ echo "${ECHO_T}$as_dir/$ac_word$ac_exec_
- fi
- done
- done
-- test "x$as_found" == "x" && {
-+ test "x$as_found" = "x" && {
- echo "$as_me:$LINENO: checking for $ac_word" >&5
- echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
- echo "$as_me:$LINENO: result: no" >&5
-@@ -6336,7 +6336,7 @@ echo "${ECHO_T}$as_dir/$ac_word$ac_exec_
- fi
- done
- done
-- test "x$as_found" == "x" && {
-+ test "x$as_found" = "x" && {
- echo "$as_me:$LINENO: checking for $ac_word" >&5
- echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
- echo "$as_me:$LINENO: result: no" >&5
-@@ -6423,7 +6423,7 @@ echo "${ECHO_T}$as_dir/$ac_word$ac_exec_
- fi
- done
- done
-- test "x$as_found" == "x" && {
-+ test "x$as_found" = "x" && {
- echo "$as_me:$LINENO: checking for $ac_word" >&5
- echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
- echo "$as_me:$LINENO: result: no" >&5
-@@ -6733,7 +6733,7 @@ case $LANG_JAVA in
- ## This variables can be used in antlr/Makefile
-
- file_list="${ANTLR_ACTION_FILES} ${ANTLR_ANTLR_FILES} ${ANTLR_TOKDEF_FILES}"
-- if test "x${file_list}" == "x" ; then
-+ if test "x${file_list}" = "x" ; then
- :
- else
- ANTLR_CONFIG_FILES=""
diff --git a/antlr/patches/patch-lib__cpp__antlr__ANTLRException.hpp b/antlr/patches/patch-lib__cpp__antlr__ANTLRException.hpp
deleted file mode 100644
index 18581d8079..0000000000
--- a/antlr/patches/patch-lib__cpp__antlr__ANTLRException.hpp
+++ /dev/null
@@ -1,14 +0,0 @@
-$NetBSD$
-
-# Missing header
-
---- lib/cpp/antlr/ANTLRException.hpp.orig 2006-11-01 21:37:17.000000000 +0000
-+++ lib/cpp/antlr/ANTLRException.hpp
-@@ -9,6 +9,7 @@
- */
-
- #include <antlr/config.hpp>
-+#include <exception>
- #include <string>
-
- #ifdef ANTLR_CXX_SUPPORTS_NAMESPACE
diff --git a/antlr/patches/patch-lib_cpp_antlr_CharScanner.hpp b/antlr/patches/patch-lib_cpp_antlr_CharScanner.hpp
deleted file mode 100644
index ffd966cbc9..0000000000
--- a/antlr/patches/patch-lib_cpp_antlr_CharScanner.hpp
+++ /dev/null
@@ -1,16 +0,0 @@
-$NetBSD$
-
-# Missing headers
-
---- lib/cpp/antlr/CharScanner.hpp.orig 2006-11-01 21:37:17.000000000 +0000
-+++ lib/cpp/antlr/CharScanner.hpp
-@@ -24,6 +24,9 @@
- # include <stdio.h>
- #endif
-
-+#include <cstdio>
-+#include <cstring>
-+
- #include <antlr/TokenStream.hpp>
- #include <antlr/RecognitionException.hpp>
- #include <antlr/SemanticException.hpp>
diff --git a/armadillo/DESCR b/armadillo/DESCR
deleted file mode 100644
index 1fe431a8c2..0000000000
--- a/armadillo/DESCR
+++ /dev/null
@@ -1,4 +0,0 @@
-Armadillo is an open-source C++ linear algebra library (matrix maths) aiming
-towards a good balance between speed and ease of use. Integer, floating point
-and complex numbers are supported, as well as a subset of trigonometric and
-statistics functions.
diff --git a/armadillo/PLIST b/armadillo/PLIST
deleted file mode 100644
index f69a9d0789..0000000000
--- a/armadillo/PLIST
+++ /dev/null
@@ -1,575 +0,0 @@
-@comment $NetBSD$
-include/armadillo
-include/armadillo_bits/BaseCube_bones.hpp
-include/armadillo_bits/BaseCube_meat.hpp
-include/armadillo_bits/Base_bones.hpp
-include/armadillo_bits/Base_meat.hpp
-include/armadillo_bits/Col_bones.hpp
-include/armadillo_bits/Col_meat.hpp
-include/armadillo_bits/Cube_bones.hpp
-include/armadillo_bits/Cube_meat.hpp
-include/armadillo_bits/GenCube_bones.hpp
-include/armadillo_bits/GenCube_meat.hpp
-include/armadillo_bits/GenSpecialiser.hpp
-include/armadillo_bits/Gen_bones.hpp
-include/armadillo_bits/Gen_meat.hpp
-include/armadillo_bits/GlueCube_bones.hpp
-include/armadillo_bits/GlueCube_meat.hpp
-include/armadillo_bits/Glue_bones.hpp
-include/armadillo_bits/Glue_meat.hpp
-include/armadillo_bits/MapMat_bones.hpp
-include/armadillo_bits/MapMat_meat.hpp
-include/armadillo_bits/Mat_bones.hpp
-include/armadillo_bits/Mat_meat.hpp
-include/armadillo_bits/OpCube_bones.hpp
-include/armadillo_bits/OpCube_meat.hpp
-include/armadillo_bits/Op_bones.hpp
-include/armadillo_bits/Op_meat.hpp
-include/armadillo_bits/Proxy.hpp
-include/armadillo_bits/ProxyCube.hpp
-include/armadillo_bits/Row_bones.hpp
-include/armadillo_bits/Row_meat.hpp
-include/armadillo_bits/SizeCube_bones.hpp
-include/armadillo_bits/SizeCube_meat.hpp
-include/armadillo_bits/SizeMat_bones.hpp
-include/armadillo_bits/SizeMat_meat.hpp
-include/armadillo_bits/SpBase_bones.hpp
-include/armadillo_bits/SpBase_meat.hpp
-include/armadillo_bits/SpCol_bones.hpp
-include/armadillo_bits/SpCol_meat.hpp
-include/armadillo_bits/SpGlue_bones.hpp
-include/armadillo_bits/SpGlue_meat.hpp
-include/armadillo_bits/SpMat_bones.hpp
-include/armadillo_bits/SpMat_iterators_meat.hpp
-include/armadillo_bits/SpMat_meat.hpp
-include/armadillo_bits/SpOp_bones.hpp
-include/armadillo_bits/SpOp_meat.hpp
-include/armadillo_bits/SpProxy.hpp
-include/armadillo_bits/SpRow_bones.hpp
-include/armadillo_bits/SpRow_meat.hpp
-include/armadillo_bits/SpSubview_bones.hpp
-include/armadillo_bits/SpSubview_iterators_meat.hpp
-include/armadillo_bits/SpSubview_meat.hpp
-include/armadillo_bits/SpToDOp_bones.hpp
-include/armadillo_bits/SpToDOp_meat.hpp
-include/armadillo_bits/SpValProxy_bones.hpp
-include/armadillo_bits/SpValProxy_meat.hpp
-include/armadillo_bits/access.hpp
-include/armadillo_bits/arma_cmath.hpp
-include/armadillo_bits/arma_config.hpp
-include/armadillo_bits/arma_forward.hpp
-include/armadillo_bits/arma_ostream_bones.hpp
-include/armadillo_bits/arma_ostream_meat.hpp
-include/armadillo_bits/arma_rel_comparators.hpp
-include/armadillo_bits/arma_rng.hpp
-include/armadillo_bits/arma_rng_cxx11.hpp
-include/armadillo_bits/arma_rng_cxx98.hpp
-include/armadillo_bits/arma_static_check.hpp
-include/armadillo_bits/arma_str.hpp
-include/armadillo_bits/arma_version.hpp
-include/armadillo_bits/arrayops_bones.hpp
-include/armadillo_bits/arrayops_meat.hpp
-include/armadillo_bits/auxlib_bones.hpp
-include/armadillo_bits/auxlib_meat.hpp
-include/armadillo_bits/band_helper.hpp
-include/armadillo_bits/compiler_extra.hpp
-include/armadillo_bits/compiler_setup.hpp
-include/armadillo_bits/compiler_setup_post.hpp
-include/armadillo_bits/cond_rel_bones.hpp
-include/armadillo_bits/cond_rel_meat.hpp
-include/armadillo_bits/config.hpp
-include/armadillo_bits/constants.hpp
-include/armadillo_bits/constants_old.hpp
-include/armadillo_bits/debug.hpp
-include/armadillo_bits/def_arpack.hpp
-include/armadillo_bits/def_atlas.hpp
-include/armadillo_bits/def_blas.hpp
-include/armadillo_bits/def_hdf5.hpp
-include/armadillo_bits/def_lapack.hpp
-include/armadillo_bits/def_superlu.hpp
-include/armadillo_bits/diagmat_proxy.hpp
-include/armadillo_bits/diagview_bones.hpp
-include/armadillo_bits/diagview_meat.hpp
-include/armadillo_bits/diskio_bones.hpp
-include/armadillo_bits/diskio_meat.hpp
-include/armadillo_bits/distr_param.hpp
-include/armadillo_bits/eGlueCube_bones.hpp
-include/armadillo_bits/eGlueCube_meat.hpp
-include/armadillo_bits/eGlue_bones.hpp
-include/armadillo_bits/eGlue_meat.hpp
-include/armadillo_bits/eOpCube_bones.hpp
-include/armadillo_bits/eOpCube_meat.hpp
-include/armadillo_bits/eOp_bones.hpp
-include/armadillo_bits/eOp_meat.hpp
-include/armadillo_bits/eglue_core_bones.hpp
-include/armadillo_bits/eglue_core_meat.hpp
-include/armadillo_bits/eop_aux.hpp
-include/armadillo_bits/eop_core_bones.hpp
-include/armadillo_bits/eop_core_meat.hpp
-include/armadillo_bits/fft_engine.hpp
-include/armadillo_bits/field_bones.hpp
-include/armadillo_bits/field_meat.hpp
-include/armadillo_bits/fn_accu.hpp
-include/armadillo_bits/fn_all.hpp
-include/armadillo_bits/fn_any.hpp
-include/armadillo_bits/fn_approx_equal.hpp
-include/armadillo_bits/fn_as_scalar.hpp
-include/armadillo_bits/fn_chi2rnd.hpp
-include/armadillo_bits/fn_chol.hpp
-include/armadillo_bits/fn_clamp.hpp
-include/armadillo_bits/fn_cond.hpp
-include/armadillo_bits/fn_conv.hpp
-include/armadillo_bits/fn_conv_to.hpp
-include/armadillo_bits/fn_cor.hpp
-include/armadillo_bits/fn_cov.hpp
-include/armadillo_bits/fn_cross.hpp
-include/armadillo_bits/fn_cumprod.hpp
-include/armadillo_bits/fn_cumsum.hpp
-include/armadillo_bits/fn_det.hpp
-include/armadillo_bits/fn_diagmat.hpp
-include/armadillo_bits/fn_diagvec.hpp
-include/armadillo_bits/fn_diff.hpp
-include/armadillo_bits/fn_dot.hpp
-include/armadillo_bits/fn_eig_gen.hpp
-include/armadillo_bits/fn_eig_pair.hpp
-include/armadillo_bits/fn_eig_sym.hpp
-include/armadillo_bits/fn_eigs_gen.hpp
-include/armadillo_bits/fn_eigs_sym.hpp
-include/armadillo_bits/fn_elem.hpp
-include/armadillo_bits/fn_eps.hpp
-include/armadillo_bits/fn_expmat.hpp
-include/armadillo_bits/fn_eye.hpp
-include/armadillo_bits/fn_fft.hpp
-include/armadillo_bits/fn_fft2.hpp
-include/armadillo_bits/fn_find.hpp
-include/armadillo_bits/fn_find_unique.hpp
-include/armadillo_bits/fn_flip.hpp
-include/armadillo_bits/fn_hess.hpp
-include/armadillo_bits/fn_hist.hpp
-include/armadillo_bits/fn_histc.hpp
-include/armadillo_bits/fn_index_max.hpp
-include/armadillo_bits/fn_index_min.hpp
-include/armadillo_bits/fn_inplace_strans.hpp
-include/armadillo_bits/fn_inplace_trans.hpp
-include/armadillo_bits/fn_interp1.hpp
-include/armadillo_bits/fn_interp2.hpp
-include/armadillo_bits/fn_intersect.hpp
-include/armadillo_bits/fn_inv.hpp
-include/armadillo_bits/fn_join.hpp
-include/armadillo_bits/fn_kmeans.hpp
-include/armadillo_bits/fn_kron.hpp
-include/armadillo_bits/fn_log_det.hpp
-include/armadillo_bits/fn_logmat.hpp
-include/armadillo_bits/fn_lu.hpp
-include/armadillo_bits/fn_max.hpp
-include/armadillo_bits/fn_mean.hpp
-include/armadillo_bits/fn_median.hpp
-include/armadillo_bits/fn_min.hpp
-include/armadillo_bits/fn_misc.hpp
-include/armadillo_bits/fn_mvnrnd.hpp
-include/armadillo_bits/fn_n_unique.hpp
-include/armadillo_bits/fn_nonzeros.hpp
-include/armadillo_bits/fn_norm.hpp
-include/armadillo_bits/fn_normalise.hpp
-include/armadillo_bits/fn_normcdf.hpp
-include/armadillo_bits/fn_normpdf.hpp
-include/armadillo_bits/fn_numel.hpp
-include/armadillo_bits/fn_ones.hpp
-include/armadillo_bits/fn_orth_null.hpp
-include/armadillo_bits/fn_pinv.hpp
-include/armadillo_bits/fn_polyfit.hpp
-include/armadillo_bits/fn_polyval.hpp
-include/armadillo_bits/fn_princomp.hpp
-include/armadillo_bits/fn_prod.hpp
-include/armadillo_bits/fn_qr.hpp
-include/armadillo_bits/fn_qz.hpp
-include/armadillo_bits/fn_randg.hpp
-include/armadillo_bits/fn_randi.hpp
-include/armadillo_bits/fn_randn.hpp
-include/armadillo_bits/fn_randu.hpp
-include/armadillo_bits/fn_range.hpp
-include/armadillo_bits/fn_rank.hpp
-include/armadillo_bits/fn_regspace.hpp
-include/armadillo_bits/fn_repelem.hpp
-include/armadillo_bits/fn_repmat.hpp
-include/armadillo_bits/fn_reshape.hpp
-include/armadillo_bits/fn_resize.hpp
-include/armadillo_bits/fn_reverse.hpp
-include/armadillo_bits/fn_roots.hpp
-include/armadillo_bits/fn_schur.hpp
-include/armadillo_bits/fn_shift.hpp
-include/armadillo_bits/fn_shuffle.hpp
-include/armadillo_bits/fn_size.hpp
-include/armadillo_bits/fn_solve.hpp
-include/armadillo_bits/fn_sort.hpp
-include/armadillo_bits/fn_sort_index.hpp
-include/armadillo_bits/fn_speye.hpp
-include/armadillo_bits/fn_spones.hpp
-include/armadillo_bits/fn_sprandn.hpp
-include/armadillo_bits/fn_sprandu.hpp
-include/armadillo_bits/fn_spsolve.hpp
-include/armadillo_bits/fn_sqrtmat.hpp
-include/armadillo_bits/fn_stddev.hpp
-include/armadillo_bits/fn_strans.hpp
-include/armadillo_bits/fn_sum.hpp
-include/armadillo_bits/fn_svd.hpp
-include/armadillo_bits/fn_svds.hpp
-include/armadillo_bits/fn_syl_lyap.hpp
-include/armadillo_bits/fn_symmat.hpp
-include/armadillo_bits/fn_toeplitz.hpp
-include/armadillo_bits/fn_trace.hpp
-include/armadillo_bits/fn_trans.hpp
-include/armadillo_bits/fn_trapz.hpp
-include/armadillo_bits/fn_trig.hpp
-include/armadillo_bits/fn_trimat.hpp
-include/armadillo_bits/fn_trunc_exp.hpp
-include/armadillo_bits/fn_trunc_log.hpp
-include/armadillo_bits/fn_unique.hpp
-include/armadillo_bits/fn_var.hpp
-include/armadillo_bits/fn_vectorise.hpp
-include/armadillo_bits/fn_wishrnd.hpp
-include/armadillo_bits/fn_zeros.hpp
-include/armadillo_bits/glue_affmul_bones.hpp
-include/armadillo_bits/glue_affmul_meat.hpp
-include/armadillo_bits/glue_atan2_bones.hpp
-include/armadillo_bits/glue_atan2_meat.hpp
-include/armadillo_bits/glue_conv_bones.hpp
-include/armadillo_bits/glue_conv_meat.hpp
-include/armadillo_bits/glue_cor_bones.hpp
-include/armadillo_bits/glue_cor_meat.hpp
-include/armadillo_bits/glue_cov_bones.hpp
-include/armadillo_bits/glue_cov_meat.hpp
-include/armadillo_bits/glue_cross_bones.hpp
-include/armadillo_bits/glue_cross_meat.hpp
-include/armadillo_bits/glue_hist_bones.hpp
-include/armadillo_bits/glue_hist_meat.hpp
-include/armadillo_bits/glue_histc_bones.hpp
-include/armadillo_bits/glue_histc_meat.hpp
-include/armadillo_bits/glue_hypot_bones.hpp
-include/armadillo_bits/glue_hypot_meat.hpp
-include/armadillo_bits/glue_intersect_bones.hpp
-include/armadillo_bits/glue_intersect_meat.hpp
-include/armadillo_bits/glue_join_bones.hpp
-include/armadillo_bits/glue_join_meat.hpp
-include/armadillo_bits/glue_kron_bones.hpp
-include/armadillo_bits/glue_kron_meat.hpp
-include/armadillo_bits/glue_max_bones.hpp
-include/armadillo_bits/glue_max_meat.hpp
-include/armadillo_bits/glue_min_bones.hpp
-include/armadillo_bits/glue_min_meat.hpp
-include/armadillo_bits/glue_mixed_bones.hpp
-include/armadillo_bits/glue_mixed_meat.hpp
-include/armadillo_bits/glue_mvnrnd_bones.hpp
-include/armadillo_bits/glue_mvnrnd_meat.hpp
-include/armadillo_bits/glue_polyfit_bones.hpp
-include/armadillo_bits/glue_polyfit_meat.hpp
-include/armadillo_bits/glue_polyval_bones.hpp
-include/armadillo_bits/glue_polyval_meat.hpp
-include/armadillo_bits/glue_relational_bones.hpp
-include/armadillo_bits/glue_relational_meat.hpp
-include/armadillo_bits/glue_solve_bones.hpp
-include/armadillo_bits/glue_solve_meat.hpp
-include/armadillo_bits/glue_times_bones.hpp
-include/armadillo_bits/glue_times_meat.hpp
-include/armadillo_bits/glue_toeplitz_bones.hpp
-include/armadillo_bits/glue_toeplitz_meat.hpp
-include/armadillo_bits/glue_trapz_bones.hpp
-include/armadillo_bits/glue_trapz_meat.hpp
-include/armadillo_bits/gmm_diag_bones.hpp
-include/armadillo_bits/gmm_diag_meat.hpp
-include/armadillo_bits/gmm_full_bones.hpp
-include/armadillo_bits/gmm_full_meat.hpp
-include/armadillo_bits/gmm_misc_bones.hpp
-include/armadillo_bits/gmm_misc_meat.hpp
-include/armadillo_bits/hdf5_misc.hpp
-include/armadillo_bits/include_atlas.hpp
-include/armadillo_bits/include_hdf5.hpp
-include/armadillo_bits/include_superlu.hpp
-include/armadillo_bits/injector_bones.hpp
-include/armadillo_bits/injector_meat.hpp
-include/armadillo_bits/memory.hpp
-include/armadillo_bits/mp_misc.hpp
-include/armadillo_bits/mtGlueCube_bones.hpp
-include/armadillo_bits/mtGlueCube_meat.hpp
-include/armadillo_bits/mtGlue_bones.hpp
-include/armadillo_bits/mtGlue_meat.hpp
-include/armadillo_bits/mtOpCube_bones.hpp
-include/armadillo_bits/mtOpCube_meat.hpp
-include/armadillo_bits/mtOp_bones.hpp
-include/armadillo_bits/mtOp_meat.hpp
-include/armadillo_bits/mtSpGlue_bones.hpp
-include/armadillo_bits/mtSpGlue_meat.hpp
-include/armadillo_bits/mtSpOp_bones.hpp
-include/armadillo_bits/mtSpOp_meat.hpp
-include/armadillo_bits/mul_gemm.hpp
-include/armadillo_bits/mul_gemm_mixed.hpp
-include/armadillo_bits/mul_gemv.hpp
-include/armadillo_bits/mul_herk.hpp
-include/armadillo_bits/mul_syrk.hpp
-include/armadillo_bits/newarp_DenseGenMatProd_bones.hpp
-include/armadillo_bits/newarp_DenseGenMatProd_meat.hpp
-include/armadillo_bits/newarp_DoubleShiftQR_bones.hpp
-include/armadillo_bits/newarp_DoubleShiftQR_meat.hpp
-include/armadillo_bits/newarp_EigsSelect.hpp
-include/armadillo_bits/newarp_GenEigsSolver_bones.hpp
-include/armadillo_bits/newarp_GenEigsSolver_meat.hpp
-include/armadillo_bits/newarp_SortEigenvalue.hpp
-include/armadillo_bits/newarp_SparseGenMatProd_bones.hpp
-include/armadillo_bits/newarp_SparseGenMatProd_meat.hpp
-include/armadillo_bits/newarp_SymEigsSolver_bones.hpp
-include/armadillo_bits/newarp_SymEigsSolver_meat.hpp
-include/armadillo_bits/newarp_TridiagEigen_bones.hpp
-include/armadillo_bits/newarp_TridiagEigen_meat.hpp
-include/armadillo_bits/newarp_UpperHessenbergEigen_bones.hpp
-include/armadillo_bits/newarp_UpperHessenbergEigen_meat.hpp
-include/armadillo_bits/newarp_UpperHessenbergQR_bones.hpp
-include/armadillo_bits/newarp_UpperHessenbergQR_meat.hpp
-include/armadillo_bits/newarp_cx_attrib.hpp
-include/armadillo_bits/op_all_bones.hpp
-include/armadillo_bits/op_all_meat.hpp
-include/armadillo_bits/op_any_bones.hpp
-include/armadillo_bits/op_any_meat.hpp
-include/armadillo_bits/op_chi2rnd_bones.hpp
-include/armadillo_bits/op_chi2rnd_meat.hpp
-include/armadillo_bits/op_chol_bones.hpp
-include/armadillo_bits/op_chol_meat.hpp
-include/armadillo_bits/op_clamp_bones.hpp
-include/armadillo_bits/op_clamp_meat.hpp
-include/armadillo_bits/op_cond_bones.hpp
-include/armadillo_bits/op_cond_meat.hpp
-include/armadillo_bits/op_cor_bones.hpp
-include/armadillo_bits/op_cor_meat.hpp
-include/armadillo_bits/op_cov_bones.hpp
-include/armadillo_bits/op_cov_meat.hpp
-include/armadillo_bits/op_cumprod_bones.hpp
-include/armadillo_bits/op_cumprod_meat.hpp
-include/armadillo_bits/op_cumsum_bones.hpp
-include/armadillo_bits/op_cumsum_meat.hpp
-include/armadillo_bits/op_cx_scalar_bones.hpp
-include/armadillo_bits/op_cx_scalar_meat.hpp
-include/armadillo_bits/op_diagmat_bones.hpp
-include/armadillo_bits/op_diagmat_meat.hpp
-include/armadillo_bits/op_diagvec_bones.hpp
-include/armadillo_bits/op_diagvec_meat.hpp
-include/armadillo_bits/op_diff_bones.hpp
-include/armadillo_bits/op_diff_meat.hpp
-include/armadillo_bits/op_dot_bones.hpp
-include/armadillo_bits/op_dot_meat.hpp
-include/armadillo_bits/op_dotext_bones.hpp
-include/armadillo_bits/op_dotext_meat.hpp
-include/armadillo_bits/op_expmat_bones.hpp
-include/armadillo_bits/op_expmat_meat.hpp
-include/armadillo_bits/op_fft_bones.hpp
-include/armadillo_bits/op_fft_meat.hpp
-include/armadillo_bits/op_find_bones.hpp
-include/armadillo_bits/op_find_meat.hpp
-include/armadillo_bits/op_find_unique_bones.hpp
-include/armadillo_bits/op_find_unique_meat.hpp
-include/armadillo_bits/op_flip_bones.hpp
-include/armadillo_bits/op_flip_meat.hpp
-include/armadillo_bits/op_hist_bones.hpp
-include/armadillo_bits/op_hist_meat.hpp
-include/armadillo_bits/op_htrans_bones.hpp
-include/armadillo_bits/op_htrans_meat.hpp
-include/armadillo_bits/op_index_max_bones.hpp
-include/armadillo_bits/op_index_max_meat.hpp
-include/armadillo_bits/op_index_min_bones.hpp
-include/armadillo_bits/op_index_min_meat.hpp
-include/armadillo_bits/op_inv_bones.hpp
-include/armadillo_bits/op_inv_meat.hpp
-include/armadillo_bits/op_logmat_bones.hpp
-include/armadillo_bits/op_logmat_meat.hpp
-include/armadillo_bits/op_max_bones.hpp
-include/armadillo_bits/op_max_meat.hpp
-include/armadillo_bits/op_mean_bones.hpp
-include/armadillo_bits/op_mean_meat.hpp
-include/armadillo_bits/op_median_bones.hpp
-include/armadillo_bits/op_median_meat.hpp
-include/armadillo_bits/op_min_bones.hpp
-include/armadillo_bits/op_min_meat.hpp
-include/armadillo_bits/op_misc_bones.hpp
-include/armadillo_bits/op_misc_meat.hpp
-include/armadillo_bits/op_nonzeros_bones.hpp
-include/armadillo_bits/op_nonzeros_meat.hpp
-include/armadillo_bits/op_norm_bones.hpp
-include/armadillo_bits/op_norm_meat.hpp
-include/armadillo_bits/op_normalise_bones.hpp
-include/armadillo_bits/op_normalise_meat.hpp
-include/armadillo_bits/op_orth_null_bones.hpp
-include/armadillo_bits/op_orth_null_meat.hpp
-include/armadillo_bits/op_pinv_bones.hpp
-include/armadillo_bits/op_pinv_meat.hpp
-include/armadillo_bits/op_princomp_bones.hpp
-include/armadillo_bits/op_princomp_meat.hpp
-include/armadillo_bits/op_prod_bones.hpp
-include/armadillo_bits/op_prod_meat.hpp
-include/armadillo_bits/op_range_bones.hpp
-include/armadillo_bits/op_range_meat.hpp
-include/armadillo_bits/op_relational_bones.hpp
-include/armadillo_bits/op_relational_meat.hpp
-include/armadillo_bits/op_repelem_bones.hpp
-include/armadillo_bits/op_repelem_meat.hpp
-include/armadillo_bits/op_repmat_bones.hpp
-include/armadillo_bits/op_repmat_meat.hpp
-include/armadillo_bits/op_reshape_bones.hpp
-include/armadillo_bits/op_reshape_meat.hpp
-include/armadillo_bits/op_resize_bones.hpp
-include/armadillo_bits/op_resize_meat.hpp
-include/armadillo_bits/op_reverse_bones.hpp
-include/armadillo_bits/op_reverse_meat.hpp
-include/armadillo_bits/op_roots_bones.hpp
-include/armadillo_bits/op_roots_meat.hpp
-include/armadillo_bits/op_shift_bones.hpp
-include/armadillo_bits/op_shift_meat.hpp
-include/armadillo_bits/op_shuffle_bones.hpp
-include/armadillo_bits/op_shuffle_meat.hpp
-include/armadillo_bits/op_sort_bones.hpp
-include/armadillo_bits/op_sort_index_bones.hpp
-include/armadillo_bits/op_sort_index_meat.hpp
-include/armadillo_bits/op_sort_meat.hpp
-include/armadillo_bits/op_sp_minus_bones.hpp
-include/armadillo_bits/op_sp_minus_meat.hpp
-include/armadillo_bits/op_sp_plus_bones.hpp
-include/armadillo_bits/op_sp_plus_meat.hpp
-include/armadillo_bits/op_sqrtmat_bones.hpp
-include/armadillo_bits/op_sqrtmat_meat.hpp
-include/armadillo_bits/op_stddev_bones.hpp
-include/armadillo_bits/op_stddev_meat.hpp
-include/armadillo_bits/op_strans_bones.hpp
-include/armadillo_bits/op_strans_meat.hpp
-include/armadillo_bits/op_sum_bones.hpp
-include/armadillo_bits/op_sum_meat.hpp
-include/armadillo_bits/op_symmat_bones.hpp
-include/armadillo_bits/op_symmat_meat.hpp
-include/armadillo_bits/op_toeplitz_bones.hpp
-include/armadillo_bits/op_toeplitz_meat.hpp
-include/armadillo_bits/op_trimat_bones.hpp
-include/armadillo_bits/op_trimat_meat.hpp
-include/armadillo_bits/op_unique_bones.hpp
-include/armadillo_bits/op_unique_meat.hpp
-include/armadillo_bits/op_var_bones.hpp
-include/armadillo_bits/op_var_meat.hpp
-include/armadillo_bits/op_vectorise_bones.hpp
-include/armadillo_bits/op_vectorise_meat.hpp
-include/armadillo_bits/op_wishrnd_bones.hpp
-include/armadillo_bits/op_wishrnd_meat.hpp
-include/armadillo_bits/operator_cube_div.hpp
-include/armadillo_bits/operator_cube_minus.hpp
-include/armadillo_bits/operator_cube_plus.hpp
-include/armadillo_bits/operator_cube_relational.hpp
-include/armadillo_bits/operator_cube_schur.hpp
-include/armadillo_bits/operator_cube_times.hpp
-include/armadillo_bits/operator_div.hpp
-include/armadillo_bits/operator_minus.hpp
-include/armadillo_bits/operator_ostream.hpp
-include/armadillo_bits/operator_plus.hpp
-include/armadillo_bits/operator_relational.hpp
-include/armadillo_bits/operator_schur.hpp
-include/armadillo_bits/operator_times.hpp
-include/armadillo_bits/podarray_bones.hpp
-include/armadillo_bits/podarray_meat.hpp
-include/armadillo_bits/promote_type.hpp
-include/armadillo_bits/restrictors.hpp
-include/armadillo_bits/running_stat_bones.hpp
-include/armadillo_bits/running_stat_meat.hpp
-include/armadillo_bits/running_stat_vec_bones.hpp
-include/armadillo_bits/running_stat_vec_meat.hpp
-include/armadillo_bits/sp_auxlib_bones.hpp
-include/armadillo_bits/sp_auxlib_meat.hpp
-include/armadillo_bits/span.hpp
-include/armadillo_bits/spdiagview_bones.hpp
-include/armadillo_bits/spdiagview_meat.hpp
-include/armadillo_bits/spglue_elem_helper_bones.hpp
-include/armadillo_bits/spglue_elem_helper_meat.hpp
-include/armadillo_bits/spglue_join_bones.hpp
-include/armadillo_bits/spglue_join_meat.hpp
-include/armadillo_bits/spglue_kron_bones.hpp
-include/armadillo_bits/spglue_kron_meat.hpp
-include/armadillo_bits/spglue_max_bones.hpp
-include/armadillo_bits/spglue_max_meat.hpp
-include/armadillo_bits/spglue_min_bones.hpp
-include/armadillo_bits/spglue_min_meat.hpp
-include/armadillo_bits/spglue_minus_bones.hpp
-include/armadillo_bits/spglue_minus_meat.hpp
-include/armadillo_bits/spglue_plus_bones.hpp
-include/armadillo_bits/spglue_plus_meat.hpp
-include/armadillo_bits/spglue_schur_bones.hpp
-include/armadillo_bits/spglue_schur_meat.hpp
-include/armadillo_bits/spglue_times_bones.hpp
-include/armadillo_bits/spglue_times_meat.hpp
-include/armadillo_bits/spop_diagmat_bones.hpp
-include/armadillo_bits/spop_diagmat_meat.hpp
-include/armadillo_bits/spop_htrans_bones.hpp
-include/armadillo_bits/spop_htrans_meat.hpp
-include/armadillo_bits/spop_max_bones.hpp
-include/armadillo_bits/spop_max_meat.hpp
-include/armadillo_bits/spop_mean_bones.hpp
-include/armadillo_bits/spop_mean_meat.hpp
-include/armadillo_bits/spop_min_bones.hpp
-include/armadillo_bits/spop_min_meat.hpp
-include/armadillo_bits/spop_misc_bones.hpp
-include/armadillo_bits/spop_misc_meat.hpp
-include/armadillo_bits/spop_normalise_bones.hpp
-include/armadillo_bits/spop_normalise_meat.hpp
-include/armadillo_bits/spop_repmat_bones.hpp
-include/armadillo_bits/spop_repmat_meat.hpp
-include/armadillo_bits/spop_reverse_bones.hpp
-include/armadillo_bits/spop_reverse_meat.hpp
-include/armadillo_bits/spop_strans_bones.hpp
-include/armadillo_bits/spop_strans_meat.hpp
-include/armadillo_bits/spop_sum_bones.hpp
-include/armadillo_bits/spop_sum_meat.hpp
-include/armadillo_bits/spop_symmat_bones.hpp
-include/armadillo_bits/spop_symmat_meat.hpp
-include/armadillo_bits/spop_trimat_bones.hpp
-include/armadillo_bits/spop_trimat_meat.hpp
-include/armadillo_bits/spop_var_bones.hpp
-include/armadillo_bits/spop_var_meat.hpp
-include/armadillo_bits/spop_vectorise_bones.hpp
-include/armadillo_bits/spop_vectorise_meat.hpp
-include/armadillo_bits/strip.hpp
-include/armadillo_bits/subview_bones.hpp
-include/armadillo_bits/subview_cube_bones.hpp
-include/armadillo_bits/subview_cube_each_bones.hpp
-include/armadillo_bits/subview_cube_each_meat.hpp
-include/armadillo_bits/subview_cube_meat.hpp
-include/armadillo_bits/subview_cube_slices_bones.hpp
-include/armadillo_bits/subview_cube_slices_meat.hpp
-include/armadillo_bits/subview_each_bones.hpp
-include/armadillo_bits/subview_each_meat.hpp
-include/armadillo_bits/subview_elem1_bones.hpp
-include/armadillo_bits/subview_elem1_meat.hpp
-include/armadillo_bits/subview_elem2_bones.hpp
-include/armadillo_bits/subview_elem2_meat.hpp
-include/armadillo_bits/subview_field_bones.hpp
-include/armadillo_bits/subview_field_meat.hpp
-include/armadillo_bits/subview_meat.hpp
-include/armadillo_bits/sympd_helper.hpp
-include/armadillo_bits/traits.hpp
-include/armadillo_bits/typedef_elem.hpp
-include/armadillo_bits/typedef_elem_check.hpp
-include/armadillo_bits/typedef_mat.hpp
-include/armadillo_bits/typedef_mat_fixed.hpp
-include/armadillo_bits/unwrap.hpp
-include/armadillo_bits/unwrap_cube.hpp
-include/armadillo_bits/unwrap_spmat.hpp
-include/armadillo_bits/upgrade_val.hpp
-include/armadillo_bits/wall_clock_bones.hpp
-include/armadillo_bits/wall_clock_meat.hpp
-include/armadillo_bits/wrapper_arpack.hpp
-include/armadillo_bits/wrapper_atlas.hpp
-include/armadillo_bits/wrapper_blas.hpp
-include/armadillo_bits/wrapper_lapack.hpp
-include/armadillo_bits/wrapper_superlu.hpp
-include/armadillo_bits/xtrans_mat_bones.hpp
-include/armadillo_bits/xtrans_mat_meat.hpp
-include/armadillo_bits/xvec_htrans_bones.hpp
-include/armadillo_bits/xvec_htrans_meat.hpp
-lib/libarmadillo.so
-lib/libarmadillo.so.9
-lib/libarmadillo.so.9.400.3
-lib/pkgconfig/armadillo.pc
-share/Armadillo/CMake/ArmadilloConfig.cmake
-share/Armadillo/CMake/ArmadilloConfigVersion.cmake
-share/Armadillo/CMake/ArmadilloLibraryDepends-noconfig.cmake
-share/Armadillo/CMake/ArmadilloLibraryDepends.cmake
diff --git a/armadillo/buildlink3.mk b/armadillo/buildlink3.mk
deleted file mode 100644
index 70a305e68f..0000000000
--- a/armadillo/buildlink3.mk
+++ /dev/null
@@ -1,17 +0,0 @@
-# $NetBSD: buildlink3.mk,v 1.7 2014/10/02 15:31:39 uccwen Exp $
-
-BUILDLINK_TREE+= armadillo
-
-.if !defined(ARMADILLO_BUILDLINK3_MK)
-ARMADILLO_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.armadillo+= armadillo>=4.45.2
-BUILDLINK_ABI_DEPENDS.armadillo?= armadillo>=4.45.2
-BUILDLINK_PKGSRCDIR.armadillo?= ../../wip/armadillo
-
-.include "../../mk/blas.buildlink3.mk"
-.include "../../devel/boost-libs/buildlink3.mk"
-.include "../../devel/boost-headers/buildlink3.mk"
-.endif # ARMADILLO_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -armadillo
diff --git a/armadillo/distinfo b/armadillo/distinfo
deleted file mode 100644
index 1a9efc89ef..0000000000
--- a/armadillo/distinfo
+++ /dev/null
@@ -1,6 +0,0 @@
-$NetBSD$
-
-RMD160 (armadillo-9.400.3.tar.xz) = e1d73d9c5cb9eed997ca294fee85d5c649a8ef90
-SHA512 (armadillo-9.400.3.tar.xz) = ae35f6d2e45202af4f5ef4516467c38a064ca2c1796d5c03ab389c31b800e8eea110b9035912a742c3f297234890b57f91918a40df071db5ebb20ec74b18ada5
-Size (armadillo-9.400.3.tar.xz) = 4798164 bytes
-SHA1 (patch-CMakeLists.txt) = 21d73fdb47a1a5e957121c223f1671c35a7f6612
diff --git a/armadillo/patches/patch-CMakeLists.txt b/armadillo/patches/patch-CMakeLists.txt
deleted file mode 100644
index cd3e1ea819..0000000000
--- a/armadillo/patches/patch-CMakeLists.txt
+++ /dev/null
@@ -1,72 +0,0 @@
-$Netbsd$
-
-Make the build use LAPACK_LIBS and BLAS_LIBS from the environment.
-Could this be acceptible to upstream?
-
-Also, override the possibly badly detected HDF5 include directory.
-On my system, where there are some paths external to pkgrc (compiler,
-Open MPI), and HDF5 is just available without any extra hassle,
-the firsts of the external include paths is picked up as alleged
-HDF5 include directory. It's Open MPI's include directory. No
-hdf5.h in there! This breaks users of armadillo, obviously. I don't
-get the sense of hardcoding the path to hdf5.h at all. This is all
-so wrong.
-
---- CMakeLists.txt.orig 2020-02-24 22:11:41.093696230 +0100
-+++ CMakeLists.txt 2020-02-24 22:14:52.780347663 +0100
-@@ -151,6 +151,16 @@
- ##
-
- set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_CURRENT_SOURCE_DIR}/cmake_aux/Modules/")
-+if(APPLE)
-+ if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
-+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
-+ message(STATUS "Clang compiler on MacOS X detected. Added '-stdlib=libc++' to compiler flags")
-+ endif()
-+
-+ set(CMAKE_MACOSX_RPATH 1)
-+endif()
-+
-+if("$ENV{BLAS_LIBS}" STREQUAL "")
-
- if(APPLE)
-
-@@ -162,13 +172,6 @@
- set(ARMA_LIBS ${ARMA_LIBS} "-framework Accelerate") # or "-framework accelerate" ?
- message(STATUS "MacOS X detected. Added '-framework Accelerate' to compiler flags")
-
-- if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
-- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
-- message(STATUS "Clang compiler on MacOS X detected. Added '-stdlib=libc++' to compiler flags")
-- endif()
--
-- set(CMAKE_MACOSX_RPATH 1)
--
- else()
-
- set(ARMA_OS unix)
-@@ -284,6 +287,14 @@
-
- endif()
-
-+else()
-+
-+set(ARMA_USE_BLAS true)
-+set(ARMA_USE_LAPACK true)
-+set(ARMA_LIBS ${ARMA_LIBS} $ENV{LAPACK_LIBS} $ENV{BLAS_LIBS})
-+message(STATUS "Using BLAS/LAPACK from BLAS_LIBS and LAPACK_LIBS environment variables.")
-+
-+endif()
-
- find_package(PkgConfig)
-
-@@ -334,6 +345,9 @@ if(DETECT_HDF5)
- message(STATUS "*** rerun cmake with HDF5 detection disabled:")
- message(STATUS "*** cmake -D DETECT_HDF5=false .")
- message(STATUS "")
-+ set(ARMA_HDF5_INCLUDE_DIR ${CMAKE_INSTALL_PREFIX}/include)
-+ message(STATUS "Overriding silly HDF5 include dir hardcode to common install prefix for pkgsrc.")
-+ message(STATUS "ARMA_HDF5_INCLUDE_DIR = ${ARMA_HDF5_INCLUDE_DIR}")
- endif()
- endif()
-
diff --git a/blasr/DESCR b/blasr/DESCR
deleted file mode 100644
index a3f8db85e9..0000000000
--- a/blasr/DESCR
+++ /dev/null
@@ -1,3 +0,0 @@
-PacBio(R) long read aligner.
-
-WWW: https://github.com/PacificBiosciences/blasr
diff --git a/blasr/PLIST b/blasr/PLIST
deleted file mode 100644
index 75b72a03d1..0000000000
--- a/blasr/PLIST
+++ /dev/null
@@ -1,10 +0,0 @@
-@comment $NetBSD$
-bin/blasr
-bin/loadPulses
-bin/pls2fasta
-bin/samFilter
-bin/samtoh5
-bin/samtom4
-bin/sawriter
-bin/sdpMatcher
-bin/toAfg
diff --git a/blasr/TODO b/blasr/TODO
deleted file mode 100644
index b687356e6b..0000000000
--- a/blasr/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test
diff --git a/blasr/buildlink3.mk b/blasr/buildlink3.mk
deleted file mode 100644
index 2920513938..0000000000
--- a/blasr/buildlink3.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-# $NetBSD$
-
-BUILDLINK_TREE+= blasr
-
-.if !defined(BLASR_BUILDLINK3_MK)
-BLASR_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.blasr+= blasr>=2015.08.17
-BUILDLINK_PKGSRCDIR.blasr?= ../../wip/blasr
-.endif # BLASR_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -blasr
diff --git a/blasr/distinfo b/blasr/distinfo
deleted file mode 100644
index e137bce10e..0000000000
--- a/blasr/distinfo
+++ /dev/null
@@ -1,6 +0,0 @@
-$NetBSD$
-
-RMD160 (blasr-2015.08.17.tar.xz) = d85998bc824b6ad3319e140478d86b8ac6ffb056
-SHA512 (blasr-2015.08.17.tar.xz) = dcb3e9df039a09862bc25b9d4b9120e65bae7c8f3d7f38a81db21a8687c86d50ecacf32640af13ea8dfbd1b8d6adf198e7f58b3cc7b38022f1552e37046eb81d
-Size (blasr-2015.08.17.tar.xz) = 1027344 bytes
-SHA1 (patch-Blasr.cpp) = 663437d839027a7a6f057cf44234a96f6eb7299c
diff --git a/blasr/patches/patch-Blasr.cpp b/blasr/patches/patch-Blasr.cpp
deleted file mode 100644
index 7025346f12..0000000000
--- a/blasr/patches/patch-Blasr.cpp
+++ /dev/null
@@ -1,21 +0,0 @@
-$NetBSD$
-# Replce C++11ism
-
---- Blasr.cpp.orig 2015-08-13 20:42:14.000000000 +0000
-+++ Blasr.cpp
-@@ -2655,9 +2655,12 @@ SelectAlignmentsToPrint(vector<T_Alignme
- // Apply filter criteria and hit policy.
- // Shallow copy AlignmentCandidate pointers.
- vector<T_AlignmentCandidate*> filtered;
-- for (auto ptr: alignmentPtrs) {
-- if (params.filterCriteria.Satisfy(ptr)) {
-- filtered.push_back(ptr);
-+ // for (auto ptr: alignmentPtrs) {
-+ // if (params.filterCriteria.Satisfy(ptr)) {
-+ // filtered.push_back(ptr);
-+ for (int i = 0; i < alignmentPtrs.size(); ++i) {
-+ if (params.filterCriteria.Satisfy(alignmentPtrs[i])) {
-+ filtered.push_back(alignmentPtrs[i]);
- if (filtered.size() == params.nBest) break;
- }
- }
diff --git a/blasr_libcpp/DESCR b/blasr_libcpp/DESCR
deleted file mode 100644
index ba39f25b29..0000000000
--- a/blasr_libcpp/DESCR
+++ /dev/null
@@ -1,4 +0,0 @@
-Blasr_libcpp is a library used by blasr and other executables such as samtoh5,
-loadPulses for analyzing PacBio sequences.
-
-WWW: https://github.com/PacificBiosciences/blasr_libcpp
diff --git a/blasr_libcpp/PLIST b/blasr_libcpp/PLIST
deleted file mode 100644
index 2b0a85e6ad..0000000000
--- a/blasr_libcpp/PLIST
+++ /dev/null
@@ -1,290 +0,0 @@
-@comment $NetBSD: PLIST,v 1.2 2015/09/11 16:48:33 outpaddling Exp $
-include/blasr_libcpp/alignment/MappingMetrics.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/AffineGuidedAlign.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/AffineKBandAlign.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/AlignmentFormats.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/AlignmentUtils.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/BaseScoreFunction.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/ExtendAlign.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/FullQVAlign.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/GraphPaper.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/GraphPaperImpl.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/GuidedAlign.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/IDSScoreFunction.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/KBandAlign.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/OneGapAlignment.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/QualityValueScoreFunction.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/SDPAlign.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/SDPAlignImpl.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/SWAlign.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/SWAlignImpl.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/ScoreMatrices.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/StringToScoreMatrix.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/sdp/FragmentSort.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/sdp/FragmentSortImpl.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/sdp/NonoverlappingSparseDynamicProgramming.h
-include/blasr_libcpp/alignment/algorithms/alignment/sdp/SDPColumn.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/sdp/SDPFragment.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/sdp/SDPSet.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/sdp/SDPSetImpl.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp
-include/blasr_libcpp/alignment/algorithms/alignment/sdp/VariableLengthSDPFragment.h
-include/blasr_libcpp/alignment/algorithms/anchoring/BWTSearch.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/BWTSearchImpl.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/BasicEndpoint.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/BasicEndpointImpl.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/ClusterProbability.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/Coordinate.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/FindMaxInterval.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/GlobalChain.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/GlobalChainImpl.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/LISPValue.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/LISPValueImpl.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/LISPValueWeightor.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/LISPValueWeightorImpl.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/LISQValueWeightor.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/LISSizeWeightor.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/LISSizeWeightorImpl.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/LongestIncreasingSubsequence.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/LongestIncreasingSubsequenceImpl.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/MapBySuffixArray.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/PrioritySearchTree.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/PrioritySearchTreeImpl.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/ScoreAnchors.hpp
-include/blasr_libcpp/alignment/algorithms/anchoring/ScoreAnchorsImpl.hpp
-include/blasr_libcpp/alignment/algorithms/compare/CompareStrings.hpp
-include/blasr_libcpp/alignment/algorithms/sorting/DifferenceCovers.hpp
-include/blasr_libcpp/alignment/algorithms/sorting/Karkkainen.hpp
-include/blasr_libcpp/alignment/algorithms/sorting/LightweightSuffixArray.hpp
-include/blasr_libcpp/alignment/algorithms/sorting/MultikeyQuicksort.hpp
-include/blasr_libcpp/alignment/algorithms/sorting/qsufsort.hpp
-include/blasr_libcpp/alignment/anchoring/AnchorParameters.hpp
-include/blasr_libcpp/alignment/bwt/BWT.hpp
-include/blasr_libcpp/alignment/bwt/Occ.hpp
-include/blasr_libcpp/alignment/bwt/PackedHash.hpp
-include/blasr_libcpp/alignment/bwt/Pos.hpp
-include/blasr_libcpp/alignment/datastructures/alignment/AlignedPair.h
-include/blasr_libcpp/alignment/datastructures/alignment/Alignment.hpp
-include/blasr_libcpp/alignment/datastructures/alignment/AlignmentCandidate.hpp
-include/blasr_libcpp/alignment/datastructures/alignment/AlignmentContext.hpp
-include/blasr_libcpp/alignment/datastructures/alignment/AlignmentGapList.h
-include/blasr_libcpp/alignment/datastructures/alignment/AlignmentMap.hpp
-include/blasr_libcpp/alignment/datastructures/alignment/AlignmentStats.hpp
-include/blasr_libcpp/alignment/datastructures/alignment/ByteAlignment.h
-include/blasr_libcpp/alignment/datastructures/alignment/CmpFile.hpp
-include/blasr_libcpp/alignment/datastructures/alignment/CmpIndexedStringTable.h
-include/blasr_libcpp/alignment/datastructures/alignment/CmpReadGroupTable.h
-include/blasr_libcpp/alignment/datastructures/alignment/CmpRefSeqTable.h
-include/blasr_libcpp/alignment/datastructures/alignment/FilterCriteria.hpp
-include/blasr_libcpp/alignment/datastructures/alignment/Path.h
-include/blasr_libcpp/alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.hpp
-include/blasr_libcpp/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp
-include/blasr_libcpp/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp
-include/blasr_libcpp/alignment/datastructures/alignmentset/SAMQVConversion.hpp
-include/blasr_libcpp/alignment/datastructures/alignmentset/SAMSupplementalQVList.hpp
-include/blasr_libcpp/alignment/datastructures/anchoring/AnchorParameters.hpp
-include/blasr_libcpp/alignment/datastructures/anchoring/ClusterList.hpp
-include/blasr_libcpp/alignment/datastructures/anchoring/MatchPos.hpp
-include/blasr_libcpp/alignment/datastructures/anchoring/WeightedInterval.hpp
-include/blasr_libcpp/alignment/files/BaseSequenceIO.hpp
-include/blasr_libcpp/alignment/files/CCSIterator.hpp
-include/blasr_libcpp/alignment/files/FragmentCCSIterator.hpp
-include/blasr_libcpp/alignment/files/ReaderAgglomerate.hpp
-include/blasr_libcpp/alignment/files/ReaderAgglomerateImpl.hpp
-include/blasr_libcpp/alignment/format/BAMPrinter.hpp
-include/blasr_libcpp/alignment/format/BAMPrinterImpl.hpp
-include/blasr_libcpp/alignment/format/CompareSequencesPrinter.hpp
-include/blasr_libcpp/alignment/format/CompareSequencesPrinterImpl.hpp
-include/blasr_libcpp/alignment/format/IntervalPrinter.hpp
-include/blasr_libcpp/alignment/format/SAMHeaderPrinter.hpp
-include/blasr_libcpp/alignment/format/SAMPrinter.hpp
-include/blasr_libcpp/alignment/format/SAMPrinterImpl.hpp
-include/blasr_libcpp/alignment/format/StickAlignmentPrinter.hpp
-include/blasr_libcpp/alignment/format/SummaryPrinter.hpp
-include/blasr_libcpp/alignment/format/VulgarPrinter.hpp
-include/blasr_libcpp/alignment/format/XMLPrinter.hpp
-include/blasr_libcpp/alignment/ipc/SharedMemoryAllocator.hpp
-include/blasr_libcpp/alignment/qvs/QualityValueProfile.hpp
-include/blasr_libcpp/alignment/simulator/CDFMap.hpp
-include/blasr_libcpp/alignment/simulator/ContextOutputList.hpp
-include/blasr_libcpp/alignment/simulator/ContextSample.hpp
-include/blasr_libcpp/alignment/simulator/ContextSet.hpp
-include/blasr_libcpp/alignment/simulator/LengthHistogram.hpp
-include/blasr_libcpp/alignment/simulator/OutputList.hpp
-include/blasr_libcpp/alignment/simulator/OutputSample.hpp
-include/blasr_libcpp/alignment/simulator/OutputSampleList.hpp
-include/blasr_libcpp/alignment/simulator/OutputSampleListSet.hpp
-include/blasr_libcpp/alignment/simulator/QualitySample.hpp
-include/blasr_libcpp/alignment/statistics/AnchorDistributionTable.hpp
-include/blasr_libcpp/alignment/statistics/LookupAnchorDistribution.hpp
-include/blasr_libcpp/alignment/statistics/StatUtils.hpp
-include/blasr_libcpp/alignment/statistics/StatUtilsImpl.hpp
-include/blasr_libcpp/alignment/statistics/VarianceAccumulator.hpp
-include/blasr_libcpp/alignment/statistics/VarianceAccumulatorImpl.hpp
-include/blasr_libcpp/alignment/statistics/cdfs.hpp
-include/blasr_libcpp/alignment/statistics/pdfs.hpp
-include/blasr_libcpp/alignment/suffixarray/LCPTable.hpp
-include/blasr_libcpp/alignment/suffixarray/SharedSuffixArray.hpp
-include/blasr_libcpp/alignment/suffixarray/SuffixArray.hpp
-include/blasr_libcpp/alignment/suffixarray/SuffixArrayTypes.hpp
-include/blasr_libcpp/alignment/suffixarray/ssort.hpp
-include/blasr_libcpp/alignment/tuples/BaseTuple.hpp
-include/blasr_libcpp/alignment/tuples/CompressedDNATuple.hpp
-include/blasr_libcpp/alignment/tuples/CountedTuple.h
-include/blasr_libcpp/alignment/tuples/DNATuple.hpp
-include/blasr_libcpp/alignment/tuples/DNATupleImpl.hpp
-include/blasr_libcpp/alignment/tuples/DNATupleList.h
-include/blasr_libcpp/alignment/tuples/HashedTupleList.hpp
-include/blasr_libcpp/alignment/tuples/HashedTupleListImpl.hpp
-include/blasr_libcpp/alignment/tuples/TupleCountTable.hpp
-include/blasr_libcpp/alignment/tuples/TupleCountTableImpl.hpp
-include/blasr_libcpp/alignment/tuples/TupleList.hpp
-include/blasr_libcpp/alignment/tuples/TupleListImpl.hpp
-include/blasr_libcpp/alignment/tuples/TupleMask.h
-include/blasr_libcpp/alignment/tuples/TupleMatching.hpp
-include/blasr_libcpp/alignment/tuples/TupleMatchingImpl.hpp
-include/blasr_libcpp/alignment/tuples/TupleMetrics.hpp
-include/blasr_libcpp/alignment/tuples/TupleOperations.h
-include/blasr_libcpp/alignment/tuples/TupleTranslations.h
-include/blasr_libcpp/alignment/tuples/tuple.h
-include/blasr_libcpp/alignment/utils/FileOfFileNames.hpp
-include/blasr_libcpp/alignment/utils/FileUtils.hpp
-include/blasr_libcpp/alignment/utils/LogUtils.hpp
-include/blasr_libcpp/alignment/utils/PhredUtils.hpp
-include/blasr_libcpp/alignment/utils/RangeUtils.hpp
-include/blasr_libcpp/alignment/utils/RegionUtils.hpp
-include/blasr_libcpp/alignment/utils/RegionUtilsImpl.hpp
-include/blasr_libcpp/alignment/utils/SimpleXMLUtils.hpp
-include/blasr_libcpp/alignment/utils/TimeUtils.hpp
-include/blasr_libcpp/hdf/BufferedHDF2DArray.hpp
-include/blasr_libcpp/hdf/BufferedHDF2DArrayImpl.hpp
-include/blasr_libcpp/hdf/BufferedHDFArray.hpp
-include/blasr_libcpp/hdf/BufferedHDFArrayImpl.hpp
-include/blasr_libcpp/hdf/DatasetCollection.hpp
-include/blasr_libcpp/hdf/DatasetCollectionImpl.hpp
-include/blasr_libcpp/hdf/HDF2DArray.hpp
-include/blasr_libcpp/hdf/HDFAlnGroup.hpp
-include/blasr_libcpp/hdf/HDFAlnGroupGroup.hpp
-include/blasr_libcpp/hdf/HDFAlnInfoGroup.hpp
-include/blasr_libcpp/hdf/HDFArray.hpp
-include/blasr_libcpp/hdf/HDFAtom.hpp
-include/blasr_libcpp/hdf/HDFAttributable.hpp
-include/blasr_libcpp/hdf/HDFBasReader.hpp
-include/blasr_libcpp/hdf/HDFBasWriter.hpp
-include/blasr_libcpp/hdf/HDFCCSReader.hpp
-include/blasr_libcpp/hdf/HDFCmpData.hpp
-include/blasr_libcpp/hdf/HDFCmpExperimentGroup.hpp
-include/blasr_libcpp/hdf/HDFCmpFile.hpp
-include/blasr_libcpp/hdf/HDFCmpReader.hpp
-include/blasr_libcpp/hdf/HDFCmpRefAlignmentGroup.hpp
-include/blasr_libcpp/hdf/HDFCmpRootGroup.hpp
-include/blasr_libcpp/hdf/HDFCmpSupportedFields.hpp
-include/blasr_libcpp/hdf/HDFCommonFG.hpp
-include/blasr_libcpp/hdf/HDFConfig.hpp
-include/blasr_libcpp/hdf/HDFData.hpp
-include/blasr_libcpp/hdf/HDFFile.hpp
-include/blasr_libcpp/hdf/HDFFileLogGroup.hpp
-include/blasr_libcpp/hdf/HDFGroup.hpp
-include/blasr_libcpp/hdf/HDFMovieInfoGroup.hpp
-include/blasr_libcpp/hdf/HDFNewBasReader.hpp
-include/blasr_libcpp/hdf/HDFPlsReader.hpp
-include/blasr_libcpp/hdf/HDFPlsWriter.hpp
-include/blasr_libcpp/hdf/HDFPulseDataFile.hpp
-include/blasr_libcpp/hdf/HDFRefGroupGroup.hpp
-include/blasr_libcpp/hdf/HDFRefInfoGroup.hpp
-include/blasr_libcpp/hdf/HDFRegionTableReader.hpp
-include/blasr_libcpp/hdf/HDFRegionTableWriter.hpp
-include/blasr_libcpp/hdf/HDFSMRTSequenceReader.hpp
-include/blasr_libcpp/hdf/HDFScanDataReader.hpp
-include/blasr_libcpp/hdf/HDFScanDataWriter.hpp
-include/blasr_libcpp/hdf/HDFSentinalFile.hpp
-include/blasr_libcpp/hdf/HDFUtils.hpp
-include/blasr_libcpp/hdf/HDFWriteBuffer.hpp
-include/blasr_libcpp/hdf/HDFZMWReader.hpp
-include/blasr_libcpp/libconfig.h
-include/blasr_libcpp/pbdata/CCSSequence.hpp
-include/blasr_libcpp/pbdata/ChangeListID.hpp
-include/blasr_libcpp/pbdata/CommandLineParser.hpp
-include/blasr_libcpp/pbdata/Compare4BitCompressed.hpp
-include/blasr_libcpp/pbdata/CompressedDNASequence.hpp
-include/blasr_libcpp/pbdata/CompressedSequence.hpp
-include/blasr_libcpp/pbdata/CompressedSequenceImpl.hpp
-include/blasr_libcpp/pbdata/DNASequence.hpp
-include/blasr_libcpp/pbdata/Enumerations.h
-include/blasr_libcpp/pbdata/FASTAReader.hpp
-include/blasr_libcpp/pbdata/FASTASequence.hpp
-include/blasr_libcpp/pbdata/FASTQReader.hpp
-include/blasr_libcpp/pbdata/FASTQSequence.hpp
-include/blasr_libcpp/pbdata/GFFFile.hpp
-include/blasr_libcpp/pbdata/MD5Utils.hpp
-include/blasr_libcpp/pbdata/MD5UtilsImpl.hpp
-include/blasr_libcpp/pbdata/NucConversion.hpp
-include/blasr_libcpp/pbdata/PackedDNASequence.hpp
-include/blasr_libcpp/pbdata/ReverseCompressIndex.hpp
-include/blasr_libcpp/pbdata/SMRTSequence.hpp
-include/blasr_libcpp/pbdata/SeqUtils.hpp
-include/blasr_libcpp/pbdata/SeqUtilsImpl.hpp
-include/blasr_libcpp/pbdata/StringUtils.hpp
-include/blasr_libcpp/pbdata/Types.h
-include/blasr_libcpp/pbdata/VectorUtils.hpp
-include/blasr_libcpp/pbdata/alignment/CmpAlignment.hpp
-include/blasr_libcpp/pbdata/alignment/CmpAlignmentImpl.hpp
-include/blasr_libcpp/pbdata/amos/AfgBasWriter.hpp
-include/blasr_libcpp/pbdata/defs.h
-include/blasr_libcpp/pbdata/loadpulses/MetricField.hpp
-include/blasr_libcpp/pbdata/loadpulses/MovieAlnIndexLookupTable.hpp
-include/blasr_libcpp/pbdata/matrix/FlatMatrix.hpp
-include/blasr_libcpp/pbdata/matrix/FlatMatrixImpl.hpp
-include/blasr_libcpp/pbdata/matrix/Matrix.hpp
-include/blasr_libcpp/pbdata/matrix/MatrixImpl.hpp
-include/blasr_libcpp/pbdata/metagenome/FindRandomSequence.hpp
-include/blasr_libcpp/pbdata/metagenome/SequenceIndexDatabase.hpp
-include/blasr_libcpp/pbdata/metagenome/SequenceIndexDatabaseImpl.hpp
-include/blasr_libcpp/pbdata/metagenome/TitleTable.hpp
-include/blasr_libcpp/pbdata/qvs/QualityTransform.hpp
-include/blasr_libcpp/pbdata/qvs/QualityValue.hpp
-include/blasr_libcpp/pbdata/qvs/QualityValueVector.hpp
-include/blasr_libcpp/pbdata/qvs/QualityValueVectorImpl.hpp
-include/blasr_libcpp/pbdata/reads/BaseFile.hpp
-include/blasr_libcpp/pbdata/reads/BaseFileImpl.hpp
-include/blasr_libcpp/pbdata/reads/HoleXY.hpp
-include/blasr_libcpp/pbdata/reads/PulseBaseCommon.hpp
-include/blasr_libcpp/pbdata/reads/PulseFile.hpp
-include/blasr_libcpp/pbdata/reads/PulseFileImpl.hpp
-include/blasr_libcpp/pbdata/reads/ReadInterval.hpp
-include/blasr_libcpp/pbdata/reads/ReadType.hpp
-include/blasr_libcpp/pbdata/reads/RegionTable.hpp
-include/blasr_libcpp/pbdata/reads/ScanData.hpp
-include/blasr_libcpp/pbdata/reads/ZMWGroupEntry.hpp
-include/blasr_libcpp/pbdata/saf/AlnGroup.hpp
-include/blasr_libcpp/pbdata/saf/AlnInfo.hpp
-include/blasr_libcpp/pbdata/saf/MovieInfo.hpp
-include/blasr_libcpp/pbdata/saf/RefGroup.hpp
-include/blasr_libcpp/pbdata/saf/RefInfo.hpp
-include/blasr_libcpp/pbdata/sam/AlignmentSet.hpp
-include/blasr_libcpp/pbdata/sam/AlignmentSetImpl.hpp
-include/blasr_libcpp/pbdata/sam/CigarString.h
-include/blasr_libcpp/pbdata/sam/ReadGroup.hpp
-include/blasr_libcpp/pbdata/sam/ReferenceSequence.hpp
-include/blasr_libcpp/pbdata/sam/SAMAlignment.hpp
-include/blasr_libcpp/pbdata/sam/SAMFlag.h
-include/blasr_libcpp/pbdata/sam/SAMHeader.hpp
-include/blasr_libcpp/pbdata/sam/SAMKeywordValuePair.hpp
-include/blasr_libcpp/pbdata/sam/SAMKeywordValuePairImpl.hpp
-include/blasr_libcpp/pbdata/sam/SAMReader.hpp
-include/blasr_libcpp/pbdata/sam/SAMReaderImpl.hpp
-include/blasr_libcpp/pbdata/utils.hpp
-include/blasr_libcpp/pbdata/utils/BitUtils.hpp
-include/blasr_libcpp/pbdata/utils/SMRTReadUtils.hpp
-include/blasr_libcpp/pbdata/utils/SMRTTitle.hpp
-include/blasr_libcpp/pbdata/utilsImpl.hpp
-include/blasr_libcpp/unittest/pbdata/testdata.h
-lib/libblasr.a
-lib/libpbdata.a
-lib/libpbihdf.a
diff --git a/blasr_libcpp/TODO b/blasr_libcpp/TODO
deleted file mode 100644
index 50a8cc38e6..0000000000
--- a/blasr_libcpp/TODO
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Some code is commented out by patches because it doesn't compile under GCC 4.4
-on CentOS.
diff --git a/blasr_libcpp/buildlink3.mk b/blasr_libcpp/buildlink3.mk
deleted file mode 100644
index 269f7bcceb..0000000000
--- a/blasr_libcpp/buildlink3.mk
+++ /dev/null
@@ -1,23 +0,0 @@
-# $NetBSD: buildlink3.mk,v 1.3 2015/09/16 02:36:53 outpaddling Exp $
-# XXX
-# XXX This file was created automatically using createbuildlink-3.16.
-# XXX After this file has been verified as correct, the comment lines
-# XXX beginning with "XXX" should be removed. Please do not commit
-# XXX unverified buildlink3.mk files.
-# XXX
-# XXX Packages that only install static libraries or headers should
-# XXX include the following line:
-# XXX
-# XXX BUILDLINK_DEPMETHOD.blasr_libcpp?= build
-
-BUILDLINK_TREE+= blasr_libcpp
-
-.if !defined(BLASR_LIBCPP_BUILDLINK3_MK)
-BLASR_LIBCPP_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.blasr_libcpp+= blasr_libcpp>=2015.08.17
-BUILDLINK_PKGSRCDIR.blasr_libcpp?= ../../wip/blasr_libcpp
-=======
-.endif # BLASR_LIBCPP_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -blasr_libcpp
diff --git a/blasr_libcpp/distinfo b/blasr_libcpp/distinfo
deleted file mode 100644
index 2486cc19ec..0000000000
--- a/blasr_libcpp/distinfo
+++ /dev/null
@@ -1,12 +0,0 @@
-$NetBSD: distinfo,v 1.3 2015/09/16 15:50:08 outpaddling Exp $
-
-RMD160 (blasr_libcpp-2015.08.17.tar.xz) = 28c95ad27b0a4de94cdfa378954f6af059b75269
-Size (blasr_libcpp-2015.08.17.tar.xz) = 935436 bytes
-SHA1 (patch-alignment_MappingMetrics.cpp) = 27a2e437437d5abcda08a7e4ba111cfb7bcf7431
-SHA1 (patch-alignment_datastructures_alignment_FilterCriteria.cpp) = 34a53f90f1b16d5121d4c0099a43888ccbe4d14d
-SHA1 (patch-alignment_datastructures_alignment_FilterCriteria.hpp) = 89b6ae88a0882cec0688a949f386bbe35d68afe4
-SHA1 (patch-alignment_format_SAMHeaderPrinter.cpp) = e1e2b9d945a2a3ef31df58cb9ff747f2c755c40e
-SHA1 (patch-alignment_ipc_SharedMemoryAllocator.hpp) = a8d062fc5ee416b9d40c84d7237aaba1e798a878
-SHA1 (patch-configure.py) = c64b88725254593f3d18468f31a3f70d6a3229cc
-SHA1 (patch-pbdata_reads_HoleXY.hpp) = a59816df93098d4e538031ca93fb5acf06f8aa33
-SHA1 (patch-pbdata_utils_SMRTTitle.cpp) = c10115f37146c40d2500312c4a8380d06a4d3b4f
diff --git a/blasr_libcpp/patches/patch-alignment_MappingMetrics.cpp b/blasr_libcpp/patches/patch-alignment_MappingMetrics.cpp
deleted file mode 100644
index dbc01a2f56..0000000000
--- a/blasr_libcpp/patches/patch-alignment_MappingMetrics.cpp
+++ /dev/null
@@ -1,20 +0,0 @@
-$NetBSD: patch-alignment_MappingMetrics.cpp,v 1.1 2015/09/16 02:36:53 outpaddling Exp $
-
---- alignment/MappingMetrics.cpp.orig 2015-08-12 17:41:23.000000000 +0000
-+++ alignment/MappingMetrics.cpp
-@@ -34,6 +34,7 @@ int clock_gettime(clockid_t clk_id, stru
- retval = -1;
- }
- break;
-+#ifndef __NetBSD__
- case CLOCK_PROCESS_CPUTIME_ID:
- case CLOCK_THREAD_CPUTIME_ID:
- start = mach_absolute_time();
-@@ -52,6 +53,7 @@ int clock_gettime(clockid_t clk_id, stru
- tp->tv_nsec = nano - (tp->tv_sec * 1e9);
- retval = 0;
- break;
-+#endif
- default:
- errno = EINVAL;
- retval = -1;
diff --git a/blasr_libcpp/patches/patch-alignment_datastructures_alignment_FilterCriteria.cpp b/blasr_libcpp/patches/patch-alignment_datastructures_alignment_FilterCriteria.cpp
deleted file mode 100644
index 31f742982a..0000000000
--- a/blasr_libcpp/patches/patch-alignment_datastructures_alignment_FilterCriteria.cpp
+++ /dev/null
@@ -1,65 +0,0 @@
-$NetBSD: patch-alignment_datastructures_alignment_FilterCriteria.cpp,v 1.1 2015/09/11 16:48:33 outpaddling Exp $
-
---- alignment/datastructures/alignment/FilterCriteria.cpp.orig 2015-08-12 17:41:23.000000000 +0000
-+++ alignment/datastructures/alignment/FilterCriteria.cpp
-@@ -21,12 +21,12 @@
- Score::Score(const float & value, const ScoreSign & sign)
- : _value(value)
- , _sign(sign)
--{ }
-+{ errorunit = 1e-6; }
-
- Score::Score(const Score & another)
- : _value(another._value)
- , _sign(another._sign)
--{ }
-+{ errorunit = 1e-6; }
-
- Score::~Score() { }
-
-@@ -144,9 +144,18 @@ HitPolicy::Apply(const std::vector<T_Ali
- // Assume that input alignments share the same query name and
- // are sorted by score and tPos asscendingly: worst, ...., best
- int bestScore = ret[0]->score;
-+
-+ /* Not sure how to convert this. C++11ism?
- ret.erase(std::remove_if(ret.begin(), ret.end(),
- [&bestScore](const T_AlignmentCandidate* x)->bool{return x->score != bestScore;}),
- ret.end());
-+ */
-+
-+ // Attempt to replace lambda function. Double check this...
-+ std::vector<T_AlignmentCandidate *>::iterator i = ret.begin();
-+ while ( (*i)->score == bestScore )
-+ ++i;
-+ ret.erase( i, ret.end() );
-
- if (IsAllbest()) {
- return ret;
-@@ -267,18 +276,23 @@ const std::string FilterCriteria::Help(c
- pad + scoreCutoffHelp());
- }*/
-
-+// FIXME: Strange error from CentOS 6.7 g++ 4.4:
-+// /home/bacon/blasr_libcpp/branches/c++0x/alignment/datastructures/alignment/FilterCriteria.cpp:285: error: call of overloaded to_string(int) is ambiguous
-+// /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h:2604: note: candidates are: std::string std::to_string(long long int)
-+// /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h:2610: note: std::string std::to_string(long long unsigned int)
-+// /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h:2616: note: std::string std::to_string(long double)
- const std::string FilterCriteria::MinAlnLengthHelp() {
-- return std::string("(") + std::to_string(_minAlnLength) + ") " +
-+ return std::string("(") + std::to_string(static_cast<long long>(_minAlnLength)) + ") " +
- "Report alignments only if their lengths are greater than minAlnLength.";
- }
-
- const std::string FilterCriteria::MinPctSimilarityHelp() {
-- return std::string("(") + std::to_string(static_cast<int>(_minPctSimilarity)) + ") " +
-+ return std::string("(") + std::to_string(static_cast<long long>(_minPctSimilarity)) + ") " +
- "Report alignments only if their percentage similairty is greater than minPctSimilarity.";
- }
-
- const std::string FilterCriteria::MinPctAccuracyHelp() {
-- return std::string("(") + std::to_string(static_cast<int>(_minPctAccuracy)) + ") " +
-+ return std::string("(") + std::to_string(static_cast<long long>(_minPctAccuracy)) + ") " +
- "Report alignments only if their percentage accuray is greater than minAccuracy.";
- }
-
diff --git a/blasr_libcpp/patches/patch-alignment_datastructures_alignment_FilterCriteria.hpp b/blasr_libcpp/patches/patch-alignment_datastructures_alignment_FilterCriteria.hpp
deleted file mode 100644
index 6040b6dc3a..0000000000
--- a/blasr_libcpp/patches/patch-alignment_datastructures_alignment_FilterCriteria.hpp
+++ /dev/null
@@ -1,14 +0,0 @@
-$NetBSD: patch-alignment_datastructures_alignment_FilterCriteria.hpp,v 1.1 2015/09/11 16:48:33 outpaddling Exp $
-
---- alignment/datastructures/alignment/FilterCriteria.hpp.orig 2015-08-12 17:41:23.000000000 +0000
-+++ alignment/datastructures/alignment/FilterCriteria.hpp
-@@ -39,7 +39,8 @@ public:
- private:
- float _value;
- ScoreSign _sign;
-- static constexpr float errorunit = 1e-6;
-+ //static constexpr float errorunit = 1e-6;
-+ float errorunit;
- };
-
- class HitPolicy {
diff --git a/blasr_libcpp/patches/patch-alignment_format_SAMHeaderPrinter.cpp b/blasr_libcpp/patches/patch-alignment_format_SAMHeaderPrinter.cpp
deleted file mode 100644
index b08395df7b..0000000000
--- a/blasr_libcpp/patches/patch-alignment_format_SAMHeaderPrinter.cpp
+++ /dev/null
@@ -1,26 +0,0 @@
-$NetBSD: patch-alignment_format_SAMHeaderPrinter.cpp,v 1.1 2015/09/11 16:48:33 outpaddling Exp $
-
---- alignment/format/SAMHeaderPrinter.cpp.orig 2015-08-12 17:41:23.000000000 +0000
-+++ alignment/format/SAMHeaderPrinter.cpp
-@@ -183,8 +183,10 @@ SAMHeaderPG::SAMHeaderPG(const std::stri
- }
-
- // SAMHeaderSQ
--SAMHeaderSQ::SAMHeaderSQ(const std::string & sn, const DNALength & ln, const std::string & md5)
--: SAMHeaderSQ(sn, std::to_string(ln), md5) {}
-+SAMHeaderSQ::SAMHeaderSQ(const std::string & sn, const DNALength & ln, const std::string & md5) {}
-+
-+// Doesn't compile in GCC 4.4.7. C++11ism?
-+// : SAMHeaderSQ(sn, std::to_string(static_cast<unsigned long long>(ln)), md5) {}
-
- SAMHeaderSQ::SAMHeaderSQ(const std::string & sn, const string & ln, const std::string & md5)
- : SAMHeaderGroup() {
-@@ -400,7 +402,7 @@ SAMHeaderPGs SAMHeaderPrinter::MakePGs(c
- #endif
- }
-
-- pgs.Add(SAMHeaderPG(std::to_string(prog_id), progName, progVersion, commandLine));
-+ pgs.Add(SAMHeaderPG(std::to_string(static_cast<unsigned long long>(prog_id)), progName, progVersion, commandLine));
- return pgs;
- }
-
diff --git a/blasr_libcpp/patches/patch-alignment_ipc_SharedMemoryAllocator.hpp b/blasr_libcpp/patches/patch-alignment_ipc_SharedMemoryAllocator.hpp
deleted file mode 100644
index f9ed567144..0000000000
--- a/blasr_libcpp/patches/patch-alignment_ipc_SharedMemoryAllocator.hpp
+++ /dev/null
@@ -1,12 +0,0 @@
-$NetBSD: patch-alignment_ipc_SharedMemoryAllocator.hpp,v 1.2 2015/09/11 16:48:33 outpaddling Exp $
-
---- alignment/ipc/SharedMemoryAllocator.hpp.orig 2015-08-12 17:41:23.000000000 +0000
-+++ alignment/ipc/SharedMemoryAllocator.hpp
-@@ -7,6 +7,7 @@
- #include <fcntl.h>
- #include <unistd.h>
- #include <sys/mman.h>
-+#include <sys/stat.h>
-
- template<typename T_Data>
- int AllocateMappedShare(std::string &handle, int dataLength, T_Data *&dataPtr, int &shmId) {
diff --git a/blasr_libcpp/patches/patch-configure.py b/blasr_libcpp/patches/patch-configure.py
deleted file mode 100644
index 906f08d53a..0000000000
--- a/blasr_libcpp/patches/patch-configure.py
+++ /dev/null
@@ -1,19 +0,0 @@
-$NetBSD: patch-configure.py,v 1.3 2015/09/16 02:36:53 outpaddling Exp $
-
---- configure.py.orig 2015-08-12 17:41:23.000000000 +0000
-+++ configure.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python
-+#!/usr/bin/env python2.7
- """Configure the build.
-
- - Fetch HDF5 headers.
-@@ -93,7 +93,7 @@ nohdf ?=1
- """%(dict(thisdir=thisdir))
-
- def get_OS_STRING():
-- G_BUILDOS_CMD = """bash -c 'set -e; set -o pipefail; id=$(lsb_release -si | tr "[:upper:]" "[:lower:]"); rel=$(lsb_release -sr); case $id in ubuntu) printf "$id-%04d\n" ${rel/./};; centos) echo "$id-${rel%%.*}";; *) echo "$id-$rel";; esac' 2>/dev/null"""
-+ G_BUILDOS_CMD = """printf `uname`-`uname -r | cut -d - -f 1`'\n'"""
- return shell(G_BUILDOS_CMD)
-
- def get_PBBAM(env, prefix):
diff --git a/blasr_libcpp/patches/patch-pbdata_reads_HoleXY.hpp b/blasr_libcpp/patches/patch-pbdata_reads_HoleXY.hpp
deleted file mode 100644
index cccd96fc07..0000000000
--- a/blasr_libcpp/patches/patch-pbdata_reads_HoleXY.hpp
+++ /dev/null
@@ -1,12 +0,0 @@
-$NetBSD: patch-pbdata_reads_HoleXY.hpp,v 1.2 2015/09/11 16:48:33 outpaddling Exp $
-
---- pbdata/reads/HoleXY.hpp.orig 2015-08-12 17:41:23.000000000 +0000
-+++ pbdata/reads/HoleXY.hpp
-@@ -2,6 +2,7 @@
- #define _BLASR_HOLE_XY_HPP_
-
- #include <stdlib.h>
-+#include <stdint.h>
-
- class HoleXY {
- public:
diff --git a/blasr_libcpp/patches/patch-pbdata_utils_SMRTTitle.cpp b/blasr_libcpp/patches/patch-pbdata_utils_SMRTTitle.cpp
deleted file mode 100644
index fab3edd924..0000000000
--- a/blasr_libcpp/patches/patch-pbdata_utils_SMRTTitle.cpp
+++ /dev/null
@@ -1,9 +0,0 @@
-$NetBSD: patch-pbdata_utils_SMRTTitle.cpp,v 1.1 2015/09/16 02:36:53 outpaddling Exp $
-
---- pbdata/utils/SMRTTitle.cpp.orig 2015-08-12 17:41:23.000000000 +0000
-+++ pbdata/utils/SMRTTitle.cpp
-@@ -1,3 +1,4 @@
-+#include <cstdlib>
- #include "utils/SMRTTitle.hpp"
-
- /// Parse a Pacbio read name, it is a SMRTTitle, get movieName,
diff --git a/bowtie/DESCR b/bowtie/DESCR
deleted file mode 100644
index 03d1a2c426..0000000000
--- a/bowtie/DESCR
+++ /dev/null
@@ -1,5 +0,0 @@
-Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
-DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
-reads per hour.
-
-WWW: http://bowtie-bio.sourceforge.net/index.shtml
diff --git a/bowtie/PLIST b/bowtie/PLIST
deleted file mode 100644
index 483a68db8a..0000000000
--- a/bowtie/PLIST
+++ /dev/null
@@ -1,91 +0,0 @@
-@comment $NetBSD$
-bin/best_verify.pl
-bin/bowtie
-bin/bowtie-align-l
-bin/bowtie-align-s
-bin/bowtie-build
-bin/bowtie-build-l
-bin/bowtie-build-s
-bin/bowtie-inspect
-bin/bowtie-inspect-l
-bin/bowtie-inspect-s
-bin/bs_mapability.pl
-bin/build_test.sh
-bin/colorize_fasta.pl
-bin/colorize_fastq.pl
-bin/convert_quals.pl
-bin/fastq_to_tabbed.pl
-bin/gen_2b_occ_lookup.pl
-bin/gen_dnamasks2colormask.pl
-bin/gen_occ_lookup.pl
-bin/gen_solqual_lookup.pl
-bin/infer_fraglen.pl
-bin/make_a_thaliana_tair.sh
-bin/make_b_taurus_UMD3.sh
-bin/make_c_elegans.sh
-bin/make_canFam2.sh
-bin/make_d_melanogaster.sh
-bin/make_e_coli.sh
-bin/make_galGal3.sh
-bin/make_h_sapiens_ncbi36.sh
-bin/make_h_sapiens_ncbi37.sh
-bin/make_hg18.sh
-bin/make_hg19.sh
-bin/make_m_musculus_ncbi37.sh
-bin/make_mm8.sh
-bin/make_mm9.sh
-bin/make_rn4.sh
-bin/make_s_cerevisiae.sh
-bin/mapability.pl
-bin/pe_verify.pl
-bin/reconcile_alignments.pl
-bin/reconcile_alignments_pe.pl
-share/bowtie/genomes/.cvsignore
-share/bowtie/genomes/NC_008253.fna
-share/bowtie/indexes/e_coli.1.ebwt
-share/bowtie/indexes/e_coli.2.ebwt
-share/bowtie/indexes/e_coli.3.ebwt
-share/bowtie/indexes/e_coli.4.ebwt
-share/bowtie/indexes/e_coli.README
-share/bowtie/indexes/e_coli.rev.1.ebwt
-share/bowtie/indexes/e_coli.rev.2.ebwt
-share/bowtie/reads/e_coli_1000.fa
-share/bowtie/reads/e_coli_1000.fq
-share/bowtie/reads/e_coli_1000.raw
-share/bowtie/reads/e_coli_10000snp.csfasta
-share/bowtie/reads/e_coli_10000snp.fa
-share/bowtie/reads/e_coli_10000snp.fq
-share/bowtie/reads/e_coli_1000_1.fa
-share/bowtie/reads/e_coli_1000_1.fq
-share/bowtie/reads/e_coli_1000_2.fa
-share/bowtie/reads/e_coli_1000_2.fq
-share/doc/bowtie/README
-share/doc/bowtie/manual.html
-share/doc/bowtie/release.txt
-share/doc/bowtie/strip_markdown.pl
-share/doc/bowtie/style.css
-share/doc/bowtie/website/css/style.css
-share/doc/bowtie/website/foot.ssi
-share/doc/bowtie/website/images/bowtie_logo.png
-share/doc/bowtie/website/images/osi-certified.gif
-share/doc/bowtie/website/images/sflogo.png
-share/doc/bowtie/website/images/university.small.horizontal.white.png
-share/doc/bowtie/website/index.html
-share/doc/bowtie/website/index.shtml
-share/doc/bowtie/website/latest-version.txt
-share/doc/bowtie/website/manual.html
-share/doc/bowtie/website/manual.shtml
-share/doc/bowtie/website/manual.ssi
-share/doc/bowtie/website/md5s.shtml
-share/doc/bowtie/website/md5s.ssi
-share/doc/bowtie/website/news.shtml
-share/doc/bowtie/website/old_news.ssi
-share/doc/bowtie/website/other_tools.shtml
-share/doc/bowtie/website/other_tools.ssi
-share/doc/bowtie/website/push_langmead.sh
-share/doc/bowtie/website/recent_news.ssi
-share/doc/bowtie/website/rhsidebar.ssi
-share/doc/bowtie/website/top.ssi
-share/doc/bowtie/website/tutorial.html
-share/doc/bowtie/website/tutorial.shtml
-@pkgdir share/docs/bowtie
diff --git a/bowtie/buildlink3.mk b/bowtie/buildlink3.mk
deleted file mode 100644
index 7c97c47730..0000000000
--- a/bowtie/buildlink3.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-# $NetBSD: buildlink3.mk,v 1.1 2015/01/28 20:52:06 outpaddling Exp $
-
-BUILDLINK_TREE+= bowtie
-
-.if !defined(BOWTIE_BUILDLINK3_MK)
-BOWTIE_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.bowtie+= bowtie>=1.0.1
-BUILDLINK_PKGSRCDIR.bowtie?= ../../wip/bowtie
-.endif # BOWTIE_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -bowtie
diff --git a/bowtie/distinfo b/bowtie/distinfo
deleted file mode 100644
index 1f9a504077..0000000000
--- a/bowtie/distinfo
+++ /dev/null
@@ -1,7 +0,0 @@
-$NetBSD$
-
-RMD160 (bowtie-1.1.2.tar.gz) = 723f8cc273c6db3031c2dc4b8bd7fab70fbd78f2
-SHA512 (bowtie-1.1.2.tar.gz) = 81f8df4b292b70d57a545b3d485d166b92cdd68be144f7fe60215de1175a85c815c584559f647c097fc03eccfa24eff91c816a6db8b11ea162287a3a8e500701
-Size (bowtie-1.1.2.tar.gz) = 7831346 bytes
-SHA1 (patch-Makefile) = f38c82018fc458511bf40bb6baf0e6b1bd6c7faf
-SHA1 (patch-scripts_test_random__bowtie__tests.sh) = aaa2911d4b5e15082eb0857f00c8f53c4508688c
diff --git a/bowtie/patches/patch-Makefile b/bowtie/patches/patch-Makefile
deleted file mode 100644
index a754534e7f..0000000000
--- a/bowtie/patches/patch-Makefile
+++ /dev/null
@@ -1,18 +0,0 @@
-$NetBSD$
-
-# Respect env
---- Makefile.orig 2018-09-14 16:04:25.976840223 +0000
-+++ Makefile
-@@ -8,9 +8,9 @@ bindir = $(prefix)/bin
- SEQAN_DIR = SeqAn-1.1
- SEQAN_INC = -I $(SEQAN_DIR)
- INC = $(SEQAN_INC) -I third_party
--CPP = g++
--CXX = $(CPP)
--CC = gcc
-+CPP ?= g++
-+CXX ?= $(CPP)
-+CC ?= gcc
- HEADERS = $(wildcard *.h)
- BOWTIE_MM = 1
- BOWTIE_SHARED_MEM = 1
diff --git a/bowtie/patches/patch-scripts_test_random__bowtie__tests.sh b/bowtie/patches/patch-scripts_test_random__bowtie__tests.sh
deleted file mode 100644
index 61dd92127d..0000000000
--- a/bowtie/patches/patch-scripts_test_random__bowtie__tests.sh
+++ /dev/null
@@ -1,20 +0,0 @@
-$NetBSD$
-
-# Remove bashisms
---- scripts/test/random_bowtie_tests.sh.orig 2018-09-14 16:08:02.613191531 +0000
-+++ scripts/test/random_bowtie_tests.sh
-@@ -1,4 +1,4 @@
--#!/bin/bash
-+#!/bin/sh
-
- PREFIX=${0%/*}
-
-@@ -9,7 +9,7 @@ else
- shift
- fi
-
--if [ "$1" == "-c" ] ; then
-+if [ "$1" = "-c" ] ; then
- make clean
- shift
- fi
diff --git a/cdbfasta/DESCR b/cdbfasta/DESCR
deleted file mode 100644
index 9676c40a92..0000000000
--- a/cdbfasta/DESCR
+++ /dev/null
@@ -1,3 +0,0 @@
-Fast indexing and retrieval of fasta records from flat file data bases.
-
-WWW: http://sourceforge.net/projects/cdbfasta/
diff --git a/cdbfasta/PLIST b/cdbfasta/PLIST
deleted file mode 100644
index 66edc1ab05..0000000000
--- a/cdbfasta/PLIST
+++ /dev/null
@@ -1,3 +0,0 @@
-@comment $NetBSD$
-bin/cdbfasta
-bin/cdbyank
diff --git a/cdbfasta/TODO b/cdbfasta/TODO
deleted file mode 100644
index b687356e6b..0000000000
--- a/cdbfasta/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test
diff --git a/cdbfasta/buildlink3.mk b/cdbfasta/buildlink3.mk
deleted file mode 100644
index bc87acc702..0000000000
--- a/cdbfasta/buildlink3.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-# $NetBSD$
-
-BUILDLINK_TREE+= cdbfasta
-
-.if !defined(CDBFASTA_BUILDLINK3_MK)
-CDBFASTA_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.cdbfasta+= cdbfasta>=2010.07.22
-BUILDLINK_PKGSRCDIR.cdbfasta?= ../../wip/cdbfasta
-.endif # CDBFASTA_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -cdbfasta
diff --git a/cdbfasta/distinfo b/cdbfasta/distinfo
deleted file mode 100644
index b7363d0153..0000000000
--- a/cdbfasta/distinfo
+++ /dev/null
@@ -1,6 +0,0 @@
-$NetBSD$
-
-RMD160 (cdbfasta-2010.07.22.tar.gz) = c90e0ede03a01bf2da77f9beaa3c97fa7e46ff2a
-SHA512 (cdbfasta-2010.07.22.tar.gz) = 500b3cdf4bf4e21c78a285739c6544e3f2bed377f8e3858c8ace240a9107d765c89cff8004ca2ea001860abc04fc48bc37c03569da5b16115f4419f5fd9bcd5e
-Size (cdbfasta-2010.07.22.tar.gz) = 59735 bytes
-SHA1 (patch-Makefile) = 9ac728af0e7f1149ab1ae226759591df2e34096e
diff --git a/cdbfasta/patches/patch-Makefile b/cdbfasta/patches/patch-Makefile
deleted file mode 100644
index 5df71c6fe4..0000000000
--- a/cdbfasta/patches/patch-Makefile
+++ /dev/null
@@ -1,61 +0,0 @@
-$NetBSD$
-
---- Makefile.orig 2015-02-18 10:08:59.000000000 -0600
-+++ Makefile 2015-02-18 10:41:31.000000000 -0600
-@@ -18,7 +18,9 @@
- MARCH =
- endif
-
--CC := g++
-+# Use the correct compiler (CXX, not CC) and respect the environment
-++CXX?=g++
-+
- BASEFLAGS = -Wall ${SEARCHDIRS} $(MARCH) -DENABLE_COMPRESSION=0 -D_FILE_OFFSET_BITS=64 \
- -D_LARGEFILE_SOURCE -fno-exceptions -fno-rtti -fno-strict-aliasing \
- -D_REENTRANT
-@@ -33,25 +35,25 @@
- endif
-
- ifeq ($(findstring nommap,$(MAKECMDGOALS)),)
-- CFLAGS = $(DBGFLAGS) $(BASEFLAGS)
-+ CXXFLAGS = $(DBGFLAGS) $(BASEFLAGS)
- else
-- CFLAGS = $(DBGFLAGS) $(BASEFLAGS) -DNO_MMAP
-+ CXXFLAGS = $(DBGFLAGS) $(BASEFLAGS) -DNO_MMAP
- endif
-
- %.o : %.c
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- %.o : %.cc
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- %.o : %.C
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- %.o : %.cpp
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- %.o : %.cxx
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CXX} ${CXXFLAGS} -c $< -o $@
-
- # C/C++ linker
-
-@@ -65,10 +67,10 @@
- debug: all
- nommap: all
- cdbfasta: ./cdbfasta.o ./gcdbz.o $(LIBS) ${GCLDIR}/gcdb.o ${GCLDIR}/GBase.o ${GCLDIR}/GStr.o ${GCLDIR}/GArgs.o
-- ${LINKER} -o $@ ${filter-out %.a %.so, $^} $(LDFLAGS)
-+ ${CXX} -o $@ ${filter-out %.a %.so, $^} $(LDFLAGS)
-
- cdbyank : ./cdbyank.o ./gcdbz.o ${GCLDIR}/gcdb.o ${GCLDIR}/GBase.o ${GCLDIR}/GStr.o ${GCLDIR}/GArgs.o
-- ${LINKER} -o $@ ${filter-out %.a %.so, $^} $(LDFLAGS)
-+ ${CXX} -o $@ ${filter-out %.a %.so, $^} $(LDFLAGS)
-
- # target for removing all object files
-
diff --git a/cluster-admin/DESCR b/cluster-admin/DESCR
deleted file mode 100644
index 4b45b7edac..0000000000
--- a/cluster-admin/DESCR
+++ /dev/null
@@ -1,3 +0,0 @@
-Cluster-admin is a suite of tools for building and managing FreeBSD clusters.
-It automates the processing of creating a head node and compute nodes, and
-managing configuration and software after installation.
diff --git a/cluster-admin/PLIST b/cluster-admin/PLIST
deleted file mode 100644
index 66efd5055c..0000000000
--- a/cluster-admin/PLIST
+++ /dev/null
@@ -1,119 +0,0 @@
-@comment $NetBSD$
-bin/cluster-all-nodes
-bin/cluster-backup-nodes
-bin/cluster-compute-nodes
-bin/cluster-down-nodes
-bin/cluster-file-servers
-bin/cluster-passwd
-bin/cluster-pfs-nodes
-bin/cluster-pw-check
-bin/cluster-raid-nodes
-bin/cluster-vis-nodes
-bin/cluster-zfs-nodes
-bin/condor-build-R-packages
-bin/condor-cpus
-bin/condor-list-packages
-bin/psnode
-bin/slurm-cluster-load
-bin/slurm-find-strays
-bin/slurm-gui-job
-bin/slurm-job-hist
-bin/slurm-job-stats
-bin/slurm-job-status
-bin/slurm-load-summary
-bin/slurm-memory-use
-bin/slurm-node-info
-bin/slurm-pending-jobs
-bin/slurm-shell
-bin/slurm-user-cores
-bin/topjob
-bin/topnode
-libexec/add-gecos.awk
-sbin/cluster-add-to-group
-sbin/cluster-adduser
-sbin/cluster-admin
-sbin/cluster-archive-user-dir
-sbin/cluster-change-group-gid
-sbin/cluster-change-nfsd-count
-sbin/cluster-change-primary-group
-sbin/cluster-change-uid
-sbin/cluster-check-cron-updates
-sbin/cluster-create-pw-age
-sbin/cluster-diagnostics
-sbin/cluster-dist-file
-sbin/cluster-enable-autologout
-sbin/cluster-firewalld-config
-sbin/cluster-ganglia-restart
-sbin/cluster-get-sync-file
-sbin/cluster-head-check
-sbin/cluster-highest-uid
-sbin/cluster-idrac-config
-sbin/cluster-init-node
-sbin/cluster-krb-auth-setup
-sbin/cluster-lock-local-pw
-sbin/cluster-lock-user
-sbin/cluster-lowest-uid
-sbin/cluster-munge-enable
-sbin/cluster-node-admin
-sbin/cluster-node-type
-sbin/cluster-passwd-expiration
-sbin/cluster-passwd-user-expiration
-sbin/cluster-pkgsrc-admin
-sbin/cluster-recreate-user
-sbin/cluster-remove-from-group
-sbin/cluster-remove-from-known-hosts
-sbin/cluster-remove-user
-sbin/cluster-restore-user
-sbin/cluster-run
-sbin/cluster-set-compute-memory-limits
-sbin/cluster-setup
-sbin/cluster-shutdown
-sbin/cluster-slurm-enable
-sbin/cluster-ssh-keygen
-sbin/cluster-stay-down
-sbin/cluster-sync-backup-nodes
-sbin/cluster-sync-files
-sbin/cluster-sync-node
-sbin/cluster-sync-packages
-sbin/cluster-sync-pw
-sbin/cluster-sync-sysfiles
-sbin/cluster-sync-user
-sbin/cluster-transfer-pw
-sbin/cluster-unlock-local-pw
-sbin/cluster-unlock-user
-sbin/cluster-update-backup-nodes
-sbin/cluster-update-file-servers
-sbin/cluster-update-vis-nodes
-sbin/cluster-user-admin
-sbin/cluster-user-cleanup
-sbin/cluster-useradd
-sbin/cluster-users
-sbin/condor-build-R-packages
-sbin/condor-list-packages
-sbin/ganglia-web-setup
-sbin/node-sync-all-users
-sbin/node-sync-groups
-sbin/node-sync-users
-sbin/slurm-admin
-sbin/slurm-cron-updates
-sbin/slurm-drain-all
-sbin/slurm-restart
-sbin/slurm-resume-nodes
-sbin/slurm-resume-updated-nodes
-sbin/slurm-shutdown-idle-nodes
-sbin/slurm-sync-backup
-sbin/slurm-sync-config
-sbin/slurm-update-idle-nodes
-sbin/slurm-usage-report
-sbin/spcm-banner
-sbin/ssh-keygen-for-user
-sbin/update-cluster-admin-wip
-share/cluster-admin/WWW/centos-power.jpg
-share/cluster-admin/WWW/global_styles.css
-share/cluster-admin/WWW/gmetad.conf.template
-share/cluster-admin/WWW/gmond.conf.template
-share/cluster-admin/WWW/index.php
-share/cluster-admin/WWW/pkgsrc.jpg
-share/cluster-admin/profile.d/zzz-cluster.csh
-share/cluster-admin/profile.d/zzz-cluster.sh
-share/cluster-admin/sys-update.sbatch
diff --git a/cluster-admin/distinfo b/cluster-admin/distinfo
deleted file mode 100644
index 36f891bd09..0000000000
--- a/cluster-admin/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD$
-
-RMD160 (cluster-admin-0.4.tar.xz) = 438266ecca81c2bad64bf0095145b01819196ab2
-SHA512 (cluster-admin-0.4.tar.xz) = 1eb25336b56eb2b685404351d21b823202146b20ce7f0aef618fbcbfa6e8edc7075629a7d3badc88537e9cecdaada97f37864c3df58f0440f1781484a07ae8f4
-Size (cluster-admin-0.4.tar.xz) = 115368 bytes
diff --git a/daligner/DESCR b/daligner/DESCR
deleted file mode 100644
index 9b0ea503eb..0000000000
--- a/daligner/DESCR
+++ /dev/null
@@ -1,3 +0,0 @@
-Find all significant local alignments between reads.
-
-WWW: https://github.com/thegenemyers/DALIGNER
diff --git a/daligner/PLIST b/daligner/PLIST
deleted file mode 100644
index 34feb32a51..0000000000
--- a/daligner/PLIST
+++ /dev/null
@@ -1,21 +0,0 @@
-@comment $NetBSD$
-bin/DAPI.py
-bin/DAPipe.py
-bin/DB2Falcon
-bin/DBLA_to_falcon.py
-bin/HPCdaligner
-bin/HPCmapper
-bin/LA4Falcon
-bin/LAPI.py
-bin/LAPipe.py
-bin/LAcat
-bin/LAcheck
-bin/LAmerge
-bin/LAshow
-bin/LAsort
-bin/LAsplit
-bin/daligner
-bin/daligner_p
-include/align.h
-include/filter.h
-lib/libdaligner.a
diff --git a/daligner/TODO b/daligner/TODO
deleted file mode 100644
index b687356e6b..0000000000
--- a/daligner/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test
diff --git a/daligner/buildlink3.mk b/daligner/buildlink3.mk
deleted file mode 100644
index 6215ee13f5..0000000000
--- a/daligner/buildlink3.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-# $NetBSD$
-
-BUILDLINK_TREE+= daligner
-
-.if !defined(DALIGNER_BUILDLINK3_MK)
-DALIGNER_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.daligner+= daligner-2015.10.28{,nb*}
-BUILDLINK_PKGSRCDIR.daligner?= ../../wip/daligner
-.endif # DALIGNER_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -daligner
diff --git a/daligner/distinfo b/daligner/distinfo
deleted file mode 100644
index ee0c9a56b7..0000000000
--- a/daligner/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD$
-
-RMD160 (daligner-2015.10.28.tar.xz) = 813725f49fb82431b7c0397874732bc5368c84c6
-SHA512 (daligner-2015.10.28.tar.xz) = 39e3e760b378711df043223805670ee256ac7f0a8c29d74bc103ffd09844fa09fdfb02925c76ce841fa5c3b51f53f385f3edb66fafed824411f7cc60f3655579
-Size (daligner-2015.10.28.tar.xz) = 57128 bytes
diff --git a/dazz_db/DESCR b/dazz_db/DESCR
deleted file mode 100644
index c86c5a0f6a..0000000000
--- a/dazz_db/DESCR
+++ /dev/null
@@ -1,3 +0,0 @@
-The Dazzler Data Base.
-
-WWW: https://github.com/thegenemyers/DAZZ_DB
diff --git a/dazz_db/PLIST b/dazz_db/PLIST
deleted file mode 100644
index 890a485d77..0000000000
--- a/dazz_db/PLIST
+++ /dev/null
@@ -1,17 +0,0 @@
-@comment $NetBSD$
-bin/Catrack
-bin/DAM2fasta
-bin/DB2fasta
-bin/DB2quiva
-bin/DBdust
-bin/DBrm
-bin/DBshow
-bin/DBsplit
-bin/DBstats
-bin/fasta2DAM
-bin/fasta2DB
-bin/quiva2DB
-bin/simulator
-include/DB.h
-include/QV.h
-lib/libdazzdb.a
diff --git a/dazz_db/TODO b/dazz_db/TODO
deleted file mode 100644
index b687356e6b..0000000000
--- a/dazz_db/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test
diff --git a/dazz_db/buildlink3.mk b/dazz_db/buildlink3.mk
deleted file mode 100644
index 88c09a6a0d..0000000000
--- a/dazz_db/buildlink3.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-# $NetBSD$
-
-BUILDLINK_TREE+= dazz_db
-
-.if !defined(DAZZ_DB_BUILDLINK3_MK)
-DAZZ_DB_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.dazz_db+= dazz_db>=2015.08.17
-BUILDLINK_PKGSRCDIR.dazz_db?= ../../wip/dazz_db
-.endif # DAZZ_DB_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -dazz_db
diff --git a/dazz_db/distinfo b/dazz_db/distinfo
deleted file mode 100644
index 632f605b9a..0000000000
--- a/dazz_db/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD$
-
-RMD160 (dazz_db-2015.10.28.tar.xz) = a3324f7e13ad7069ff2214afdf1e1fb94a1802e6
-SHA512 (dazz_db-2015.10.28.tar.xz) = 9262a5e3259b99ff70fe56111be708963e1b9e25af62c1d3289a7abc6d825ce957949d1b90db441ac9057a37665fbc4017ccef0f1fe78f27877b3c92a25e2f68
-Size (dazz_db-2015.10.28.tar.xz) = 49300 bytes
diff --git a/denyhosts/DESCR b/denyhosts/DESCR
deleted file mode 100644
index 81f4a513b4..0000000000
--- a/denyhosts/DESCR
+++ /dev/null
@@ -1,3 +0,0 @@
-DenyHosts is a script intended to be run by system administrators to help
-thwart SSH server attacks (also known as dictionary based attacks and brute
-force attacks).
diff --git a/denyhosts/PLIST b/denyhosts/PLIST
deleted file mode 100644
index 39f155d4f6..0000000000
--- a/denyhosts/PLIST
+++ /dev/null
@@ -1,78 +0,0 @@
-@comment $NetBSD$
-bin/denyhosts.py
-${PYSITELIB}/DenyHosts/__init__.py
-${PYSITELIB}/DenyHosts/__init__.pyc
-${PYSITELIB}/DenyHosts/__init__.pyo
-${PYSITELIB}/DenyHosts/allowedhosts.py
-${PYSITELIB}/DenyHosts/allowedhosts.pyc
-${PYSITELIB}/DenyHosts/allowedhosts.pyo
-${PYSITELIB}/DenyHosts/constants.py
-${PYSITELIB}/DenyHosts/constants.pyc
-${PYSITELIB}/DenyHosts/constants.pyo
-${PYSITELIB}/DenyHosts/counter.py
-${PYSITELIB}/DenyHosts/counter.pyc
-${PYSITELIB}/DenyHosts/counter.pyo
-${PYSITELIB}/DenyHosts/daemon.py
-${PYSITELIB}/DenyHosts/daemon.pyc
-${PYSITELIB}/DenyHosts/daemon.pyo
-${PYSITELIB}/DenyHosts/deny_hosts.py
-${PYSITELIB}/DenyHosts/deny_hosts.pyc
-${PYSITELIB}/DenyHosts/deny_hosts.pyo
-${PYSITELIB}/DenyHosts/denyfileutil.py
-${PYSITELIB}/DenyHosts/denyfileutil.pyc
-${PYSITELIB}/DenyHosts/denyfileutil.pyo
-${PYSITELIB}/DenyHosts/filetracker.py
-${PYSITELIB}/DenyHosts/filetracker.pyc
-${PYSITELIB}/DenyHosts/filetracker.pyo
-${PYSITELIB}/DenyHosts/lockfile.py
-${PYSITELIB}/DenyHosts/lockfile.pyc
-${PYSITELIB}/DenyHosts/lockfile.pyo
-${PYSITELIB}/DenyHosts/loginattempt.py
-${PYSITELIB}/DenyHosts/loginattempt.pyc
-${PYSITELIB}/DenyHosts/loginattempt.pyo
-${PYSITELIB}/DenyHosts/old-daemon.py
-${PYSITELIB}/DenyHosts/old-daemon.pyc
-${PYSITELIB}/DenyHosts/old-daemon.pyo
-${PYSITELIB}/DenyHosts/plugin.py
-${PYSITELIB}/DenyHosts/plugin.pyc
-${PYSITELIB}/DenyHosts/plugin.pyo
-${PYSITELIB}/DenyHosts/prefs.py
-${PYSITELIB}/DenyHosts/prefs.pyc
-${PYSITELIB}/DenyHosts/prefs.pyo
-${PYSITELIB}/DenyHosts/purgecounter.py
-${PYSITELIB}/DenyHosts/purgecounter.pyc
-${PYSITELIB}/DenyHosts/purgecounter.pyo
-${PYSITELIB}/DenyHosts/python_version.py
-${PYSITELIB}/DenyHosts/python_version.pyc
-${PYSITELIB}/DenyHosts/python_version.pyo
-${PYSITELIB}/DenyHosts/regex.py
-${PYSITELIB}/DenyHosts/regex.pyc
-${PYSITELIB}/DenyHosts/regex.pyo
-${PYSITELIB}/DenyHosts/report.py
-${PYSITELIB}/DenyHosts/report.pyc
-${PYSITELIB}/DenyHosts/report.pyo
-${PYSITELIB}/DenyHosts/restricted.py
-${PYSITELIB}/DenyHosts/restricted.pyc
-${PYSITELIB}/DenyHosts/restricted.pyo
-${PYSITELIB}/DenyHosts/sync.py
-${PYSITELIB}/DenyHosts/sync.pyc
-${PYSITELIB}/DenyHosts/sync.pyo
-${PYSITELIB}/DenyHosts/util.py
-${PYSITELIB}/DenyHosts/util.pyc
-${PYSITELIB}/DenyHosts/util.pyo
-${PYSITELIB}/DenyHosts/version.py
-${PYSITELIB}/DenyHosts/version.pyc
-${PYSITELIB}/DenyHosts/version.pyo
-share/denyhosts/CHANGELOG.txt
-share/denyhosts/LICENSE.txt
-share/denyhosts/README.txt
-share/denyhosts/daemon-control-dist
-share/denyhosts/denyhosts.cfg
-share/denyhosts/denyhosts.cfg-dist
-share/denyhosts/plugins/README.contrib
-share/denyhosts/plugins/shorewall_allow.sh
-share/denyhosts/plugins/shorewall_deny.sh
-share/denyhosts/plugins/test_deny.py
-share/denyhosts/scripts/restricted_from_invalid.py
-share/denyhosts/scripts/restricted_from_passwd.py
-share/denyhosts/setup.py
diff --git a/denyhosts/TODO b/denyhosts/TODO
deleted file mode 100644
index b687356e6b..0000000000
--- a/denyhosts/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test
diff --git a/denyhosts/distinfo b/denyhosts/distinfo
deleted file mode 100644
index 48de88044f..0000000000
--- a/denyhosts/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD$
-
-RMD160 (DenyHosts-2.6.tar.gz) = cab4206af992f5405ed1c9b302341c7b5649c71a
-SHA512 (DenyHosts-2.6.tar.gz) = 331144348d4930e2fa7a057a779bb7504dfa8ec348660e1a73fcd6a9195258408abb7c77de2bcc96724dfc42afbee918320eebfbc3b380d6ac4ff2d275e89600
-Size (DenyHosts-2.6.tar.gz) = 42667 bytes
diff --git a/diffanal/DESCR b/diffanal/DESCR
deleted file mode 100644
index 1e328481ba..0000000000
--- a/diffanal/DESCR
+++ /dev/null
@@ -1,5 +0,0 @@
-Diffanal aims to provide a fast and simple differential analysis tool
-that just works and does not require any knowledge beyond basic Unix
-command-line skills. The code is written entirely in C to maximize
-efficiency and portability, and to provide a simple command-line user
-interface.
diff --git a/diffanal/PLIST b/diffanal/PLIST
deleted file mode 100644
index 48bc504bb9..0000000000
--- a/diffanal/PLIST
+++ /dev/null
@@ -1,9 +0,0 @@
-@comment $NetBSD$
-bin/diffanal
-libexec/diffanal/abundance
-libexec/diffanal/fold-change
-libexec/diffanal/normalize
-man/man1/diffanal-abundance.1
-man/man1/diffanal-fold-change.1
-man/man1/diffanal-normalize.1
-man/man1/diffanal.1
diff --git a/diffanal/distinfo b/diffanal/distinfo
deleted file mode 100644
index 71b290d557..0000000000
--- a/diffanal/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD$
-
-BLAKE2s (diffanal-0.1.0.21-f5f29e07e345829c82cab97b8e4245cc41deab3c.tar.gz) = f9656ffd830f0b5635bdfe8fb45d21fe986db11a8437da02a666bd1a61f47822
-SHA512 (diffanal-0.1.0.21-f5f29e07e345829c82cab97b8e4245cc41deab3c.tar.gz) = dc66c1645521f37196e3bd5db105ace91926e99e08f1419adae2c4c80c7e4d6ba6775fb6ed90db497c520237c471425ccb4de339615fec4838a7c825fd07ac07
-Size (diffanal-0.1.0.21-f5f29e07e345829c82cab97b8e4245cc41deab3c.tar.gz) = 37792 bytes
diff --git a/dlpoly-classic/DESCR b/dlpoly-classic/DESCR
deleted file mode 100644
index 2ec3ea56a9..0000000000
--- a/dlpoly-classic/DESCR
+++ /dev/null
@@ -1,2 +0,0 @@
-DL_POLY is a general purpose classical molecular dynamics (MD) simulation
-software developed at Daresbury Laboratory by I.T. Todorov and W. Smith.
diff --git a/dlpoly-classic/PLIST b/dlpoly-classic/PLIST
deleted file mode 100644
index cc54c2db7a..0000000000
--- a/dlpoly-classic/PLIST
+++ /dev/null
@@ -1,3 +0,0 @@
-@comment $NetBSD: PLIST,v 1.1.1.1 2012/03/30 19:54:21 outpaddling Exp $
-bin/dlpoly-classic
-bin/dlpoly-classic-mpi
diff --git a/dlpoly-classic/distinfo b/dlpoly-classic/distinfo
deleted file mode 100644
index 795dbaaf58..0000000000
--- a/dlpoly-classic/distinfo
+++ /dev/null
@@ -1,6 +0,0 @@
-$NetBSD: distinfo,v 1.1.1.1 2012/03/30 19:54:21 outpaddling Exp $
-
-RMD160 (dl_class_1.8.tar.gz) = 727af316e3b8a817cf5d53a02834060d234215d4
-Size (dl_class_1.8.tar.gz) = 2769075 bytes
-SHA1 (patch-build_MakePAR) = ddc36087885326fff603cfc89e0c8d741f12cbcf
-SHA1 (patch-build_MakeSEQ) = baef00cb934e2475709b679fd557db3f3ccb58ad
diff --git a/dlpoly-classic/patches/patch-build_MakePAR b/dlpoly-classic/patches/patch-build_MakePAR
deleted file mode 100644
index e24eacb065..0000000000
--- a/dlpoly-classic/patches/patch-build_MakePAR
+++ /dev/null
@@ -1,32 +0,0 @@
-$NetBSD: patch-build_MakePAR,v 1.1.1.1 2012/03/30 19:54:21 outpaddling Exp $
-
---- build/MakePAR.orig 2011-02-22 11:46:11.000000000 +0000
-+++ build/MakePAR
-@@ -7,7 +7,7 @@
-
- BINROOT = ../execute
- CC = gcc
--EX = DLPOLY.X
-+EX = dlpoly-classic-mpi
- EXE = $(BINROOT)/$(EX)
- FC=undefined
- SHELL=/bin/sh
-@@ -54,15 +54,15 @@ all:
-
- #================== GNU Fortran, MPI version ==============================
- gfortran:
-- $(MAKE) FC="mpif90" LD="mpif90 -o" \
-+ $(MAKE) FC="mpif77" LD="mpif77 -o" \
- LDFLAGS="-O2 -ffast-math" \
- FFLAGS="-c -O2 -ffast-math" \
- EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
-
- #================= Woodcrest =========================================
- woodcrest:
-- $(MAKE) LD="mpif90 -o" LDFLAGS="" \
-- FC=mpif90 FFLAGS="-c -O3" \
-+ $(MAKE) LD="mpif77 -o" LDFLAGS="" \
-+ FC=mpif77 FFLAGS="-c -O3" \
- EX=$(EX) BINROOT=$(BINROOT) $(TYPE)
-
- #=====================================================================
diff --git a/dlpoly-classic/patches/patch-build_MakeSEQ b/dlpoly-classic/patches/patch-build_MakeSEQ
deleted file mode 100644
index b69af50af3..0000000000
--- a/dlpoly-classic/patches/patch-build_MakeSEQ
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-build_MakeSEQ,v 1.1.1.1 2012/03/30 19:54:21 outpaddling Exp $
-
---- build/MakeSEQ.orig 2011-02-22 11:46:11.000000000 +0000
-+++ build/MakeSEQ
-@@ -7,7 +7,7 @@
-
- BINROOT = ../execute
- CC = gcc
--EX = DLPOLY.X
-+EX = dlpoly-classic
- EXE = $(BINROOT)/$(EX)
- FC=undefined
- SHELL=/bin/sh
diff --git a/gromacs/DESCR b/gromacs/DESCR
deleted file mode 100644
index 17d86649e9..0000000000
--- a/gromacs/DESCR
+++ /dev/null
@@ -1,10 +0,0 @@
-GROMACS is a versatile package to perform molecular dynamics,
-i.e. simulate the Newtonian equations of motion for systems with
-hundreds to millions of particles.
-
-It is primarily designed for biochemical molecules like proteins,
-lipids and nucleic acids that have a lot of complicated bonded
-interactions, but since GROMACS is extremely fast at calculating
-the nonbonded interactions (that usually dominate simulations)
-many groups are also using it for research on non-biological
-systems, e.g. polymers.
diff --git a/gromacs/PLIST b/gromacs/PLIST
deleted file mode 100644
index d59d493591..0000000000
--- a/gromacs/PLIST
+++ /dev/null
@@ -1,699 +0,0 @@
-@comment $NetBSD$
-bin/GMXRC
-bin/GMXRC.bash
-bin/GMXRC.csh
-bin/GMXRC.zsh
-bin/demux.pl
-bin/gmx
-bin/gmx-completion-gmx.bash
-bin/gmx-completion.bash
-bin/xplor2gmx.pl
-include/gromacs/analysisdata.h
-include/gromacs/analysisdata/abstractdata.h
-include/gromacs/analysisdata/analysisdata.h
-include/gromacs/analysisdata/arraydata.h
-include/gromacs/analysisdata/dataframe.h
-include/gromacs/analysisdata/datamodule.h
-include/gromacs/analysisdata/modules/average.h
-include/gromacs/analysisdata/modules/displacement.h
-include/gromacs/analysisdata/modules/histogram.h
-include/gromacs/analysisdata/modules/lifetime.h
-include/gromacs/analysisdata/modules/plot.h
-include/gromacs/commandline.h
-include/gromacs/commandline/cmdlinehelpwriter.h
-include/gromacs/commandline/cmdlineinit.h
-include/gromacs/commandline/cmdlinemodule.h
-include/gromacs/commandline/cmdlineoptionsmodule.h
-include/gromacs/commandline/cmdlineparser.h
-include/gromacs/commandline/cmdlineprogramcontext.h
-include/gromacs/commandline/filenm.h
-include/gromacs/commandline/pargs.h
-include/gromacs/commandline/viewit.h
-include/gromacs/compat/make_unique.h
-include/gromacs/fft/fft.h
-include/gromacs/fileio/confio.h
-include/gromacs/fileio/enxio.h
-include/gromacs/fileio/filetypes.h
-include/gromacs/fileio/gmxfio.h
-include/gromacs/fileio/matio.h
-include/gromacs/fileio/mtxio.h
-include/gromacs/fileio/oenv.h
-include/gromacs/fileio/pdbio.h
-include/gromacs/fileio/rgb.h
-include/gromacs/fileio/tpxio.h
-include/gromacs/fileio/trrio.h
-include/gromacs/fileio/trxio.h
-include/gromacs/fileio/xdr_datatype.h
-include/gromacs/fileio/xtcio.h
-include/gromacs/fileio/xvgr.h
-include/gromacs/gmxana/gstat.h
-include/gromacs/gpu_utils/hostallocator.h
-include/gromacs/linearalgebra/eigensolver.h
-include/gromacs/linearalgebra/matrix.h
-include/gromacs/linearalgebra/sparsematrix.h
-include/gromacs/math/3dtransforms.h
-include/gromacs/math/arrayrefwithpadding.h
-include/gromacs/math/do_fit.h
-include/gromacs/math/functions.h
-include/gromacs/math/gmxcomplex.h
-include/gromacs/math/paddedvector.h
-include/gromacs/math/units.h
-include/gromacs/math/utilities.h
-include/gromacs/math/vec.h
-include/gromacs/math/vectypes.h
-include/gromacs/mdlib/simulationsignal.h
-include/gromacs/mdtypes/inputrec.h
-include/gromacs/mdtypes/md_enums.h
-include/gromacs/mdtypes/mdatom.h
-include/gromacs/mdtypes/state.h
-include/gromacs/options.h
-include/gromacs/options/abstractoption.h
-include/gromacs/options/abstractsection.h
-include/gromacs/options/basicoptions.h
-include/gromacs/options/filenameoption.h
-include/gromacs/options/filenameoptionmanager.h
-include/gromacs/options/ioptionsbehavior.h
-include/gromacs/options/ioptionscontainer.h
-include/gromacs/options/ioptionscontainerwithsections.h
-include/gromacs/options/isectionstorage.h
-include/gromacs/options/ivaluestore.h
-include/gromacs/options/optionfiletype.h
-include/gromacs/options/optionflags.h
-include/gromacs/options/options.h
-include/gromacs/options/optionsection.h
-include/gromacs/options/repeatingsection.h
-include/gromacs/options/timeunitmanager.h
-include/gromacs/options/valuestore.h
-include/gromacs/pbcutil/ishift.h
-include/gromacs/pbcutil/pbc.h
-include/gromacs/pbcutil/rmpbc.h
-include/gromacs/random.h
-include/gromacs/random/exponentialdistribution.h
-include/gromacs/random/gammadistribution.h
-include/gromacs/random/normaldistribution.h
-include/gromacs/random/seed.h
-include/gromacs/random/tabulatednormaldistribution.h
-include/gromacs/random/threefry.h
-include/gromacs/random/uniformintdistribution.h
-include/gromacs/random/uniformrealdistribution.h
-include/gromacs/restraint/restraintpotential.h
-include/gromacs/selection.h
-include/gromacs/selection/indexutil.h
-include/gromacs/selection/nbsearch.h
-include/gromacs/selection/position.h
-include/gromacs/selection/selection.h
-include/gromacs/selection/selectioncollection.h
-include/gromacs/selection/selectionenums.h
-include/gromacs/selection/selectionoption.h
-include/gromacs/selection/selectionoptionbehavior.h
-include/gromacs/selection/selectionoptionmanager.h
-include/gromacs/timing/wallcycle.h
-include/gromacs/timing/walltime_accounting.h
-include/gromacs/topology/atomprop.h
-include/gromacs/topology/atoms.h
-include/gromacs/topology/block.h
-include/gromacs/topology/forcefieldparameters.h
-include/gromacs/topology/idef.h
-include/gromacs/topology/ifunc.h
-include/gromacs/topology/index.h
-include/gromacs/topology/mtop_util.h
-include/gromacs/topology/symtab.h
-include/gromacs/topology/topology.h
-include/gromacs/trajectory/energyframe.h
-include/gromacs/trajectory/trajectoryframe.h
-include/gromacs/trajectoryanalysis.h
-include/gromacs/trajectoryanalysis/analysismodule.h
-include/gromacs/trajectoryanalysis/analysissettings.h
-include/gromacs/trajectoryanalysis/cmdlinerunner.h
-include/gromacs/trajectoryanalysis/topologyinformation.h
-include/gromacs/utility.h
-include/gromacs/utility/alignedallocator.h
-include/gromacs/utility/allocator.h
-include/gromacs/utility/arrayref.h
-include/gromacs/utility/arraysize.h
-include/gromacs/utility/basedefinitions.h
-include/gromacs/utility/baseversion.h
-include/gromacs/utility/classhelpers.h
-include/gromacs/utility/cstringutil.h
-include/gromacs/utility/current_function.h
-include/gromacs/utility/datafilefinder.h
-include/gromacs/utility/errorcodes.h
-include/gromacs/utility/exceptions.h
-include/gromacs/utility/fatalerror.h
-include/gromacs/utility/fileptr.h
-include/gromacs/utility/flags.h
-include/gromacs/utility/futil.h
-include/gromacs/utility/gmxassert.h
-include/gromacs/utility/init.h
-include/gromacs/utility/programcontext.h
-include/gromacs/utility/real.h
-include/gromacs/utility/smalloc.h
-include/gromacs/utility/stringutil.h
-include/gromacs/utility/unique_cptr.h
-include/gromacs/version.h
-lib/libgromacs.so
-lib/libgromacs.so.4
-lib/libgromacs.so.4.0.0
-lib/pkgconfig/libgromacs.pc
-man/man1/gmx-anadock.1
-man/man1/gmx-anaeig.1
-man/man1/gmx-analyze.1
-man/man1/gmx-angle.1
-man/man1/gmx-awh.1
-man/man1/gmx-bar.1
-man/man1/gmx-bundle.1
-man/man1/gmx-check.1
-man/man1/gmx-chi.1
-man/man1/gmx-cluster.1
-man/man1/gmx-clustsize.1
-man/man1/gmx-confrms.1
-man/man1/gmx-convert-tpr.1
-man/man1/gmx-covar.1
-man/man1/gmx-current.1
-man/man1/gmx-density.1
-man/man1/gmx-densmap.1
-man/man1/gmx-densorder.1
-man/man1/gmx-dielectric.1
-man/man1/gmx-dipoles.1
-man/man1/gmx-disre.1
-man/man1/gmx-distance.1
-man/man1/gmx-do_dssp.1
-man/man1/gmx-dos.1
-man/man1/gmx-dump.1
-man/man1/gmx-dyecoupl.1
-man/man1/gmx-dyndom.1
-man/man1/gmx-editconf.1
-man/man1/gmx-eneconv.1
-man/man1/gmx-enemat.1
-man/man1/gmx-energy.1
-man/man1/gmx-filter.1
-man/man1/gmx-freevolume.1
-man/man1/gmx-gangle.1
-man/man1/gmx-genconf.1
-man/man1/gmx-genion.1
-man/man1/gmx-genrestr.1
-man/man1/gmx-grompp.1
-man/man1/gmx-gyrate.1
-man/man1/gmx-h2order.1
-man/man1/gmx-hbond.1
-man/man1/gmx-helix.1
-man/man1/gmx-helixorient.1
-man/man1/gmx-help.1
-man/man1/gmx-hydorder.1
-man/man1/gmx-insert-molecules.1
-man/man1/gmx-lie.1
-man/man1/gmx-make_edi.1
-man/man1/gmx-make_ndx.1
-man/man1/gmx-mdmat.1
-man/man1/gmx-mdrun.1
-man/man1/gmx-mindist.1
-man/man1/gmx-mk_angndx.1
-man/man1/gmx-morph.1
-man/man1/gmx-msd.1
-man/man1/gmx-nmeig.1
-man/man1/gmx-nmens.1
-man/man1/gmx-nmr.1
-man/man1/gmx-nmtraj.1
-man/man1/gmx-order.1
-man/man1/gmx-pairdist.1
-man/man1/gmx-pdb2gmx.1
-man/man1/gmx-pme_error.1
-man/man1/gmx-polystat.1
-man/man1/gmx-potential.1
-man/man1/gmx-principal.1
-man/man1/gmx-rama.1
-man/man1/gmx-rdf.1
-man/man1/gmx-report-methods.1
-man/man1/gmx-rms.1
-man/man1/gmx-rmsdist.1
-man/man1/gmx-rmsf.1
-man/man1/gmx-rotacf.1
-man/man1/gmx-rotmat.1
-man/man1/gmx-saltbr.1
-man/man1/gmx-sans.1
-man/man1/gmx-sasa.1
-man/man1/gmx-saxs.1
-man/man1/gmx-select.1
-man/man1/gmx-sham.1
-man/man1/gmx-sigeps.1
-man/man1/gmx-solvate.1
-man/man1/gmx-sorient.1
-man/man1/gmx-spatial.1
-man/man1/gmx-spol.1
-man/man1/gmx-tcaf.1
-man/man1/gmx-traj.1
-man/man1/gmx-trajectory.1
-man/man1/gmx-trjcat.1
-man/man1/gmx-trjconv.1
-man/man1/gmx-trjorder.1
-man/man1/gmx-tune_pme.1
-man/man1/gmx-vanhove.1
-man/man1/gmx-velacc.1
-man/man1/gmx-view.1
-man/man1/gmx-wham.1
-man/man1/gmx-wheel.1
-man/man1/gmx-x2top.1
-man/man1/gmx-xpm2ps.1
-man/man1/gmx.1
-share/cmake/gromacs/gromacs-config-version.cmake
-share/cmake/gromacs/gromacs-config.cmake
-share/cmake/gromacs/libgromacs-release.cmake
-share/cmake/gromacs/libgromacs.cmake
-share/gromacs/COPYING
-share/gromacs/README.tutor
-share/gromacs/README_FreeEnergyModifications.txt
-share/gromacs/template/CMakeLists.txt
-share/gromacs/template/Makefile.pkg
-share/gromacs/template/README
-share/gromacs/template/cmake/FindGROMACS.cmake
-share/gromacs/template/template.cpp
-share/gromacs/top/README
-share/gromacs/top/amber03.ff/aminoacids.arn
-share/gromacs/top/amber03.ff/aminoacids.c.tdb
-share/gromacs/top/amber03.ff/aminoacids.hdb
-share/gromacs/top/amber03.ff/aminoacids.n.tdb
-share/gromacs/top/amber03.ff/aminoacids.r2b
-share/gromacs/top/amber03.ff/aminoacids.rtp
-share/gromacs/top/amber03.ff/aminoacids.vsd
-share/gromacs/top/amber03.ff/atomtypes.atp
-share/gromacs/top/amber03.ff/dna.arn
-share/gromacs/top/amber03.ff/dna.hdb
-share/gromacs/top/amber03.ff/dna.r2b
-share/gromacs/top/amber03.ff/dna.rtp
-share/gromacs/top/amber03.ff/ffbonded.itp
-share/gromacs/top/amber03.ff/ffnonbonded.itp
-share/gromacs/top/amber03.ff/forcefield.doc
-share/gromacs/top/amber03.ff/forcefield.itp
-share/gromacs/top/amber03.ff/ions.itp
-share/gromacs/top/amber03.ff/rna.arn
-share/gromacs/top/amber03.ff/rna.hdb
-share/gromacs/top/amber03.ff/rna.r2b
-share/gromacs/top/amber03.ff/rna.rtp
-share/gromacs/top/amber03.ff/spc.itp
-share/gromacs/top/amber03.ff/spce.itp
-share/gromacs/top/amber03.ff/tip3p.itp
-share/gromacs/top/amber03.ff/tip4p.itp
-share/gromacs/top/amber03.ff/tip4pew.itp
-share/gromacs/top/amber03.ff/tip5p.itp
-share/gromacs/top/amber03.ff/urea.itp
-share/gromacs/top/amber03.ff/watermodels.dat
-share/gromacs/top/amber94.ff/aminoacids.arn
-share/gromacs/top/amber94.ff/aminoacids.c.tdb
-share/gromacs/top/amber94.ff/aminoacids.hdb
-share/gromacs/top/amber94.ff/aminoacids.n.tdb
-share/gromacs/top/amber94.ff/aminoacids.r2b
-share/gromacs/top/amber94.ff/aminoacids.rtp
-share/gromacs/top/amber94.ff/aminoacids.vsd
-share/gromacs/top/amber94.ff/atomtypes.atp
-share/gromacs/top/amber94.ff/dna.arn
-share/gromacs/top/amber94.ff/dna.hdb
-share/gromacs/top/amber94.ff/dna.r2b
-share/gromacs/top/amber94.ff/dna.rtp
-share/gromacs/top/amber94.ff/ffbonded.itp
-share/gromacs/top/amber94.ff/ffnonbonded.itp
-share/gromacs/top/amber94.ff/forcefield.doc
-share/gromacs/top/amber94.ff/forcefield.itp
-share/gromacs/top/amber94.ff/ions.itp
-share/gromacs/top/amber94.ff/rna.arn
-share/gromacs/top/amber94.ff/rna.hdb
-share/gromacs/top/amber94.ff/rna.r2b
-share/gromacs/top/amber94.ff/rna.rtp
-share/gromacs/top/amber94.ff/spc.itp
-share/gromacs/top/amber94.ff/spce.itp
-share/gromacs/top/amber94.ff/tip3p.itp
-share/gromacs/top/amber94.ff/tip4p.itp
-share/gromacs/top/amber94.ff/tip4pew.itp
-share/gromacs/top/amber94.ff/tip5p.itp
-share/gromacs/top/amber94.ff/urea.itp
-share/gromacs/top/amber94.ff/watermodels.dat
-share/gromacs/top/amber96.ff/aminoacids.arn
-share/gromacs/top/amber96.ff/aminoacids.c.tdb
-share/gromacs/top/amber96.ff/aminoacids.hdb
-share/gromacs/top/amber96.ff/aminoacids.n.tdb
-share/gromacs/top/amber96.ff/aminoacids.r2b
-share/gromacs/top/amber96.ff/aminoacids.rtp
-share/gromacs/top/amber96.ff/aminoacids.vsd
-share/gromacs/top/amber96.ff/atomtypes.atp
-share/gromacs/top/amber96.ff/dna.arn
-share/gromacs/top/amber96.ff/dna.hdb
-share/gromacs/top/amber96.ff/dna.r2b
-share/gromacs/top/amber96.ff/dna.rtp
-share/gromacs/top/amber96.ff/ffbonded.itp
-share/gromacs/top/amber96.ff/ffnonbonded.itp
-share/gromacs/top/amber96.ff/forcefield.doc
-share/gromacs/top/amber96.ff/forcefield.itp
-share/gromacs/top/amber96.ff/ions.itp
-share/gromacs/top/amber96.ff/rna.arn
-share/gromacs/top/amber96.ff/rna.hdb
-share/gromacs/top/amber96.ff/rna.r2b
-share/gromacs/top/amber96.ff/rna.rtp
-share/gromacs/top/amber96.ff/spc.itp
-share/gromacs/top/amber96.ff/spce.itp
-share/gromacs/top/amber96.ff/tip3p.itp
-share/gromacs/top/amber96.ff/tip4p.itp
-share/gromacs/top/amber96.ff/tip4pew.itp
-share/gromacs/top/amber96.ff/tip5p.itp
-share/gromacs/top/amber96.ff/urea.itp
-share/gromacs/top/amber96.ff/watermodels.dat
-share/gromacs/top/amber99.ff/aminoacids.arn
-share/gromacs/top/amber99.ff/aminoacids.c.tdb
-share/gromacs/top/amber99.ff/aminoacids.hdb
-share/gromacs/top/amber99.ff/aminoacids.n.tdb
-share/gromacs/top/amber99.ff/aminoacids.r2b
-share/gromacs/top/amber99.ff/aminoacids.rtp
-share/gromacs/top/amber99.ff/aminoacids.vsd
-share/gromacs/top/amber99.ff/atomtypes.atp
-share/gromacs/top/amber99.ff/dna.arn
-share/gromacs/top/amber99.ff/dna.hdb
-share/gromacs/top/amber99.ff/dna.r2b
-share/gromacs/top/amber99.ff/dna.rtp
-share/gromacs/top/amber99.ff/ffbonded.itp
-share/gromacs/top/amber99.ff/ffnonbonded.itp
-share/gromacs/top/amber99.ff/forcefield.doc
-share/gromacs/top/amber99.ff/forcefield.itp
-share/gromacs/top/amber99.ff/ions.itp
-share/gromacs/top/amber99.ff/rna.arn
-share/gromacs/top/amber99.ff/rna.hdb
-share/gromacs/top/amber99.ff/rna.r2b
-share/gromacs/top/amber99.ff/rna.rtp
-share/gromacs/top/amber99.ff/spc.itp
-share/gromacs/top/amber99.ff/spce.itp
-share/gromacs/top/amber99.ff/tip3p.itp
-share/gromacs/top/amber99.ff/tip4p.itp
-share/gromacs/top/amber99.ff/tip4pew.itp
-share/gromacs/top/amber99.ff/tip5p.itp
-share/gromacs/top/amber99.ff/urea.itp
-share/gromacs/top/amber99.ff/watermodels.dat
-share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
-share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb
-share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb
-share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb
-share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b
-share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp
-share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd
-share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp
-share/gromacs/top/amber99sb-ildn.ff/dna.arn
-share/gromacs/top/amber99sb-ildn.ff/dna.hdb
-share/gromacs/top/amber99sb-ildn.ff/dna.r2b
-share/gromacs/top/amber99sb-ildn.ff/dna.rtp
-share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp
-share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp
-share/gromacs/top/amber99sb-ildn.ff/forcefield.doc
-share/gromacs/top/amber99sb-ildn.ff/forcefield.itp
-share/gromacs/top/amber99sb-ildn.ff/ions.itp
-share/gromacs/top/amber99sb-ildn.ff/rna.arn
-share/gromacs/top/amber99sb-ildn.ff/rna.hdb
-share/gromacs/top/amber99sb-ildn.ff/rna.r2b
-share/gromacs/top/amber99sb-ildn.ff/rna.rtp
-share/gromacs/top/amber99sb-ildn.ff/spc.itp
-share/gromacs/top/amber99sb-ildn.ff/spce.itp
-share/gromacs/top/amber99sb-ildn.ff/tip3p.itp
-share/gromacs/top/amber99sb-ildn.ff/tip4p.itp
-share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp
-share/gromacs/top/amber99sb-ildn.ff/tip5p.itp
-share/gromacs/top/amber99sb-ildn.ff/urea.itp
-share/gromacs/top/amber99sb-ildn.ff/watermodels.dat
-share/gromacs/top/amber99sb.ff/aminoacids.arn
-share/gromacs/top/amber99sb.ff/aminoacids.c.tdb
-share/gromacs/top/amber99sb.ff/aminoacids.hdb
-share/gromacs/top/amber99sb.ff/aminoacids.n.tdb
-share/gromacs/top/amber99sb.ff/aminoacids.r2b
-share/gromacs/top/amber99sb.ff/aminoacids.rtp
-share/gromacs/top/amber99sb.ff/aminoacids.vsd
-share/gromacs/top/amber99sb.ff/atomtypes.atp
-share/gromacs/top/amber99sb.ff/dna.arn
-share/gromacs/top/amber99sb.ff/dna.hdb
-share/gromacs/top/amber99sb.ff/dna.r2b
-share/gromacs/top/amber99sb.ff/dna.rtp
-share/gromacs/top/amber99sb.ff/ffbonded.itp
-share/gromacs/top/amber99sb.ff/ffnonbonded.itp
-share/gromacs/top/amber99sb.ff/forcefield.doc
-share/gromacs/top/amber99sb.ff/forcefield.itp
-share/gromacs/top/amber99sb.ff/ions.itp
-share/gromacs/top/amber99sb.ff/rna.arn
-share/gromacs/top/amber99sb.ff/rna.hdb
-share/gromacs/top/amber99sb.ff/rna.r2b
-share/gromacs/top/amber99sb.ff/rna.rtp
-share/gromacs/top/amber99sb.ff/spc.itp
-share/gromacs/top/amber99sb.ff/spce.itp
-share/gromacs/top/amber99sb.ff/tip3p.itp
-share/gromacs/top/amber99sb.ff/tip4p.itp
-share/gromacs/top/amber99sb.ff/tip4pew.itp
-share/gromacs/top/amber99sb.ff/tip5p.itp
-share/gromacs/top/amber99sb.ff/urea.itp
-share/gromacs/top/amber99sb.ff/watermodels.dat
-share/gromacs/top/amberGS.ff/aminoacids.arn
-share/gromacs/top/amberGS.ff/aminoacids.c.tdb
-share/gromacs/top/amberGS.ff/aminoacids.hdb
-share/gromacs/top/amberGS.ff/aminoacids.n.tdb
-share/gromacs/top/amberGS.ff/aminoacids.r2b
-share/gromacs/top/amberGS.ff/aminoacids.rtp
-share/gromacs/top/amberGS.ff/aminoacids.vsd
-share/gromacs/top/amberGS.ff/atomtypes.atp
-share/gromacs/top/amberGS.ff/dna.arn
-share/gromacs/top/amberGS.ff/dna.hdb
-share/gromacs/top/amberGS.ff/dna.r2b
-share/gromacs/top/amberGS.ff/dna.rtp
-share/gromacs/top/amberGS.ff/ffbonded.itp
-share/gromacs/top/amberGS.ff/ffnonbonded.itp
-share/gromacs/top/amberGS.ff/forcefield.doc
-share/gromacs/top/amberGS.ff/forcefield.itp
-share/gromacs/top/amberGS.ff/ions.itp
-share/gromacs/top/amberGS.ff/rna.arn
-share/gromacs/top/amberGS.ff/rna.hdb
-share/gromacs/top/amberGS.ff/rna.r2b
-share/gromacs/top/amberGS.ff/rna.rtp
-share/gromacs/top/amberGS.ff/spc.itp
-share/gromacs/top/amberGS.ff/spce.itp
-share/gromacs/top/amberGS.ff/tip3p.itp
-share/gromacs/top/amberGS.ff/tip4p.itp
-share/gromacs/top/amberGS.ff/tip4pew.itp
-share/gromacs/top/amberGS.ff/tip5p.itp
-share/gromacs/top/amberGS.ff/urea.itp
-share/gromacs/top/amberGS.ff/watermodels.dat
-share/gromacs/top/atom_nom.tbl
-share/gromacs/top/atommass.dat
-share/gromacs/top/bonds.dlg
-share/gromacs/top/ca-shift.dat
-share/gromacs/top/cb-shift.dat
-share/gromacs/top/charmm27.ff/aminoacids.arn
-share/gromacs/top/charmm27.ff/aminoacids.c.tdb
-share/gromacs/top/charmm27.ff/aminoacids.hdb
-share/gromacs/top/charmm27.ff/aminoacids.n.tdb
-share/gromacs/top/charmm27.ff/aminoacids.r2b
-share/gromacs/top/charmm27.ff/aminoacids.rtp
-share/gromacs/top/charmm27.ff/aminoacids.vsd
-share/gromacs/top/charmm27.ff/atomtypes.atp
-share/gromacs/top/charmm27.ff/cmap.itp
-share/gromacs/top/charmm27.ff/dna.arn
-share/gromacs/top/charmm27.ff/dna.c.tdb
-share/gromacs/top/charmm27.ff/dna.hdb
-share/gromacs/top/charmm27.ff/dna.n.tdb
-share/gromacs/top/charmm27.ff/dna.rtp
-share/gromacs/top/charmm27.ff/ffbonded.itp
-share/gromacs/top/charmm27.ff/ffnabonded.itp
-share/gromacs/top/charmm27.ff/ffnanonbonded.itp
-share/gromacs/top/charmm27.ff/ffnonbonded.itp
-share/gromacs/top/charmm27.ff/forcefield.doc
-share/gromacs/top/charmm27.ff/forcefield.itp
-share/gromacs/top/charmm27.ff/ions.itp
-share/gromacs/top/charmm27.ff/lipids.hdb
-share/gromacs/top/charmm27.ff/lipids.rtp
-share/gromacs/top/charmm27.ff/rna.arn
-share/gromacs/top/charmm27.ff/rna.c.tdb
-share/gromacs/top/charmm27.ff/rna.hdb
-share/gromacs/top/charmm27.ff/rna.n.tdb
-share/gromacs/top/charmm27.ff/rna.r2b
-share/gromacs/top/charmm27.ff/rna.rtp
-share/gromacs/top/charmm27.ff/spc.itp
-share/gromacs/top/charmm27.ff/spce.itp
-share/gromacs/top/charmm27.ff/tip3p.itp
-share/gromacs/top/charmm27.ff/tip4p.itp
-share/gromacs/top/charmm27.ff/tip5p.itp
-share/gromacs/top/charmm27.ff/tips3p.itp
-share/gromacs/top/charmm27.ff/watermodels.dat
-share/gromacs/top/co-shift.dat
-share/gromacs/top/defselection.dat
-share/gromacs/top/dgsolv.dat
-share/gromacs/top/edissoc.dat
-share/gromacs/top/electroneg.dat
-share/gromacs/top/elements.dat
-share/gromacs/top/export.dlg
-share/gromacs/top/ffG43a1.itp
-share/gromacs/top/ffG43a2.itp
-share/gromacs/top/ffG45a3.itp
-share/gromacs/top/ffG53a5.itp
-share/gromacs/top/ffG53a6.itp
-share/gromacs/top/ffoplsaa-n.tst
-share/gromacs/top/ffoplsaa.itp
-share/gromacs/top/flexspc.itp
-share/gromacs/top/flexspce.itp
-share/gromacs/top/flexwat-ferguson.itp
-share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb
-share/gromacs/top/gromos43a1.ff/aminoacids.hdb
-share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb
-share/gromacs/top/gromos43a1.ff/aminoacids.r2b
-share/gromacs/top/gromos43a1.ff/aminoacids.rtp
-share/gromacs/top/gromos43a1.ff/aminoacids.vsd
-share/gromacs/top/gromos43a1.ff/atomtypes.atp
-share/gromacs/top/gromos43a1.ff/ff_dum.itp
-share/gromacs/top/gromos43a1.ff/ffbonded.itp
-share/gromacs/top/gromos43a1.ff/ffnonbonded.itp
-share/gromacs/top/gromos43a1.ff/forcefield.doc
-share/gromacs/top/gromos43a1.ff/forcefield.itp
-share/gromacs/top/gromos43a1.ff/ions.itp
-share/gromacs/top/gromos43a1.ff/methanol.itp
-share/gromacs/top/gromos43a1.ff/methanol216.gro
-share/gromacs/top/gromos43a1.ff/spc.itp
-share/gromacs/top/gromos43a1.ff/spce.itp
-share/gromacs/top/gromos43a1.ff/tip3p.itp
-share/gromacs/top/gromos43a1.ff/tip4p.itp
-share/gromacs/top/gromos43a1.ff/watermodels.dat
-share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb
-share/gromacs/top/gromos43a2.ff/aminoacids.hdb
-share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb
-share/gromacs/top/gromos43a2.ff/aminoacids.r2b
-share/gromacs/top/gromos43a2.ff/aminoacids.rtp
-share/gromacs/top/gromos43a2.ff/aminoacids.vsd
-share/gromacs/top/gromos43a2.ff/atomtypes.atp
-share/gromacs/top/gromos43a2.ff/ff_dum.itp
-share/gromacs/top/gromos43a2.ff/ffbonded.itp
-share/gromacs/top/gromos43a2.ff/ffnonbonded.itp
-share/gromacs/top/gromos43a2.ff/forcefield.doc
-share/gromacs/top/gromos43a2.ff/forcefield.itp
-share/gromacs/top/gromos43a2.ff/ions.itp
-share/gromacs/top/gromos43a2.ff/spc.itp
-share/gromacs/top/gromos43a2.ff/spce.itp
-share/gromacs/top/gromos43a2.ff/tip3p.itp
-share/gromacs/top/gromos43a2.ff/tip4p.itp
-share/gromacs/top/gromos43a2.ff/watermodels.dat
-share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb
-share/gromacs/top/gromos45a3.ff/aminoacids.hdb
-share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb
-share/gromacs/top/gromos45a3.ff/aminoacids.r2b
-share/gromacs/top/gromos45a3.ff/aminoacids.rtp
-share/gromacs/top/gromos45a3.ff/aminoacids.vsd
-share/gromacs/top/gromos45a3.ff/atomtypes.atp
-share/gromacs/top/gromos45a3.ff/ff_dum.itp
-share/gromacs/top/gromos45a3.ff/ffbonded.itp
-share/gromacs/top/gromos45a3.ff/ffnonbonded.itp
-share/gromacs/top/gromos45a3.ff/forcefield.doc
-share/gromacs/top/gromos45a3.ff/forcefield.itp
-share/gromacs/top/gromos45a3.ff/ions.itp
-share/gromacs/top/gromos45a3.ff/spc.itp
-share/gromacs/top/gromos45a3.ff/spce.itp
-share/gromacs/top/gromos45a3.ff/tip3p.itp
-share/gromacs/top/gromos45a3.ff/tip4p.itp
-share/gromacs/top/gromos45a3.ff/watermodels.dat
-share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb
-share/gromacs/top/gromos53a5.ff/aminoacids.hdb
-share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb
-share/gromacs/top/gromos53a5.ff/aminoacids.r2b
-share/gromacs/top/gromos53a5.ff/aminoacids.rtp
-share/gromacs/top/gromos53a5.ff/aminoacids.vsd
-share/gromacs/top/gromos53a5.ff/atomname2type.n2t
-share/gromacs/top/gromos53a5.ff/atomtypes.atp
-share/gromacs/top/gromos53a5.ff/ff_dum.itp
-share/gromacs/top/gromos53a5.ff/ffbonded.itp
-share/gromacs/top/gromos53a5.ff/ffnonbonded.itp
-share/gromacs/top/gromos53a5.ff/forcefield.doc
-share/gromacs/top/gromos53a5.ff/forcefield.itp
-share/gromacs/top/gromos53a5.ff/ions.itp
-share/gromacs/top/gromos53a5.ff/spc.itp
-share/gromacs/top/gromos53a5.ff/spce.itp
-share/gromacs/top/gromos53a5.ff/tip3p.itp
-share/gromacs/top/gromos53a5.ff/tip4p.itp
-share/gromacs/top/gromos53a5.ff/watermodels.dat
-share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb
-share/gromacs/top/gromos53a6.ff/aminoacids.hdb
-share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb
-share/gromacs/top/gromos53a6.ff/aminoacids.r2b
-share/gromacs/top/gromos53a6.ff/aminoacids.rtp
-share/gromacs/top/gromos53a6.ff/aminoacids.vsd
-share/gromacs/top/gromos53a6.ff/atomtypes.atp
-share/gromacs/top/gromos53a6.ff/ff_dum.itp
-share/gromacs/top/gromos53a6.ff/ffbonded.itp
-share/gromacs/top/gromos53a6.ff/ffnonbonded.itp
-share/gromacs/top/gromos53a6.ff/forcefield.doc
-share/gromacs/top/gromos53a6.ff/forcefield.itp
-share/gromacs/top/gromos53a6.ff/ions.itp
-share/gromacs/top/gromos53a6.ff/spc.itp
-share/gromacs/top/gromos53a6.ff/spce.itp
-share/gromacs/top/gromos53a6.ff/tip3p.itp
-share/gromacs/top/gromos53a6.ff/tip4p.itp
-share/gromacs/top/gromos53a6.ff/watermodels.dat
-share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb
-share/gromacs/top/gromos54a7.ff/aminoacids.hdb
-share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb
-share/gromacs/top/gromos54a7.ff/aminoacids.r2b
-share/gromacs/top/gromos54a7.ff/aminoacids.rtp
-share/gromacs/top/gromos54a7.ff/aminoacids.vsd
-share/gromacs/top/gromos54a7.ff/atomtypes.atp
-share/gromacs/top/gromos54a7.ff/dppc.itp
-share/gromacs/top/gromos54a7.ff/ff_dum.itp
-share/gromacs/top/gromos54a7.ff/ffbonded.itp
-share/gromacs/top/gromos54a7.ff/ffnonbonded.itp
-share/gromacs/top/gromos54a7.ff/forcefield.doc
-share/gromacs/top/gromos54a7.ff/forcefield.itp
-share/gromacs/top/gromos54a7.ff/ions.itp
-share/gromacs/top/gromos54a7.ff/popc.itp
-share/gromacs/top/gromos54a7.ff/spc.itp
-share/gromacs/top/gromos54a7.ff/spce.itp
-share/gromacs/top/gromos54a7.ff/tip3p.itp
-share/gromacs/top/gromos54a7.ff/tip4p.itp
-share/gromacs/top/gromos54a7.ff/tmcl.itp
-share/gromacs/top/gromos54a7.ff/watermodels.dat
-share/gromacs/top/ha-shift.dat
-share/gromacs/top/ions.itp
-share/gromacs/top/nsfactor.dat
-share/gromacs/top/oplsaa.ff/1propanol.itp
-share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
-share/gromacs/top/oplsaa.ff/aminoacids.hdb
-share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
-share/gromacs/top/oplsaa.ff/aminoacids.r2b
-share/gromacs/top/oplsaa.ff/aminoacids.rtp
-share/gromacs/top/oplsaa.ff/aminoacids.vsd
-share/gromacs/top/oplsaa.ff/atomname2type.n2t
-share/gromacs/top/oplsaa.ff/atomtypes.atp
-share/gromacs/top/oplsaa.ff/ethanol.itp
-share/gromacs/top/oplsaa.ff/ffbonded.itp
-share/gromacs/top/oplsaa.ff/ffnonbonded.itp
-share/gromacs/top/oplsaa.ff/forcefield.doc
-share/gromacs/top/oplsaa.ff/forcefield.itp
-share/gromacs/top/oplsaa.ff/ions.itp
-share/gromacs/top/oplsaa.ff/methanol.itp
-share/gromacs/top/oplsaa.ff/spc.itp
-share/gromacs/top/oplsaa.ff/spce.itp
-share/gromacs/top/oplsaa.ff/tip3p.itp
-share/gromacs/top/oplsaa.ff/tip4p.itp
-share/gromacs/top/oplsaa.ff/tip4pew.itp
-share/gromacs/top/oplsaa.ff/tip5p.itp
-share/gromacs/top/oplsaa.ff/tip5pe.itp
-share/gromacs/top/oplsaa.ff/watermodels.dat
-share/gromacs/top/phbres.dat
-share/gromacs/top/ps.m2p
-share/gromacs/top/random.dat
-share/gromacs/top/refi_aa.dat
-share/gromacs/top/residues.dtd
-share/gromacs/top/residues.xml
-share/gromacs/top/residuetypes.dat
-share/gromacs/top/sfactor.dat
-share/gromacs/top/spc.itp
-share/gromacs/top/spc216.gro
-share/gromacs/top/spce.itp
-share/gromacs/top/specbond.dat
-share/gromacs/top/ss.map
-share/gromacs/top/surface.dat
-share/gromacs/top/sw.itp
-share/gromacs/top/table6-10.xvg
-share/gromacs/top/table6-11.xvg
-share/gromacs/top/table6-12.xvg
-share/gromacs/top/table6-8.xvg
-share/gromacs/top/table6-9.xvg
-share/gromacs/top/tip3p.itp
-share/gromacs/top/tip4p.gro
-share/gromacs/top/tip4p.itp
-share/gromacs/top/tip5p.gro
-share/gromacs/top/vdw-msms.dat
-share/gromacs/top/vdwradii.dat
-share/gromacs/top/xlateat.dat
diff --git a/gromacs/distinfo b/gromacs/distinfo
deleted file mode 100644
index 5db3c65ff3..0000000000
--- a/gromacs/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD$
-
-RMD160 (gromacs-2019.tar.gz) = 598f0b3b797a801ff5b4acef38cc248f69656fc2
-SHA512 (gromacs-2019.tar.gz) = 54b11530e8ff671461e3ae9418d991fe242957943c944798cddf6efe740eee670a562cd5201dbba68b045f4bafd3afa2dc8de27e0643c7def4e05eaf0ccb5769
-Size (gromacs-2019.tar.gz) = 33428725 bytes
diff --git a/gromacs/options.mk b/gromacs/options.mk
deleted file mode 100644
index a7660f3965..0000000000
--- a/gromacs/options.mk
+++ /dev/null
@@ -1,28 +0,0 @@
-# $NetBSD: options.mk,v 1.2 2010/05/16 12:04:03 asau Exp $
-
-PKG_OPTIONS_VAR= PKG_OPTIONS.gromacs
-PKG_SUPPORTED_OPTIONS+= mpi x11
-PKG_SUGGESTED_OPTIONS+= mpi x11
-
-.include "../../mk/bsd.options.mk"
-
-PLIST_VARS= x11
-
-# MPI support:
-.if !empty(PKG_OPTIONS:Mmpi)
-CONFIGURE_ARGS+= --enable-mpi
-PLIST_SUBST+= MPI=_mpi
-.include "../../mk/mpi.buildlink3.mk"
-.else
-PLIST_SUBST+= MPI=
-.endif
-
-# X support:
-.if !empty(PKG_OPTIONS:Mx11)
-CONFIGURE_ARGS+= --with-x
-PLIST.x11= yes
-
-.include "../../x11/libX11/buildlink3.mk"
-.include "../../x11/libICE/buildlink3.mk"
-.include "../../x11/libSM/buildlink3.mk"
-.endif
diff --git a/gromacs2018/DESCR b/gromacs2018/DESCR
deleted file mode 100644
index 17d86649e9..0000000000
--- a/gromacs2018/DESCR
+++ /dev/null
@@ -1,10 +0,0 @@
-GROMACS is a versatile package to perform molecular dynamics,
-i.e. simulate the Newtonian equations of motion for systems with
-hundreds to millions of particles.
-
-It is primarily designed for biochemical molecules like proteins,
-lipids and nucleic acids that have a lot of complicated bonded
-interactions, but since GROMACS is extremely fast at calculating
-the nonbonded interactions (that usually dominate simulations)
-many groups are also using it for research on non-biological
-systems, e.g. polymers.
diff --git a/gromacs2018/PLIST b/gromacs2018/PLIST
deleted file mode 100644
index 72c5ee7d82..0000000000
--- a/gromacs2018/PLIST
+++ /dev/null
@@ -1,699 +0,0 @@
-@comment $NetBSD$
-bin/GMXRC
-bin/GMXRC.bash
-bin/GMXRC.csh
-bin/GMXRC.zsh
-bin/demux.pl
-bin/gmx
-bin/gmx-completion-gmx.bash
-bin/gmx-completion.bash
-bin/xplor2gmx.pl
-include/gromacs/analysisdata.h
-include/gromacs/analysisdata/abstractdata.h
-include/gromacs/analysisdata/analysisdata.h
-include/gromacs/analysisdata/arraydata.h
-include/gromacs/analysisdata/dataframe.h
-include/gromacs/analysisdata/datamodule.h
-include/gromacs/analysisdata/modules/average.h
-include/gromacs/analysisdata/modules/displacement.h
-include/gromacs/analysisdata/modules/histogram.h
-include/gromacs/analysisdata/modules/lifetime.h
-include/gromacs/analysisdata/modules/plot.h
-include/gromacs/commandline.h
-include/gromacs/commandline/cmdlinehelpwriter.h
-include/gromacs/commandline/cmdlineinit.h
-include/gromacs/commandline/cmdlinemodule.h
-include/gromacs/commandline/cmdlineoptionsmodule.h
-include/gromacs/commandline/cmdlineparser.h
-include/gromacs/commandline/cmdlineprogramcontext.h
-include/gromacs/commandline/filenm.h
-include/gromacs/commandline/pargs.h
-include/gromacs/commandline/viewit.h
-include/gromacs/fft/fft.h
-include/gromacs/fileio/confio.h
-include/gromacs/fileio/enxio.h
-include/gromacs/fileio/filetypes.h
-include/gromacs/fileio/gmxfio.h
-include/gromacs/fileio/matio.h
-include/gromacs/fileio/mtxio.h
-include/gromacs/fileio/oenv.h
-include/gromacs/fileio/pdbio.h
-include/gromacs/fileio/rgb.h
-include/gromacs/fileio/tpxio.h
-include/gromacs/fileio/trrio.h
-include/gromacs/fileio/trxio.h
-include/gromacs/fileio/xdr_datatype.h
-include/gromacs/fileio/xtcio.h
-include/gromacs/fileio/xvgr.h
-include/gromacs/gmxana/gstat.h
-include/gromacs/gpu_utils/hostallocator.h
-include/gromacs/linearalgebra/eigensolver.h
-include/gromacs/linearalgebra/matrix.h
-include/gromacs/linearalgebra/sparsematrix.h
-include/gromacs/listed-forces/listed-forces.h
-include/gromacs/math/3dtransforms.h
-include/gromacs/math/do_fit.h
-include/gromacs/math/functions.h
-include/gromacs/math/gmxcomplex.h
-include/gromacs/math/paddedvector.h
-include/gromacs/math/units.h
-include/gromacs/math/utilities.h
-include/gromacs/math/vec.h
-include/gromacs/math/vectypes.h
-include/gromacs/mdtypes/inputrec.h
-include/gromacs/mdtypes/md_enums.h
-include/gromacs/mdtypes/mdatom.h
-include/gromacs/mdtypes/state.h
-include/gromacs/options.h
-include/gromacs/options/abstractoption.h
-include/gromacs/options/abstractsection.h
-include/gromacs/options/basicoptions.h
-include/gromacs/options/filenameoption.h
-include/gromacs/options/filenameoptionmanager.h
-include/gromacs/options/ioptionsbehavior.h
-include/gromacs/options/ioptionscontainer.h
-include/gromacs/options/ioptionscontainerwithsections.h
-include/gromacs/options/isectionstorage.h
-include/gromacs/options/ivaluestore.h
-include/gromacs/options/optionfiletype.h
-include/gromacs/options/optionflags.h
-include/gromacs/options/options.h
-include/gromacs/options/optionsection.h
-include/gromacs/options/repeatingsection.h
-include/gromacs/options/timeunitmanager.h
-include/gromacs/options/valuestore.h
-include/gromacs/pbcutil/ishift.h
-include/gromacs/pbcutil/pbc.h
-include/gromacs/pbcutil/rmpbc.h
-include/gromacs/random.h
-include/gromacs/random/exponentialdistribution.h
-include/gromacs/random/gammadistribution.h
-include/gromacs/random/normaldistribution.h
-include/gromacs/random/seed.h
-include/gromacs/random/tabulatednormaldistribution.h
-include/gromacs/random/threefry.h
-include/gromacs/random/uniformintdistribution.h
-include/gromacs/random/uniformrealdistribution.h
-include/gromacs/selection.h
-include/gromacs/selection/indexutil.h
-include/gromacs/selection/nbsearch.h
-include/gromacs/selection/position.h
-include/gromacs/selection/selection.h
-include/gromacs/selection/selectioncollection.h
-include/gromacs/selection/selectionenums.h
-include/gromacs/selection/selectionoption.h
-include/gromacs/selection/selectionoptionbehavior.h
-include/gromacs/selection/selectionoptionmanager.h
-include/gromacs/timing/wallcycle.h
-include/gromacs/timing/walltime_accounting.h
-include/gromacs/topology/atomprop.h
-include/gromacs/topology/atoms.h
-include/gromacs/topology/block.h
-include/gromacs/topology/idef.h
-include/gromacs/topology/index.h
-include/gromacs/topology/mtop_util.h
-include/gromacs/topology/symtab.h
-include/gromacs/topology/topology.h
-include/gromacs/trajectory/energy.h
-include/gromacs/trajectory/trajectoryframe.h
-include/gromacs/trajectoryanalysis.h
-include/gromacs/trajectoryanalysis/analysismodule.h
-include/gromacs/trajectoryanalysis/analysissettings.h
-include/gromacs/trajectoryanalysis/cmdlinerunner.h
-include/gromacs/utility.h
-include/gromacs/utility/alignedallocator.h
-include/gromacs/utility/allocator.h
-include/gromacs/utility/arrayref.h
-include/gromacs/utility/arraysize.h
-include/gromacs/utility/basedefinitions.h
-include/gromacs/utility/baseversion.h
-include/gromacs/utility/classhelpers.h
-include/gromacs/utility/cstringutil.h
-include/gromacs/utility/current_function.h
-include/gromacs/utility/datafilefinder.h
-include/gromacs/utility/errorcodes.h
-include/gromacs/utility/exceptions.h
-include/gromacs/utility/fatalerror.h
-include/gromacs/utility/flags.h
-include/gromacs/utility/futil.h
-include/gromacs/utility/gmxassert.h
-include/gromacs/utility/init.h
-include/gromacs/utility/programcontext.h
-include/gromacs/utility/real.h
-include/gromacs/utility/smalloc.h
-include/gromacs/utility/stringutil.h
-include/gromacs/version.h
-lib/libgromacs.so
-lib/libgromacs.so.3
-lib/libgromacs.so.3.4.0
-lib/pkgconfig/libgromacs.pc
-man/man1/gmx-anadock.1
-man/man1/gmx-anaeig.1
-man/man1/gmx-analyze.1
-man/man1/gmx-angle.1
-man/man1/gmx-awh.1
-man/man1/gmx-bar.1
-man/man1/gmx-bundle.1
-man/man1/gmx-check.1
-man/man1/gmx-chi.1
-man/man1/gmx-cluster.1
-man/man1/gmx-clustsize.1
-man/man1/gmx-confrms.1
-man/man1/gmx-convert-tpr.1
-man/man1/gmx-covar.1
-man/man1/gmx-current.1
-man/man1/gmx-density.1
-man/man1/gmx-densmap.1
-man/man1/gmx-densorder.1
-man/man1/gmx-dielectric.1
-man/man1/gmx-dipoles.1
-man/man1/gmx-disre.1
-man/man1/gmx-distance.1
-man/man1/gmx-do_dssp.1
-man/man1/gmx-dos.1
-man/man1/gmx-dump.1
-man/man1/gmx-dyecoupl.1
-man/man1/gmx-dyndom.1
-man/man1/gmx-editconf.1
-man/man1/gmx-eneconv.1
-man/man1/gmx-enemat.1
-man/man1/gmx-energy.1
-man/man1/gmx-filter.1
-man/man1/gmx-freevolume.1
-man/man1/gmx-gangle.1
-man/man1/gmx-genconf.1
-man/man1/gmx-genion.1
-man/man1/gmx-genrestr.1
-man/man1/gmx-grompp.1
-man/man1/gmx-gyrate.1
-man/man1/gmx-h2order.1
-man/man1/gmx-hbond.1
-man/man1/gmx-helix.1
-man/man1/gmx-helixorient.1
-man/man1/gmx-help.1
-man/man1/gmx-hydorder.1
-man/man1/gmx-insert-molecules.1
-man/man1/gmx-lie.1
-man/man1/gmx-make_edi.1
-man/man1/gmx-make_ndx.1
-man/man1/gmx-mdmat.1
-man/man1/gmx-mdrun.1
-man/man1/gmx-mindist.1
-man/man1/gmx-mk_angndx.1
-man/man1/gmx-morph.1
-man/man1/gmx-msd.1
-man/man1/gmx-nmeig.1
-man/man1/gmx-nmens.1
-man/man1/gmx-nmr.1
-man/man1/gmx-nmtraj.1
-man/man1/gmx-order.1
-man/man1/gmx-pairdist.1
-man/man1/gmx-pdb2gmx.1
-man/man1/gmx-pme_error.1
-man/man1/gmx-polystat.1
-man/man1/gmx-potential.1
-man/man1/gmx-principal.1
-man/man1/gmx-rama.1
-man/man1/gmx-rdf.1
-man/man1/gmx-rms.1
-man/man1/gmx-rmsdist.1
-man/man1/gmx-rmsf.1
-man/man1/gmx-rotacf.1
-man/man1/gmx-rotmat.1
-man/man1/gmx-saltbr.1
-man/man1/gmx-sans.1
-man/man1/gmx-sasa.1
-man/man1/gmx-saxs.1
-man/man1/gmx-select.1
-man/man1/gmx-sham.1
-man/man1/gmx-sigeps.1
-man/man1/gmx-solvate.1
-man/man1/gmx-sorient.1
-man/man1/gmx-spatial.1
-man/man1/gmx-spol.1
-man/man1/gmx-tcaf.1
-man/man1/gmx-traj.1
-man/man1/gmx-trajectory.1
-man/man1/gmx-trjcat.1
-man/man1/gmx-trjconv.1
-man/man1/gmx-trjorder.1
-man/man1/gmx-tune_pme.1
-man/man1/gmx-vanhove.1
-man/man1/gmx-velacc.1
-man/man1/gmx-view.1
-man/man1/gmx-wham.1
-man/man1/gmx-wheel.1
-man/man1/gmx-x2top.1
-man/man1/gmx-xpm2ps.1
-man/man1/gmx.1
-share/cmake/gromacs/gromacs-config-version.cmake
-share/cmake/gromacs/gromacs-config.cmake
-share/cmake/gromacs/libgromacs-release.cmake
-share/cmake/gromacs/libgromacs.cmake
-share/gromacs/COPYING
-share/gromacs/README.tutor
-share/gromacs/README_FreeEnergyModifications.txt
-share/gromacs/template/CMakeLists.txt
-share/gromacs/template/Makefile.pkg
-share/gromacs/template/README
-share/gromacs/template/cmake/FindGROMACS.cmake
-share/gromacs/template/template.cpp
-share/gromacs/top/README
-share/gromacs/top/amber03.ff/aminoacids.arn
-share/gromacs/top/amber03.ff/aminoacids.c.tdb
-share/gromacs/top/amber03.ff/aminoacids.hdb
-share/gromacs/top/amber03.ff/aminoacids.n.tdb
-share/gromacs/top/amber03.ff/aminoacids.r2b
-share/gromacs/top/amber03.ff/aminoacids.rtp
-share/gromacs/top/amber03.ff/aminoacids.vsd
-share/gromacs/top/amber03.ff/atomtypes.atp
-share/gromacs/top/amber03.ff/dna.arn
-share/gromacs/top/amber03.ff/dna.hdb
-share/gromacs/top/amber03.ff/dna.r2b
-share/gromacs/top/amber03.ff/dna.rtp
-share/gromacs/top/amber03.ff/ffbonded.itp
-share/gromacs/top/amber03.ff/ffnonbonded.itp
-share/gromacs/top/amber03.ff/forcefield.doc
-share/gromacs/top/amber03.ff/forcefield.itp
-share/gromacs/top/amber03.ff/gbsa.itp
-share/gromacs/top/amber03.ff/ions.itp
-share/gromacs/top/amber03.ff/rna.arn
-share/gromacs/top/amber03.ff/rna.hdb
-share/gromacs/top/amber03.ff/rna.r2b
-share/gromacs/top/amber03.ff/rna.rtp
-share/gromacs/top/amber03.ff/spc.itp
-share/gromacs/top/amber03.ff/spce.itp
-share/gromacs/top/amber03.ff/tip3p.itp
-share/gromacs/top/amber03.ff/tip4p.itp
-share/gromacs/top/amber03.ff/tip4pew.itp
-share/gromacs/top/amber03.ff/tip5p.itp
-share/gromacs/top/amber03.ff/urea.itp
-share/gromacs/top/amber03.ff/watermodels.dat
-share/gromacs/top/amber94.ff/aminoacids.arn
-share/gromacs/top/amber94.ff/aminoacids.c.tdb
-share/gromacs/top/amber94.ff/aminoacids.hdb
-share/gromacs/top/amber94.ff/aminoacids.n.tdb
-share/gromacs/top/amber94.ff/aminoacids.r2b
-share/gromacs/top/amber94.ff/aminoacids.rtp
-share/gromacs/top/amber94.ff/aminoacids.vsd
-share/gromacs/top/amber94.ff/atomtypes.atp
-share/gromacs/top/amber94.ff/dna.arn
-share/gromacs/top/amber94.ff/dna.hdb
-share/gromacs/top/amber94.ff/dna.r2b
-share/gromacs/top/amber94.ff/dna.rtp
-share/gromacs/top/amber94.ff/ffbonded.itp
-share/gromacs/top/amber94.ff/ffnonbonded.itp
-share/gromacs/top/amber94.ff/forcefield.doc
-share/gromacs/top/amber94.ff/forcefield.itp
-share/gromacs/top/amber94.ff/gbsa.itp
-share/gromacs/top/amber94.ff/ions.itp
-share/gromacs/top/amber94.ff/rna.arn
-share/gromacs/top/amber94.ff/rna.hdb
-share/gromacs/top/amber94.ff/rna.r2b
-share/gromacs/top/amber94.ff/rna.rtp
-share/gromacs/top/amber94.ff/spc.itp
-share/gromacs/top/amber94.ff/spce.itp
-share/gromacs/top/amber94.ff/tip3p.itp
-share/gromacs/top/amber94.ff/tip4p.itp
-share/gromacs/top/amber94.ff/tip4pew.itp
-share/gromacs/top/amber94.ff/tip5p.itp
-share/gromacs/top/amber94.ff/urea.itp
-share/gromacs/top/amber94.ff/watermodels.dat
-share/gromacs/top/amber96.ff/aminoacids.arn
-share/gromacs/top/amber96.ff/aminoacids.c.tdb
-share/gromacs/top/amber96.ff/aminoacids.hdb
-share/gromacs/top/amber96.ff/aminoacids.n.tdb
-share/gromacs/top/amber96.ff/aminoacids.r2b
-share/gromacs/top/amber96.ff/aminoacids.rtp
-share/gromacs/top/amber96.ff/aminoacids.vsd
-share/gromacs/top/amber96.ff/atomtypes.atp
-share/gromacs/top/amber96.ff/dna.arn
-share/gromacs/top/amber96.ff/dna.hdb
-share/gromacs/top/amber96.ff/dna.r2b
-share/gromacs/top/amber96.ff/dna.rtp
-share/gromacs/top/amber96.ff/ffbonded.itp
-share/gromacs/top/amber96.ff/ffnonbonded.itp
-share/gromacs/top/amber96.ff/forcefield.doc
-share/gromacs/top/amber96.ff/forcefield.itp
-share/gromacs/top/amber96.ff/gbsa.itp
-share/gromacs/top/amber96.ff/ions.itp
-share/gromacs/top/amber96.ff/rna.arn
-share/gromacs/top/amber96.ff/rna.hdb
-share/gromacs/top/amber96.ff/rna.r2b
-share/gromacs/top/amber96.ff/rna.rtp
-share/gromacs/top/amber96.ff/spc.itp
-share/gromacs/top/amber96.ff/spce.itp
-share/gromacs/top/amber96.ff/tip3p.itp
-share/gromacs/top/amber96.ff/tip4p.itp
-share/gromacs/top/amber96.ff/tip4pew.itp
-share/gromacs/top/amber96.ff/tip5p.itp
-share/gromacs/top/amber96.ff/urea.itp
-share/gromacs/top/amber96.ff/watermodels.dat
-share/gromacs/top/amber99.ff/aminoacids.arn
-share/gromacs/top/amber99.ff/aminoacids.c.tdb
-share/gromacs/top/amber99.ff/aminoacids.hdb
-share/gromacs/top/amber99.ff/aminoacids.n.tdb
-share/gromacs/top/amber99.ff/aminoacids.r2b
-share/gromacs/top/amber99.ff/aminoacids.rtp
-share/gromacs/top/amber99.ff/aminoacids.vsd
-share/gromacs/top/amber99.ff/atomtypes.atp
-share/gromacs/top/amber99.ff/dna.arn
-share/gromacs/top/amber99.ff/dna.hdb
-share/gromacs/top/amber99.ff/dna.r2b
-share/gromacs/top/amber99.ff/dna.rtp
-share/gromacs/top/amber99.ff/ffbonded.itp
-share/gromacs/top/amber99.ff/ffnonbonded.itp
-share/gromacs/top/amber99.ff/forcefield.doc
-share/gromacs/top/amber99.ff/forcefield.itp
-share/gromacs/top/amber99.ff/gbsa.itp
-share/gromacs/top/amber99.ff/ions.itp
-share/gromacs/top/amber99.ff/rna.arn
-share/gromacs/top/amber99.ff/rna.hdb
-share/gromacs/top/amber99.ff/rna.r2b
-share/gromacs/top/amber99.ff/rna.rtp
-share/gromacs/top/amber99.ff/spc.itp
-share/gromacs/top/amber99.ff/spce.itp
-share/gromacs/top/amber99.ff/tip3p.itp
-share/gromacs/top/amber99.ff/tip4p.itp
-share/gromacs/top/amber99.ff/tip4pew.itp
-share/gromacs/top/amber99.ff/tip5p.itp
-share/gromacs/top/amber99.ff/urea.itp
-share/gromacs/top/amber99.ff/watermodels.dat
-share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
-share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb
-share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb
-share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb
-share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b
-share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp
-share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd
-share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp
-share/gromacs/top/amber99sb-ildn.ff/dna.arn
-share/gromacs/top/amber99sb-ildn.ff/dna.hdb
-share/gromacs/top/amber99sb-ildn.ff/dna.r2b
-share/gromacs/top/amber99sb-ildn.ff/dna.rtp
-share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp
-share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp
-share/gromacs/top/amber99sb-ildn.ff/forcefield.doc
-share/gromacs/top/amber99sb-ildn.ff/forcefield.itp
-share/gromacs/top/amber99sb-ildn.ff/gbsa.itp
-share/gromacs/top/amber99sb-ildn.ff/ions.itp
-share/gromacs/top/amber99sb-ildn.ff/rna.arn
-share/gromacs/top/amber99sb-ildn.ff/rna.hdb
-share/gromacs/top/amber99sb-ildn.ff/rna.r2b
-share/gromacs/top/amber99sb-ildn.ff/rna.rtp
-share/gromacs/top/amber99sb-ildn.ff/spc.itp
-share/gromacs/top/amber99sb-ildn.ff/spce.itp
-share/gromacs/top/amber99sb-ildn.ff/tip3p.itp
-share/gromacs/top/amber99sb-ildn.ff/tip4p.itp
-share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp
-share/gromacs/top/amber99sb-ildn.ff/tip5p.itp
-share/gromacs/top/amber99sb-ildn.ff/urea.itp
-share/gromacs/top/amber99sb-ildn.ff/watermodels.dat
-share/gromacs/top/amber99sb.ff/aminoacids.arn
-share/gromacs/top/amber99sb.ff/aminoacids.c.tdb
-share/gromacs/top/amber99sb.ff/aminoacids.hdb
-share/gromacs/top/amber99sb.ff/aminoacids.n.tdb
-share/gromacs/top/amber99sb.ff/aminoacids.r2b
-share/gromacs/top/amber99sb.ff/aminoacids.rtp
-share/gromacs/top/amber99sb.ff/aminoacids.vsd
-share/gromacs/top/amber99sb.ff/atomtypes.atp
-share/gromacs/top/amber99sb.ff/dna.arn
-share/gromacs/top/amber99sb.ff/dna.hdb
-share/gromacs/top/amber99sb.ff/dna.r2b
-share/gromacs/top/amber99sb.ff/dna.rtp
-share/gromacs/top/amber99sb.ff/ffbonded.itp
-share/gromacs/top/amber99sb.ff/ffnonbonded.itp
-share/gromacs/top/amber99sb.ff/forcefield.doc
-share/gromacs/top/amber99sb.ff/forcefield.itp
-share/gromacs/top/amber99sb.ff/gbsa.itp
-share/gromacs/top/amber99sb.ff/ions.itp
-share/gromacs/top/amber99sb.ff/rna.arn
-share/gromacs/top/amber99sb.ff/rna.hdb
-share/gromacs/top/amber99sb.ff/rna.r2b
-share/gromacs/top/amber99sb.ff/rna.rtp
-share/gromacs/top/amber99sb.ff/spc.itp
-share/gromacs/top/amber99sb.ff/spce.itp
-share/gromacs/top/amber99sb.ff/tip3p.itp
-share/gromacs/top/amber99sb.ff/tip4p.itp
-share/gromacs/top/amber99sb.ff/tip4pew.itp
-share/gromacs/top/amber99sb.ff/tip5p.itp
-share/gromacs/top/amber99sb.ff/urea.itp
-share/gromacs/top/amber99sb.ff/watermodels.dat
-share/gromacs/top/amberGS.ff/aminoacids.arn
-share/gromacs/top/amberGS.ff/aminoacids.c.tdb
-share/gromacs/top/amberGS.ff/aminoacids.hdb
-share/gromacs/top/amberGS.ff/aminoacids.n.tdb
-share/gromacs/top/amberGS.ff/aminoacids.r2b
-share/gromacs/top/amberGS.ff/aminoacids.rtp
-share/gromacs/top/amberGS.ff/aminoacids.vsd
-share/gromacs/top/amberGS.ff/atomtypes.atp
-share/gromacs/top/amberGS.ff/dna.arn
-share/gromacs/top/amberGS.ff/dna.hdb
-share/gromacs/top/amberGS.ff/dna.r2b
-share/gromacs/top/amberGS.ff/dna.rtp
-share/gromacs/top/amberGS.ff/ffbonded.itp
-share/gromacs/top/amberGS.ff/ffnonbonded.itp
-share/gromacs/top/amberGS.ff/forcefield.doc
-share/gromacs/top/amberGS.ff/forcefield.itp
-share/gromacs/top/amberGS.ff/gbsa.itp
-share/gromacs/top/amberGS.ff/ions.itp
-share/gromacs/top/amberGS.ff/rna.arn
-share/gromacs/top/amberGS.ff/rna.hdb
-share/gromacs/top/amberGS.ff/rna.r2b
-share/gromacs/top/amberGS.ff/rna.rtp
-share/gromacs/top/amberGS.ff/spc.itp
-share/gromacs/top/amberGS.ff/spce.itp
-share/gromacs/top/amberGS.ff/tip3p.itp
-share/gromacs/top/amberGS.ff/tip4p.itp
-share/gromacs/top/amberGS.ff/tip4pew.itp
-share/gromacs/top/amberGS.ff/tip5p.itp
-share/gromacs/top/amberGS.ff/urea.itp
-share/gromacs/top/amberGS.ff/watermodels.dat
-share/gromacs/top/atom_nom.tbl
-share/gromacs/top/atommass.dat
-share/gromacs/top/bonds.dlg
-share/gromacs/top/ca-shift.dat
-share/gromacs/top/cb-shift.dat
-share/gromacs/top/charmm27.ff/aminoacids.arn
-share/gromacs/top/charmm27.ff/aminoacids.c.tdb
-share/gromacs/top/charmm27.ff/aminoacids.hdb
-share/gromacs/top/charmm27.ff/aminoacids.n.tdb
-share/gromacs/top/charmm27.ff/aminoacids.r2b
-share/gromacs/top/charmm27.ff/aminoacids.rtp
-share/gromacs/top/charmm27.ff/aminoacids.vsd
-share/gromacs/top/charmm27.ff/atomtypes.atp
-share/gromacs/top/charmm27.ff/cmap.itp
-share/gromacs/top/charmm27.ff/dna.arn
-share/gromacs/top/charmm27.ff/dna.c.tdb
-share/gromacs/top/charmm27.ff/dna.hdb
-share/gromacs/top/charmm27.ff/dna.n.tdb
-share/gromacs/top/charmm27.ff/dna.rtp
-share/gromacs/top/charmm27.ff/ffbonded.itp
-share/gromacs/top/charmm27.ff/ffnabonded.itp
-share/gromacs/top/charmm27.ff/ffnanonbonded.itp
-share/gromacs/top/charmm27.ff/ffnonbonded.itp
-share/gromacs/top/charmm27.ff/forcefield.doc
-share/gromacs/top/charmm27.ff/forcefield.itp
-share/gromacs/top/charmm27.ff/gb.itp
-share/gromacs/top/charmm27.ff/ions.itp
-share/gromacs/top/charmm27.ff/lipids.hdb
-share/gromacs/top/charmm27.ff/lipids.rtp
-share/gromacs/top/charmm27.ff/rna.arn
-share/gromacs/top/charmm27.ff/rna.c.tdb
-share/gromacs/top/charmm27.ff/rna.hdb
-share/gromacs/top/charmm27.ff/rna.n.tdb
-share/gromacs/top/charmm27.ff/rna.r2b
-share/gromacs/top/charmm27.ff/rna.rtp
-share/gromacs/top/charmm27.ff/spc.itp
-share/gromacs/top/charmm27.ff/spce.itp
-share/gromacs/top/charmm27.ff/tip3p.itp
-share/gromacs/top/charmm27.ff/tip4p.itp
-share/gromacs/top/charmm27.ff/tip5p.itp
-share/gromacs/top/charmm27.ff/tips3p.itp
-share/gromacs/top/charmm27.ff/watermodels.dat
-share/gromacs/top/co-shift.dat
-share/gromacs/top/defselection.dat
-share/gromacs/top/dgsolv.dat
-share/gromacs/top/edissoc.dat
-share/gromacs/top/electroneg.dat
-share/gromacs/top/elements.dat
-share/gromacs/top/export.dlg
-share/gromacs/top/ffG43a1.itp
-share/gromacs/top/ffG43a2.itp
-share/gromacs/top/ffG45a3.itp
-share/gromacs/top/ffG53a5.itp
-share/gromacs/top/ffG53a6.itp
-share/gromacs/top/ffoplsaa-n.tst
-share/gromacs/top/ffoplsaa.itp
-share/gromacs/top/flexspc.itp
-share/gromacs/top/flexspce.itp
-share/gromacs/top/flexwat-ferguson.itp
-share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb
-share/gromacs/top/gromos43a1.ff/aminoacids.hdb
-share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb
-share/gromacs/top/gromos43a1.ff/aminoacids.r2b
-share/gromacs/top/gromos43a1.ff/aminoacids.rtp
-share/gromacs/top/gromos43a1.ff/aminoacids.vsd
-share/gromacs/top/gromos43a1.ff/atomtypes.atp
-share/gromacs/top/gromos43a1.ff/ff_dum.itp
-share/gromacs/top/gromos43a1.ff/ffbonded.itp
-share/gromacs/top/gromos43a1.ff/ffnonbonded.itp
-share/gromacs/top/gromos43a1.ff/forcefield.doc
-share/gromacs/top/gromos43a1.ff/forcefield.itp
-share/gromacs/top/gromos43a1.ff/ions.itp
-share/gromacs/top/gromos43a1.ff/methanol.itp
-share/gromacs/top/gromos43a1.ff/methanol216.gro
-share/gromacs/top/gromos43a1.ff/spc.itp
-share/gromacs/top/gromos43a1.ff/spce.itp
-share/gromacs/top/gromos43a1.ff/tip3p.itp
-share/gromacs/top/gromos43a1.ff/tip4p.itp
-share/gromacs/top/gromos43a1.ff/watermodels.dat
-share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb
-share/gromacs/top/gromos43a2.ff/aminoacids.hdb
-share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb
-share/gromacs/top/gromos43a2.ff/aminoacids.r2b
-share/gromacs/top/gromos43a2.ff/aminoacids.rtp
-share/gromacs/top/gromos43a2.ff/aminoacids.vsd
-share/gromacs/top/gromos43a2.ff/atomtypes.atp
-share/gromacs/top/gromos43a2.ff/ff_dum.itp
-share/gromacs/top/gromos43a2.ff/ffbonded.itp
-share/gromacs/top/gromos43a2.ff/ffnonbonded.itp
-share/gromacs/top/gromos43a2.ff/forcefield.doc
-share/gromacs/top/gromos43a2.ff/forcefield.itp
-share/gromacs/top/gromos43a2.ff/ions.itp
-share/gromacs/top/gromos43a2.ff/spc.itp
-share/gromacs/top/gromos43a2.ff/spce.itp
-share/gromacs/top/gromos43a2.ff/tip3p.itp
-share/gromacs/top/gromos43a2.ff/tip4p.itp
-share/gromacs/top/gromos43a2.ff/watermodels.dat
-share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb
-share/gromacs/top/gromos45a3.ff/aminoacids.hdb
-share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb
-share/gromacs/top/gromos45a3.ff/aminoacids.r2b
-share/gromacs/top/gromos45a3.ff/aminoacids.rtp
-share/gromacs/top/gromos45a3.ff/aminoacids.vsd
-share/gromacs/top/gromos45a3.ff/atomtypes.atp
-share/gromacs/top/gromos45a3.ff/ff_dum.itp
-share/gromacs/top/gromos45a3.ff/ffbonded.itp
-share/gromacs/top/gromos45a3.ff/ffnonbonded.itp
-share/gromacs/top/gromos45a3.ff/forcefield.doc
-share/gromacs/top/gromos45a3.ff/forcefield.itp
-share/gromacs/top/gromos45a3.ff/ions.itp
-share/gromacs/top/gromos45a3.ff/spc.itp
-share/gromacs/top/gromos45a3.ff/spce.itp
-share/gromacs/top/gromos45a3.ff/tip3p.itp
-share/gromacs/top/gromos45a3.ff/tip4p.itp
-share/gromacs/top/gromos45a3.ff/watermodels.dat
-share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb
-share/gromacs/top/gromos53a5.ff/aminoacids.hdb
-share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb
-share/gromacs/top/gromos53a5.ff/aminoacids.r2b
-share/gromacs/top/gromos53a5.ff/aminoacids.rtp
-share/gromacs/top/gromos53a5.ff/aminoacids.vsd
-share/gromacs/top/gromos53a5.ff/atomname2type.n2t
-share/gromacs/top/gromos53a5.ff/atomtypes.atp
-share/gromacs/top/gromos53a5.ff/ff_dum.itp
-share/gromacs/top/gromos53a5.ff/ffbonded.itp
-share/gromacs/top/gromos53a5.ff/ffnonbonded.itp
-share/gromacs/top/gromos53a5.ff/forcefield.doc
-share/gromacs/top/gromos53a5.ff/forcefield.itp
-share/gromacs/top/gromos53a5.ff/ions.itp
-share/gromacs/top/gromos53a5.ff/spc.itp
-share/gromacs/top/gromos53a5.ff/spce.itp
-share/gromacs/top/gromos53a5.ff/tip3p.itp
-share/gromacs/top/gromos53a5.ff/tip4p.itp
-share/gromacs/top/gromos53a5.ff/watermodels.dat
-share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb
-share/gromacs/top/gromos53a6.ff/aminoacids.hdb
-share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb
-share/gromacs/top/gromos53a6.ff/aminoacids.r2b
-share/gromacs/top/gromos53a6.ff/aminoacids.rtp
-share/gromacs/top/gromos53a6.ff/aminoacids.vsd
-share/gromacs/top/gromos53a6.ff/atomtypes.atp
-share/gromacs/top/gromos53a6.ff/ff_dum.itp
-share/gromacs/top/gromos53a6.ff/ffbonded.itp
-share/gromacs/top/gromos53a6.ff/ffnonbonded.itp
-share/gromacs/top/gromos53a6.ff/forcefield.doc
-share/gromacs/top/gromos53a6.ff/forcefield.itp
-share/gromacs/top/gromos53a6.ff/ions.itp
-share/gromacs/top/gromos53a6.ff/spc.itp
-share/gromacs/top/gromos53a6.ff/spce.itp
-share/gromacs/top/gromos53a6.ff/tip3p.itp
-share/gromacs/top/gromos53a6.ff/tip4p.itp
-share/gromacs/top/gromos53a6.ff/watermodels.dat
-share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb
-share/gromacs/top/gromos54a7.ff/aminoacids.hdb
-share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb
-share/gromacs/top/gromos54a7.ff/aminoacids.r2b
-share/gromacs/top/gromos54a7.ff/aminoacids.rtp
-share/gromacs/top/gromos54a7.ff/aminoacids.vsd
-share/gromacs/top/gromos54a7.ff/atomtypes.atp
-share/gromacs/top/gromos54a7.ff/dppc.itp
-share/gromacs/top/gromos54a7.ff/ff_dum.itp
-share/gromacs/top/gromos54a7.ff/ffbonded.itp
-share/gromacs/top/gromos54a7.ff/ffnonbonded.itp
-share/gromacs/top/gromos54a7.ff/forcefield.doc
-share/gromacs/top/gromos54a7.ff/forcefield.itp
-share/gromacs/top/gromos54a7.ff/ions.itp
-share/gromacs/top/gromos54a7.ff/popc.itp
-share/gromacs/top/gromos54a7.ff/spc.itp
-share/gromacs/top/gromos54a7.ff/spce.itp
-share/gromacs/top/gromos54a7.ff/tip3p.itp
-share/gromacs/top/gromos54a7.ff/tip4p.itp
-share/gromacs/top/gromos54a7.ff/tmcl.itp
-share/gromacs/top/gromos54a7.ff/watermodels.dat
-share/gromacs/top/ha-shift.dat
-share/gromacs/top/ions.itp
-share/gromacs/top/nsfactor.dat
-share/gromacs/top/oplsaa.ff/1propanol.itp
-share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
-share/gromacs/top/oplsaa.ff/aminoacids.hdb
-share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
-share/gromacs/top/oplsaa.ff/aminoacids.r2b
-share/gromacs/top/oplsaa.ff/aminoacids.rtp
-share/gromacs/top/oplsaa.ff/aminoacids.vsd
-share/gromacs/top/oplsaa.ff/atomname2type.n2t
-share/gromacs/top/oplsaa.ff/atomtypes.atp
-share/gromacs/top/oplsaa.ff/ethanol.itp
-share/gromacs/top/oplsaa.ff/ffbonded.itp
-share/gromacs/top/oplsaa.ff/ffnonbonded.itp
-share/gromacs/top/oplsaa.ff/forcefield.doc
-share/gromacs/top/oplsaa.ff/forcefield.itp
-share/gromacs/top/oplsaa.ff/gbsa.itp
-share/gromacs/top/oplsaa.ff/ions.itp
-share/gromacs/top/oplsaa.ff/methanol.itp
-share/gromacs/top/oplsaa.ff/spc.itp
-share/gromacs/top/oplsaa.ff/spce.itp
-share/gromacs/top/oplsaa.ff/tip3p.itp
-share/gromacs/top/oplsaa.ff/tip4p.itp
-share/gromacs/top/oplsaa.ff/tip4pew.itp
-share/gromacs/top/oplsaa.ff/tip5p.itp
-share/gromacs/top/oplsaa.ff/tip5pe.itp
-share/gromacs/top/oplsaa.ff/watermodels.dat
-share/gromacs/top/phbres.dat
-share/gromacs/top/ps.m2p
-share/gromacs/top/random.dat
-share/gromacs/top/refi_aa.dat
-share/gromacs/top/residues.dtd
-share/gromacs/top/residues.xml
-share/gromacs/top/residuetypes.dat
-share/gromacs/top/sfactor.dat
-share/gromacs/top/spc.itp
-share/gromacs/top/spc216.gro
-share/gromacs/top/spce.itp
-share/gromacs/top/specbond.dat
-share/gromacs/top/ss.map
-share/gromacs/top/surface.dat
-share/gromacs/top/sw.itp
-share/gromacs/top/table6-10.xvg
-share/gromacs/top/table6-11.xvg
-share/gromacs/top/table6-12.xvg
-share/gromacs/top/table6-8.xvg
-share/gromacs/top/table6-9.xvg
-share/gromacs/top/tip3p.itp
-share/gromacs/top/tip4p.gro
-share/gromacs/top/tip4p.itp
-share/gromacs/top/tip5p.gro
-share/gromacs/top/vdw-msms.dat
-share/gromacs/top/vdwradii.dat
-share/gromacs/top/xlateat.dat
diff --git a/gromacs2018/distinfo b/gromacs2018/distinfo
deleted file mode 100644
index 3d8621f99a..0000000000
--- a/gromacs2018/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD$
-
-RMD160 (gromacs-2018.4.tar.gz) = 88fba994a6fb944f2b8afcb83755399b010a951e
-SHA512 (gromacs-2018.4.tar.gz) = 8ef0b90b2c266bb706c8fdba12e763de9c21aad197c1c71f48c06378644a734a3694172804db6c916a4974a9832b128512f2445d0b72783811e64edd22d27955
-Size (gromacs-2018.4.tar.gz) = 29918276 bytes
diff --git a/gromacs2018/options.mk b/gromacs2018/options.mk
deleted file mode 100644
index cea1e5dec6..0000000000
--- a/gromacs2018/options.mk
+++ /dev/null
@@ -1,28 +0,0 @@
-# $NetBSD: options.mk,v 1.2 2010/05/16 12:04:03 asau Exp $
-
-PKG_OPTIONS_VAR= PKG_OPTIONS.gromacs
-PKG_SUPPORTED_OPTIONS+= mpich x11
-PKG_SUGGESTED_OPTIONS+= x11
-
-.include "../../mk/bsd.options.mk"
-
-PLIST_VARS= x11
-
-# MPI support:
-.if !empty(PKG_OPTIONS:Mmpich)
-CONFIGURE_ARGS+= --enable-mpi
-PLIST_SUBST+= MPI=_mpi
-.include "../../mk/mpi.buildlink3.mk"
-.else
-PLIST_SUBST+= MPI=
-.endif
-
-# X support:
-.if !empty(PKG_OPTIONS:Mx11)
-CONFIGURE_ARGS+= --with-x
-PLIST.x11= yes
-
-.include "../../x11/libX11/buildlink3.mk"
-.include "../../x11/libICE/buildlink3.mk"
-.include "../../x11/libSM/buildlink3.mk"
-.endif
diff --git a/hmmer/DESCR b/hmmer/DESCR
deleted file mode 100644
index fdc94b9677..0000000000
--- a/hmmer/DESCR
+++ /dev/null
@@ -1,7 +0,0 @@
-HMMER is an implementation of profile hidden Markov model methods for
-sensitive searches of biological sequence databases using multiple sequence
-alignments as queries.
-Given a multiple sequence alignment as input, HMMER builds a statistical
-model called a "hidden Markov model" which can then be used as a query into
-a sequence database to find (and/or align) additional homologues of the
-sequence family.
diff --git a/hmmer/PLIST b/hmmer/PLIST
deleted file mode 100644
index cbee4cedf9..0000000000
--- a/hmmer/PLIST
+++ /dev/null
@@ -1,38 +0,0 @@
-@comment $NetBSD$
-bin/alimask
-bin/hmmalign
-bin/hmmbuild
-bin/hmmconvert
-bin/hmmemit
-bin/hmmfetch
-bin/hmmlogo
-bin/hmmpgmd
-bin/hmmpress
-bin/hmmscan
-bin/hmmsearch
-bin/hmmsim
-bin/hmmstat
-bin/jackhmmer
-bin/makehmmerdb
-bin/nhmmer
-bin/nhmmscan
-bin/phmmer
-man/man1/alimask.1
-man/man1/hmmalign.1
-man/man1/hmmbuild.1
-man/man1/hmmconvert.1
-man/man1/hmmemit.1
-man/man1/hmmer.1
-man/man1/hmmfetch.1
-man/man1/hmmlogo.1
-man/man1/hmmpgmd.1
-man/man1/hmmpress.1
-man/man1/hmmscan.1
-man/man1/hmmsearch.1
-man/man1/hmmsim.1
-man/man1/hmmstat.1
-man/man1/jackhmmer.1
-man/man1/makehmmerdb.1
-man/man1/nhmmer.1
-man/man1/nhmmscan.1
-man/man1/phmmer.1
diff --git a/hmmer/distinfo b/hmmer/distinfo
deleted file mode 100644
index 8775350d24..0000000000
--- a/hmmer/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD$
-
-RMD160 (hmmer-3.2.1.tar.gz) = 68d395678ee9881c956359c84514d715b0f0e30e
-SHA512 (hmmer-3.2.1.tar.gz) = e3303710c6748ffdf952c89b6202a2c322b984eca2141fe072f2f280a70e559c61d5224b3570bb8fb5bc34c49e63c9bbc56d0495898c446dd0f8df33b594b4c0
-Size (hmmer-3.2.1.tar.gz) = 7670274 bytes
diff --git a/lmod/DESCR b/lmod/DESCR
deleted file mode 100644
index 8319199171..0000000000
--- a/lmod/DESCR
+++ /dev/null
@@ -1,8 +0,0 @@
-Lmod is a Lua based module system. Modules allow for dynamic modification of
-a user's environment under Unix systems.
-
-See www.tacc.utexas.edu/tacc-projects/lmod for a complete description.
-
-Lmod is a new implementation that easily handles the MODULEPATH Hierarchical
-problem. It is drop-in replacement for TCL/C modules and reads TCL modulefiles
-directly.
diff --git a/lmod/PLIST b/lmod/PLIST
deleted file mode 100644
index 2a02d7f3ef..0000000000
--- a/lmod/PLIST
+++ /dev/null
@@ -1,120 +0,0 @@
-@comment $NetBSD: PLIST,v 1.1 2013/12/11 19:13:31 outpaddling Exp $
-bin/lmod
-lmod/${PKGVERSION}/init/bash
-lmod/${PKGVERSION}/init/csh
-lmod/${PKGVERSION}/init/cshrc
-lmod/${PKGVERSION}/init/env_modules_python.py
-lmod/${PKGVERSION}/init/ksh
-lmod/${PKGVERSION}/init/lmod_bash_completions
-lmod/${PKGVERSION}/init/.lmodrc.lua
-lmod/${PKGVERSION}/init/perl
-lmod/${PKGVERSION}/init/profile
-lmod/${PKGVERSION}/init/sh
-lmod/${PKGVERSION}/init/tcsh
-lmod/${PKGVERSION}/init/zsh
-lmod/${PKGVERSION}/libexec/addto
-lmod/${PKGVERSION}/libexec/Bare.lua
-lmod/${PKGVERSION}/libexec/BaseShell.lua
-lmod/${PKGVERSION}/libexec/Bash.lua
-lmod/${PKGVERSION}/libexec/Between.lua
-lmod/${PKGVERSION}/libexec/Cache.lua
-lmod/${PKGVERSION}/libexec/clearMT_cmd
-lmod/${PKGVERSION}/libexec/cmdfuncs.lua
-lmod/${PKGVERSION}/libexec/colorize.lua
-lmod/${PKGVERSION}/libexec/computeHashSum
-lmod/${PKGVERSION}/libexec/Configuration.lua
-lmod/${PKGVERSION}/libexec/Csh.lua
-lmod/${PKGVERSION}/libexec/CTimer.lua
-lmod/${PKGVERSION}/libexec/Exec.lua
-lmod/${PKGVERSION}/libexec/getmt
-lmod/${PKGVERSION}/libexec/Hook.lua
-lmod/${PKGVERSION}/libexec/Latest.lua
-lmod/${PKGVERSION}/libexec/lmod
-lmod/${PKGVERSION}/libexec/loadModuleFile.lua
-lmod/${PKGVERSION}/libexec/MasterControl.lua
-lmod/${PKGVERSION}/libexec/Master.lua
-lmod/${PKGVERSION}/libexec/Match.lua
-lmod/${PKGVERSION}/libexec/MC_Access.lua
-lmod/${PKGVERSION}/libexec/MC_ComputeHash.lua
-lmod/${PKGVERSION}/libexec/MC_Load.lua
-lmod/${PKGVERSION}/libexec/MC_MgrLoad.lua
-lmod/${PKGVERSION}/libexec/MC_Refresh.lua
-lmod/${PKGVERSION}/libexec/MC_Show.lua
-lmod/${PKGVERSION}/libexec/MC_Spider.lua
-lmod/${PKGVERSION}/libexec/MC_Unload.lua
-lmod/${PKGVERSION}/libexec/ml_cmd
-lmod/${PKGVERSION}/libexec/MName.lua
-lmod/${PKGVERSION}/libexec/modfuncs.lua
-lmod/${PKGVERSION}/libexec/ModuleStack.lua
-lmod/${PKGVERSION}/libexec/ModulesVersion.tcl
-lmod/${PKGVERSION}/libexec/MT.lua
-lmod/${PKGVERSION}/libexec/myGlobals.lua
-lmod/${PKGVERSION}/libexec/Options.lua
-lmod/${PKGVERSION}/libexec/pager.lua
-lmod/${PKGVERSION}/libexec/parseVersion.lua
-lmod/${PKGVERSION}/libexec/Perl.lua
-lmod/${PKGVERSION}/libexec/PkgBase.lua
-lmod/${PKGVERSION}/libexec/Pkg.lua
-lmod/${PKGVERSION}/libexec/PkgTACC.lua
-lmod/${PKGVERSION}/libexec/processModuleUsage
-lmod/${PKGVERSION}/libexec/processMT
-lmod/${PKGVERSION}/libexec/Python.lua
-lmod/${PKGVERSION}/libexec/reportUsers
-lmod/${PKGVERSION}/libexec/sandbox.lua
-lmod/${PKGVERSION}/libexec/SitePackage.lua
-lmod/${PKGVERSION}/libexec/spider
-lmod/${PKGVERSION}/libexec/spiderCacheSupport
-lmod/${PKGVERSION}/libexec/Spider.lua
-lmod/${PKGVERSION}/libexec/StandardPackage.lua
-lmod/${PKGVERSION}/libexec/tcl2lua.tcl
-lmod/${PKGVERSION}/libexec/term/colors.lua
-lmod/${PKGVERSION}/libexec/term/cursor.lua
-lmod/${PKGVERSION}/libexec/term/init.lua
-lmod/${PKGVERSION}/libexec/Timer.lua
-lmod/${PKGVERSION}/libexec/utils.lua
-lmod/${PKGVERSION}/libexec/Var.lua
-lmod/${PKGVERSION}/libexec/Version.lua
-lmod/${PKGVERSION}/lib/term/core.so
-lmod/${PKGVERSION}/lib/term/core.so.1
-lmod/${PKGVERSION}/lib/term/core.so.1.0.1
-lmod/${PKGVERSION}/modulefiles/Core/lmod/lmod.lua
-lmod/${PKGVERSION}/modulefiles/Core/settarg/settarg.lua
-lmod/${PKGVERSION}/settarg/Bare.lua
-lmod/${PKGVERSION}/settarg/BaseShell.lua
-lmod/${PKGVERSION}/settarg/Bash.lua
-lmod/${PKGVERSION}/settarg/BuildTarget.lua
-lmod/${PKGVERSION}/settarg/CmdLineOptions.lua
-lmod/${PKGVERSION}/settarg/Csh.lua
-lmod/${PKGVERSION}/settarg/getUname.lua
-lmod/${PKGVERSION}/settarg/ModifyPath.lua
-lmod/${PKGVERSION}/settarg/Output.lua
-lmod/${PKGVERSION}/settarg/ProcessModuleTable.lua
-lmod/${PKGVERSION}/settarg/settarg_cmd
-lmod/${PKGVERSION}/settarg/.settarg.lua
-lmod/${PKGVERSION}/settarg/STT.lua
-lmod/${PKGVERSION}/settarg/targ
-lmod/${PKGVERSION}/settarg/utils.lua
-lmod/${PKGVERSION}/settarg/Version.lua
-lmod/${PKGVERSION}/tools/base64.lua
-lmod/${PKGVERSION}/tools/BeautifulTbl.lua
-lmod/${PKGVERSION}/tools/capture.lua
-lmod/${PKGVERSION}/tools/ColumnTable.lua
-lmod/${PKGVERSION}/tools/Dbg.lua
-lmod/${PKGVERSION}/tools/declare.lua
-lmod/${PKGVERSION}/tools/deepcopy.lua
-lmod/${PKGVERSION}/tools/escape.lua
-lmod/${PKGVERSION}/tools/fileOps.lua
-lmod/${PKGVERSION}/tools/fillWords.lua
-lmod/${PKGVERSION}/tools/inherits.lua
-lmod/${PKGVERSION}/tools/json.lua
-lmod/${PKGVERSION}/tools/Optiks.lua
-lmod/${PKGVERSION}/tools/Optiks_Option.lua
-lmod/${PKGVERSION}/tools/pairsByKeys.lua
-lmod/${PKGVERSION}/tools/ProgressBar.lua
-lmod/${PKGVERSION}/tools/Queue.lua
-lmod/${PKGVERSION}/tools/serializeTbl.lua
-lmod/${PKGVERSION}/tools/strict.lua
-lmod/${PKGVERSION}/tools/string_split.lua
-lmod/${PKGVERSION}/tools/string_trim.lua
-lmod/${PKGVERSION}/tools/TermWidth.lua
-lmod/lmod
diff --git a/lmod/distinfo b/lmod/distinfo
deleted file mode 100644
index a1f7ad8c2f..0000000000
--- a/lmod/distinfo
+++ /dev/null
@@ -1,4 +0,0 @@
-$NetBSD: distinfo,v 1.1 2013/12/11 19:13:31 outpaddling Exp $
-
-RMD160 (Lmod-5.2.tar.bz2) = 6601f7b45a47b5ac81456c125b5ed10e792b52ff
-Size (Lmod-5.2.tar.bz2) = 167035 bytes
diff --git a/man2html/DESCR b/man2html/DESCR
deleted file mode 100644
index 374f05f4a4..0000000000
--- a/man2html/DESCR
+++ /dev/null
@@ -1 +0,0 @@
-Convert UNIX nroff(1) manual pages to HTML format.
diff --git a/man2html/PLIST b/man2html/PLIST
deleted file mode 100644
index 4f71eb2bbf..0000000000
--- a/man2html/PLIST
+++ /dev/null
@@ -1,3 +0,0 @@
-@comment $NetBSD$
-bin/man2html
-man/man1/man2html.1
diff --git a/man2html/distinfo b/man2html/distinfo
deleted file mode 100644
index 321ccb9ced..0000000000
--- a/man2html/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD$
-
-RMD160 (man2html3.0.1.tar.gz) = f3463926acc414a5f934e2cf1fd6fd59dcc454bd
-SHA512 (man2html3.0.1.tar.gz) = 6a57ff109cfc9d8a31150990f3a2304ee46956feeead9d528344be19ac252afb47bed36a470d3a9e9505ef7134b77a1edf30f5c97e8215c2c5d235cf8aee8565
-Size (man2html3.0.1.tar.gz) = 45371 bytes
diff --git a/meep-mpi/DESCR b/meep-mpi/DESCR
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/meep-mpi/PLIST b/meep-mpi/PLIST
deleted file mode 100644
index c153974b8f..0000000000
--- a/meep-mpi/PLIST
+++ /dev/null
@@ -1,10 +0,0 @@
-@comment $NetBSD: PLIST,v 1.1.1.1 2012/05/15 22:29:58 outpaddling Exp $
-bin/meep-mpi
-include/meep-mpi/meep.hpp
-include/meep-mpi/meep/mympi.hpp
-include/meep-mpi/meep/vec.hpp
-lib/libmeep_mpi.la
-lib/pkgconfig/meep_mpi.pc
-share/meep-mpi/meep/casimir.scm
-share/meep-mpi/meep/meep-enums.scm
-share/meep-mpi/meep/meep.scm
diff --git a/meep-mpi/distinfo b/meep-mpi/distinfo
deleted file mode 100644
index 25be764a53..0000000000
--- a/meep-mpi/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD: distinfo,v 1.1.1.1 2012/05/15 22:29:58 outpaddling Exp $
-
-RMD160 (meep-1.1.1.tar.gz) = 5b74b172678d5ce7e8d7ac2d7b78649aafdb11cb
-Size (meep-1.1.1.tar.gz) = 751244 bytes
-SHA1 (patch-configure) = 6ef2401ba74775f8af24cd58cb6c4d1ecf2e12b9
diff --git a/meep-mpi/patches/patch-configure b/meep-mpi/patches/patch-configure
deleted file mode 100644
index e8cfe8ac8d..0000000000
--- a/meep-mpi/patches/patch-configure
+++ /dev/null
@@ -1,19 +0,0 @@
-$NetBSD: patch-configure,v 1.1.1.1 2012/05/15 22:29:58 outpaddling Exp $
-
---- configure.orig 2011-12-27 21:51:55.000000000 +0000
-+++ configure
-@@ -1,4 +1,4 @@
--#! /bin/sh
-+#!/usr/bin/env bash
- # Guess values for system-dependent variables and create Makefiles.
- # Generated by GNU Autoconf 2.63 for meep 1.1.1.
- #
-@@ -10318,7 +10318,7 @@ fi
- LIBTOOL_DEPS="$ltmain"
-
- # Always use our own libtool.
--LIBTOOL='$(SHELL) $(top_builddir)/libtool'
-+LIBTOOL='/usr/bin/env bash $(top_builddir)/libtool'
-
-
-
diff --git a/meep-openmpi/DESCR b/meep-openmpi/DESCR
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/meep-openmpi/MESSAGE b/meep-openmpi/MESSAGE
deleted file mode 100644
index 35aaafe5de..0000000000
--- a/meep-openmpi/MESSAGE
+++ /dev/null
@@ -1,6 +0,0 @@
-
-You may need to add LD_LIBRARY_PATH to
-
-${PREFIX}/lib
-
-in order to work around a problem locating libguile-srfi*.
diff --git a/meep-openmpi/PLIST b/meep-openmpi/PLIST
deleted file mode 100644
index ff66d1a258..0000000000
--- a/meep-openmpi/PLIST
+++ /dev/null
@@ -1,10 +0,0 @@
-@comment $NetBSD: PLIST,v 1.1 2013/06/24 18:52:04 outpaddling Exp $
-openmpi/bin/meep-mpi
-openmpi/include/meep.hpp
-openmpi/include/meep/mympi.hpp
-openmpi/include/meep/vec.hpp
-openmpi/lib/libmeep_mpi.la
-openmpi/lib/pkgconfig/meep_mpi.pc
-openmpi/share/meep/casimir.scm
-openmpi/share/meep/meep-enums.scm
-openmpi/share/meep/meep.scm
diff --git a/meep-openmpi/distinfo b/meep-openmpi/distinfo
deleted file mode 100644
index a413edea4d..0000000000
--- a/meep-openmpi/distinfo
+++ /dev/null
@@ -1,7 +0,0 @@
-$NetBSD: distinfo,v 1.1 2013/06/24 18:52:04 outpaddling Exp $
-
-RMD160 (meep-1.2.tar.gz) = 2b76ea516f7ba1cae6b211ff5e623edfe88186ac
-SHA512 (meep-1.2.tar.gz) = f7b25183491881d59653ba5bc727a2b4f5deb126d515ff7ed5df7a1f9d31a5161b720348e65f45b9c76004be44714c606c4b8063f855b5cc97ff7757bd5a5656
-Size (meep-1.2.tar.gz) = 807522 bytes
-SHA1 (patch-configure) = dd626b44af862f1a93a888ea9dd1ca9c6f3ea6fe
-SHA1 (patch-configure.ac) = 54e60d25f5cd3a2dff406142860538c43043b207
diff --git a/meep-openmpi/patches/patch-configure b/meep-openmpi/patches/patch-configure
deleted file mode 100644
index 7c63cff966..0000000000
--- a/meep-openmpi/patches/patch-configure
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-configure,v 1.1 2013/06/24 18:52:04 outpaddling Exp $
-
---- configure.orig 2012-07-20 01:29:15.000000000 +0000
-+++ configure
-@@ -25552,7 +25552,7 @@ $as_echo "readline-activator" >&6; }
- ACTIVATE_READLINE="$ractivate"
- else
- ractivate="(use-modules (ice-9 readline)) (activate-readline)"
-- if guile -c "$ractivate" >& /dev/null; then
-+ if guile -c "$ractivate" > /dev/null 2>&1; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: ice-9 readline" >&5
- $as_echo "ice-9 readline" >&6; }
- ACTIVATE_READLINE="$ractivate"
diff --git a/meep-openmpi/patches/patch-configure.ac b/meep-openmpi/patches/patch-configure.ac
deleted file mode 100644
index 3698e84902..0000000000
--- a/meep-openmpi/patches/patch-configure.ac
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-configure.ac,v 1.1 2013/06/24 18:52:04 outpaddling Exp $
-
---- configure.ac.orig 2012-07-20 01:27:20.000000000 +0000
-+++ configure.ac
-@@ -307,7 +307,7 @@ if guile -c "$ractivate" > /dev/null 2>&
- ACTIVATE_READLINE="$ractivate"
- else
- ractivate="(use-modules (ice-9 readline)) (activate-readline)"
-- if guile -c "$ractivate" >& /dev/null; then
-+ if guile -c "$ractivate" > /dev/null 2>&1; then
- AC_MSG_RESULT(ice-9 readline)
- ACTIVATE_READLINE="$ractivate"
- else
diff --git a/meep/DESCR b/meep/DESCR
deleted file mode 100644
index f369570ce6..0000000000
--- a/meep/DESCR
+++ /dev/null
@@ -1,3 +0,0 @@
-Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation
-software package developed at MIT to model electromagnetic systems, along
-with our MPB eigenmode package.
diff --git a/meep/MESSAGE b/meep/MESSAGE
deleted file mode 100644
index 35aaafe5de..0000000000
--- a/meep/MESSAGE
+++ /dev/null
@@ -1,6 +0,0 @@
-
-You may need to add LD_LIBRARY_PATH to
-
-${PREFIX}/lib
-
-in order to work around a problem locating libguile-srfi*.
diff --git a/meep/PLIST b/meep/PLIST
deleted file mode 100644
index ead8208209..0000000000
--- a/meep/PLIST
+++ /dev/null
@@ -1,10 +0,0 @@
-@comment $NetBSD: PLIST,v 1.3 2013/06/24 20:21:03 outpaddling Exp $
-bin/meep
-include/meep.hpp
-include/meep/mympi.hpp
-include/meep/vec.hpp
-lib/libmeep.la
-lib/pkgconfig/meep.pc
-share/meep/casimir.scm
-share/meep/meep-enums.scm
-share/meep/meep.scm
diff --git a/meep/buildlink3.mk b/meep/buildlink3.mk
deleted file mode 100644
index 417a56def2..0000000000
--- a/meep/buildlink3.mk
+++ /dev/null
@@ -1,18 +0,0 @@
-# $NetBSD: buildlink3.mk,v 1.3 2012/10/15 19:21:45 asau Exp $
-
-BUILDLINK_TREE+= meep
-
-.if !defined(MEEP_BUILDLINK3_MK)
-MEEP_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.meep+= meep>=1.1.1
-BUILDLINK_PKGSRCDIR.meep?= ../../wip/meep
-
-.include "../../math/harminv/buildlink3.mk"
-.include "../../wip/libctl/buildlink3.mk"
-.include "../../devel/hdf5/buildlink3.mk"
-.include "../../devel/gettext-lib/buildlink3.mk"
-.include "../../converters/libiconv/buildlink3.mk"
-.endif # MEEP_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -meep
diff --git a/meep/distinfo b/meep/distinfo
deleted file mode 100644
index 759900f122..0000000000
--- a/meep/distinfo
+++ /dev/null
@@ -1,7 +0,0 @@
-$NetBSD: distinfo,v 1.3 2012/10/15 21:50:13 asau Exp $
-
-RMD160 (meep-1.2.tar.gz) = 2b76ea516f7ba1cae6b211ff5e623edfe88186ac
-SHA512 (meep-1.2.tar.gz) = f7b25183491881d59653ba5bc727a2b4f5deb126d515ff7ed5df7a1f9d31a5161b720348e65f45b9c76004be44714c606c4b8063f855b5cc97ff7757bd5a5656
-Size (meep-1.2.tar.gz) = 807522 bytes
-SHA1 (patch-configure) = dd626b44af862f1a93a888ea9dd1ca9c6f3ea6fe
-SHA1 (patch-configure.ac) = 54e60d25f5cd3a2dff406142860538c43043b207
diff --git a/meep/patches/patch-configure b/meep/patches/patch-configure
deleted file mode 100644
index ca302a992f..0000000000
--- a/meep/patches/patch-configure
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-configure,v 1.3 2012/10/15 21:53:37 asau Exp $
-
---- configure.orig 2012-07-20 01:29:15.000000000 +0000
-+++ configure
-@@ -25552,7 +25552,7 @@ $as_echo "readline-activator" >&6; }
- ACTIVATE_READLINE="$ractivate"
- else
- ractivate="(use-modules (ice-9 readline)) (activate-readline)"
-- if guile -c "$ractivate" >& /dev/null; then
-+ if guile -c "$ractivate" > /dev/null 2>&1; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: ice-9 readline" >&5
- $as_echo "ice-9 readline" >&6; }
- ACTIVATE_READLINE="$ractivate"
diff --git a/meep/patches/patch-configure.ac b/meep/patches/patch-configure.ac
deleted file mode 100644
index 1fe5b6070d..0000000000
--- a/meep/patches/patch-configure.ac
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-configure.ac,v 1.1 2012/10/15 21:53:37 asau Exp $
-
---- configure.ac.orig 2012-07-20 01:27:20.000000000 +0000
-+++ configure.ac
-@@ -307,7 +307,7 @@ if guile -c "$ractivate" > /dev/null 2>&
- ACTIVATE_READLINE="$ractivate"
- else
- ractivate="(use-modules (ice-9 readline)) (activate-readline)"
-- if guile -c "$ractivate" >& /dev/null; then
-+ if guile -c "$ractivate" > /dev/null 2>&1; then
- AC_MSG_RESULT(ice-9 readline)
- ACTIVATE_READLINE="$ractivate"
- else
diff --git a/mpb-openmpi/DESCR b/mpb-openmpi/DESCR
deleted file mode 100644
index 9602c9b4c4..0000000000
--- a/mpb-openmpi/DESCR
+++ /dev/null
@@ -1,3 +0,0 @@
-The MIT Photonic-Bands (MPB) package is a free program for computing the band
-structures (dispersion relations) and electromagnetic modes of periodic
-dielectric structures, on both serial and parallel computers.
diff --git a/mpb-openmpi/PLIST b/mpb-openmpi/PLIST
deleted file mode 100644
index 0fe701b0b3..0000000000
--- a/mpb-openmpi/PLIST
+++ /dev/null
@@ -1,5 +0,0 @@
-@comment $NetBSD: PLIST,v 1.1 2013/06/23 18:33:44 outpaddling Exp $
-openmpi/bin/mpb-mpi
-openmpi/man/man1/mpb.1
-openmpi/share/libctl/specs/mpb.scm
-@pkgdir openmpi/lib
diff --git a/mpb-openmpi/buildlink3.mk b/mpb-openmpi/buildlink3.mk
deleted file mode 100644
index 2668906d8e..0000000000
--- a/mpb-openmpi/buildlink3.mk
+++ /dev/null
@@ -1,19 +0,0 @@
-# $NetBSD: buildlink3.mk,v 1.3 2013/06/23 18:44:16 outpaddling Exp $
-# XXX BUILDLINK_DEPMETHOD.mpb-openmpi?= build
-
-BUILDLINK_TREE+= mpb-openmpi
-
-.if !defined(MPB_BUILDLINK3_MK)
-MPB_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.mpb-openmpi+= mpb-openmpi>=1.4.2
-BUILDLINK_PKGSRCDIR.mpb-openmpi?= ../../wip/mpb-openmpi
-
-.include "../../mk/blas.buildlink3.mk"
-.include "../../devel/hdf5/buildlink3.mk"
-.include "../../math/fftw2/buildlink3.mk"
-.include "../../devel/readline/buildlink3.mk"
-.include "../../devel/libctl/buildlink3.mk"
-.endif # MPB_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -mpb-openmpi
diff --git a/mpb-openmpi/distinfo b/mpb-openmpi/distinfo
deleted file mode 100644
index 5e4026cd38..0000000000
--- a/mpb-openmpi/distinfo
+++ /dev/null
@@ -1,10 +0,0 @@
-$NetBSD: distinfo,v 1.1 2013/06/23 18:33:44 outpaddling Exp $
-
-RMD160 (mpb-1.4.2.tar.gz) = 6440f0e19d4b5b8354c135034429ea2031c4301d
-SHA512 (mpb-1.4.2.tar.gz) = 4151612b8868b324353556f46aeccdce2726d8938ab8cf7404c36da68e90ec0de1799d4e23b2d5bbe5853d0c0329ba0ee1a2fdb2745aed43c34759084b62fbac
-Size (mpb-1.4.2.tar.gz) = 686488 bytes
-SHA1 (patch-mpb-ctl_Makefile.in) = 822a94fe7239664002daf45d0bee94b415af15c4
-SHA1 (patch-src_util_Makefile.in) = a2ed814bf1ad94d4192fa82fc1cdbcc926eb53b2
-SHA1 (patch-src_util_check.c) = 59fb816d555bf7baf718253bde3bca8516da6d69
-SHA1 (patch-src_util_check.h) = 278a7c27ec3d0e06c1d9611f99b1d4a5d4f3d2de
-SHA1 (patch-utils_Makefile.in) = bcdc8b28a2bf29c1e94b38a9b5dd7d93073a00a6
diff --git a/mpb-openmpi/patches/patch-mpb-ctl_Makefile.in b/mpb-openmpi/patches/patch-mpb-ctl_Makefile.in
deleted file mode 100644
index 8d96f6f59b..0000000000
--- a/mpb-openmpi/patches/patch-mpb-ctl_Makefile.in
+++ /dev/null
@@ -1,51 +0,0 @@
-$NetBSD: patch-mpb-ctl_Makefile.in,v 1.1 2013/06/23 18:33:44 outpaddling Exp $
-
---- mpb-ctl/Makefile.in.orig 2002-09-14 22:20:55.000000000 +0000
-+++ mpb-ctl/Makefile.in
-@@ -66,7 +66,12 @@ LDFLAGS = $(MY_LDFLAGS) @LDFLAGS@
- ##############################################################################
-
- INSTALL = @INSTALL@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_DATA = @INSTALL_DATA@
- prefix = @prefix@
-+exec_prefix = @exec_prefix@
-+bindir = @bindir@
- mandir = @mandir@
- # c.f. AC_ARG_PROGRAM autoconf docs:
- transform=@program_transform_name@
-@@ -133,23 +138,23 @@ geom.c: $(LIBCTL_DIR)/utils/geom.c
- install: install-mpb @INSTALL_MPB_SPLIT@
-
- install-mpb: $(PROGRAM_NAME)
-- $(INSTALL) -d $(prefix)/bin
-- $(INSTALL) -m 0755 -s .$(PROGRAM_NAME) $(prefix)/bin/`echo $(PROGRAM_NAME)|sed '$(transform)'`
-- $(INSTALL) -d $(prefix)/share/libctl/specs
-- $(INSTALL) -m 0644 $(SPECIFICATION_FILE) $(prefix)/share/libctl/specs
-- $(INSTALL) -d $(mandir)/man1
-- $(INSTALL) -m 0644 $(PROGRAM_NAME).1 $(mandir)/man1
-+ $(INSTALL) -d $(DESTDIR)$(prefix)/bin
-+ $(INSTALL_PROGRAM) .$(PROGRAM_NAME) $(DESTDIR)$(bindir)/`echo $(PROGRAM_NAME)|sed '$(transform)'`
-+ $(INSTALL) -d $(DESTDIR)$(prefix)/share/libctl/specs
-+ $(INSTALL_DATA) $(SPECIFICATION_FILE) $(DESTDIR)$(prefix)/share/libctl/specs
-+ $(INSTALL) -d $(DESTDIR)$(mandir)/man1
-+ $(INSTALL_DATA) $(PROGRAM_NAME).1 $(DESTDIR)$(mandir)/man1
-
- mpb-split-tmp:
- rm -f mpb-split-tmp
- mpb_name=`echo mpb | sed '$(transform)'`; \
-- sed "s%\./mpb%"$(prefix)/bin/"$$mpb_name%g" mpb-split > mpb-split-tmp;
-+ sed "s%\./mpb%"$(bindir)/"$$mpb_name%g" mpb-split > mpb-split-tmp;
-
- install-mpb-split: mpb-split-tmp
- mpb_name=`echo mpb | sed '$(transform)'`; \
-- $(INSTALL) -m 0755 mpb-split-tmp $(prefix)/bin/$${mpb_name}-split
-- $(INSTALL) -d $(mandir)/man1
-- $(INSTALL) -m 0644 mpb-split.1 $(mandir)/man1
-+ $(INSTALL_SCRIPT) mpb-split-tmp $(DESTDIR)$(bindir)/$${mpb_name}-split
-+ $(INSTALL) -d $(DESTDIR)$(mandir)/man1
-+ $(INSTALL_DATA) mpb-split.1 $(DESTDIR)$(mandir)/man1
-
- clean:
- rm -f $(ALL_OBJECTS) ctl-io.c ctl-io.h main.c geom.c \
diff --git a/mpb-openmpi/patches/patch-src_util_Makefile.in b/mpb-openmpi/patches/patch-src_util_Makefile.in
deleted file mode 100644
index 060487f89b..0000000000
--- a/mpb-openmpi/patches/patch-src_util_Makefile.in
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-src_util_Makefile.in,v 1.1 2013/06/23 18:33:44 outpaddling Exp $
-
---- src/util/Makefile.in.orig 2002-09-14 22:20:55.000000000 +0000
-+++ src/util/Makefile.in
-@@ -15,7 +15,7 @@ AR = ar
-
- all: libs
-
--OBJECTS = debug_malloc.o mpi_utils.o
-+OBJECTS = debug_malloc.o mpi_utils.o check.o
- LIBNAME = util.a
-
- libs: $(LIBNAME)
diff --git a/mpb-openmpi/patches/patch-src_util_check.c b/mpb-openmpi/patches/patch-src_util_check.c
deleted file mode 100644
index 749bf8eb7e..0000000000
--- a/mpb-openmpi/patches/patch-src_util_check.c
+++ /dev/null
@@ -1,20 +0,0 @@
-$NetBSD: patch-src_util_check.c,v 1.1 2013/06/23 18:33:44 outpaddling Exp $
-
---- src/util/check.c.orig 2013-04-03 21:01:44.000000000 +0000
-+++ src/util/check.c
-@@ -0,0 +1,15 @@
-+#include <libguile.h>
-+
-+void
-+scm_mpb_error (const char *file, int line, const char *message)
-+{
-+ char buf[256];
-+ sprintf (buf, "%s, line %d", file, line);
-+ scm_error(
-+ scm_string_to_symbol (scm_makfrom0str("mpb-error")),
-+ buf,
-+ message,
-+ SCM_BOOL_F, /* no args */
-+ SCM_BOOL_F /* no rest */
-+ );
-+}
diff --git a/mpb-openmpi/patches/patch-src_util_check.h b/mpb-openmpi/patches/patch-src_util_check.h
deleted file mode 100644
index 8370ca99ca..0000000000
--- a/mpb-openmpi/patches/patch-src_util_check.h
+++ /dev/null
@@ -1,27 +0,0 @@
-$NetBSD: patch-src_util_check.h,v 1.1 2013/06/23 18:33:44 outpaddling Exp $
-
---- src/util/check.h.orig 2013-04-03 21:02:05.000000000 +0000
-+++ src/util/check.h
-@@ -33,6 +33,7 @@ extern void check_breakpoint(void);
- #define CHECK_BREAKPOINT /* nothing */
- #endif
-
-+#ifdef HAVE_MPI
- #define CHECK(condition, message) do { \
- if (!(condition)) { \
- CHECK_BREAKPOINT; \
-@@ -40,6 +41,14 @@ extern void check_breakpoint(void);
- message "\n", __LINE__); \
- } \
- } while (0)
-+#else
-+extern void scm_mpb_error (const char *file, int line, const char *message);
-+#define CHECK(condition, message) \
-+ if (!(condition)) { \
-+ CHECK_BREAKPOINT; \
-+ scm_mpb_error(__FILE__, __LINE__, message); \
-+ }
-+#endif
-
- #endif /* not CHECK_DISABLE */
-
diff --git a/mpb-openmpi/patches/patch-utils_Makefile.in b/mpb-openmpi/patches/patch-utils_Makefile.in
deleted file mode 100644
index 0c46d324e4..0000000000
--- a/mpb-openmpi/patches/patch-utils_Makefile.in
+++ /dev/null
@@ -1,32 +0,0 @@
-$NetBSD: patch-utils_Makefile.in,v 1.1 2013/06/23 18:33:44 outpaddling Exp $
-
---- utils/Makefile.in.orig 2002-09-14 22:20:55.000000000 +0000
-+++ utils/Makefile.in
-@@ -12,7 +12,12 @@ RANLIB = @RANLIB@
- @SET_MAKE@
-
- INSTALL = @INSTALL@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_DATA = @INSTALL_DATA@
- prefix = @prefix@
-+exec_prefix = @exec_prefix@
-+bindir = @bindir@
- mandir = @mandir@
- # c.f. AC_ARG_PROGRAM autoconf docs:
- transform=@program_transform_name@
-@@ -35,10 +40,10 @@ install: install-@BUILD_MPB_DATA@
- install-: # dummy target for when BUILD_MPB_DATA is ""
-
- install-mpb-data: mpb-data
-- $(INSTALL) -d $(prefix)/bin
-- $(INSTALL) -m 0755 -s mpb-data $(prefix)/bin/`echo mpb-data|sed '$(transform)'`
-- $(INSTALL) -d $(mandir)/man1
-- $(INSTALL) -m 0644 mpb-data.1 $(mandir)/man1
-+ $(INSTALL) -d $(DESTDIR)$(bindir)
-+ $(INSTALL_PROGRAM) mpb-data $(DESTDIR)$(bindir)/`echo mpb-data|sed '$(transform)'`
-+ $(INSTALL) -d $(DESTDIR)$(mandir)/man1
-+ $(INSTALL_DATA) mpb-data.1 $(DESTDIR)$(mandir)/man1
-
- clean:
- rm -f mpb-data mpb-data.o core
diff --git a/mpb/DESCR b/mpb/DESCR
deleted file mode 100644
index 9602c9b4c4..0000000000
--- a/mpb/DESCR
+++ /dev/null
@@ -1,3 +0,0 @@
-The MIT Photonic-Bands (MPB) package is a free program for computing the band
-structures (dispersion relations) and electromagnetic modes of periodic
-dielectric structures, on both serial and parallel computers.
diff --git a/mpb/PLIST b/mpb/PLIST
deleted file mode 100644
index 1ffb9a43ed..0000000000
--- a/mpb/PLIST
+++ /dev/null
@@ -1,8 +0,0 @@
-@comment $NetBSD: PLIST,v 1.1.1.1 2012/03/23 02:21:07 outpaddling Exp $
-bin/mpb
-bin/mpb-data
-bin/mpb-split
-man/man1/mpb-data.1
-man/man1/mpb-split.1
-man/man1/mpb.1
-share/libctl/specs/mpb.scm
diff --git a/mpb/buildlink3.mk b/mpb/buildlink3.mk
deleted file mode 100644
index b6560229f3..0000000000
--- a/mpb/buildlink3.mk
+++ /dev/null
@@ -1,19 +0,0 @@
-# $NetBSD: buildlink3.mk,v 1.2 2013/02/22 22:51:42 kristerw Exp $
-# XXX BUILDLINK_DEPMETHOD.mpb?= build
-
-BUILDLINK_TREE+= mpb
-
-.if !defined(MPB_BUILDLINK3_MK)
-MPB_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.mpb+= mpb>=1.4.2
-BUILDLINK_PKGSRCDIR.mpb?= ../../wip/mpb
-
-.include "../../mk/blas.buildlink3.mk"
-.include "../../devel/hdf5/buildlink3.mk"
-.include "../../math/fftw2/buildlink3.mk"
-.include "../../devel/readline/buildlink3.mk"
-.include "../../devel/libctl/buildlink3.mk"
-.endif # MPB_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -mpb
diff --git a/mpb/distinfo b/mpb/distinfo
deleted file mode 100644
index f47bbae2c8..0000000000
--- a/mpb/distinfo
+++ /dev/null
@@ -1,10 +0,0 @@
-$NetBSD: distinfo,v 1.3 2013/04/03 21:21:04 outpaddling Exp $
-
-RMD160 (mpb-1.4.2.tar.gz) = 6440f0e19d4b5b8354c135034429ea2031c4301d
-SHA512 (mpb-1.4.2.tar.gz) = 4151612b8868b324353556f46aeccdce2726d8938ab8cf7404c36da68e90ec0de1799d4e23b2d5bbe5853d0c0329ba0ee1a2fdb2745aed43c34759084b62fbac
-Size (mpb-1.4.2.tar.gz) = 686488 bytes
-SHA1 (patch-mpb-ctl_Makefile.in) = 822a94fe7239664002daf45d0bee94b415af15c4
-SHA1 (patch-src_util_Makefile.in) = a2ed814bf1ad94d4192fa82fc1cdbcc926eb53b2
-SHA1 (patch-src_util_check.c) = 59fb816d555bf7baf718253bde3bca8516da6d69
-SHA1 (patch-src_util_check.h) = 278a7c27ec3d0e06c1d9611f99b1d4a5d4f3d2de
-SHA1 (patch-utils_Makefile.in) = bcdc8b28a2bf29c1e94b38a9b5dd7d93073a00a6
diff --git a/mpb/patches/patch-mpb-ctl_Makefile.in b/mpb/patches/patch-mpb-ctl_Makefile.in
deleted file mode 100644
index 45a92727d5..0000000000
--- a/mpb/patches/patch-mpb-ctl_Makefile.in
+++ /dev/null
@@ -1,51 +0,0 @@
-$NetBSD: patch-mpb-ctl_Makefile.in,v 1.1 2012/10/15 21:01:15 asau Exp $
-
---- mpb-ctl/Makefile.in.orig 2002-09-14 22:20:55.000000000 +0000
-+++ mpb-ctl/Makefile.in
-@@ -66,7 +66,12 @@ LDFLAGS = $(MY_LDFLAGS) @LDFLAGS@
- ##############################################################################
-
- INSTALL = @INSTALL@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_DATA = @INSTALL_DATA@
- prefix = @prefix@
-+exec_prefix = @exec_prefix@
-+bindir = @bindir@
- mandir = @mandir@
- # c.f. AC_ARG_PROGRAM autoconf docs:
- transform=@program_transform_name@
-@@ -133,23 +138,23 @@ geom.c: $(LIBCTL_DIR)/utils/geom.c
- install: install-mpb @INSTALL_MPB_SPLIT@
-
- install-mpb: $(PROGRAM_NAME)
-- $(INSTALL) -d $(prefix)/bin
-- $(INSTALL) -m 0755 -s .$(PROGRAM_NAME) $(prefix)/bin/`echo $(PROGRAM_NAME)|sed '$(transform)'`
-- $(INSTALL) -d $(prefix)/share/libctl/specs
-- $(INSTALL) -m 0644 $(SPECIFICATION_FILE) $(prefix)/share/libctl/specs
-- $(INSTALL) -d $(mandir)/man1
-- $(INSTALL) -m 0644 $(PROGRAM_NAME).1 $(mandir)/man1
-+ $(INSTALL) -d $(DESTDIR)$(prefix)/bin
-+ $(INSTALL_PROGRAM) .$(PROGRAM_NAME) $(DESTDIR)$(bindir)/`echo $(PROGRAM_NAME)|sed '$(transform)'`
-+ $(INSTALL) -d $(DESTDIR)$(prefix)/share/libctl/specs
-+ $(INSTALL_DATA) $(SPECIFICATION_FILE) $(DESTDIR)$(prefix)/share/libctl/specs
-+ $(INSTALL) -d $(DESTDIR)$(mandir)/man1
-+ $(INSTALL_DATA) $(PROGRAM_NAME).1 $(DESTDIR)$(mandir)/man1
-
- mpb-split-tmp:
- rm -f mpb-split-tmp
- mpb_name=`echo mpb | sed '$(transform)'`; \
-- sed "s%\./mpb%"$(prefix)/bin/"$$mpb_name%g" mpb-split > mpb-split-tmp;
-+ sed "s%\./mpb%"$(bindir)/"$$mpb_name%g" mpb-split > mpb-split-tmp;
-
- install-mpb-split: mpb-split-tmp
- mpb_name=`echo mpb | sed '$(transform)'`; \
-- $(INSTALL) -m 0755 mpb-split-tmp $(prefix)/bin/$${mpb_name}-split
-- $(INSTALL) -d $(mandir)/man1
-- $(INSTALL) -m 0644 mpb-split.1 $(mandir)/man1
-+ $(INSTALL_SCRIPT) mpb-split-tmp $(DESTDIR)$(bindir)/$${mpb_name}-split
-+ $(INSTALL) -d $(DESTDIR)$(mandir)/man1
-+ $(INSTALL_DATA) mpb-split.1 $(DESTDIR)$(mandir)/man1
-
- clean:
- rm -f $(ALL_OBJECTS) ctl-io.c ctl-io.h main.c geom.c \
diff --git a/mpb/patches/patch-src_util_Makefile.in b/mpb/patches/patch-src_util_Makefile.in
deleted file mode 100644
index 2408f48d92..0000000000
--- a/mpb/patches/patch-src_util_Makefile.in
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-src_util_Makefile.in,v 1.1 2013/04/03 21:21:04 outpaddling Exp $
-
---- src/util/Makefile.in.orig 2002-09-14 22:20:55.000000000 +0000
-+++ src/util/Makefile.in
-@@ -15,7 +15,7 @@ AR = ar
-
- all: libs
-
--OBJECTS = debug_malloc.o mpi_utils.o
-+OBJECTS = debug_malloc.o mpi_utils.o check.o
- LIBNAME = util.a
-
- libs: $(LIBNAME)
diff --git a/mpb/patches/patch-src_util_check.c b/mpb/patches/patch-src_util_check.c
deleted file mode 100644
index 64740ae5f7..0000000000
--- a/mpb/patches/patch-src_util_check.c
+++ /dev/null
@@ -1,20 +0,0 @@
-$NetBSD: patch-src_util_check.c,v 1.1 2013/04/03 21:21:05 outpaddling Exp $
-
---- src/util/check.c.orig 2013-04-03 21:01:44.000000000 +0000
-+++ src/util/check.c
-@@ -0,0 +1,15 @@
-+#include <libguile.h>
-+
-+void
-+scm_mpb_error (const char *file, int line, const char *message)
-+{
-+ char buf[256];
-+ sprintf (buf, "%s, line %d", file, line);
-+ scm_error(
-+ scm_string_to_symbol (scm_makfrom0str("mpb-error")),
-+ buf,
-+ message,
-+ SCM_BOOL_F, /* no args */
-+ SCM_BOOL_F /* no rest */
-+ );
-+}
diff --git a/mpb/patches/patch-src_util_check.h b/mpb/patches/patch-src_util_check.h
deleted file mode 100644
index e32f803e69..0000000000
--- a/mpb/patches/patch-src_util_check.h
+++ /dev/null
@@ -1,27 +0,0 @@
-$NetBSD: patch-src_util_check.h,v 1.1 2013/04/03 21:21:05 outpaddling Exp $
-
---- src/util/check.h.orig 2013-04-03 21:02:05.000000000 +0000
-+++ src/util/check.h
-@@ -33,6 +33,7 @@ extern void check_breakpoint(void);
- #define CHECK_BREAKPOINT /* nothing */
- #endif
-
-+#ifdef HAVE_MPI
- #define CHECK(condition, message) do { \
- if (!(condition)) { \
- CHECK_BREAKPOINT; \
-@@ -40,6 +41,14 @@ extern void check_breakpoint(void);
- message "\n", __LINE__); \
- } \
- } while (0)
-+#else
-+extern void scm_mpb_error (const char *file, int line, const char *message);
-+#define CHECK(condition, message) \
-+ if (!(condition)) { \
-+ CHECK_BREAKPOINT; \
-+ scm_mpb_error(__FILE__, __LINE__, message); \
-+ }
-+#endif
-
- #endif /* not CHECK_DISABLE */
-
diff --git a/mpb/patches/patch-utils_Makefile.in b/mpb/patches/patch-utils_Makefile.in
deleted file mode 100644
index f6fddda5b3..0000000000
--- a/mpb/patches/patch-utils_Makefile.in
+++ /dev/null
@@ -1,32 +0,0 @@
-$NetBSD: patch-utils_Makefile.in,v 1.1 2012/10/15 21:01:15 asau Exp $
-
---- utils/Makefile.in.orig 2002-09-14 22:20:55.000000000 +0000
-+++ utils/Makefile.in
-@@ -12,7 +12,12 @@ RANLIB = @RANLIB@
- @SET_MAKE@
-
- INSTALL = @INSTALL@
-+INSTALL_PROGRAM = @INSTALL_PROGRAM@
-+INSTALL_SCRIPT = @INSTALL_SCRIPT@
-+INSTALL_DATA = @INSTALL_DATA@
- prefix = @prefix@
-+exec_prefix = @exec_prefix@
-+bindir = @bindir@
- mandir = @mandir@
- # c.f. AC_ARG_PROGRAM autoconf docs:
- transform=@program_transform_name@
-@@ -35,10 +40,10 @@ install: install-@BUILD_MPB_DATA@
- install-: # dummy target for when BUILD_MPB_DATA is ""
-
- install-mpb-data: mpb-data
-- $(INSTALL) -d $(prefix)/bin
-- $(INSTALL) -m 0755 -s mpb-data $(prefix)/bin/`echo mpb-data|sed '$(transform)'`
-- $(INSTALL) -d $(mandir)/man1
-- $(INSTALL) -m 0644 mpb-data.1 $(mandir)/man1
-+ $(INSTALL) -d $(DESTDIR)$(bindir)
-+ $(INSTALL_PROGRAM) mpb-data $(DESTDIR)$(bindir)/`echo mpb-data|sed '$(transform)'`
-+ $(INSTALL) -d $(DESTDIR)$(mandir)/man1
-+ $(INSTALL_DATA) mpb-data.1 $(DESTDIR)$(mandir)/man1
-
- clean:
- rm -f mpb-data mpb-data.o core
diff --git a/multichoose/DESCR b/multichoose/DESCR
deleted file mode 100644
index 6c1d61f8d1..0000000000
--- a/multichoose/DESCR
+++ /dev/null
@@ -1,4 +0,0 @@
-Efficient loopless multiset combination generation algorithm which is
-(approximately) described in "Loopless algorithms for generating permutations,
-combinations, and other combinatorial configurations." G Ehrlich - Journal of
-the ACM (JACM), 1973. (Algorithm 7.)
diff --git a/multichoose/PLIST b/multichoose/PLIST
deleted file mode 100644
index 3412967736..0000000000
--- a/multichoose/PLIST
+++ /dev/null
@@ -1,8 +0,0 @@
-@comment $NetBSD$
-bin/cmultichoose
-bin/multichoose
-bin/multichoose.py
-bin/multipermute
-bin/multipermute.py
-include/multichoose/multichoose.h
-include/multichoose/multipermute.h
diff --git a/multichoose/TODO b/multichoose/TODO
deleted file mode 100644
index b687356e6b..0000000000
--- a/multichoose/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test
diff --git a/multichoose/buildlink3.mk b/multichoose/buildlink3.mk
deleted file mode 100644
index f773f46fd9..0000000000
--- a/multichoose/buildlink3.mk
+++ /dev/null
@@ -1,13 +0,0 @@
-# $NetBSD$
-# XXX BUILDLINK_DEPMETHOD.multichoose?= build
-
-BUILDLINK_TREE+= multichoose
-
-.if !defined(MULTICHOOSE_BUILDLINK3_MK)
-MULTICHOOSE_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.multichoose+= multichoose>=0.0.0.20151117
-BUILDLINK_PKGSRCDIR.multichoose?= ../../wip/multichoose
-.endif # MULTICHOOSE_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -multichoose
diff --git a/multichoose/distinfo b/multichoose/distinfo
deleted file mode 100644
index 31d1f04dfa..0000000000
--- a/multichoose/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD$
-
-RMD160 (multichoose-0.0.0.20151117-3b8d14e616c719de88261614f0e78195d8ed49e9.tar.gz) = 2de518cc97c5b0e2bb635e4673cd8434fefd2cff
-SHA512 (multichoose-0.0.0.20151117-3b8d14e616c719de88261614f0e78195d8ed49e9.tar.gz) = af300100ee40c9038b0a0bbdb5351cff68721176b968ae04ede7fb1cb9f8462eb46c6563e20f1ccba9a1058520b2b996d1fb675cb62ffa6c020cbacdc0dda2b9
-Size (multichoose-0.0.0.20151117-3b8d14e616c719de88261614f0e78195d8ed49e9.tar.gz) = 6551 bytes
diff --git a/multichoose/files/Makefile b/multichoose/files/Makefile
deleted file mode 100644
index 4dbae01af9..0000000000
--- a/multichoose/files/Makefile
+++ /dev/null
@@ -1,46 +0,0 @@
-
-# Use ?= to allow overriding from the env or command-line, e.g.
-#
-# make CXXFLAGS="-O3 -fPIC" install
-#
-# Package managers will override many of these variables automatically, so
-# this is aimed at making it easy to create packages (Debian packages,
-# FreeBSD ports, MacPorts, pkgsrc, etc.)
-
-CC ?= cc
-CXX ?= c++
-DESTDIR ?= stage
-PREFIX ?= /usr/local
-MKDIR ?= mkdir
-INSTALL ?= install -c
-STRIP ?= strip
-AR ?= ar
-
-BINS = multichoose cmultichoose multipermute
-
-all: ${BINS}
-
-#multichoose_recursive: multichoose_recursive.cpp
-# ${CXX} multichoose_recursive.cpp -o multichoose_recursive
-
-multichoose: multichoose.cpp multichoose.h
- ${CXX} multichoose.cpp -o multichoose
-
-multipermute: multipermute.cpp multipermute.h
- ${CXX} multipermute.cpp -o multipermute
-
-cmultichoose: multichoose.c
- ${CC} multichoose.c -o cmultichoose
-
-install: all
- ${MKDIR} -p ${DESTDIR}${PREFIX}/bin
- ${MKDIR} -p ${DESTDIR}${PREFIX}/include/multichoose
- ${INSTALL} ${BINS} ${DESTDIR}${PREFIX}/bin
- ${INSTALL} *.py ${DESTDIR}${PREFIX}/bin
- ${INSTALL} -m644 *.h ${DESTDIR}${PREFIX}/include/multichoose
-
-install-strip: install
- ${STRIP} ${DESTDIR}${PREFIX}/bin/*e
-
-clean:
- rm -rf ${BINS} ${DESTDIR}
diff --git a/numactl/DESCR b/numactl/DESCR
deleted file mode 100644
index 8037e20f24..0000000000
--- a/numactl/DESCR
+++ /dev/null
@@ -1,4 +0,0 @@
-The numactl program allows you to run your application program on specific
-cpu's and memory nodes. The libnuma library provides convenient ways for you
-to add NUMA memory policies into your own program. It is a shared object (.so)
-library.
diff --git a/numactl/PLIST b/numactl/PLIST
deleted file mode 100644
index 4b347958a0..0000000000
--- a/numactl/PLIST
+++ /dev/null
@@ -1,17 +0,0 @@
-@comment $NetBSD$
-bin/memhog
-bin/migratepages
-bin/migspeed
-bin/numactl
-bin/numademo
-bin/numastat
-include/numa.h
-include/numacompat1.h
-include/numaif.h
-lib/libnuma.la
-man/man2/move_pages.2
-man/man3/numa.3
-man/man8/migratepages.8
-man/man8/migspeed.8
-man/man8/numactl.8
-man/man8/numastat.8
diff --git a/numactl/TODO b/numactl/TODO
deleted file mode 100644
index b687356e6b..0000000000
--- a/numactl/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test
diff --git a/numactl/buildlink3.mk b/numactl/buildlink3.mk
deleted file mode 100644
index fdde3cfc36..0000000000
--- a/numactl/buildlink3.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-# $NetBSD$
-
-BUILDLINK_TREE+= numactl
-
-.if !defined(NUMACTL_BUILDLINK3_MK)
-NUMACTL_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.numactl+= numactl>=2.0.11
-BUILDLINK_PKGSRCDIR.numactl?= ../../wip/numactl
-.endif # NUMACTL_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -numactl
diff --git a/numactl/distinfo b/numactl/distinfo
deleted file mode 100644
index 63e6555ab3..0000000000
--- a/numactl/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD$
-
-RMD160 (numactl-2.0.11.tar.gz) = af5ebcb438993febaf15523f9ae26f1399ee16cb
-SHA512 (numactl-2.0.11.tar.gz) = 1969d7ee0ff3de0d6f1fa42ec089a17cdb3f92cb35d453b8f8b2eec49724c43787ecbd213357013a8f2500a260b0df9844d515815ca3a0376314a0eed050a0d4
-Size (numactl-2.0.11.tar.gz) = 408175 bytes
diff --git a/openmx-openmpi/DESCR b/openmx-openmpi/DESCR
deleted file mode 100644
index fe6dba78f1..0000000000
--- a/openmx-openmpi/DESCR
+++ /dev/null
@@ -1 +0,0 @@
-OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT) [1], norm-conserving pseudopotentials [19,20,21,22,23], and pseudo-atomic localized basis functions [28].
diff --git a/openmx-openmpi/PLIST b/openmx-openmpi/PLIST
deleted file mode 100644
index 6726f4f72f..0000000000
--- a/openmx-openmpi/PLIST
+++ /dev/null
@@ -1,342 +0,0 @@
-@comment $NetBSD: PLIST,v 1.2 2013/06/22 13:20:19 outpaddling Exp $
-openmpi/bin/DosMain
-openmpi/bin/OpticalConductivityMain
-openmpi/bin/TranMain
-openmpi/bin/TranMain_NC
-openmpi/bin/analysis_example
-openmpi/bin/esp
-openmpi/bin/jx
-openmpi/bin/openmx
-openmpi/bin/polB
-openmpi/bin/test_mpi
-openmpi/share/openmx/work/Al-Si111_ESM.dat
-openmpi/share/openmx/work/C2H4_NEB.dat
-openmpi/share/openmx/work/C60.dat
-openmpi/share/openmx/work/C60_DC.dat
-openmpi/share/openmx/work/C60_LO.dat
-openmpi/share/openmx/work/CG15c_DC.dat
-openmpi/share/openmx/work/Cafcc_FS.dat
-openmpi/share/openmx/work/Cdia.dat
-openmpi/share/openmx/work/CoO_NC.dat
-openmpi/share/openmx/work/Cr2_CNC.dat
-openmpi/share/openmx/work/Crys-NiO.dat
-openmpi/share/openmx/work/DIA216_DC.dat
-openmpi/share/openmx/work/DIA512-1.dat
-openmpi/share/openmx/work/DIA512_DC.dat
-openmpi/share/openmx/work/DIA64_Band.dat
-openmpi/share/openmx/work/DIA64_DC.dat
-openmpi/share/openmx/work/DIA8-VA.dat
-openmpi/share/openmx/work/DIA8_DC.dat
-openmpi/share/openmx/work/Doped_NT.dat
-openmpi/share/openmx/work/Fe2.dat
-openmpi/share/openmx/work/FeO+U.dat
-openmpi/share/openmx/work/FeO_NC.dat
-openmpi/share/openmx/work/Febcc2.dat
-openmpi/share/openmx/work/GaAs.dat
-openmpi/share/openmx/work/Gly_NH.dat
-openmpi/share/openmx/work/Gly_VS.dat
-openmpi/share/openmx/work/Graphite_STM.dat
-openmpi/share/openmx/work/H2O.dat
-openmpi/share/openmx/work/MCCN.dat
-openmpi/share/openmx/work/Methane.dat
-openmpi/share/openmx/work/Methane2.dat
-openmpi/share/openmx/work/Methane_OO.dat
-openmpi/share/openmx/work/Mn12.dat
-openmpi/share/openmx/work/MnO_NC.dat
-openmpi/share/openmx/work/Mnfcc-EvsLC.dat
-openmpi/share/openmx/work/Mol_MnO_NC.dat
-openmpi/share/openmx/work/NaCl.dat
-openmpi/share/openmx/work/NaCl_FC.dat
-openmpi/share/openmx/work/NiO_NC.dat
-openmpi/share/openmx/work/Nitro_Benzene.dat
-openmpi/share/openmx/work/Pt13.dat
-openmpi/share/openmx/work/Pt63.dat
-openmpi/share/openmx/work/Si8.dat
-openmpi/share/openmx/work/Si8_NEB.dat
-openmpi/share/openmx/work/SialicAcid.dat
-openmpi/share/openmx/work/Valorphin_DC.dat
-openmpi/share/openmx/work/force_example/C2_GGA.dat
-openmpi/share/openmx/work/force_example/C2_LDA.dat
-openmpi/share/openmx/work/force_example/CH3F_GGA.dat
-openmpi/share/openmx/work/force_example/CH3F_LDA.dat
-openmpi/share/openmx/work/force_example/CH_GGA.dat
-openmpi/share/openmx/work/force_example/CH_LDA+U.dat
-openmpi/share/openmx/work/force_example/CH_LSDA.dat
-openmpi/share/openmx/work/force_example/CH_NC.dat
-openmpi/share/openmx/work/force_example/Cdia_GGA.dat
-openmpi/share/openmx/work/force_example/Cdia_LDA.dat
-openmpi/share/openmx/work/force_example/Cr2.dat
-openmpi/share/openmx/work/force_example/Crys-MnO_GGA.dat
-openmpi/share/openmx/work/force_example/Crys-MnO_LSDA.dat
-openmpi/share/openmx/work/force_example/F2_GGA.dat
-openmpi/share/openmx/work/force_example/F2_LDA.dat
-openmpi/share/openmx/work/force_example/Fe2_GGA.dat
-openmpi/share/openmx/work/force_example/Fe2_LSDA.dat
-openmpi/share/openmx/work/force_example/FeCrH_GGA.dat
-openmpi/share/openmx/work/force_example/FeCrH_LSDA.dat
-openmpi/share/openmx/work/force_example/GaAs+05.dat
-openmpi/share/openmx/work/force_example/GaAs_GGA.dat
-openmpi/share/openmx/work/force_example/GaAs_LDA.dat
-openmpi/share/openmx/work/force_example/GaAs_NC_SO+U.dat
-openmpi/share/openmx/work/force_example/GaAs_NC_SO.dat
-openmpi/share/openmx/work/force_example/H2_GGA.dat
-openmpi/share/openmx/work/force_example/H2_LDA.dat
-openmpi/share/openmx/work/force_example/HHdia_GGA.dat
-openmpi/share/openmx/work/force_example/HHdia_LDA.dat
-openmpi/share/openmx/work/force_example/Hdia_GGA.dat
-openmpi/share/openmx/work/force_example/Hdia_LDA.dat
-openmpi/share/openmx/work/force_example/Methane+EF.dat
-openmpi/share/openmx/work/force_example/Methane-1.dat
-openmpi/share/openmx/work/force_example/Methane_GGA.dat
-openmpi/share/openmx/work/force_example/Methane_LDA.dat
-openmpi/share/openmx/work/force_example/Mn2O_LDA+U.dat
-openmpi/share/openmx/work/force_example/MnO_LDA+U.dat
-openmpi/share/openmx/work/force_example/forcetest.result
-openmpi/share/openmx/work/geoopt_example/B2C62_BFGS.dat
-openmpi/share/openmx/work/geoopt_example/B2C62_BFGS.out
-openmpi/share/openmx/work/geoopt_example/B2C62_DIIS.dat
-openmpi/share/openmx/work/geoopt_example/B2C62_DIIS.out
-openmpi/share/openmx/work/geoopt_example/B2C62_EF.dat
-openmpi/share/openmx/work/geoopt_example/B2C62_EF.out
-openmpi/share/openmx/work/geoopt_example/B2C62_RF.dat
-openmpi/share/openmx/work/geoopt_example/B2C62_RF.out
-openmpi/share/openmx/work/geoopt_example/C16_BFGS.dat
-openmpi/share/openmx/work/geoopt_example/C16_BFGS.out
-openmpi/share/openmx/work/geoopt_example/C16_DIIS.dat
-openmpi/share/openmx/work/geoopt_example/C16_DIIS.out
-openmpi/share/openmx/work/geoopt_example/C16_EF.dat
-openmpi/share/openmx/work/geoopt_example/C16_EF.out
-openmpi/share/openmx/work/geoopt_example/C16_RF.dat
-openmpi/share/openmx/work/geoopt_example/C16_RF.out
-openmpi/share/openmx/work/geoopt_example/C60_BFGS.dat
-openmpi/share/openmx/work/geoopt_example/C60_BFGS.out
-openmpi/share/openmx/work/geoopt_example/C60_DIIS.dat
-openmpi/share/openmx/work/geoopt_example/C60_DIIS.out
-openmpi/share/openmx/work/geoopt_example/C60_EF.dat
-openmpi/share/openmx/work/geoopt_example/C60_EF.out
-openmpi/share/openmx/work/geoopt_example/C60_RF.dat
-openmpi/share/openmx/work/geoopt_example/C60_RF.out
-openmpi/share/openmx/work/geoopt_example/Glycine_BFGS.dat
-openmpi/share/openmx/work/geoopt_example/Glycine_BFGS.out
-openmpi/share/openmx/work/geoopt_example/Glycine_DIIS.dat
-openmpi/share/openmx/work/geoopt_example/Glycine_DIIS.out
-openmpi/share/openmx/work/geoopt_example/Glycine_EF.dat
-openmpi/share/openmx/work/geoopt_example/Glycine_EF.out
-openmpi/share/openmx/work/geoopt_example/Glycine_RF.dat
-openmpi/share/openmx/work/geoopt_example/Glycine_RF.out
-openmpi/share/openmx/work/geoopt_example/Methane_BFGS.dat
-openmpi/share/openmx/work/geoopt_example/Methane_BFGS.out
-openmpi/share/openmx/work/geoopt_example/Methane_DIIS.dat
-openmpi/share/openmx/work/geoopt_example/Methane_DIIS.out
-openmpi/share/openmx/work/geoopt_example/Methane_EF.dat
-openmpi/share/openmx/work/geoopt_example/Methane_EF.out
-openmpi/share/openmx/work/geoopt_example/Methane_RF.dat
-openmpi/share/openmx/work/geoopt_example/Methane_RF.out
-openmpi/share/openmx/work/geoopt_example/NBen_BFGS.dat
-openmpi/share/openmx/work/geoopt_example/NBen_BFGS.out
-openmpi/share/openmx/work/geoopt_example/NBen_DIIS.dat
-openmpi/share/openmx/work/geoopt_example/NBen_DIIS.out
-openmpi/share/openmx/work/geoopt_example/NBen_EF.dat
-openmpi/share/openmx/work/geoopt_example/NBen_EF.out
-openmpi/share/openmx/work/geoopt_example/NBen_RF.dat
-openmpi/share/openmx/work/geoopt_example/NBen_RF.out
-openmpi/share/openmx/work/geoopt_example/NaCl_BFGS.dat
-openmpi/share/openmx/work/geoopt_example/NaCl_BFGS.out
-openmpi/share/openmx/work/geoopt_example/NaCl_DIIS.dat
-openmpi/share/openmx/work/geoopt_example/NaCl_DIIS.out
-openmpi/share/openmx/work/geoopt_example/NaCl_EF.dat
-openmpi/share/openmx/work/geoopt_example/NaCl_EF.out
-openmpi/share/openmx/work/geoopt_example/NaCl_RF.dat
-openmpi/share/openmx/work/geoopt_example/NaCl_RF.out
-openmpi/share/openmx/work/geoopt_example/Si7C_BFGS.dat
-openmpi/share/openmx/work/geoopt_example/Si7C_BFGS.out
-openmpi/share/openmx/work/geoopt_example/Si7C_DIIS.dat
-openmpi/share/openmx/work/geoopt_example/Si7C_DIIS.out
-openmpi/share/openmx/work/geoopt_example/Si7C_EF.dat
-openmpi/share/openmx/work/geoopt_example/Si7C_EF.out
-openmpi/share/openmx/work/geoopt_example/Si7C_RF.dat
-openmpi/share/openmx/work/geoopt_example/Si7C_RF.out
-openmpi/share/openmx/work/geoopt_example/SialicAcid_BFGS.dat
-openmpi/share/openmx/work/geoopt_example/SialicAcid_BFGS.out
-openmpi/share/openmx/work/geoopt_example/SialicAcid_DIIS.dat
-openmpi/share/openmx/work/geoopt_example/SialicAcid_DIIS.out
-openmpi/share/openmx/work/geoopt_example/SialicAcid_EF.dat
-openmpi/share/openmx/work/geoopt_example/SialicAcid_EF.out
-openmpi/share/openmx/work/geoopt_example/SialicAcid_RF.dat
-openmpi/share/openmx/work/geoopt_example/SialicAcid_RF.out
-openmpi/share/openmx/work/geoopt_example/TiO2_BFGS.dat
-openmpi/share/openmx/work/geoopt_example/TiO2_BFGS.out
-openmpi/share/openmx/work/geoopt_example/TiO2_DIIS.dat
-openmpi/share/openmx/work/geoopt_example/TiO2_DIIS.out
-openmpi/share/openmx/work/geoopt_example/TiO2_EF.dat
-openmpi/share/openmx/work/geoopt_example/TiO2_EF.out
-openmpi/share/openmx/work/geoopt_example/TiO2_RF.dat
-openmpi/share/openmx/work/geoopt_example/TiO2_RF.out
-openmpi/share/openmx/work/geoopt_example/V2O5_BFGS.dat
-openmpi/share/openmx/work/geoopt_example/V2O5_BFGS.out
-openmpi/share/openmx/work/geoopt_example/V2O5_DIIS.dat
-openmpi/share/openmx/work/geoopt_example/V2O5_DIIS.out
-openmpi/share/openmx/work/geoopt_example/V2O5_EF.dat
-openmpi/share/openmx/work/geoopt_example/V2O5_EF.out
-openmpi/share/openmx/work/geoopt_example/V2O5_RF.dat
-openmpi/share/openmx/work/geoopt_example/V2O5_RF.out
-openmpi/share/openmx/work/geoopt_example/d-H2O_BFGS.dat
-openmpi/share/openmx/work/geoopt_example/d-H2O_BFGS.out
-openmpi/share/openmx/work/geoopt_example/d-H2O_DIIS.dat
-openmpi/share/openmx/work/geoopt_example/d-H2O_DIIS.out
-openmpi/share/openmx/work/geoopt_example/d-H2O_EF.dat
-openmpi/share/openmx/work/geoopt_example/d-H2O_EF.out
-openmpi/share/openmx/work/geoopt_example/d-H2O_RF.dat
-openmpi/share/openmx/work/geoopt_example/d-H2O_RF.out
-openmpi/share/openmx/work/input_example/Benzene.dat
-openmpi/share/openmx/work/input_example/Benzene.out
-openmpi/share/openmx/work/input_example/C60.dat
-openmpi/share/openmx/work/input_example/C60.out
-openmpi/share/openmx/work/input_example/CO.dat
-openmpi/share/openmx/work/input_example/CO.out
-openmpi/share/openmx/work/input_example/Cr2.dat
-openmpi/share/openmx/work/input_example/Cr2.out
-openmpi/share/openmx/work/input_example/Crys-MnO.dat
-openmpi/share/openmx/work/input_example/Crys-MnO.out
-openmpi/share/openmx/work/input_example/GaAs.dat
-openmpi/share/openmx/work/input_example/GaAs.out
-openmpi/share/openmx/work/input_example/Glycine.dat
-openmpi/share/openmx/work/input_example/Glycine.out
-openmpi/share/openmx/work/input_example/Graphite4.dat
-openmpi/share/openmx/work/input_example/Graphite4.out
-openmpi/share/openmx/work/input_example/H2O-EF.dat
-openmpi/share/openmx/work/input_example/H2O-EF.out
-openmpi/share/openmx/work/input_example/H2O.dat
-openmpi/share/openmx/work/input_example/H2O.out
-openmpi/share/openmx/work/input_example/HMn.dat
-openmpi/share/openmx/work/input_example/HMn.out
-openmpi/share/openmx/work/input_example/Methane.dat
-openmpi/share/openmx/work/input_example/Methane.out
-openmpi/share/openmx/work/input_example/Mol_MnO.dat
-openmpi/share/openmx/work/input_example/Mol_MnO.out
-openmpi/share/openmx/work/input_example/Ndia2.dat
-openmpi/share/openmx/work/input_example/Ndia2.out
-openmpi/share/openmx/work/input_example/runtest.result_FX10
-openmpi/share/openmx/work/input_example/runtest.result_K
-openmpi/share/openmx/work/input_example/runtest.result_PCC
-openmpi/share/openmx/work/input_example/runtest.result_abacus2
-openmpi/share/openmx/work/input_example/runtest.result_altix
-openmpi/share/openmx/work/input_example/runtest.result_s078-065
-openmpi/share/openmx/work/input_example/runtest.result_vsmp
-openmpi/share/openmx/work/input_example/runtest.result_vtpcc01
-openmpi/share/openmx/work/input_example/runtest.result_xc30
-openmpi/share/openmx/work/input_example/runtest.result_xc30_v3.6
-openmpi/share/openmx/work/large2_example/C1000.dat
-openmpi/share/openmx/work/large2_example/C1000.out
-openmpi/share/openmx/work/large2_example/Fe1000.dat
-openmpi/share/openmx/work/large2_example/Fe1000.out
-openmpi/share/openmx/work/large2_example/GRA1024.dat
-openmpi/share/openmx/work/large2_example/GRA1024.out
-openmpi/share/openmx/work/large2_example/Ih-Ice1200.dat
-openmpi/share/openmx/work/large2_example/Ih-Ice1200.out
-openmpi/share/openmx/work/large2_example/Pt500.dat
-openmpi/share/openmx/work/large2_example/Pt500.out
-openmpi/share/openmx/work/large2_example/R-TiO2-1050.dat
-openmpi/share/openmx/work/large2_example/R-TiO2-1050.out
-openmpi/share/openmx/work/large2_example/Si1000.dat
-openmpi/share/openmx/work/large2_example/Si1000.out
-openmpi/share/openmx/work/large2_example/runtestL2.result_xc30
-openmpi/share/openmx/work/large_example/5_5_13COb2.dat
-openmpi/share/openmx/work/large_example/5_5_13COb2.out
-openmpi/share/openmx/work/large_example/B2C62_Band.dat
-openmpi/share/openmx/work/large_example/B2C62_Band.out
-openmpi/share/openmx/work/large_example/CG15c-Kry.dat
-openmpi/share/openmx/work/large_example/CG15c-Kry.out
-openmpi/share/openmx/work/large_example/DIA512-1.dat
-openmpi/share/openmx/work/large_example/DIA512-1.out
-openmpi/share/openmx/work/large_example/FeBCC.dat
-openmpi/share/openmx/work/large_example/FeBCC.out
-openmpi/share/openmx/work/large_example/GEL.dat
-openmpi/share/openmx/work/large_example/GEL.out
-openmpi/share/openmx/work/large_example/GFRAG.dat
-openmpi/share/openmx/work/large_example/GFRAG.out
-openmpi/share/openmx/work/large_example/GGFF.dat
-openmpi/share/openmx/work/large_example/GGFF.out
-openmpi/share/openmx/work/large_example/MCCN.dat
-openmpi/share/openmx/work/large_example/MCCN.out
-openmpi/share/openmx/work/large_example/Mn12_148_F.dat
-openmpi/share/openmx/work/large_example/Mn12_148_F.out
-openmpi/share/openmx/work/large_example/N1C999.dat
-openmpi/share/openmx/work/large_example/N1C999.out
-openmpi/share/openmx/work/large_example/Ni63-O64.dat
-openmpi/share/openmx/work/large_example/Ni63-O64.out
-openmpi/share/openmx/work/large_example/Pt63.dat
-openmpi/share/openmx/work/large_example/Pt63.out
-openmpi/share/openmx/work/large_example/SialicAcid.dat
-openmpi/share/openmx/work/large_example/SialicAcid.out
-openmpi/share/openmx/work/large_example/ZrB2_2x2.dat
-openmpi/share/openmx/work/large_example/ZrB2_2x2.out
-openmpi/share/openmx/work/large_example/nsV4Bz5.dat
-openmpi/share/openmx/work/large_example/nsV4Bz5.out
-openmpi/share/openmx/work/large_example/runtestL.result_FX10
-openmpi/share/openmx/work/large_example/runtestL.result_K
-openmpi/share/openmx/work/large_example/runtestL.result_PCC
-openmpi/share/openmx/work/large_example/runtestL.result_abacus2
-openmpi/share/openmx/work/large_example/runtestL.result_altix
-openmpi/share/openmx/work/large_example/runtestL.result_vsmp
-openmpi/share/openmx/work/large_example/runtestL.result_vtpcc01
-openmpi/share/openmx/work/large_example/runtestL.result_xc30
-openmpi/share/openmx/work/large_example/runtestL.result_xc30_v3.6
-openmpi/share/openmx/work/ml_example/Co4+U.dat
-openmpi/share/openmx/work/ml_example/Co4.dat
-openmpi/share/openmx/work/ml_example/DIA8.dat
-openmpi/share/openmx/work/ml_example/DIA8_DC.dat
-openmpi/share/openmx/work/ml_example/DIA8_Krylov.dat
-openmpi/share/openmx/work/ml_example/FeO+U.dat
-openmpi/share/openmx/work/ml_example/Febcc2.dat
-openmpi/share/openmx/work/ml_example/GaAs.dat
-openmpi/share/openmx/work/ml_example/Glycine-H.dat
-openmpi/share/openmx/work/ml_example/Glycine.dat
-openmpi/share/openmx/work/ml_example/Glycine_Kry.dat
-openmpi/share/openmx/work/ml_example/Methane.dat
-openmpi/share/openmx/work/ml_example/SialicAcid.dat
-openmpi/share/openmx/work/ml_example/mltest.result
-openmpi/share/openmx/work/negf_example/Lead-Au-Chain-NC.dat
-openmpi/share/openmx/work/negf_example/Lead-Chain.dat
-openmpi/share/openmx/work/negf_example/Lead-Graphene.dat
-openmpi/share/openmx/work/negf_example/Lead-L-8ZGNR-NC.dat
-openmpi/share/openmx/work/negf_example/Lead-L-8ZGNR.dat
-openmpi/share/openmx/work/negf_example/Lead-R-8ZGNR-NC.dat
-openmpi/share/openmx/work/negf_example/Lead-R-8ZGNR.dat
-openmpi/share/openmx/work/negf_example/NEGF-8ZGNR-0.3.dat
-openmpi/share/openmx/work/negf_example/NEGF-8ZGNR-NC.dat
-openmpi/share/openmx/work/negf_example/NEGF-Au-Chain-NC.dat
-openmpi/share/openmx/work/negf_example/NEGF-Chain.dat
-openmpi/share/openmx/work/negf_example/NEGF-Graphene.dat
-openmpi/share/openmx/work/negf_example/lead-au-chain-nc.out
-openmpi/share/openmx/work/negf_example/lead-chain.out
-openmpi/share/openmx/work/negf_example/lead-graphene.out
-openmpi/share/openmx/work/negf_example/lead-l-8zgnr-nc.out
-openmpi/share/openmx/work/negf_example/lead-l-8zgnr.out
-openmpi/share/openmx/work/negf_example/lead-r-8zgnr-nc.out
-openmpi/share/openmx/work/negf_example/lead-r-8zgnr.out
-openmpi/share/openmx/work/negf_example/negf-8zgnr-0.3.out
-openmpi/share/openmx/work/negf_example/negf-8zgnr-nc.out
-openmpi/share/openmx/work/negf_example/negf-au-chain-nc.out
-openmpi/share/openmx/work/negf_example/negf-chain.out
-openmpi/share/openmx/work/negf_example/negf-graphene.out
-openmpi/share/openmx/work/negf_example/runtestNEGF.result_vtpcc
-openmpi/share/openmx/work/wf_example/Benzene.dat
-openmpi/share/openmx/work/wf_example/Benzene.out
-openmpi/share/openmx/work/wf_example/GaAs.dat
-openmpi/share/openmx/work/wf_example/GaAs.out
-openmpi/share/openmx/work/wf_example/GaAs_NC.dat
-openmpi/share/openmx/work/wf_example/GaAs_NC.out
-openmpi/share/openmx/work/wf_example/NC_CVO.dat
-openmpi/share/openmx/work/wf_example/NC_CVO.out
-openmpi/share/openmx/work/wf_example/NC_SVO.dat
-openmpi/share/openmx/work/wf_example/NC_SVO.out
-openmpi/share/openmx/work/wf_example/Si.dat
-openmpi/share/openmx/work/wf_example/Si.out
-openmpi/share/openmx/work/wf_example/VBz.dat
-openmpi/share/openmx/work/wf_example/VBz.out
-openmpi/share/openmx/work/wf_example/pmCVO.dat
-openmpi/share/openmx/work/wf_example/pmCVO.out
-openmpi/share/openmx/work/wf_example/runtestWF.result_vtpcc01
-openmpi/share/openmx/work/wf_example/symGra.dat
-openmpi/share/openmx/work/wf_example/symGra.out
diff --git a/openmx-openmpi/distinfo b/openmx-openmpi/distinfo
deleted file mode 100644
index cd3ddbae7e..0000000000
--- a/openmx-openmpi/distinfo
+++ /dev/null
@@ -1,4 +0,0 @@
-$NetBSD: distinfo,v 1.1 2013/06/21 19:39:11 outpaddling Exp $
-
-RMD160 (openmx3.7.tar.gz) = cea6ea8e27c7ab5bcf2dd1a05b06698e5834a595
-Size (openmx3.7.tar.gz) = 117784869 bytes
diff --git a/py-ffc/DESCR b/py-ffc/DESCR
deleted file mode 100644
index 1e941cbc1f..0000000000
--- a/py-ffc/DESCR
+++ /dev/null
@@ -1,2 +0,0 @@
-FFC works as a compiler for multilinear forms by generating code (C++) for
-the evaluation of a multilinear form given in mathematical notation.
diff --git a/py-ffc/PLIST b/py-ffc/PLIST
deleted file mode 100644
index d0a45f8174..0000000000
--- a/py-ffc/PLIST
+++ /dev/null
@@ -1,195 +0,0 @@
-@comment $NetBSD: PLIST,v 1.5 2013/03/24 20:42:27 outpaddling Exp $
-bin/ffc
-${PYSITELIB}/ffc/__init__.py
-${PYSITELIB}/ffc/__init__.pyc
-${PYSITELIB}/ffc/__init__.pyo
-${PYSITELIB}/ffc/analysis.py
-${PYSITELIB}/ffc/analysis.pyc
-${PYSITELIB}/ffc/analysis.pyo
-${PYSITELIB}/ffc/codegeneration.py
-${PYSITELIB}/ffc/codegeneration.pyc
-${PYSITELIB}/ffc/codegeneration.pyo
-${PYSITELIB}/ffc/codesnippets.py
-${PYSITELIB}/ffc/codesnippets.pyc
-${PYSITELIB}/ffc/codesnippets.pyo
-${PYSITELIB}/ffc/compiler.py
-${PYSITELIB}/ffc/compiler.pyc
-${PYSITELIB}/ffc/compiler.pyo
-${PYSITELIB}/ffc/constants.py
-${PYSITELIB}/ffc/constants.pyc
-${PYSITELIB}/ffc/constants.pyo
-${PYSITELIB}/ffc/cpp.py
-${PYSITELIB}/ffc/cpp.pyc
-${PYSITELIB}/ffc/cpp.pyo
-${PYSITELIB}/ffc/enrichedelement.py
-${PYSITELIB}/ffc/enrichedelement.pyc
-${PYSITELIB}/ffc/enrichedelement.pyo
-${PYSITELIB}/ffc/errorcontrol/__init__.py
-${PYSITELIB}/ffc/errorcontrol/__init__.pyc
-${PYSITELIB}/ffc/errorcontrol/__init__.pyo
-${PYSITELIB}/ffc/errorcontrol/errorcontrol.py
-${PYSITELIB}/ffc/errorcontrol/errorcontrol.pyc
-${PYSITELIB}/ffc/errorcontrol/errorcontrol.pyo
-${PYSITELIB}/ffc/errorcontrol/errorcontrolgenerators.py
-${PYSITELIB}/ffc/errorcontrol/errorcontrolgenerators.pyc
-${PYSITELIB}/ffc/errorcontrol/errorcontrolgenerators.pyo
-${PYSITELIB}/ffc/evaluatebasis.py
-${PYSITELIB}/ffc/evaluatebasis.pyc
-${PYSITELIB}/ffc/evaluatebasis.pyo
-${PYSITELIB}/ffc/evaluatebasisderivatives.py
-${PYSITELIB}/ffc/evaluatebasisderivatives.pyc
-${PYSITELIB}/ffc/evaluatebasisderivatives.pyo
-${PYSITELIB}/ffc/evaluatedof.py
-${PYSITELIB}/ffc/evaluatedof.pyc
-${PYSITELIB}/ffc/evaluatedof.pyo
-${PYSITELIB}/ffc/extras.py
-${PYSITELIB}/ffc/extras.pyc
-${PYSITELIB}/ffc/extras.pyo
-${PYSITELIB}/ffc/fiatinterface.py
-${PYSITELIB}/ffc/fiatinterface.pyc
-${PYSITELIB}/ffc/fiatinterface.pyo
-${PYSITELIB}/ffc/formatting.py
-${PYSITELIB}/ffc/formatting.pyc
-${PYSITELIB}/ffc/formatting.pyo
-${PYSITELIB}/ffc/interpolatevertexvalues.py
-${PYSITELIB}/ffc/interpolatevertexvalues.pyc
-${PYSITELIB}/ffc/interpolatevertexvalues.pyo
-${PYSITELIB}/ffc/jitcompiler.py
-${PYSITELIB}/ffc/jitcompiler.pyc
-${PYSITELIB}/ffc/jitcompiler.pyo
-${PYSITELIB}/ffc/jitobject.py
-${PYSITELIB}/ffc/jitobject.pyc
-${PYSITELIB}/ffc/jitobject.pyo
-${PYSITELIB}/ffc/log.py
-${PYSITELIB}/ffc/log.pyc
-${PYSITELIB}/ffc/log.pyo
-${PYSITELIB}/ffc/mixedelement.py
-${PYSITELIB}/ffc/mixedelement.pyc
-${PYSITELIB}/ffc/mixedelement.pyo
-${PYSITELIB}/ffc/optimization.py
-${PYSITELIB}/ffc/optimization.pyc
-${PYSITELIB}/ffc/optimization.pyo
-${PYSITELIB}/ffc/parameters.py
-${PYSITELIB}/ffc/parameters.pyc
-${PYSITELIB}/ffc/parameters.pyo
-${PYSITELIB}/ffc/plot.py
-${PYSITELIB}/ffc/plot.pyc
-${PYSITELIB}/ffc/plot.pyo
-${PYSITELIB}/ffc/quadrature/__init__.py
-${PYSITELIB}/ffc/quadrature/__init__.pyc
-${PYSITELIB}/ffc/quadrature/__init__.pyo
-${PYSITELIB}/ffc/quadrature/expr.py
-${PYSITELIB}/ffc/quadrature/expr.pyc
-${PYSITELIB}/ffc/quadrature/expr.pyo
-${PYSITELIB}/ffc/quadrature/floatvalue.py
-${PYSITELIB}/ffc/quadrature/floatvalue.pyc
-${PYSITELIB}/ffc/quadrature/floatvalue.pyo
-${PYSITELIB}/ffc/quadrature/fraction.py
-${PYSITELIB}/ffc/quadrature/fraction.pyc
-${PYSITELIB}/ffc/quadrature/fraction.pyo
-${PYSITELIB}/ffc/quadrature/optimisedquadraturetransformer.py
-${PYSITELIB}/ffc/quadrature/optimisedquadraturetransformer.pyc
-${PYSITELIB}/ffc/quadrature/optimisedquadraturetransformer.pyo
-${PYSITELIB}/ffc/quadrature/product.py
-${PYSITELIB}/ffc/quadrature/product.pyc
-${PYSITELIB}/ffc/quadrature/product.pyo
-${PYSITELIB}/ffc/quadrature/quadraturegenerator.py
-${PYSITELIB}/ffc/quadrature/quadraturegenerator.pyc
-${PYSITELIB}/ffc/quadrature/quadraturegenerator.pyo
-${PYSITELIB}/ffc/quadrature/quadratureoptimization.py
-${PYSITELIB}/ffc/quadrature/quadratureoptimization.pyc
-${PYSITELIB}/ffc/quadrature/quadratureoptimization.pyo
-${PYSITELIB}/ffc/quadrature/quadraturerepresentation.py
-${PYSITELIB}/ffc/quadrature/quadraturerepresentation.pyc
-${PYSITELIB}/ffc/quadrature/quadraturerepresentation.pyo
-${PYSITELIB}/ffc/quadrature/quadraturetransformer.py
-${PYSITELIB}/ffc/quadrature/quadraturetransformer.pyc
-${PYSITELIB}/ffc/quadrature/quadraturetransformer.pyo
-${PYSITELIB}/ffc/quadrature/quadraturetransformerbase.py
-${PYSITELIB}/ffc/quadrature/quadraturetransformerbase.pyc
-${PYSITELIB}/ffc/quadrature/quadraturetransformerbase.pyo
-${PYSITELIB}/ffc/quadrature/quadratureutils.py
-${PYSITELIB}/ffc/quadrature/quadratureutils.pyc
-${PYSITELIB}/ffc/quadrature/quadratureutils.pyo
-${PYSITELIB}/ffc/quadrature/reduce_operations.py
-${PYSITELIB}/ffc/quadrature/reduce_operations.pyc
-${PYSITELIB}/ffc/quadrature/reduce_operations.pyo
-${PYSITELIB}/ffc/quadrature/sumobj.py
-${PYSITELIB}/ffc/quadrature/sumobj.pyc
-${PYSITELIB}/ffc/quadrature/sumobj.pyo
-${PYSITELIB}/ffc/quadrature/symbol.py
-${PYSITELIB}/ffc/quadrature/symbol.pyc
-${PYSITELIB}/ffc/quadrature/symbol.pyo
-${PYSITELIB}/ffc/quadrature/symbolics.py
-${PYSITELIB}/ffc/quadrature/symbolics.pyc
-${PYSITELIB}/ffc/quadrature/symbolics.pyo
-${PYSITELIB}/ffc/quadrature_schemes.py
-${PYSITELIB}/ffc/quadrature_schemes.pyc
-${PYSITELIB}/ffc/quadrature_schemes.pyo
-${PYSITELIB}/ffc/quadratureelement.py
-${PYSITELIB}/ffc/quadratureelement.pyc
-${PYSITELIB}/ffc/quadratureelement.pyo
-${PYSITELIB}/ffc/representation.py
-${PYSITELIB}/ffc/representation.pyc
-${PYSITELIB}/ffc/representation.pyo
-${PYSITELIB}/ffc/representationutils.py
-${PYSITELIB}/ffc/representationutils.pyc
-${PYSITELIB}/ffc/representationutils.pyo
-${PYSITELIB}/ffc/restrictedelement.py
-${PYSITELIB}/ffc/restrictedelement.pyc
-${PYSITELIB}/ffc/restrictedelement.pyo
-${PYSITELIB}/ffc/tensor/__init__.py
-${PYSITELIB}/ffc/tensor/__init__.pyc
-${PYSITELIB}/ffc/tensor/__init__.pyo
-${PYSITELIB}/ffc/tensor/costestimation.py
-${PYSITELIB}/ffc/tensor/costestimation.pyc
-${PYSITELIB}/ffc/tensor/costestimation.pyo
-${PYSITELIB}/ffc/tensor/geometrytensor.py
-${PYSITELIB}/ffc/tensor/geometrytensor.pyc
-${PYSITELIB}/ffc/tensor/geometrytensor.pyo
-${PYSITELIB}/ffc/tensor/monomialextraction.py
-${PYSITELIB}/ffc/tensor/monomialextraction.pyc
-${PYSITELIB}/ffc/tensor/monomialextraction.pyo
-${PYSITELIB}/ffc/tensor/monomialintegration.py
-${PYSITELIB}/ffc/tensor/monomialintegration.pyc
-${PYSITELIB}/ffc/tensor/monomialintegration.pyo
-${PYSITELIB}/ffc/tensor/monomialtransformation.py
-${PYSITELIB}/ffc/tensor/monomialtransformation.pyc
-${PYSITELIB}/ffc/tensor/monomialtransformation.pyo
-${PYSITELIB}/ffc/tensor/multiindex.py
-${PYSITELIB}/ffc/tensor/multiindex.pyc
-${PYSITELIB}/ffc/tensor/multiindex.pyo
-${PYSITELIB}/ffc/tensor/referencetensor.py
-${PYSITELIB}/ffc/tensor/referencetensor.pyc
-${PYSITELIB}/ffc/tensor/referencetensor.pyo
-${PYSITELIB}/ffc/tensor/tensorgenerator.py
-${PYSITELIB}/ffc/tensor/tensorgenerator.pyc
-${PYSITELIB}/ffc/tensor/tensorgenerator.pyo
-${PYSITELIB}/ffc/tensor/tensoroptimization.py
-${PYSITELIB}/ffc/tensor/tensoroptimization.pyc
-${PYSITELIB}/ffc/tensor/tensoroptimization.pyo
-${PYSITELIB}/ffc/tensor/tensorreordering.py
-${PYSITELIB}/ffc/tensor/tensorreordering.pyc
-${PYSITELIB}/ffc/tensor/tensorreordering.pyo
-${PYSITELIB}/ffc/tensor/tensorrepresentation.py
-${PYSITELIB}/ffc/tensor/tensorrepresentation.pyc
-${PYSITELIB}/ffc/tensor/tensorrepresentation.pyo
-${PYSITELIB}/ffc/uflacsrepr/__init__.py
-${PYSITELIB}/ffc/uflacsrepr/__init__.pyc
-${PYSITELIB}/ffc/uflacsrepr/__init__.pyo
-${PYSITELIB}/ffc/uflacsrepr/uflacsgenerator.py
-${PYSITELIB}/ffc/uflacsrepr/uflacsgenerator.pyc
-${PYSITELIB}/ffc/uflacsrepr/uflacsgenerator.pyo
-${PYSITELIB}/ffc/uflacsrepr/uflacsoptimization.py
-${PYSITELIB}/ffc/uflacsrepr/uflacsoptimization.pyc
-${PYSITELIB}/ffc/uflacsrepr/uflacsoptimization.pyo
-${PYSITELIB}/ffc/uflacsrepr/uflacsrepresentation.py
-${PYSITELIB}/ffc/uflacsrepr/uflacsrepresentation.pyc
-${PYSITELIB}/ffc/uflacsrepr/uflacsrepresentation.pyo
-${PYSITELIB}/ffc/utils.py
-${PYSITELIB}/ffc/utils.pyc
-${PYSITELIB}/ffc/utils.pyo
-${PYSITELIB}/ffc/wrappers.py
-${PYSITELIB}/ffc/wrappers.pyc
-${PYSITELIB}/ffc/wrappers.pyo
-man/man1/ffc.1
diff --git a/py-ffc/buildlink3.mk b/py-ffc/buildlink3.mk
deleted file mode 100644
index 462f9759fb..0000000000
--- a/py-ffc/buildlink3.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-# $NetBSD: buildlink3.mk,v 1.5 2013/03/23 13:33:57 outpaddling Exp $
-
-BUILDLINK_TREE+= py-ffc
-
-.if !defined(PY_FFC_BUILDLINK3_MK)
-PY_FFC_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.py-ffc+= ${PYPKGPREFIX}-ffc>=1.0.0
-BUILDLINK_PKGSRCDIR.py-ffc?= ../../wip/py-ffc
-.endif # PY_FFC_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -py-ffc
diff --git a/py-ffc/distinfo b/py-ffc/distinfo
deleted file mode 100644
index 33371cdf09..0000000000
--- a/py-ffc/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD: distinfo,v 1.3 2013/03/24 20:37:45 outpaddling Exp $
-
-RMD160 (ffc-1.2.0.tar.gz) = 7d62c9c903b5eb64dc7d5e67eaeb4617aa82e6dc
-SHA512 (ffc-1.2.0.tar.gz) = fd2a54764716c03894d779c6574deaea732df8e925e9c77474b969168fa2add8c189e0e9e7e163aa67008650fd1918dd2257cc990b5ab19e65a86b95f5eaed1b
-Size (ffc-1.2.0.tar.gz) = 4457544 bytes
diff --git a/py-fiat/DESCR b/py-fiat/DESCR
deleted file mode 100644
index 2ca3b2d8f7..0000000000
--- a/py-fiat/DESCR
+++ /dev/null
@@ -1,2 +0,0 @@
-The FInite element Automatic Tabulator FIAT supports generation of arbitrary
-order instances of the Lagrange elements on lines, triangles, and tetrahedra.
diff --git a/py-fiat/PLIST b/py-fiat/PLIST
deleted file mode 100644
index 416154adc3..0000000000
--- a/py-fiat/PLIST
+++ /dev/null
@@ -1,91 +0,0 @@
-@comment $NetBSD: PLIST,v 1.2 2013/03/23 13:41:02 outpaddling Exp $
-${PYSITELIB}/FIAT/P0.py
-${PYSITELIB}/FIAT/P0.pyc
-${PYSITELIB}/FIAT/P0.pyo
-${PYSITELIB}/FIAT/__init__.py
-${PYSITELIB}/FIAT/__init__.pyc
-${PYSITELIB}/FIAT/__init__.pyo
-${PYSITELIB}/FIAT/argyris.py
-${PYSITELIB}/FIAT/argyris.pyc
-${PYSITELIB}/FIAT/argyris.pyo
-${PYSITELIB}/FIAT/asci2vtk2d.py
-${PYSITELIB}/FIAT/asci2vtk2d.pyc
-${PYSITELIB}/FIAT/asci2vtk2d.pyo
-${PYSITELIB}/FIAT/asci2vtk3d.py
-${PYSITELIB}/FIAT/asci2vtk3d.pyc
-${PYSITELIB}/FIAT/asci2vtk3d.pyo
-${PYSITELIB}/FIAT/brezzi_douglas_fortin_marini.py
-${PYSITELIB}/FIAT/brezzi_douglas_fortin_marini.pyc
-${PYSITELIB}/FIAT/brezzi_douglas_fortin_marini.pyo
-${PYSITELIB}/FIAT/brezzi_douglas_marini.py
-${PYSITELIB}/FIAT/brezzi_douglas_marini.pyc
-${PYSITELIB}/FIAT/brezzi_douglas_marini.pyo
-${PYSITELIB}/FIAT/crouzeix_raviart.py
-${PYSITELIB}/FIAT/crouzeix_raviart.pyc
-${PYSITELIB}/FIAT/crouzeix_raviart.pyo
-${PYSITELIB}/FIAT/discontinuous_lagrange.py
-${PYSITELIB}/FIAT/discontinuous_lagrange.pyc
-${PYSITELIB}/FIAT/discontinuous_lagrange.pyo
-${PYSITELIB}/FIAT/dual_set.py
-${PYSITELIB}/FIAT/dual_set.pyc
-${PYSITELIB}/FIAT/dual_set.pyo
-${PYSITELIB}/FIAT/expansions.py
-${PYSITELIB}/FIAT/expansions.pyc
-${PYSITELIB}/FIAT/expansions.pyo
-${PYSITELIB}/FIAT/factorial.py
-${PYSITELIB}/FIAT/factorial.pyc
-${PYSITELIB}/FIAT/factorial.pyo
-${PYSITELIB}/FIAT/finite_element.py
-${PYSITELIB}/FIAT/finite_element.pyc
-${PYSITELIB}/FIAT/finite_element.pyo
-${PYSITELIB}/FIAT/functional.py
-${PYSITELIB}/FIAT/functional.pyc
-${PYSITELIB}/FIAT/functional.pyo
-${PYSITELIB}/FIAT/hermite.py
-${PYSITELIB}/FIAT/hermite.pyc
-${PYSITELIB}/FIAT/hermite.pyo
-${PYSITELIB}/FIAT/jacobi.py
-${PYSITELIB}/FIAT/jacobi.pyc
-${PYSITELIB}/FIAT/jacobi.pyo
-${PYSITELIB}/FIAT/lagrange.py
-${PYSITELIB}/FIAT/lagrange.pyc
-${PYSITELIB}/FIAT/lagrange.pyo
-${PYSITELIB}/FIAT/makelags.py
-${PYSITELIB}/FIAT/makelags.pyc
-${PYSITELIB}/FIAT/makelags.pyo
-${PYSITELIB}/FIAT/morley.py
-${PYSITELIB}/FIAT/morley.pyc
-${PYSITELIB}/FIAT/morley.pyo
-${PYSITELIB}/FIAT/nedelec.py
-${PYSITELIB}/FIAT/nedelec.pyc
-${PYSITELIB}/FIAT/nedelec.pyo
-${PYSITELIB}/FIAT/nedelec_second_kind.py
-${PYSITELIB}/FIAT/nedelec_second_kind.pyc
-${PYSITELIB}/FIAT/nedelec_second_kind.pyo
-${PYSITELIB}/FIAT/newdubiner.py
-${PYSITELIB}/FIAT/newdubiner.pyc
-${PYSITELIB}/FIAT/newdubiner.pyo
-${PYSITELIB}/FIAT/polynomial_set.py
-${PYSITELIB}/FIAT/polynomial_set.pyc
-${PYSITELIB}/FIAT/polynomial_set.pyo
-${PYSITELIB}/FIAT/quadrature.py
-${PYSITELIB}/FIAT/quadrature.pyc
-${PYSITELIB}/FIAT/quadrature.pyo
-${PYSITELIB}/FIAT/raviart_thomas.py
-${PYSITELIB}/FIAT/raviart_thomas.pyc
-${PYSITELIB}/FIAT/raviart_thomas.pyo
-${PYSITELIB}/FIAT/reference_element.py
-${PYSITELIB}/FIAT/reference_element.pyc
-${PYSITELIB}/FIAT/reference_element.pyo
-${PYSITELIB}/FIAT/tabarg.py
-${PYSITELIB}/FIAT/tabarg.pyc
-${PYSITELIB}/FIAT/tabarg.pyo
-${PYSITELIB}/FIAT/tablag.py
-${PYSITELIB}/FIAT/tablag.pyc
-${PYSITELIB}/FIAT/tablag.pyo
-${PYSITELIB}/FIAT/transform_hermite.py
-${PYSITELIB}/FIAT/transform_hermite.pyc
-${PYSITELIB}/FIAT/transform_hermite.pyo
-${PYSITELIB}/FIAT/transform_morley.py
-${PYSITELIB}/FIAT/transform_morley.pyc
-${PYSITELIB}/FIAT/transform_morley.pyo
diff --git a/py-fiat/buildlink3.mk b/py-fiat/buildlink3.mk
deleted file mode 100644
index 8f1f84d6c4..0000000000
--- a/py-fiat/buildlink3.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-# $NetBSD: buildlink3.mk,v 1.5 2013/03/23 13:29:16 outpaddling Exp $
-
-BUILDLINK_TREE+= py-fiat
-
-.if !defined(PY_FIAT_BUILDLINK3_MK)
-PY_FIAT_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.py-fiat+= ${PYPKGPREFIX}-fiat>=1.0.0
-BUILDLINK_PKGSRCDIR.py-fiat?= ../../wip/py-fiat
-.endif # PY_FIAT_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -py-fiat
diff --git a/py-fiat/distinfo b/py-fiat/distinfo
deleted file mode 100644
index 9d0af3b23a..0000000000
--- a/py-fiat/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD: distinfo,v 1.2 2013/03/23 13:41:02 outpaddling Exp $
-
-RMD160 (fiat-1.1.tar.gz) = b3f72af433bf359c297f877590daa611b7f86664
-SHA512 (fiat-1.1.tar.gz) = 9f65e1be1d19102fb099ec1ece587f70c04c0567c316e4fb1bcf24c93c104499b6e1baa118527b2e4c942765ea2164f7243dabac2bc0267991a23edc959d14e0
-Size (fiat-1.1.tar.gz) = 3870562 bytes
diff --git a/py-pbfalcon/DESCR b/py-pbfalcon/DESCR
deleted file mode 100644
index a96e4ea576..0000000000
--- a/py-pbfalcon/DESCR
+++ /dev/null
@@ -1,3 +0,0 @@
-Experimental PacBio diploid assembler.
-
-WWW: https://github.com/PacificBiosciences/FALCON
diff --git a/py-pbfalcon/PLIST b/py-pbfalcon/PLIST
deleted file mode 100644
index b4173efb8f..0000000000
--- a/py-pbfalcon/PLIST
+++ /dev/null
@@ -1,98 +0,0 @@
-@comment $NetBSD$
-bin/falcon-task
-bin/fc_actg_coordinate
-bin/fc_actg_coordinate.py
-bin/fc_consensus
-bin/fc_consensus.py
-bin/fc_contig_annotate
-bin/fc_contig_annotate.py
-bin/fc_ctg_link_analysis
-bin/fc_ctg_link_analysis.py
-bin/fc_dedup_a_tigs
-bin/fc_dedup_a_tigs.py
-bin/fc_graph_to_contig
-bin/fc_graph_to_contig.py
-bin/fc_graph_to_utgs
-bin/fc_graph_to_utgs.py
-bin/fc_ovlp_filter
-bin/fc_ovlp_filter.py
-bin/fc_ovlp_stats
-bin/fc_ovlp_stats.py
-bin/fc_ovlp_to_graph
-bin/fc_ovlp_to_graph.py
-bin/fc_run
-bin/fc_run.py
-${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
-${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
-${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
-${PYSITELIB}/${EGG_INFODIR}/entry_points.txt
-${PYSITELIB}/${EGG_INFODIR}/not-zip-safe
-${PYSITELIB}/${EGG_INFODIR}/requires.txt
-${PYSITELIB}/${EGG_INFODIR}/top_level.txt
-${PYSITELIB}/falcon_kit/FastaReader.py
-${PYSITELIB}/falcon_kit/FastaReader.pyc
-${PYSITELIB}/falcon_kit/FastaReader.pyo
-${PYSITELIB}/falcon_kit/__init__.py
-${PYSITELIB}/falcon_kit/__init__.pyc
-${PYSITELIB}/falcon_kit/__init__.pyo
-${PYSITELIB}/falcon_kit/ext_falcon.so
-${PYSITELIB}/falcon_kit/falcon_kit.py
-${PYSITELIB}/falcon_kit/falcon_kit.pyc
-${PYSITELIB}/falcon_kit/falcon_kit.pyo
-${PYSITELIB}/falcon_kit/fc_asm_graph.py
-${PYSITELIB}/falcon_kit/fc_asm_graph.pyc
-${PYSITELIB}/falcon_kit/fc_asm_graph.pyo
-${PYSITELIB}/falcon_kit/functional.py
-${PYSITELIB}/falcon_kit/functional.pyc
-${PYSITELIB}/falcon_kit/functional.pyo
-${PYSITELIB}/falcon_kit/mains/__init__.py
-${PYSITELIB}/falcon_kit/mains/__init__.pyc
-${PYSITELIB}/falcon_kit/mains/__init__.pyo
-${PYSITELIB}/falcon_kit/mains/actg_coordinate.py
-${PYSITELIB}/falcon_kit/mains/actg_coordinate.pyc
-${PYSITELIB}/falcon_kit/mains/actg_coordinate.pyo
-${PYSITELIB}/falcon_kit/mains/consensus.py
-${PYSITELIB}/falcon_kit/mains/consensus.pyc
-${PYSITELIB}/falcon_kit/mains/consensus.pyo
-${PYSITELIB}/falcon_kit/mains/contig_annotate.py
-${PYSITELIB}/falcon_kit/mains/contig_annotate.pyc
-${PYSITELIB}/falcon_kit/mains/contig_annotate.pyo
-${PYSITELIB}/falcon_kit/mains/ctg_link_analysis.py
-${PYSITELIB}/falcon_kit/mains/ctg_link_analysis.pyc
-${PYSITELIB}/falcon_kit/mains/ctg_link_analysis.pyo
-${PYSITELIB}/falcon_kit/mains/dedup_a_tigs.py
-${PYSITELIB}/falcon_kit/mains/dedup_a_tigs.pyc
-${PYSITELIB}/falcon_kit/mains/dedup_a_tigs.pyo
-${PYSITELIB}/falcon_kit/mains/graph_to_contig.py
-${PYSITELIB}/falcon_kit/mains/graph_to_contig.pyc
-${PYSITELIB}/falcon_kit/mains/graph_to_contig.pyo
-${PYSITELIB}/falcon_kit/mains/graph_to_utgs.py
-${PYSITELIB}/falcon_kit/mains/graph_to_utgs.pyc
-${PYSITELIB}/falcon_kit/mains/graph_to_utgs.pyo
-${PYSITELIB}/falcon_kit/mains/ovlp_filter.py
-${PYSITELIB}/falcon_kit/mains/ovlp_filter.pyc
-${PYSITELIB}/falcon_kit/mains/ovlp_filter.pyo
-${PYSITELIB}/falcon_kit/mains/ovlp_stats.py
-${PYSITELIB}/falcon_kit/mains/ovlp_stats.pyc
-${PYSITELIB}/falcon_kit/mains/ovlp_stats.pyo
-${PYSITELIB}/falcon_kit/mains/ovlp_to_graph.py
-${PYSITELIB}/falcon_kit/mains/ovlp_to_graph.pyc
-${PYSITELIB}/falcon_kit/mains/ovlp_to_graph.pyo
-${PYSITELIB}/falcon_kit/mains/run.py
-${PYSITELIB}/falcon_kit/mains/run.pyc
-${PYSITELIB}/falcon_kit/mains/run.pyo
-${PYSITELIB}/falcon_kit/mains/tasks.py
-${PYSITELIB}/falcon_kit/mains/tasks.pyc
-${PYSITELIB}/falcon_kit/mains/tasks.pyo
-${PYSITELIB}/falcon_kit/multiproc.py
-${PYSITELIB}/falcon_kit/multiproc.pyc
-${PYSITELIB}/falcon_kit/multiproc.pyo
-${PYSITELIB}/falcon_kit/run_support.py
-${PYSITELIB}/falcon_kit/run_support.pyc
-${PYSITELIB}/falcon_kit/run_support.pyo
-${PYSITELIB}/falcon_kit/util/__init__.py
-${PYSITELIB}/falcon_kit/util/__init__.pyc
-${PYSITELIB}/falcon_kit/util/__init__.pyo
-${PYSITELIB}/falcon_kit/util/io.py
-${PYSITELIB}/falcon_kit/util/io.pyc
-${PYSITELIB}/falcon_kit/util/io.pyo
diff --git a/py-pbfalcon/TODO b/py-pbfalcon/TODO
deleted file mode 100644
index b687356e6b..0000000000
--- a/py-pbfalcon/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test
diff --git a/py-pbfalcon/distinfo b/py-pbfalcon/distinfo
deleted file mode 100644
index bc5164ac2a..0000000000
--- a/py-pbfalcon/distinfo
+++ /dev/null
@@ -1,6 +0,0 @@
-$NetBSD$
-
-RMD160 (pbfalcon-2015.10.28.tar.xz) = e042a996fe813ec468974458e13631cb1c76d310
-SHA512 (pbfalcon-2015.10.28.tar.xz) = 464f1730d283be11b1aeea0ff9be98d85dbb2ec313dcdf53a9a3337790d6814a11b9d8979abf3669f1ba379c68bb1612dbe18ae9ad4a5764ef0c75aff67938dd
-Size (pbfalcon-2015.10.28.tar.xz) = 458572 bytes
-SHA1 (patch-src_py_run__support.py) = b629f948fce6ebce74c1dc8996d206e8dad98536
diff --git a/py-pbfalcon/patches/patch-src_py_run__support.py b/py-pbfalcon/patches/patch-src_py_run__support.py
deleted file mode 100644
index 207208bd68..0000000000
--- a/py-pbfalcon/patches/patch-src_py_run__support.py
+++ /dev/null
@@ -1,14 +0,0 @@
-$NetBSD$
-
-# Add portable shebang
-
---- src/py/run_support.py.orig 2015-10-28 12:31:41.000000000 -0500
-+++ src/py/run_support.py 2015-10-28 12:32:00.000000000 -0500
-@@ -33,6 +33,7 @@
- content = ifs.read()
- content = _prepend_env_paths(content, names)
- with open(fn, 'w') as ofs:
-+ ofs.write('#!/usr/bin/env bash\n\n')
- ofs.write(content)
-
- def use_tmpdir_for_files(basenames, src_dir, link_dir):
diff --git a/py-pypeflow/DESCR b/py-pypeflow/DESCR
deleted file mode 100644
index 321c4aebdd..0000000000
--- a/py-pypeflow/DESCR
+++ /dev/null
@@ -1,3 +0,0 @@
-pypeFLOW is a lightweight and reusable make/flow data process library written
-in Python. Features multiple concurrent task scheduling and a reasonable
-simple interface for declarative programming.
diff --git a/py-pypeflow/PLIST b/py-pypeflow/PLIST
deleted file mode 100644
index 0b3a6c62f1..0000000000
--- a/py-pypeflow/PLIST
+++ /dev/null
@@ -1,22 +0,0 @@
-@comment $NetBSD$
-${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
-${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
-${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
-${PYSITELIB}/${EGG_INFODIR}/not-zip-safe
-${PYSITELIB}/${EGG_INFODIR}/requires.txt
-${PYSITELIB}/${EGG_INFODIR}/top_level.txt
-${PYSITELIB}/pypeflow/__init__.py
-${PYSITELIB}/pypeflow/__init__.pyc
-${PYSITELIB}/pypeflow/__init__.pyo
-${PYSITELIB}/pypeflow/common.py
-${PYSITELIB}/pypeflow/common.pyc
-${PYSITELIB}/pypeflow/common.pyo
-${PYSITELIB}/pypeflow/controller.py
-${PYSITELIB}/pypeflow/controller.pyc
-${PYSITELIB}/pypeflow/controller.pyo
-${PYSITELIB}/pypeflow/data.py
-${PYSITELIB}/pypeflow/data.pyc
-${PYSITELIB}/pypeflow/data.pyo
-${PYSITELIB}/pypeflow/task.py
-${PYSITELIB}/pypeflow/task.pyc
-${PYSITELIB}/pypeflow/task.pyo
diff --git a/py-pypeflow/TODO b/py-pypeflow/TODO
deleted file mode 100644
index b687356e6b..0000000000
--- a/py-pypeflow/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test
diff --git a/py-pypeflow/distinfo b/py-pypeflow/distinfo
deleted file mode 100644
index ae56b8bb3e..0000000000
--- a/py-pypeflow/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD$
-
-RMD160 (pypeflow-2015.10.28.tar.xz) = 06ac42ae8be443d696018742d0cdb9793ce37402
-SHA512 (pypeflow-2015.10.28.tar.xz) = 96ba01c878d63759146ac853fc635be0152810b5fe5025ce82e092a3b677801fe29b646bfb924fc9a09b9c78bedd0ff5e88826e3f9c4b74029a9de3aff1bf9ac
-Size (pypeflow-2015.10.28.tar.xz) = 1798152 bytes
diff --git a/py-snakemake/DESCR b/py-snakemake/DESCR
deleted file mode 100644
index b5b09e9708..0000000000
--- a/py-snakemake/DESCR
+++ /dev/null
@@ -1,5 +0,0 @@
-Snakemake is a workflow management system that aims to reduce the complexity of
-creating workflows by providing a fast and comfortable execution environment,
-together with a clean and modern specification language in python style.
-Snakemake workflows are essentially Python scripts extended by declarative code
-to define rules. Rules describe how to create output files from input files.
diff --git a/py-snakemake/PLIST b/py-snakemake/PLIST
deleted file mode 100644
index f52fc8c900..0000000000
--- a/py-snakemake/PLIST
+++ /dev/null
@@ -1,143 +0,0 @@
-@comment $NetBSD$
-bin/snakemake
-bin/snakemake-bash-completion
-${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
-${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
-${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
-${PYSITELIB}/${EGG_INFODIR}/entry_points.txt
-${PYSITELIB}/${EGG_INFODIR}/not-zip-safe
-${PYSITELIB}/${EGG_INFODIR}/requires.txt
-${PYSITELIB}/${EGG_INFODIR}/top_level.txt
-${PYSITELIB}/snakemake/__init__.py
-${PYSITELIB}/snakemake/__main__.py
-${PYSITELIB}/snakemake/__init__.pyo
-${PYSITELIB}/snakemake/__init__.pyc
-${PYSITELIB}/snakemake/__main__.pyo
-${PYSITELIB}/snakemake/__main__.pyc
-${PYSITELIB}/snakemake/_version.pyo
-${PYSITELIB}/snakemake/_version.pyc
-${PYSITELIB}/snakemake/benchmark.pyo
-${PYSITELIB}/snakemake/benchmark.pyc
-${PYSITELIB}/snakemake/common.pyo
-${PYSITELIB}/snakemake/common.pyc
-${PYSITELIB}/snakemake/conda.pyo
-${PYSITELIB}/snakemake/conda.pyc
-${PYSITELIB}/snakemake/cwl.pyo
-${PYSITELIB}/snakemake/cwl.pyc
-${PYSITELIB}/snakemake/dag.pyo
-${PYSITELIB}/snakemake/dag.pyc
-${PYSITELIB}/snakemake/decorators.pyo
-${PYSITELIB}/snakemake/decorators.pyc
-${PYSITELIB}/snakemake/exceptions.pyo
-${PYSITELIB}/snakemake/exceptions.pyc
-${PYSITELIB}/snakemake/executors.pyo
-${PYSITELIB}/snakemake/executors.pyc
-${PYSITELIB}/snakemake/gui.pyo
-${PYSITELIB}/snakemake/gui.pyc
-${PYSITELIB}/snakemake/io.pyo
-${PYSITELIB}/snakemake/io.pyc
-${PYSITELIB}/snakemake/jobs.pyo
-${PYSITELIB}/snakemake/jobs.pyc
-${PYSITELIB}/snakemake/logging.pyo
-${PYSITELIB}/snakemake/logging.pyc
-${PYSITELIB}/snakemake/output_index.pyo
-${PYSITELIB}/snakemake/output_index.pyc
-${PYSITELIB}/snakemake/parser.pyo
-${PYSITELIB}/snakemake/parser.pyc
-${PYSITELIB}/snakemake/persistence.pyo
-${PYSITELIB}/snakemake/persistence.pyc
-${PYSITELIB}/snakemake/rules.pyo
-${PYSITELIB}/snakemake/rules.pyc
-${PYSITELIB}/snakemake/scheduler.pyo
-${PYSITELIB}/snakemake/scheduler.pyc
-${PYSITELIB}/snakemake/script.pyo
-${PYSITELIB}/snakemake/script.pyc
-${PYSITELIB}/snakemake/shell.pyo
-${PYSITELIB}/snakemake/shell.pyc
-${PYSITELIB}/snakemake/singularity.pyo
-${PYSITELIB}/snakemake/singularity.pyc
-${PYSITELIB}/snakemake/stats.pyo
-${PYSITELIB}/snakemake/stats.pyc
-${PYSITELIB}/snakemake/utils.pyo
-${PYSITELIB}/snakemake/utils.pyc
-${PYSITELIB}/snakemake/workflow.pyo
-${PYSITELIB}/snakemake/workflow.pyc
-${PYSITELIB}/snakemake/wrapper.pyo
-${PYSITELIB}/snakemake/wrapper.pyc
-${PYSITELIB}/snakemake/_version.py
-${PYSITELIB}/snakemake/benchmark.py
-${PYSITELIB}/snakemake/common.py
-${PYSITELIB}/snakemake/conda.py
-${PYSITELIB}/snakemake/cwl.py
-${PYSITELIB}/snakemake/dag.py
-${PYSITELIB}/snakemake/decorators.py
-${PYSITELIB}/snakemake/exceptions.py
-${PYSITELIB}/snakemake/executors.py
-${PYSITELIB}/snakemake/gui.html
-${PYSITELIB}/snakemake/gui.py
-${PYSITELIB}/snakemake/io.py
-${PYSITELIB}/snakemake/jobs.py
-${PYSITELIB}/snakemake/jobscript.sh
-${PYSITELIB}/snakemake/logging.py
-${PYSITELIB}/snakemake/output_index.py
-${PYSITELIB}/snakemake/parser.py
-${PYSITELIB}/snakemake/persistence.py
-${PYSITELIB}/snakemake/remote/EGA.py
-${PYSITELIB}/snakemake/remote/FTP.py
-${PYSITELIB}/snakemake/remote/GS.py
-${PYSITELIB}/snakemake/remote/HTTP.py
-${PYSITELIB}/snakemake/remote/NCBI.py
-${PYSITELIB}/snakemake/remote/S3.py
-${PYSITELIB}/snakemake/remote/S3Mocked.py
-${PYSITELIB}/snakemake/remote/SFTP.py
-${PYSITELIB}/snakemake/remote/XRootD.py
-${PYSITELIB}/snakemake/remote/__init__.py
-${PYSITELIB}/snakemake/remote/EGA.pyo
-${PYSITELIB}/snakemake/remote/EGA.pyc
-${PYSITELIB}/snakemake/remote/FTP.pyo
-${PYSITELIB}/snakemake/remote/FTP.pyc
-${PYSITELIB}/snakemake/remote/GS.pyo
-${PYSITELIB}/snakemake/remote/GS.pyc
-${PYSITELIB}/snakemake/remote/HTTP.pyo
-${PYSITELIB}/snakemake/remote/HTTP.pyc
-${PYSITELIB}/snakemake/remote/NCBI.pyo
-${PYSITELIB}/snakemake/remote/NCBI.pyc
-${PYSITELIB}/snakemake/remote/S3.pyo
-${PYSITELIB}/snakemake/remote/S3.pyc
-${PYSITELIB}/snakemake/remote/S3Mocked.pyo
-${PYSITELIB}/snakemake/remote/S3Mocked.pyc
-${PYSITELIB}/snakemake/remote/SFTP.pyo
-${PYSITELIB}/snakemake/remote/SFTP.pyc
-${PYSITELIB}/snakemake/remote/XRootD.pyo
-${PYSITELIB}/snakemake/remote/XRootD.pyc
-${PYSITELIB}/snakemake/remote/__init__.pyo
-${PYSITELIB}/snakemake/remote/__init__.pyc
-${PYSITELIB}/snakemake/remote/dropbox.pyo
-${PYSITELIB}/snakemake/remote/dropbox.pyc
-${PYSITELIB}/snakemake/remote/gfal.pyo
-${PYSITELIB}/snakemake/remote/gfal.pyc
-${PYSITELIB}/snakemake/remote/gridftp.pyo
-${PYSITELIB}/snakemake/remote/gridftp.pyc
-${PYSITELIB}/snakemake/remote/iRODS.pyo
-${PYSITELIB}/snakemake/remote/iRODS.pyc
-${PYSITELIB}/snakemake/remote/webdav.pyo
-${PYSITELIB}/snakemake/remote/webdav.pyc
-${PYSITELIB}/snakemake/remote/dropbox.py
-${PYSITELIB}/snakemake/remote/gfal.py
-${PYSITELIB}/snakemake/remote/gridftp.py
-${PYSITELIB}/snakemake/remote/iRODS.py
-${PYSITELIB}/snakemake/remote/webdav.py
-${PYSITELIB}/snakemake/report.css
-${PYSITELIB}/snakemake/report/__init__.py
-${PYSITELIB}/snakemake/report/__init__.pyo
-${PYSITELIB}/snakemake/report/__init__.pyc
-${PYSITELIB}/snakemake/report/report.html
-${PYSITELIB}/snakemake/rules.py
-${PYSITELIB}/snakemake/scheduler.py
-${PYSITELIB}/snakemake/script.py
-${PYSITELIB}/snakemake/shell.py
-${PYSITELIB}/snakemake/singularity.py
-${PYSITELIB}/snakemake/stats.py
-${PYSITELIB}/snakemake/utils.py
-${PYSITELIB}/snakemake/workflow.py
-${PYSITELIB}/snakemake/wrapper.py
diff --git a/py-snakemake/distinfo b/py-snakemake/distinfo
deleted file mode 100644
index 02015a7a91..0000000000
--- a/py-snakemake/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD$
-
-RMD160 (snakemake-5.2.0.tar.gz) = 63e85ba1b451a41ca81d71342978552f2df46fbf
-SHA512 (snakemake-5.2.0.tar.gz) = bab4604ceef3fb24f2236fb23c0299159aa13f224e1d7f51abf384fce690ae4bf9a9536ffc4e6a33282c8a4ab50cdc4c674ec0f9f6c4f254a98b411ac269b756
-Size (snakemake-5.2.0.tar.gz) = 163467 bytes
diff --git a/py-ufl/DESCR b/py-ufl/DESCR
deleted file mode 100644
index a16d926632..0000000000
--- a/py-ufl/DESCR
+++ /dev/null
@@ -1,2 +0,0 @@
-The Unified Form Language (UFL) is a domain specific language for declaration
-of finite element discretizations of variational forms.
diff --git a/py-ufl/PLIST b/py-ufl/PLIST
deleted file mode 100644
index c022bb8945..0000000000
--- a/py-ufl/PLIST
+++ /dev/null
@@ -1,248 +0,0 @@
-@comment $NetBSD: PLIST,v 1.3 2013/03/24 20:47:00 outpaddling Exp $
-bin/form2ufl
-bin/ufl-analyse
-bin/ufl-convert
-bin/ufl-version
-bin/ufl2py
-${PYSITELIB}/ufl/__init__.py
-${PYSITELIB}/ufl/__init__.pyc
-${PYSITELIB}/ufl/__init__.pyo
-${PYSITELIB}/ufl/algebra.py
-${PYSITELIB}/ufl/algebra.pyc
-${PYSITELIB}/ufl/algebra.pyo
-${PYSITELIB}/ufl/algorithms/__init__.py
-${PYSITELIB}/ufl/algorithms/__init__.pyc
-${PYSITELIB}/ufl/algorithms/__init__.pyo
-${PYSITELIB}/ufl/algorithms/ad.py
-${PYSITELIB}/ufl/algorithms/ad.pyc
-${PYSITELIB}/ufl/algorithms/ad.pyo
-${PYSITELIB}/ufl/algorithms/analysis.py
-${PYSITELIB}/ufl/algorithms/analysis.pyc
-${PYSITELIB}/ufl/algorithms/analysis.pyo
-${PYSITELIB}/ufl/algorithms/argument_dependencies.py
-${PYSITELIB}/ufl/algorithms/argument_dependencies.pyc
-${PYSITELIB}/ufl/algorithms/argument_dependencies.pyo
-${PYSITELIB}/ufl/algorithms/checks.py
-${PYSITELIB}/ufl/algorithms/checks.pyc
-${PYSITELIB}/ufl/algorithms/checks.pyo
-${PYSITELIB}/ufl/algorithms/deprecated.py
-${PYSITELIB}/ufl/algorithms/deprecated.pyc
-${PYSITELIB}/ufl/algorithms/deprecated.pyo
-${PYSITELIB}/ufl/algorithms/domain_analysis.py
-${PYSITELIB}/ufl/algorithms/domain_analysis.pyc
-${PYSITELIB}/ufl/algorithms/domain_analysis.pyo
-${PYSITELIB}/ufl/algorithms/elementtransformations.py
-${PYSITELIB}/ufl/algorithms/elementtransformations.pyc
-${PYSITELIB}/ufl/algorithms/elementtransformations.pyo
-${PYSITELIB}/ufl/algorithms/estimate_degrees.py
-${PYSITELIB}/ufl/algorithms/estimate_degrees.pyc
-${PYSITELIB}/ufl/algorithms/estimate_degrees.pyo
-${PYSITELIB}/ufl/algorithms/expand_compounds.py
-${PYSITELIB}/ufl/algorithms/expand_compounds.pyc
-${PYSITELIB}/ufl/algorithms/expand_compounds.pyo
-${PYSITELIB}/ufl/algorithms/expand_indices.py
-${PYSITELIB}/ufl/algorithms/expand_indices.pyc
-${PYSITELIB}/ufl/algorithms/expand_indices.pyo
-${PYSITELIB}/ufl/algorithms/formdata.py
-${PYSITELIB}/ufl/algorithms/formdata.pyc
-${PYSITELIB}/ufl/algorithms/formdata.pyo
-${PYSITELIB}/ufl/algorithms/formfiles.py
-${PYSITELIB}/ufl/algorithms/formfiles.pyc
-${PYSITELIB}/ufl/algorithms/formfiles.pyo
-${PYSITELIB}/ufl/algorithms/formtransformations.py
-${PYSITELIB}/ufl/algorithms/formtransformations.pyc
-${PYSITELIB}/ufl/algorithms/formtransformations.pyo
-${PYSITELIB}/ufl/algorithms/forward_ad.py
-${PYSITELIB}/ufl/algorithms/forward_ad.pyc
-${PYSITELIB}/ufl/algorithms/forward_ad.pyo
-${PYSITELIB}/ufl/algorithms/graph.py
-${PYSITELIB}/ufl/algorithms/graph.pyc
-${PYSITELIB}/ufl/algorithms/graph.pyo
-${PYSITELIB}/ufl/algorithms/latextools.py
-${PYSITELIB}/ufl/algorithms/latextools.pyc
-${PYSITELIB}/ufl/algorithms/latextools.pyo
-${PYSITELIB}/ufl/algorithms/multifunction.py
-${PYSITELIB}/ufl/algorithms/multifunction.pyc
-${PYSITELIB}/ufl/algorithms/multifunction.pyo
-${PYSITELIB}/ufl/algorithms/pdiffs.py
-${PYSITELIB}/ufl/algorithms/pdiffs.pyc
-${PYSITELIB}/ufl/algorithms/pdiffs.pyo
-${PYSITELIB}/ufl/algorithms/predicates.py
-${PYSITELIB}/ufl/algorithms/predicates.pyc
-${PYSITELIB}/ufl/algorithms/predicates.pyo
-${PYSITELIB}/ufl/algorithms/preprocess.py
-${PYSITELIB}/ufl/algorithms/preprocess.pyc
-${PYSITELIB}/ufl/algorithms/preprocess.pyo
-${PYSITELIB}/ufl/algorithms/printing.py
-${PYSITELIB}/ufl/algorithms/printing.pyc
-${PYSITELIB}/ufl/algorithms/printing.pyo
-${PYSITELIB}/ufl/algorithms/propagate_restrictions.py
-${PYSITELIB}/ufl/algorithms/propagate_restrictions.pyc
-${PYSITELIB}/ufl/algorithms/propagate_restrictions.pyo
-${PYSITELIB}/ufl/algorithms/renumbering.py
-${PYSITELIB}/ufl/algorithms/renumbering.pyc
-${PYSITELIB}/ufl/algorithms/renumbering.pyo
-${PYSITELIB}/ufl/algorithms/replace.py
-${PYSITELIB}/ufl/algorithms/replace.pyc
-${PYSITELIB}/ufl/algorithms/replace.pyo
-${PYSITELIB}/ufl/algorithms/signature.py
-${PYSITELIB}/ufl/algorithms/signature.pyc
-${PYSITELIB}/ufl/algorithms/signature.pyo
-${PYSITELIB}/ufl/algorithms/transformations.py
-${PYSITELIB}/ufl/algorithms/transformations.pyc
-${PYSITELIB}/ufl/algorithms/transformations.pyo
-${PYSITELIB}/ufl/algorithms/transformer.py
-${PYSITELIB}/ufl/algorithms/transformer.pyc
-${PYSITELIB}/ufl/algorithms/transformer.pyo
-${PYSITELIB}/ufl/algorithms/traversal.py
-${PYSITELIB}/ufl/algorithms/traversal.pyc
-${PYSITELIB}/ufl/algorithms/traversal.pyo
-${PYSITELIB}/ufl/algorithms/tuplenotation.py
-${PYSITELIB}/ufl/algorithms/tuplenotation.pyc
-${PYSITELIB}/ufl/algorithms/tuplenotation.pyo
-${PYSITELIB}/ufl/algorithms/ufl2dot.py
-${PYSITELIB}/ufl/algorithms/ufl2dot.pyc
-${PYSITELIB}/ufl/algorithms/ufl2dot.pyo
-${PYSITELIB}/ufl/algorithms/ufl2latex.py
-${PYSITELIB}/ufl/algorithms/ufl2latex.pyc
-${PYSITELIB}/ufl/algorithms/ufl2latex.pyo
-${PYSITELIB}/ufl/argument.py
-${PYSITELIB}/ufl/argument.pyc
-${PYSITELIB}/ufl/argument.pyo
-${PYSITELIB}/ufl/assertions.py
-${PYSITELIB}/ufl/assertions.pyc
-${PYSITELIB}/ufl/assertions.pyo
-${PYSITELIB}/ufl/classes.py
-${PYSITELIB}/ufl/classes.pyc
-${PYSITELIB}/ufl/classes.pyo
-${PYSITELIB}/ufl/coefficient.py
-${PYSITELIB}/ufl/coefficient.pyc
-${PYSITELIB}/ufl/coefficient.pyo
-${PYSITELIB}/ufl/common.py
-${PYSITELIB}/ufl/common.pyc
-${PYSITELIB}/ufl/common.pyo
-${PYSITELIB}/ufl/conditional.py
-${PYSITELIB}/ufl/conditional.pyc
-${PYSITELIB}/ufl/conditional.pyo
-${PYSITELIB}/ufl/constantvalue.py
-${PYSITELIB}/ufl/constantvalue.pyc
-${PYSITELIB}/ufl/constantvalue.pyo
-${PYSITELIB}/ufl/differentiation.py
-${PYSITELIB}/ufl/differentiation.pyc
-${PYSITELIB}/ufl/differentiation.pyo
-${PYSITELIB}/ufl/domains.py
-${PYSITELIB}/ufl/domains.pyc
-${PYSITELIB}/ufl/domains.pyo
-${PYSITELIB}/ufl/equation.py
-${PYSITELIB}/ufl/equation.pyc
-${PYSITELIB}/ufl/equation.pyo
-${PYSITELIB}/ufl/expr.py
-${PYSITELIB}/ufl/expr.pyc
-${PYSITELIB}/ufl/expr.pyo
-${PYSITELIB}/ufl/exprequals.py
-${PYSITELIB}/ufl/exprequals.pyc
-${PYSITELIB}/ufl/exprequals.pyo
-${PYSITELIB}/ufl/exproperators.py
-${PYSITELIB}/ufl/exproperators.pyc
-${PYSITELIB}/ufl/exproperators.pyo
-${PYSITELIB}/ufl/finiteelement/__init__.py
-${PYSITELIB}/ufl/finiteelement/__init__.pyc
-${PYSITELIB}/ufl/finiteelement/__init__.pyo
-${PYSITELIB}/ufl/finiteelement/elementlist.py
-${PYSITELIB}/ufl/finiteelement/elementlist.pyc
-${PYSITELIB}/ufl/finiteelement/elementlist.pyo
-${PYSITELIB}/ufl/finiteelement/enrichedelement.py
-${PYSITELIB}/ufl/finiteelement/enrichedelement.pyc
-${PYSITELIB}/ufl/finiteelement/enrichedelement.pyo
-${PYSITELIB}/ufl/finiteelement/feec.py
-${PYSITELIB}/ufl/finiteelement/feec.pyc
-${PYSITELIB}/ufl/finiteelement/feec.pyo
-${PYSITELIB}/ufl/finiteelement/finiteelement.py
-${PYSITELIB}/ufl/finiteelement/finiteelement.pyc
-${PYSITELIB}/ufl/finiteelement/finiteelement.pyo
-${PYSITELIB}/ufl/finiteelement/finiteelementbase.py
-${PYSITELIB}/ufl/finiteelement/finiteelementbase.pyc
-${PYSITELIB}/ufl/finiteelement/finiteelementbase.pyo
-${PYSITELIB}/ufl/finiteelement/mixedelement.py
-${PYSITELIB}/ufl/finiteelement/mixedelement.pyc
-${PYSITELIB}/ufl/finiteelement/mixedelement.pyo
-${PYSITELIB}/ufl/finiteelement/restrictedelement.py
-${PYSITELIB}/ufl/finiteelement/restrictedelement.pyc
-${PYSITELIB}/ufl/finiteelement/restrictedelement.pyo
-${PYSITELIB}/ufl/finiteelement/tensorproductelement.py
-${PYSITELIB}/ufl/finiteelement/tensorproductelement.pyc
-${PYSITELIB}/ufl/finiteelement/tensorproductelement.pyo
-${PYSITELIB}/ufl/form.py
-${PYSITELIB}/ufl/form.pyc
-${PYSITELIB}/ufl/form.pyo
-${PYSITELIB}/ufl/formoperators.py
-${PYSITELIB}/ufl/formoperators.pyc
-${PYSITELIB}/ufl/formoperators.pyo
-${PYSITELIB}/ufl/geometry.py
-${PYSITELIB}/ufl/geometry.pyc
-${PYSITELIB}/ufl/geometry.pyo
-${PYSITELIB}/ufl/indexed.py
-${PYSITELIB}/ufl/indexed.pyc
-${PYSITELIB}/ufl/indexed.pyo
-${PYSITELIB}/ufl/indexing.py
-${PYSITELIB}/ufl/indexing.pyc
-${PYSITELIB}/ufl/indexing.pyo
-${PYSITELIB}/ufl/indexsum.py
-${PYSITELIB}/ufl/indexsum.pyc
-${PYSITELIB}/ufl/indexsum.pyo
-${PYSITELIB}/ufl/indexutils.py
-${PYSITELIB}/ufl/indexutils.pyc
-${PYSITELIB}/ufl/indexutils.pyo
-${PYSITELIB}/ufl/integral.py
-${PYSITELIB}/ufl/integral.pyc
-${PYSITELIB}/ufl/integral.pyo
-${PYSITELIB}/ufl/log.py
-${PYSITELIB}/ufl/log.pyc
-${PYSITELIB}/ufl/log.pyo
-${PYSITELIB}/ufl/mathfunctions.py
-${PYSITELIB}/ufl/mathfunctions.pyc
-${PYSITELIB}/ufl/mathfunctions.pyo
-${PYSITELIB}/ufl/objects.py
-${PYSITELIB}/ufl/objects.pyc
-${PYSITELIB}/ufl/objects.pyo
-${PYSITELIB}/ufl/operatorbase.py
-${PYSITELIB}/ufl/operatorbase.pyc
-${PYSITELIB}/ufl/operatorbase.pyo
-${PYSITELIB}/ufl/operators.py
-${PYSITELIB}/ufl/operators.pyc
-${PYSITELIB}/ufl/operators.pyo
-${PYSITELIB}/ufl/permutation.py
-${PYSITELIB}/ufl/permutation.pyc
-${PYSITELIB}/ufl/permutation.pyo
-${PYSITELIB}/ufl/precedence.py
-${PYSITELIB}/ufl/precedence.pyc
-${PYSITELIB}/ufl/precedence.pyo
-${PYSITELIB}/ufl/restriction.py
-${PYSITELIB}/ufl/restriction.pyc
-${PYSITELIB}/ufl/restriction.pyo
-${PYSITELIB}/ufl/sorting.py
-${PYSITELIB}/ufl/sorting.pyc
-${PYSITELIB}/ufl/sorting.pyo
-${PYSITELIB}/ufl/split_functions.py
-${PYSITELIB}/ufl/split_functions.pyc
-${PYSITELIB}/ufl/split_functions.pyo
-${PYSITELIB}/ufl/tensoralgebra.py
-${PYSITELIB}/ufl/tensoralgebra.pyc
-${PYSITELIB}/ufl/tensoralgebra.pyo
-${PYSITELIB}/ufl/tensors.py
-${PYSITELIB}/ufl/tensors.pyc
-${PYSITELIB}/ufl/tensors.pyo
-${PYSITELIB}/ufl/terminal.py
-${PYSITELIB}/ufl/terminal.pyc
-${PYSITELIB}/ufl/terminal.pyo
-${PYSITELIB}/ufl/testobjects.py
-${PYSITELIB}/ufl/testobjects.pyc
-${PYSITELIB}/ufl/testobjects.pyo
-${PYSITELIB}/ufl/variable.py
-${PYSITELIB}/ufl/variable.pyc
-${PYSITELIB}/ufl/variable.pyo
-man/man1/form2ufl.1
-man/man1/ufl-analyse.1
-man/man1/ufl-convert.1
-man/man1/ufl-version.1
-man/man1/ufl2py.1
diff --git a/py-ufl/buildlink3.mk b/py-ufl/buildlink3.mk
deleted file mode 100644
index 28ba9212b8..0000000000
--- a/py-ufl/buildlink3.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-# $NetBSD: buildlink3.mk,v 1.5 2013/03/23 14:58:26 outpaddling Exp $
-
-BUILDLINK_TREE+= py-ufl
-
-.if !defined(PY_UFL_BUILDLINK3_MK)
-PY_UFL_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.py-ufl+= ${PYPKGPREFIX}-ufl>=1.0.0
-BUILDLINK_PKGSRCDIR.py-ufl?= ../../wip/py-ufl
-.endif # PY_UFL_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -py-ufl
diff --git a/py-ufl/distinfo b/py-ufl/distinfo
deleted file mode 100644
index 69734804fc..0000000000
--- a/py-ufl/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD: distinfo,v 1.3 2013/03/24 20:47:01 outpaddling Exp $
-
-RMD160 (ufl-1.2.0.tar.gz) = c0b9054affc13caffc0acdad04238eb75036f9f7
-SHA512 (ufl-1.2.0.tar.gz) = 452a9cd1eb146e8b7a05cf5eff1ea044a7736c6620939373cdaa27480f60c367677cc23c04bd0abc6868649d19d550d489f23e14f4edb614441056330a8d114b
-Size (ufl-1.2.0.tar.gz) = 748689 bytes
diff --git a/py-viper/DESCR b/py-viper/DESCR
deleted file mode 100644
index 930c6b3810..0000000000
--- a/py-viper/DESCR
+++ /dev/null
@@ -1,2 +0,0 @@
-Viper is a minimalistic scientific plotter and run-time visualization module.
-Viper has support for visualizing meshes and solutions in DOLFIN.
diff --git a/py-viper/PLIST b/py-viper/PLIST
deleted file mode 100644
index 50e765ad6e..0000000000
--- a/py-viper/PLIST
+++ /dev/null
@@ -1,43 +0,0 @@
-@comment $NetBSD: PLIST,v 1.2 2013/03/23 15:03:23 outpaddling Exp $
-bin/viper
-${PYSITELIB}/viper/__init__.py
-${PYSITELIB}/viper/__init__.pyc
-${PYSITELIB}/viper/__init__.pyo
-${PYSITELIB}/viper/data/VIF.lut
-${PYSITELIB}/viper/data/abgauss.lut
-${PYSITELIB}/viper/data/custom16.lut
-${PYSITELIB}/viper/data/gauss_075.lut
-${PYSITELIB}/viper/data/gauss_086.lut
-${PYSITELIB}/viper/data/gauss_097.lut
-${PYSITELIB}/viper/data/gauss_099.lut
-${PYSITELIB}/viper/data/gauss_100.lut
-${PYSITELIB}/viper/data/gauss_103.lut
-${PYSITELIB}/viper/data/gauss_108.lut
-${PYSITELIB}/viper/data/gauss_109.lut
-${PYSITELIB}/viper/data/gauss_113.lut
-${PYSITELIB}/viper/data/gauss_114.lut
-${PYSITELIB}/viper/data/gauss_118.lut
-${PYSITELIB}/viper/data/gauss_120.lut
-${PYSITELIB}/viper/data/gauss_121.lut
-${PYSITELIB}/viper/data/gauss_129.lut
-${PYSITELIB}/viper/data/gauss_147.lut
-${PYSITELIB}/viper/data/gauss_148.lut
-${PYSITELIB}/viper/data/gauss_164.lut
-${PYSITELIB}/viper/data/pm3d_01.lut
-${PYSITELIB}/viper/data/pm3d_03.lut
-${PYSITELIB}/viper/data/pm3d_09.lut
-${PYSITELIB}/viper/data/pm3d_10.lut
-${PYSITELIB}/viper/data/pm3d_13.lut
-${PYSITELIB}/viper/data/pm3d_18.lut
-${PYSITELIB}/viper/data/pm3d_19.lut
-${PYSITELIB}/viper/data/pm3d_22.lut
-${PYSITELIB}/viper/data/pm3d_23.lut
-${PYSITELIB}/viper/data/pm3d_24.lut
-${PYSITELIB}/viper/data/pm3d_25.lut
-${PYSITELIB}/viper/viper.py
-${PYSITELIB}/viper/viper.pyc
-${PYSITELIB}/viper/viper.pyo
-${PYSITELIB}/viper/viper_dolfin.py
-${PYSITELIB}/viper/viper_dolfin.pyc
-${PYSITELIB}/viper/viper_dolfin.pyo
-man/man1/viper.1
diff --git a/py-viper/buildlink3.mk b/py-viper/buildlink3.mk
deleted file mode 100644
index 373b0a5fc6..0000000000
--- a/py-viper/buildlink3.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-# $NetBSD: buildlink3.mk,v 1.5 2013/03/23 15:03:23 outpaddling Exp $
-
-BUILDLINK_TREE+= py-viper
-
-.if !defined(PY_VIPER_BUILDLINK3_MK)
-PY_VIPER_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.py-viper+= ${PYPKGPREFIX}-viper>=1.0.0
-BUILDLINK_PKGSRCDIR.py-viper?= ../../wip/py-viper
-.endif # PY_VIPER_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -py-viper
diff --git a/py-viper/distinfo b/py-viper/distinfo
deleted file mode 100644
index 17f5ecef12..0000000000
--- a/py-viper/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD: distinfo,v 1.2 2013/03/23 15:03:23 outpaddling Exp $
-
-RMD160 (viper-1.0.1.tar.gz) = 1266c3e796edaa8ab31f7ac5925662fa2e18215b
-SHA512 (viper-1.0.1.tar.gz) = f56c93058a3fcc904a2e2f4f5780e8b027d97a10d09867c0f66048475e07282760798f2ff446915704d49e5d1e31bb55367d3902edbce331be4936a71ca85caf
-Size (viper-1.0.1.tar.gz) = 192880 bytes
diff --git a/python3/DESCR b/python3/DESCR
deleted file mode 100644
index 00d97657cb..0000000000
--- a/python3/DESCR
+++ /dev/null
@@ -1,32 +0,0 @@
-Python is an interpreted, interactive, object-oriented
-programming language that combines remarkable power with
-very clear syntax. For an introduction to programming in
-Python you are referred to the Python Tutorial. The
-Python Library Reference documents built-in and standard
-types, constants, functions and modules. Finally, the
-Python Reference Manual describes the syntax and semantics
-of the core language in (perhaps too) much detail.
-
-Python's basic power can be extended with your own modules
-written in C or C++. On most systems such modules may be
-dynamically loaded. Python is also adaptable as an exten-
-sion language for existing applications. See the internal
-documentation for hints.
-
-This is a wrapper package for installing the default python 3
-version and links to bin/python3 and bin/python, for running
-python scripts not installed by pkgsrc, but using pkgsrc python.
-
-Currently, pkg_alternatives does not seem to have the ability
-to keep python and python3 linked to the default python version.
-Instead, it links to the latest installed version. This causes
-python scripts using #!/usr/bin/env python or #!/usr/bin/python3
-(i.e. scripts not installed by pkgsrc) to suddenly stop working
-when a python newer than the default is installed, because they
-cannot find modules installed by pkgsrc using the default version.
-pkg_altneratives has the ability to lock the links to a specific
-version, but this causes breakage when the default version changes
-and packages are updated.
-
-This wrapper package solves these problems by keeping bin/python
-and bin/python3 linked to the default python version at all times.
diff --git a/python3/PLIST b/python3/PLIST
deleted file mode 100644
index 9c68eb3036..0000000000
--- a/python3/PLIST
+++ /dev/null
@@ -1,3 +0,0 @@
-@comment $NetBSD$
-bin/python${PKGVERSION}
-bin/python
diff --git a/singularity/DESCR b/singularity/DESCR
deleted file mode 100644
index 7d48130848..0000000000
--- a/singularity/DESCR
+++ /dev/null
@@ -1,9 +0,0 @@
-Singularity is a container platform focused on supporting "Mobility of Compute"
-Mobility of Compute encapsulates the development to compute model where
-developers can work in an environment of their choosing and creation and when
-the developer needs additional compute resources, this environment can easily
-be copied and executed on other platforms. Additionally as the primary use case
-for Singularity is targeted towards computational portability, many of the
-barriers to entry of other container solutions do not apply to Singularity
-making it an ideal solution for users (both computational and
-non-computational) and HPC centers.
diff --git a/singularity/PLIST b/singularity/PLIST
deleted file mode 100644
index b3254bbcd4..0000000000
--- a/singularity/PLIST
+++ /dev/null
@@ -1,142 +0,0 @@
-@comment $NetBSD$
-bin/run-singularity
-bin/singularity
-etc/bash_completion.d/singularity
-include/singularity/bind.h
-include/singularity/image.h
-include/singularity/runtime.h
-lib/singularity/libsingularity-image.la
-lib/singularity/libsingularity-runtime.la
-libexec/singularity/bin/action
-libexec/singularity/bin/action-suid
-libexec/singularity/bin/builddef
-libexec/singularity/bin/cleanupd
-libexec/singularity/bin/docker-extract
-libexec/singularity/bin/get-section
-libexec/singularity/bin/image-type
-libexec/singularity/bin/mount
-libexec/singularity/bin/mount-suid
-libexec/singularity/bin/prepheader
-libexec/singularity/bin/start
-libexec/singularity/bin/start-suid
-libexec/singularity/bootstrap-scripts/checks.sh
-libexec/singularity/bootstrap-scripts/deffile-driver-arch.sh
-libexec/singularity/bootstrap-scripts/deffile-driver-busybox.sh
-libexec/singularity/bootstrap-scripts/deffile-driver-debootstrap.sh
-libexec/singularity/bootstrap-scripts/deffile-driver-docker.sh
-libexec/singularity/bootstrap-scripts/deffile-driver-localimage.sh
-libexec/singularity/bootstrap-scripts/deffile-driver-self.sh
-libexec/singularity/bootstrap-scripts/deffile-driver-shub.sh
-libexec/singularity/bootstrap-scripts/deffile-driver-yum.sh
-libexec/singularity/bootstrap-scripts/deffile-driver-zypper.sh
-libexec/singularity/bootstrap-scripts/deffile-post.sh
-libexec/singularity/bootstrap-scripts/deffile-sections.sh
-libexec/singularity/bootstrap-scripts/environment.sh
-libexec/singularity/bootstrap-scripts/environment.tar
-libexec/singularity/bootstrap-scripts/functions
-libexec/singularity/bootstrap-scripts/main-deffile.sh
-libexec/singularity/bootstrap-scripts/main-dockerhub.sh
-libexec/singularity/bootstrap-scripts/main-null.sh
-libexec/singularity/bootstrap-scripts/post.sh
-libexec/singularity/bootstrap-scripts/pre.sh
-libexec/singularity/cli/action_argparser.sh
-libexec/singularity/cli/apps.exec
-libexec/singularity/cli/apps.info
-libexec/singularity/cli/bootstrap.exec
-libexec/singularity/cli/bootstrap.info
-libexec/singularity/cli/build.exec
-libexec/singularity/cli/build.info
-libexec/singularity/cli/check.exec
-libexec/singularity/cli/check.info
-libexec/singularity/cli/create.exec
-libexec/singularity/cli/create.info
-libexec/singularity/cli/exec.exec
-libexec/singularity/cli/exec.info
-libexec/singularity/cli/help.exec
-libexec/singularity/cli/help.info
-libexec/singularity/cli/image.create.exec
-libexec/singularity/cli/image.create.info
-libexec/singularity/cli/image.exec
-libexec/singularity/cli/image.expand.exec
-libexec/singularity/cli/image.expand.info
-libexec/singularity/cli/image.export.exec
-libexec/singularity/cli/image.export.info
-libexec/singularity/cli/image.import.exec
-libexec/singularity/cli/image.import.info
-libexec/singularity/cli/image.info
-libexec/singularity/cli/inspect.exec
-libexec/singularity/cli/inspect.info
-libexec/singularity/cli/instance.exec
-libexec/singularity/cli/instance.info
-libexec/singularity/cli/instance.list.exec
-libexec/singularity/cli/instance.list.info
-libexec/singularity/cli/instance.start.exec
-libexec/singularity/cli/instance.start.info
-libexec/singularity/cli/instance.stop.exec
-libexec/singularity/cli/instance.stop.info
-libexec/singularity/cli/mount.exec
-libexec/singularity/cli/mount.info
-libexec/singularity/cli/pull.exec
-libexec/singularity/cli/pull.info
-libexec/singularity/cli/run.exec
-libexec/singularity/cli/run.info
-libexec/singularity/cli/selftest.exec
-libexec/singularity/cli/selftest.info
-libexec/singularity/cli/shell.exec
-libexec/singularity/cli/shell.info
-libexec/singularity/cli/test.exec
-libexec/singularity/cli/test.info
-libexec/singularity/functions
-libexec/singularity/handlers/archive-cpio.sh
-libexec/singularity/handlers/archive-tar.sh
-libexec/singularity/handlers/image-docker.sh
-libexec/singularity/handlers/image-http.sh
-libexec/singularity/handlers/image-instance.sh
-libexec/singularity/handlers/image-shub.sh
-libexec/singularity/helpers/apps/list.sh
-libexec/singularity/helpers/check.sh
-libexec/singularity/helpers/checks/1-bash-hiddens.py
-libexec/singularity/helpers/checks/1-cache-content.py
-libexec/singularity/helpers/checks/1-docker.py
-libexec/singularity/helpers/checks/1-hello-world.sh
-libexec/singularity/helpers/checks/3-cve.py
-libexec/singularity/helpers/help.sh
-libexec/singularity/helpers/image.sh
-libexec/singularity/helpers/inspect.sh
-libexec/singularity/helpers/record-env.sh
-libexec/singularity/image-handler.sh
-libexec/singularity/python/__init__.py
-libexec/singularity/python/base.py
-libexec/singularity/python/defaults.py
-libexec/singularity/python/docker/__init__.py
-libexec/singularity/python/docker/api.py
-libexec/singularity/python/docker/main.py
-libexec/singularity/python/docker/tasks.py
-libexec/singularity/python/helpers/__init__.py
-libexec/singularity/python/helpers/json/__init__.py
-libexec/singularity/python/helpers/json/add.py
-libexec/singularity/python/helpers/json/delete.py
-libexec/singularity/python/helpers/json/dump.py
-libexec/singularity/python/helpers/json/get.py
-libexec/singularity/python/helpers/json/inspect.py
-libexec/singularity/python/helpers/json/main.py
-libexec/singularity/python/import.py
-libexec/singularity/python/message.py
-libexec/singularity/python/pull.py
-libexec/singularity/python/shell.py
-libexec/singularity/python/shub/__init__.py
-libexec/singularity/python/shub/api.py
-libexec/singularity/python/shub/main.py
-libexec/singularity/python/size.py
-libexec/singularity/python/sutils.py
-libexec/singularity/python/templates.py
-man/man1/singularity.1
-share/examples/singularity/default-nsswitch.conf
-share/examples/singularity/init
-share/examples/singularity/nvliblist.conf
-share/examples/singularity/singularity.conf
-@pkgdir var/singularity/mnt/session
-@pkgdir var/singularity/mnt/overlay
-@pkgdir var/singularity/mnt/final
-@pkgdir var/singularity/mnt/container
-@pkgdir etc/singularity
diff --git a/singularity/TODO b/singularity/TODO
deleted file mode 100644
index 578fc59dc7..0000000000
--- a/singularity/TODO
+++ /dev/null
@@ -1,4 +0,0 @@
-This package has known vulnerabilities, please investigate and fix if possible:
- CVE-2018-12021, CVE-2019-11328, CVE-2019-19724
- CVE-2020-13845, CVE-2020-13846, CVE-2020-13847
- CVE-2020-15229, CVE-2021-32635
diff --git a/singularity/distinfo b/singularity/distinfo
deleted file mode 100644
index 43ab7da282..0000000000
--- a/singularity/distinfo
+++ /dev/null
@@ -1,6 +0,0 @@
-$NetBSD$
-
-RMD160 (singularity-2.5.1.tar.gz) = eb957981be467e375b0d21c39b6c9f995d7c2e5f
-SHA512 (singularity-2.5.1.tar.gz) = cbe5ca50eaf349a73702c3e8ec2d9493fa3a2309b195a1be261843f70edbab36b97dae575c56da0fb1ab2b465abb8f2b004fc72e7e2a966c71cc7bf685e4e96e
-Size (singularity-2.5.1.tar.gz) = 236497 bytes
-SHA1 (patch-configure.ac) = e2b38e24670d0518aa851eab1606f60868b3ff6b
diff --git a/singularity/patches/patch-configure.ac b/singularity/patches/patch-configure.ac
deleted file mode 100644
index f3013a8f49..0000000000
--- a/singularity/patches/patch-configure.ac
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD$
-
-# Portability
-
---- configure.ac.orig 2018-09-25 14:38:34.635766268 +0000
-+++ configure.ac
-@@ -296,7 +296,7 @@ AC_MSG_CHECKING([--with-slurm])
- AC_ARG_WITH([slurm],
- AS_HELP_STRING([--with-slurm], [This feature will no longer be part of Singularity proper]),
- )
--AS_IF([test "x$with_slurm" == "xyes"],
-+AS_IF([test "x$with_slurm" = "xyes"],
- [
- AC_MSG_RESULT([yes])
- echo
diff --git a/tophat/DESCR b/tophat/DESCR
deleted file mode 100644
index 5ec85b9261..0000000000
--- a/tophat/DESCR
+++ /dev/null
@@ -1,4 +0,0 @@
-TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq
-reads to mammalian-sized genomes using the ultra high-throughput short read
-aligner Bowtie, and then analyzes the mapping results to identify splice
-junctions between exons.
diff --git a/tophat/PLIST b/tophat/PLIST
deleted file mode 100644
index 7f15ee3d67..0000000000
--- a/tophat/PLIST
+++ /dev/null
@@ -1,29 +0,0 @@
-@comment $NetBSD$
-bin/bam2fastx
-bin/bam_merge
-bin/bed_to_juncs
-bin/contig_to_chr_coords
-bin/fix_map_ordering
-bin/gtf_juncs
-bin/gtf_to_fasta
-bin/intervaltree/__init__.py
-bin/intervaltree/interval.py
-bin/intervaltree/intervaltree.py
-bin/intervaltree/node.py
-bin/juncs_db
-bin/long_spanning_reads
-bin/map2gtf
-bin/prep_reads
-bin/sam_juncs
-bin/samtools_0.1.18
-bin/segment_juncs
-bin/sortedcontainers/__init__.py
-bin/sortedcontainers/sorteddict.py
-bin/sortedcontainers/sortedlist.py
-bin/sortedcontainers/sortedlistwithkey.py
-bin/sortedcontainers/sortedset.py
-bin/sra_to_solid
-bin/tophat
-bin/tophat-fusion-post
-bin/tophat2
-bin/tophat_reports
diff --git a/tophat/TODO b/tophat/TODO
deleted file mode 100644
index b2e3b56f25..0000000000
--- a/tophat/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test.
diff --git a/tophat/distinfo b/tophat/distinfo
deleted file mode 100644
index ca6f85e607..0000000000
--- a/tophat/distinfo
+++ /dev/null
@@ -1,8 +0,0 @@
-$NetBSD$
-
-RMD160 (tophat-2.1.1.tar.gz) = 73c06278ad8bddacc3c83f1dd7f7da6e7dd148c2
-SHA512 (tophat-2.1.1.tar.gz) = e2e0943a6f3d34b83922e6e403b65a3bee480a2b2bb4bf2de0cae7e0ef5bb166b66fec923316c2b643e8550e43c842f0f1bcc2ca7249d20fbcf5a4733fbdeabc
-Size (tophat-2.1.1.tar.gz) = 2259554 bytes
-SHA1 (patch-src-bam_merge.cpp) = 3fd585b5e1d15a3c4d42dbc152852b44bb1c6dbf
-SHA1 (patch-src-samtools-0.1.18-Makefile) = 54dfa3947fb260b2936050b1b2229a785febb327
-SHA1 (patch-src_Makefile.in) = 50aac2d59688ec99c9c6b315b79f832bf2218bd2
diff --git a/tophat/patches/patch-src-bam_merge.cpp b/tophat/patches/patch-src-bam_merge.cpp
deleted file mode 100644
index aef0c40ae1..0000000000
--- a/tophat/patches/patch-src-bam_merge.cpp
+++ /dev/null
@@ -1,10 +0,0 @@
-$NetBSD$
-
-# Missing header
---- src/bam_merge.cpp.orig 2016-02-14 18:21:17.113079000 +0000
-+++ src/bam_merge.cpp
-@@ -1,3 +1,4 @@
-+#include <getopt.h>
- #include "bam_merge.h"
-
- #define USAGE "Usage: bam_merge [-Q] <out.bam> <in1.bam> <in2.bam> [...]\n"
diff --git a/tophat/patches/patch-src-samtools-0.1.18-Makefile b/tophat/patches/patch-src-samtools-0.1.18-Makefile
deleted file mode 100644
index ce2fb3906c..0000000000
--- a/tophat/patches/patch-src-samtools-0.1.18-Makefile
+++ /dev/null
@@ -1,28 +0,0 @@
-$NetBSD$
-
-# Respect build environment
---- src/samtools-0.1.18/Makefile.orig 2016-02-14 18:21:17.376079000 +0000
-+++ src/samtools-0.1.18/Makefile
-@@ -1,5 +1,10 @@
--CC= gcc
--CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
-+CC?= gcc
-+CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc
-+CC?= gcc
-+CFLAGS?= -g -Wall -O2
-+# Link fails with clang on inlined functions with no -O
-+CFLAGS+= -O
-+RANLIB?= ranlib
- DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0
- KNETFILE_O= knetfile.o
- LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
-@@ -38,7 +43,8 @@ all:$(PROG)
- lib:libbam.a
-
- libbam.a:$(LOBJS)
-- $(AR) -csru $@ $(LOBJS)
-+ $(AR) cr $@ $(LOBJS)
-+ $(RANLIB) $@
-
- samtools_0.1.18:lib-recur $(AOBJS)
- $(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf -lm -lz #$(LIBCURSES)
diff --git a/tophat/patches/patch-src_Makefile.in b/tophat/patches/patch-src_Makefile.in
deleted file mode 100644
index e3a1f0c858..0000000000
--- a/tophat/patches/patch-src_Makefile.in
+++ /dev/null
@@ -1,23 +0,0 @@
-$NetBSD$
-
-# Allow pkgsrc to control make program
---- src/Makefile.in.orig 2016-02-24 03:08:32.568707000 +0000
-+++ src/Makefile.in
-@@ -1658,7 +1658,7 @@ uninstall-am: uninstall-binPROGRAMS unin
-
-
- clean-local:
-- cd $(SAMDIR) && make clean
-+ cd $(SAMDIR) && ${MAKE} clean
-
- tophat2: tophat2.sh
- cp tophat2.sh tophat2 && chmod 755 tophat2
-@@ -1669,7 +1669,7 @@ tophat: tophat.py
- $(SAMPROG): $(SAMLIB)
-
- $(SAMLIB):
-- cd $(SAMDIR) && make $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) ..
-+ cd $(SAMDIR) && ${MAKE} $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) ..
-
- install-data-hook:
- cp -r intervaltree sortedcontainers $(DESTDIR)$(bindir)
Home |
Main Index |
Thread Index |
Old Index