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Remove several obsolete packages Release maintainership on a few others that might be useful
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Fri Aug 19 09:02:40 2022 -0500
Changeset: f9d25ee3c9a8917ae8f4863d16258456b6a9beeb
Modified Files:
Makefile
fftw-mpich/Makefile
fftw-openmpi/Makefile
suitesparse/Makefile
Removed Files:
fvcom2/DESCR
fvcom2/Makefile
fvcom2/PLIST
fvcom2/distinfo
fvcom2/files/fvcom-license
fvcom2/patches/patch-METIS__source_makefile
fvcom2/patches/patch-Makefile
ganglia-webfrontend/DESCR
ganglia-webfrontend/MESSAGE
ganglia-webfrontend/Makefile
ganglia-webfrontend/PLIST
ganglia-webfrontend/distinfo
ganglia-webfrontend/files/apache.conf
ganglia-webfrontend/files/conf.php
ganglia-webfrontend/files/nginx.conf
ganglia-webfrontend/options.mk
ganglia-webfrontend/patches/patch-Makefile
ganglia-webfrontend/patches/patch-conf__default.php.in
ganglia-webfrontend/patches/patch-eval__conf.php
libbacon/DESCR
libbacon/Makefile
libbacon/PLIST
libbacon/buildlink3.mk
libbacon/distinfo
pbbam/DESCR
pbbam/Makefile
pbbam/PLIST
pbbam/TODO
pbbam/buildlink3.mk
pbbam/distinfo
pbbam/patches/patch-src_MD5.cpp
pbcopper/DESCR
pbcopper/Makefile
pbcopper/PLIST
pbcopper/TODO
pbcopper/buildlink3.mk
pbcopper/distinfo
pbcopper/patches/patch-cmake_pbcopper-gitsha1.cmake
pbseqan/DESCR
pbseqan/Makefile
pbseqan/PLIST
pbseqan/TODO
pbseqan/buildlink3.mk
pbseqan/distinfo
unanimity/DESCR
unanimity/Makefile
unanimity/PLIST
unanimity/TODO
unanimity/distinfo
unanimity/patches/patch-cmake_uny-gitsha1.cmake
unanimity/patches/patch-src_align_AffineAlignment.cpp
unanimity/patches/patch-src_align_LinearAlignment.cpp
unanimity/patches/patch-src_align_PairwiseAlignment.cpp
Log Message:
Remove several obsolete packages
Release maintainership on a few others that might be useful
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=f9d25ee3c9a8917ae8f4863d16258456b6a9beeb
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 7 -
fftw-mpich/Makefile | 2 +-
fftw-openmpi/Makefile | 2 +-
fvcom2/DESCR | 2 -
fvcom2/Makefile | 55 --
fvcom2/PLIST | 2 -
fvcom2/distinfo | 6 -
fvcom2/files/fvcom-license | 12 -
fvcom2/patches/patch-METIS__source_makefile | 13 -
fvcom2/patches/patch-Makefile | 108 ----
ganglia-webfrontend/DESCR | 8 -
ganglia-webfrontend/MESSAGE | 17 -
ganglia-webfrontend/Makefile | 75 ---
ganglia-webfrontend/PLIST | 356 -----------
ganglia-webfrontend/distinfo | 8 -
ganglia-webfrontend/files/apache.conf | 23 -
ganglia-webfrontend/files/conf.php | 9 -
ganglia-webfrontend/files/nginx.conf | 15 -
ganglia-webfrontend/options.mk | 34 --
ganglia-webfrontend/patches/patch-Makefile | 28 -
.../patches/patch-conf__default.php.in | 35 --
ganglia-webfrontend/patches/patch-eval__conf.php | 17 -
libbacon/DESCR | 5 -
libbacon/Makefile | 18 -
libbacon/PLIST | 3 -
libbacon/buildlink3.mk | 13 -
libbacon/distinfo | 5 -
pbbam/DESCR | 1 -
pbbam/Makefile | 52 --
pbbam/PLIST | 111 ----
pbbam/TODO | 1 -
pbbam/buildlink3.mk | 24 -
pbbam/distinfo | 6 -
pbbam/patches/patch-src_MD5.cpp | 15 -
pbcopper/DESCR | 1 -
pbcopper/Makefile | 39 --
pbcopper/PLIST | 57 --
pbcopper/TODO | 3 -
pbcopper/buildlink3.mk | 22 -
pbcopper/distinfo | 6 -
.../patches/patch-cmake_pbcopper-gitsha1.cmake | 15 -
pbseqan/DESCR | 3 -
pbseqan/Makefile | 33 --
pbseqan/PLIST | 658 ---------------------
pbseqan/TODO | 1 -
pbseqan/buildlink3.mk | 14 -
pbseqan/distinfo | 5 -
suitesparse/Makefile | 2 +-
unanimity/DESCR | 1 -
unanimity/Makefile | 52 --
unanimity/PLIST | 2 -
unanimity/TODO | 1 -
unanimity/distinfo | 9 -
unanimity/patches/patch-cmake_uny-gitsha1.cmake | 15 -
.../patches/patch-src_align_AffineAlignment.cpp | 16 -
.../patches/patch-src_align_LinearAlignment.cpp | 16 -
.../patches/patch-src_align_PairwiseAlignment.cpp | 16 -
57 files changed, 3 insertions(+), 2072 deletions(-)
diffs:
diff --git a/Makefile b/Makefile
index 63bc8fec21..af34f4e472 100644
--- a/Makefile
+++ b/Makefile
@@ -953,7 +953,6 @@ SUBDIR+= fuse-squashfuse
SUBDIR+= fuse-zip
SUBDIR+= fusefs-btfs
SUBDIR+= fusionpbx
-SUBDIR+= fvcom2
SUBDIR+= fvwm-crystal
SUBDIR+= fxrays
SUBDIR+= fxt
@@ -1061,7 +1060,6 @@ SUBDIR+= gambas3-runtime
SUBDIR+= gambas3-scripter
SUBDIR+= gambatte-dev
SUBDIR+= gambit
-SUBDIR+= ganglia-webfrontend
SUBDIR+= gappa
SUBDIR+= garage
SUBDIR+= garden
@@ -2022,7 +2020,6 @@ SUBDIR+= libalkimia
SUBDIR+= libanimal
SUBDIR+= libaudec
SUBDIR+= libavc1394
-SUBDIR+= libbacon
SUBDIR+= libbfio
SUBDIR+= libbpg
SUBDIR+= libbrahe
@@ -3062,10 +3059,7 @@ SUBDIR+= passepartout
SUBDIR+= paxmirabilis
SUBDIR+= paxtest
SUBDIR+= payara41
-SUBDIR+= pbbam
SUBDIR+= pbbuttonsd
-SUBDIR+= pbcopper
-SUBDIR+= pbseqan
SUBDIR+= pbzx
SUBDIR+= pcem
SUBDIR+= pcp
@@ -5795,7 +5789,6 @@ SUBDIR+= ulfius
SUBDIR+= umix
SUBDIR+= umurmur
SUBDIR+= unagi
-SUBDIR+= unanimity
SUBDIR+= unarchiver-clt
SUBDIR+= undo-tree
SUBDIR+= unicorn5hc
diff --git a/fftw-mpich/Makefile b/fftw-mpich/Makefile
index 058a58cdd8..cde62347af 100644
--- a/fftw-mpich/Makefile
+++ b/fftw-mpich/Makefile
@@ -6,7 +6,7 @@ CATEGORIES= math
MASTER_SITES= ftp://ftp.fftw.org/pub/fftw/ \
http://www.fftw.org/
-MAINTAINER= bacon%NetBSD.org@localhost
+MAINTAINER= pkgsrc-users%NetBSD.org@localhost
HOMEPAGE= http://www.fftw.org/
COMMENT= Collection of fast C routines to compute DFTs
LICENSE= gnu-gpl-v2
diff --git a/fftw-openmpi/Makefile b/fftw-openmpi/Makefile
index 0e5def7756..553ca230b2 100644
--- a/fftw-openmpi/Makefile
+++ b/fftw-openmpi/Makefile
@@ -6,7 +6,7 @@ CATEGORIES= math
MASTER_SITES= ftp://ftp.fftw.org/pub/fftw/ \
http://www.fftw.org/
-MAINTAINER= bacon%NetBSD.org@localhost
+MAINTAINER= pkgsrc-users%NetBSD.org@localhost
HOMEPAGE= http://www.fftw.org/
COMMENT= Collection of fast C routines to compute DFTs
LICENSE= gnu-gpl-v2
diff --git a/fvcom2/DESCR b/fvcom2/DESCR
deleted file mode 100644
index c0cd1907b7..0000000000
--- a/fvcom2/DESCR
+++ /dev/null
@@ -1,2 +0,0 @@
-FVCOM is a prognostic, unstructured-grid, finite-volume, free-surface,
-3-D primitive equation coastal ocean circulation model.
diff --git a/fvcom2/Makefile b/fvcom2/Makefile
deleted file mode 100644
index 63bba86044..0000000000
--- a/fvcom2/Makefile
+++ /dev/null
@@ -1,55 +0,0 @@
-# $NetBSD: Makefile,v 1.7 2013/01/27 22:12:38 outpaddling Exp $
-#
-
-DISTNAME= sourcecode1
-PKGNAME= fvcom-2.7.1
-CATEGORIES= science
-MASTER_SITES= http://fvcom.smast.umassd.edu/FVCOM/password_required/t2/
-
-MAINTAINER= bacon%NetBSD.org@localhost
-HOMEPAGE= http://fvcom.smast.umassd.edu/FVCOM/password_required/t2/
-COMMENT= Prognostic coastal ocean circulation model
-#LICENSE= fvcom-license
-
-WRKSRC= ${WRKDIR}/FVCOM2.7.1/FVCOM_source
-
-USE_TOOLS+= make
-# Code is actually Fortran77, even though the build system generates .f90 files
-USE_LANGUAGES= c fortran77
-
-# Use bundled metis
-# DEPENDS+= metis>=4.0:../../math/metis
-
-AUTO_MKDIRS= yes
-
-FETCH_MESSAGE= "Please download the files"
-FETCH_MESSAGE+= " "${DISTFILES:Q}
-FETCH_MESSAGE+= "manually from "${MASTER_SITES:Q}"."
-
-SUBST_CLASSES+= log2
-SUBST_FILES.log2= METIS_source/coarsen.c \
- METIS_source/kmetis.c \
- METIS_source/kvmetis.c \
- METIS_source/metis_source.c \
- METIS_source/mkmetis.c \
- METIS_source/proto.h \
- METIS_source/rename.h \
- METIS_source/util.c
-SUBST_STAGE.log2= post-patch
-SUBST_MESSAGE.log2= Fixing log2 conflict
-SUBST_SED.log2= -e 's|log2|metis_log2|g'
-
-pre-patch:
- ${MV} ${WRKSRC}/makefile ${WRKSRC}/Makefile
- ${MV} ${WRKDIR}/FVCOM2.7.1/METIS_source ${WRKSRC}
-
-pre-build:
- (cd ${WRKSRC}/METIS_source && make)
-
-do-install:
- ${INSTALL_PROGRAM} ${WRKSRC}/fvcom ${DESTDIR}${PREFIX}/bin
-
-# Current netcdf package missing mod file
-# No netcdf support until this is resolved
-#.include "../../devel/netcdf/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/fvcom2/PLIST b/fvcom2/PLIST
deleted file mode 100644
index b49df1ca4d..0000000000
--- a/fvcom2/PLIST
+++ /dev/null
@@ -1,2 +0,0 @@
-@comment $NetBSD: PLIST,v 1.1.1.1 2012/03/22 20:25:21 outpaddling Exp $
-bin/fvcom
diff --git a/fvcom2/distinfo b/fvcom2/distinfo
deleted file mode 100644
index 11f6711d1c..0000000000
--- a/fvcom2/distinfo
+++ /dev/null
@@ -1,6 +0,0 @@
-$NetBSD: distinfo,v 1.4 2012/04/02 23:11:20 outpaddling Exp $
-
-RMD160 (sourcecode1.tar.gz) = cbb865ebd3d594a5b450b49ef3f5e4a9ce7087b4
-Size (sourcecode1.tar.gz) = 6162463 bytes
-SHA1 (patch-METIS__source_makefile) = e89ffbd93143a3a8216275b15c055f2150c492ca
-SHA1 (patch-Makefile) = 6dfc6bcc483bbccfdbdd19ac82d605dfa3e39732
diff --git a/fvcom2/files/fvcom-license b/fvcom2/files/fvcom-license
deleted file mode 100644
index 5bea36a6f9..0000000000
--- a/fvcom2/files/fvcom-license
+++ /dev/null
@@ -1,12 +0,0 @@
- FVCOM Software Users’ License Agreement
-
-All users should read this agreement carefully. A user, who receives any version of the source code of FVCOM, must accept all the terms and conditions of this agreement and also agree that this agreement is like any written negotiated agreement signed by you. You may be required to have another written agreement directly with Dr. Changsheng Chen at SMAST/UMASS-D and Dr. Robert C. Beardsley at WHOI
-The Finite-Volume Coastal Ocean Model (“FVCOM”) source code has been developed in the Marine Ecosystem Dynamics Modeling Laboratory led by Dr. C. Chen at the University of Massachusetts – Dartmouth (UMASS-D) in collaboration with Dr. R. Beardsley at the Woods Hole Oceanographic Institution. All copyrights to the FVCOM code are reserved. Unauthorized reproduction and redistribution of this code are expressly prohibited except as allowed in this License.
-
-A. Permitted Use and Restrictions on Redistribution
-
-The user agrees that he/she will use the FVCOM source code, and any modifications to the FVCOM source code that the user may create, solely for internal, non-commercial purposes and shall not distribute or transfer the FVCOM source code or modifications to it to any person or third parties not participating in their primary research project without prior written permission from Dr. Chen. The term "non-commercial," as used in this End User License Agreement, means academic or other scholarly research which (a) is not undertaken for profit, or (b) is not intended to produce work, services, or data for commercial use.
-
-B. Mandatory Participation in the FVCOM Community
-
-The user agrees to openly participate in the FVCOM community through three primary mechanisms. These are (a) reporting code bugs and problems, (b) sharing major modifications made to the code, and (c) contributing to an open and ongoing discussion of model deficiencies, needed improvements and additions, and major successes. (Contact Drs. C. Chen, G. Cowles, or R. Beardsley). These mechanisms are intended to benefit the entire FVCOM user community through quick notification of code problems, possible solutions, major code improvements, and, in general, the further development of the FVCOM source code and the associated software tools needed to process, visualize and interpret FVCOM model output.
diff --git a/fvcom2/patches/patch-METIS__source_makefile b/fvcom2/patches/patch-METIS__source_makefile
deleted file mode 100644
index 5ecc64a512..0000000000
--- a/fvcom2/patches/patch-METIS__source_makefile
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-METIS__source_makefile,v 1.1 2012/04/02 20:38:52 outpaddling Exp $
-
---- METIS_source/makefile.orig 2005-01-25 17:27:40.000000000 +0000
-+++ METIS_source/makefile
-@@ -2,7 +2,7 @@ INCLUDES = -I.
- AR = ar rv
- RANLIB = ranlib
- # add path to c compiler
--CC = icc
-+CC = gcc
- # add c compiler optimization flags
- OPTFLAGS = -O2
- CFLAGS = $(COPTIONS) $(OPTFLAGS) $(INCLUDES)
diff --git a/fvcom2/patches/patch-Makefile b/fvcom2/patches/patch-Makefile
deleted file mode 100644
index f2a0712a47..0000000000
--- a/fvcom2/patches/patch-Makefile
+++ /dev/null
@@ -1,108 +0,0 @@
-$NetBSD: patch-Makefile,v 1.3 2012/04/02 23:11:21 outpaddling Exp $
-
---- Makefile.orig 2009-09-22 19:45:57.000000000 +0000
-+++ Makefile
-@@ -17,7 +17,7 @@
- # UNCOMMENT TO SELECT DOUBLE PRECISION
- #--------------------------------------------------------------------------
-
--# FLAG_1 = -DDOUBLE_PRECISION
-+ FLAG_1 = -DDOUBLE_PRECISION
-
- #--------------------------------------------------------------------------
- # SPHERICAL SELECT SPHERICAL COORDINATES FOR INTEGRATION
-@@ -35,7 +35,7 @@
- # UNCOMMENT TO INCLUDE FLOODYING/DRYING
- #--------------------------------------------------------------------------
-
--# FLAG_3 = -DWET_DRY
-+ FLAG_3 = -DWET_DRY
-
- #--------------------------------------------------------------------------
- # MULTI_PROCESSOR INCLUDES PARALLELIZATION WITH MPI
-@@ -45,14 +45,17 @@
- # UNCOMMENT TO INCLUDE MPI PARALLEL CAPABILITY
- #--------------------------------------------------------------------------
-
-- FLAG_4 = -DMULTIPROCESSOR
-+# FLAG_4 = -DMULTIPROCESSOR
-
- # For em64t computers at SMAST (guppy)
- # PARLIB = -L/hosts/salmon01/data00/medm/em64t/lib64 -lmetis
-
- # For i386 computers at SMAST (salmon and minke)
- # PARLIB = -L/hosts/salmon01/data00/medm/lib -lmetis
-- PARLIB = -L../METIS_source -lmetis
-+
-+# Why does this fail on NetBSD?
-+# PARLIB = -L${LOCALBASE}/lib -lmetis
-+ PARLIB = METIS_source/libmetis.a
-
- # For Typhoeus and Hydra
- # PARLIB = -L/usr/local/lib -lmetis
-@@ -67,7 +70,7 @@
- # UNCOMMENT TO INCLUDE WATER QUALITY MODEL
- #--------------------------------------------------------------------------
-
--# FLAG_5 = -DWATER_QUALITY
-+ FLAG_5 = -DWATER_QUALITY
-
- #--------------------------------------------------------------------------
- # NETCDF OUTPUT DUMP OUTPUT INTO NETCDF FILES (yes/no)
-@@ -78,9 +81,9 @@
- # DEFAULT: NO NETCDF OUTPUT
- # UNCOMMENT TO INCLUDE NETCDF OUTPUT CAPABILITY
- #--------------------------------------------------------------------------
-- FLAG_6 = -DNETCDF_IO
-- IOLIBS = -L/hosts/mao/usr/medm/install/netcdf/3.6.3/em64t/lib -lnetcdf
-- IOINCS = -I/hosts/mao/usr/medm/install/netcdf/3.6.3/em64t/include
-+# FLAG_6 = -DNETCDF_IO
-+# IOLIBS = -L${LOCALBASE}/lib -lnetcdf
-+# IOINCS = -I${LOCALBASE}/include
-
- # For em64t computers at SMAST (guppy)
- # IOLIBS = -L/hosts/salmon01/data00/medm/em64t/lib64 -lnetcdf
-@@ -381,10 +384,10 @@
- #--------------------------------------------------------------------------
- # Intel/MPI Compiler Definitions (SMAST)
- #--------------------------------------------------------------------------
-- CPP = /usr/bin/cpp
-- CPPFLAGS = $(DEF_FLAGS) -DINTEL
-- FC = mpif90
-- DEBFLGS = #-check all
-+# CPP = /usr/bin/cpp
-+# CPPFLAGS = $(DEF_FLAGS) -DINTEL
-+# FC = mpif90
-+# DEBFLGS = #-check all
- # Use 'OPT = -O0 -g' for fast compile to test the make
- # Use 'OPT = -xP' for fast run on em64t (Hydra, Typhoeus and Guppy)
- # Use 'OPT = -xN' for fast run on em64t (Salmon and Minke)
-@@ -397,13 +400,13 @@
- # LDFLAGS = $(VISITLIBPATH)
- #--------------------------------------------------------------------------
- # gfortran defs
-+# Take CC, FC, etc. from environment. Set by the pkgsrc framework
- #--------------------------------------------------------------------------
--# CPP = /usr/bin/cpp
--# CPPFLAGS = $(DEF_FLAGS) -DGFORTRAN
--# FC = gfortran -O3
--# DEBFLGS =
--# OPT =
--# CLIB =
-+ CPP = cpp
-+ CPPFLAGS = $(DEF_FLAGS) -DGFORTRAN
-+ DEBFLGS =
-+ OPT = -O
-+ CLIB =
- #--------------------------------------------------------------------------
- # absoft / mac os x defs
- #--------------------------------------------------------------------------
-@@ -539,6 +542,8 @@ BIOGEN = mod_bio_3D.F mod_onedtide.F
- # Linking Directives
- #--------------------------------------------------------------------------
-
-+all: $(EXEC)
-+
- $(EXEC): $(OBJS)
- $(FC) $(FFLAGS) $(VISOPT) $(LDFLAGS) $(OBJS) $(LIBS) -o $(EXEC)
-
diff --git a/ganglia-webfrontend/DESCR b/ganglia-webfrontend/DESCR
deleted file mode 100644
index f861bf9f56..0000000000
--- a/ganglia-webfrontend/DESCR
+++ /dev/null
@@ -1,8 +0,0 @@
-Ganglia provides a complete real-time monitoring and execution
-environment that is in use by hundreds of universities, private and
-government laboratories and commercial cluster implementors around the
-world. Whether you want to monitor hundreds of computers in real-time
-across a university campus or around the world, ganglia is for you.
-
-The ganglia web frontend provides access to the data collected by the
-monitoring core (parallel/ganglia-monitor-core) via the web.
diff --git a/ganglia-webfrontend/MESSAGE b/ganglia-webfrontend/MESSAGE
deleted file mode 100644
index 35c690f6ef..0000000000
--- a/ganglia-webfrontend/MESSAGE
+++ /dev/null
@@ -1,17 +0,0 @@
-===========================================================================
-$NetBSD: MESSAGE,v 1.4 2016/02/16 13:14:07 fhajny Exp $
-
-The Ganglia Web Frontend has been installed in the directory
-${PREFIX}/${DOCROOT}
-
-You must add appropriate configuration directives to your
-web server configuration file. You can use this example
-include line, for Apache:
-
- Include ${PKG_SYSCONFDIR}/apache.conf
-
-or for Nginx:
-
- include ${PKG_SYSCONFDIR}/nginx.conf;
-
-===========================================================================
diff --git a/ganglia-webfrontend/Makefile b/ganglia-webfrontend/Makefile
deleted file mode 100644
index f142c8005f..0000000000
--- a/ganglia-webfrontend/Makefile
+++ /dev/null
@@ -1,75 +0,0 @@
-# $NetBSD: Makefile,v 1.19 2017/03/12 07:20:52 maya Exp $
-#
-# Ganglia is prone to regressions. Test thoroughly before upgrading!
-
-DISTNAME= 3.7.4
-PKGNAME= ganglia-web-3.7.4
-#PKGNAME= ${DISTNAME:S/web/webfrontend/}
-CATEGORIES= www parallel
-MASTER_SITES= ${MASTER_SITE_GITHUB:=ganglia/}
-
-MAINTAINER= bacon%NetBSD.org@localhost
-HOMEPAGE= https://github.com/ganglia/ganglia-web
-COMMENT= PHP based frontend for the Ganglia Cluster Monitor
-LICENSE= modified-bsd
-
-DEPENDS+= ganglia-monitor-core>=3.7.2:../../wip/ganglia-monitor-core
-
-USE_TOOLS+= pax
-
-.include "../../mk/bsd.prefs.mk"
-.include "options.mk"
-
-MESSAGE_SUBST+= DOCROOT=${DOCROOT}
-
-PKG_SYSCONFSUBDIR= ganglia
-DOCROOT= share/ganglia
-EGDIR= share/examples/ganglia
-
-# Should match parallel/ganglia-monitor-core
-GANGLIA_VARBASE?= ${VARBASE}/db
-GWEB_DIR?= ${GANGLIA_VARBASE}/ganglia
-
-OWN_DIRS_PERMS+= ${GWEB_DIR}/dwoo ${WWW_USER} ${WWW_GROUP} 0755
-OWN_DIRS_PERMS+= ${GWEB_DIR}/dwoo/cache ${WWW_USER} ${WWW_GROUP} 0755
-OWN_DIRS_PERMS+= ${GWEB_DIR}/dwoo/compiled ${WWW_USER} ${WWW_GROUP} 0755
-PKG_SYSCONFDIR_PERMS= ${WWW_USER} ${WWW_GROUP} 0755
-MAKE_DIRS_PERMS+= ${PKG_SYSCONFDIR}/filters ${WWW_USER} ${WWW_GROUP} 0755
-
-CONF_FILES+= ${EGDIR}/conf.php ${PKG_SYSCONFDIR}/conf.php
-CONF_FILES+= ${EGDIR}/apache.conf ${PKG_SYSCONFDIR}/apache.conf
-CONF_FILES+= ${EGDIR}/nginx.conf ${PKG_SYSCONFDIR}/nginx.conf
-CONF_FILES_PERMS+= ${EGDIR}/default.json ${PKG_SYSCONFDIR}/default.json ${WWW_USER} ${WWW_GROUP} 0644
-CONF_FILES_PERMS+= ${EGDIR}/event_color.json ${PKG_SYSCONFDIR}/event_color.json ${WWW_USER} ${WWW_GROUP} 0644
-CONF_FILES_PERMS+= ${EGDIR}/events.json ${PKG_SYSCONFDIR}/events.json ${WWW_USER} ${WWW_GROUP} 0644
-CONF_FILES_PERMS+= ${EGDIR}/view_default.json ${PKG_SYSCONFDIR}/view_default.json ${WWW_USER} ${WWW_GROUP} 0644
-
-SUBST_CLASSES+= prefix
-SUBST_STAGE.prefix= pre-configure
-SUBST_MESSAGE.prefix= Fixing PREFIX
-SUBST_FILES.prefix= conf_default.php.in eval_conf.php conf/conf.php conf/apache.conf conf/nginx.conf
-SUBST_VARS.prefix= PREFIX PKG_SYSCONFDIR PKG_SYSCONFBASE VARBASE DOCROOT EGDIR
-
-REPLACE_SH+= nagios/*.sh
-
-MAKE_FLAGS+= GCONFDIR=${PKG_SYSCONFDIR}
-MAKE_FLAGS+= GDESTDIR=${PREFIX}/${DOCROOT}
-MAKE_FLAGS+= GMETAD_ROOTDIR=${GANGLIA_VARBASE}/ganglia
-MAKE_FLAGS+= GWEB_STATEDIR=${GWEB_DIR}
-
-WRKSRC= ${WRKDIR}/${PKGNAME}
-INSTALLATION_DIRS+= ${DOCROOT} ${EGDIR}
-
-post-extract:
- ${INSTALL_DATA} ${FILESDIR}/conf.php ${WRKSRC}/conf
- ${INSTALL_DATA} ${FILESDIR}/apache.conf ${WRKSRC}/conf
- ${INSTALL_DATA} ${FILESDIR}/nginx.conf ${WRKSRC}/conf
-
-do-install:
- cd ${WRKSRC} && ${PAX} -rw -pp *.php *.html *.css api css \
- docs dwoo graph.d img js lib nagios templates test \
- ${DESTDIR}${PREFIX}/${DOCROOT}
- cd ${WRKSRC}/conf && ${PAX} -rw -pp * ${DESTDIR}${PREFIX}/${EGDIR}
-
-.include "../../lang/php/phpversion.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/ganglia-webfrontend/PLIST b/ganglia-webfrontend/PLIST
deleted file mode 100644
index fd1600ab44..0000000000
--- a/ganglia-webfrontend/PLIST
+++ /dev/null
@@ -1,356 +0,0 @@
-@comment $NetBSD$
-share/examples/ganglia/apache.conf
-share/examples/ganglia/conf.php
-share/examples/ganglia/default.json
-share/examples/ganglia/event_color.json
-share/examples/ganglia/events.json
-share/examples/ganglia/nginx.conf
-share/examples/ganglia/sql/ganglia.mysql
-share/examples/ganglia/sql/ganglia.sqlite
-share/examples/ganglia/view_default.json
-share/ganglia/actions.php
-share/ganglia/aggregate_graphs.php
-share/ganglia/api/.htaccess
-share/ganglia/api/events.php
-share/ganglia/api/host.php
-share/ganglia/api/metrics.php
-share/ganglia/api/metrics_autocomplete.php
-share/ganglia/api/rundeck.php
-share/ganglia/api/search.php
-share/ganglia/api/views.php
-share/ganglia/autorotation.php
-share/ganglia/breakdown_report_results.php
-share/ganglia/breakdown_reports.php
-share/ganglia/calendar.php
-share/ganglia/cluster_legend.html
-share/ganglia/cluster_view.php
-share/ganglia/compare_hosts.php
-share/ganglia/conf_default.php
-share/ganglia/css/chosen-sprite.png
-share/ganglia/css/chosen-sprite%2x.png@localhost
-share/ganglia/css/chosen.css
-share/ganglia/css/chosen.min.css
-share/ganglia/css/cubism.css
-share/ganglia/css/fullcalendar.css
-share/ganglia/css/images/ajax-loader.png
-share/ganglia/css/images/form-check-off.png
-share/ganglia/css/images/form-check-on.png
-share/ganglia/css/images/form-radio-off.png
-share/ganglia/css/images/form-radio-on.png
-share/ganglia/css/images/icon-search-black.png
-share/ganglia/css/images/icons-18-black.png
-share/ganglia/css/images/icons-18-white.png
-share/ganglia/css/images/icons-36-black.png
-share/ganglia/css/images/icons-36-white.png
-share/ganglia/css/jquery.flot.events.css
-share/ganglia/css/jquery.liveSearch.css
-share/ganglia/css/jquery.mobile-1.4.5.min.css
-share/ganglia/css/jquery.multiselect.css
-share/ganglia/css/qtip.min.css
-share/ganglia/css/smoothness/images/animated-overlay.gif
-share/ganglia/css/smoothness/images/ui-bg_flat_0_aaaaaa_40x100.png
-share/ganglia/css/smoothness/images/ui-bg_flat_75_ffffff_40x100.png
-share/ganglia/css/smoothness/images/ui-bg_glass_55_fbf9ee_1x400.png
-share/ganglia/css/smoothness/images/ui-bg_glass_65_ffffff_1x400.png
-share/ganglia/css/smoothness/images/ui-bg_glass_75_dadada_1x400.png
-share/ganglia/css/smoothness/images/ui-bg_glass_75_e6e6e6_1x400.png
-share/ganglia/css/smoothness/images/ui-bg_glass_95_fef1ec_1x400.png
-share/ganglia/css/smoothness/images/ui-bg_highlight-soft_75_cccccc_1x100.png
-share/ganglia/css/smoothness/images/ui-icons_222222_256x240.png
-share/ganglia/css/smoothness/images/ui-icons_2e83ff_256x240.png
-share/ganglia/css/smoothness/images/ui-icons_454545_256x240.png
-share/ganglia/css/smoothness/images/ui-icons_888888_256x240.png
-share/ganglia/css/smoothness/images/ui-icons_cd0a0a_256x240.png
-share/ganglia/css/smoothness/jquery-ui-1.10.2.custom.css
-share/ganglia/css/smoothness/jquery-ui-1.10.2.custom.min.css
-share/ganglia/css/tasseo.css
-share/ganglia/cubism.php
-share/ganglia/cubism_form.php
-share/ganglia/decompose_graph.php
-share/ganglia/docs/ad-hoc-views.mdown
-share/ganglia/dwoo/Dwoo.compiled.php
-share/ganglia/dwoo/Dwoo.php
-share/ganglia/dwoo/Dwoo/Adapters/Agavi/DwooRenderer.php
-share/ganglia/dwoo/Dwoo/Adapters/Agavi/README
-share/ganglia/dwoo/Dwoo/Adapters/Agavi/dwoo_plugins/t.php
-share/ganglia/dwoo/Dwoo/Adapters/Agavi/dwoo_plugins/url.php
-share/ganglia/dwoo/Dwoo/Adapters/CakePHP/README
-share/ganglia/dwoo/Dwoo/Adapters/CakePHP/dwoo.php
-share/ganglia/dwoo/Dwoo/Adapters/CodeIgniter/README
-share/ganglia/dwoo/Dwoo/Adapters/CodeIgniter/config/dwootemplate.php
-share/ganglia/dwoo/Dwoo/Adapters/CodeIgniter/controllers/dwoowelcome.php
-share/ganglia/dwoo/Dwoo/Adapters/CodeIgniter/libraries/Dwootemplate.php
-share/ganglia/dwoo/Dwoo/Adapters/CodeIgniter/views/dwoowelcome.tpl
-share/ganglia/dwoo/Dwoo/Adapters/CodeIgniter/views/page.tpl
-share/ganglia/dwoo/Dwoo/Adapters/ZendFramework/Dwoo.php
-share/ganglia/dwoo/Dwoo/Adapters/ZendFramework/PluginProxy.php
-share/ganglia/dwoo/Dwoo/Adapters/ZendFramework/README
-share/ganglia/dwoo/Dwoo/Adapters/ZendFramework/View.php
-share/ganglia/dwoo/Dwoo/Block/Plugin.php
-share/ganglia/dwoo/Dwoo/Compilation/Exception.php
-share/ganglia/dwoo/Dwoo/Compiler.php
-share/ganglia/dwoo/Dwoo/Core.php
-share/ganglia/dwoo/Dwoo/Data.php
-share/ganglia/dwoo/Dwoo/Exception.php
-share/ganglia/dwoo/Dwoo/Filter.php
-share/ganglia/dwoo/Dwoo/ICompilable.php
-share/ganglia/dwoo/Dwoo/ICompilable/Block.php
-share/ganglia/dwoo/Dwoo/ICompiler.php
-share/ganglia/dwoo/Dwoo/IDataProvider.php
-share/ganglia/dwoo/Dwoo/IElseable.php
-share/ganglia/dwoo/Dwoo/ILoader.php
-share/ganglia/dwoo/Dwoo/IPluginProxy.php
-share/ganglia/dwoo/Dwoo/ITemplate.php
-share/ganglia/dwoo/Dwoo/Loader.php
-share/ganglia/dwoo/Dwoo/Plugin.php
-share/ganglia/dwoo/Dwoo/Processor.php
-share/ganglia/dwoo/Dwoo/Security/Exception.php
-share/ganglia/dwoo/Dwoo/Security/Policy.php
-share/ganglia/dwoo/Dwoo/Smarty/Adapter.php
-share/ganglia/dwoo/Dwoo/Template/File.php
-share/ganglia/dwoo/Dwoo/Template/String.php
-share/ganglia/dwoo/LICENSE
-share/ganglia/dwoo/dwooAutoload.php
-share/ganglia/dwoo/plugins/builtin/blocks/a.php
-share/ganglia/dwoo/plugins/builtin/blocks/auto_escape.php
-share/ganglia/dwoo/plugins/builtin/blocks/block.php
-share/ganglia/dwoo/plugins/builtin/blocks/capture.php
-share/ganglia/dwoo/plugins/builtin/blocks/dynamic.php
-share/ganglia/dwoo/plugins/builtin/blocks/else.php
-share/ganglia/dwoo/plugins/builtin/blocks/elseif.php
-share/ganglia/dwoo/plugins/builtin/blocks/for.php
-share/ganglia/dwoo/plugins/builtin/blocks/foreach.php
-share/ganglia/dwoo/plugins/builtin/blocks/foreachelse.php
-share/ganglia/dwoo/plugins/builtin/blocks/forelse.php
-share/ganglia/dwoo/plugins/builtin/blocks/if.php
-share/ganglia/dwoo/plugins/builtin/blocks/loop.php
-share/ganglia/dwoo/plugins/builtin/blocks/section.php
-share/ganglia/dwoo/plugins/builtin/blocks/smartyinterface.php
-share/ganglia/dwoo/plugins/builtin/blocks/strip.php
-share/ganglia/dwoo/plugins/builtin/blocks/template.php
-share/ganglia/dwoo/plugins/builtin/blocks/textformat.php
-share/ganglia/dwoo/plugins/builtin/blocks/topLevelBlock.php
-share/ganglia/dwoo/plugins/builtin/blocks/with.php
-share/ganglia/dwoo/plugins/builtin/blocks/withelse.php
-share/ganglia/dwoo/plugins/builtin/filters/html_format.php
-share/ganglia/dwoo/plugins/builtin/functions/assign.php
-share/ganglia/dwoo/plugins/builtin/functions/capitalize.php
-share/ganglia/dwoo/plugins/builtin/functions/cat.php
-share/ganglia/dwoo/plugins/builtin/functions/count_characters.php
-share/ganglia/dwoo/plugins/builtin/functions/count_paragraphs.php
-share/ganglia/dwoo/plugins/builtin/functions/count_sentences.php
-share/ganglia/dwoo/plugins/builtin/functions/count_words.php
-share/ganglia/dwoo/plugins/builtin/functions/counter.php
-share/ganglia/dwoo/plugins/builtin/functions/cycle.php
-share/ganglia/dwoo/plugins/builtin/functions/date_format.php
-share/ganglia/dwoo/plugins/builtin/functions/default.php
-share/ganglia/dwoo/plugins/builtin/functions/dump.php
-share/ganglia/dwoo/plugins/builtin/functions/eol.php
-share/ganglia/dwoo/plugins/builtin/functions/escape.php
-share/ganglia/dwoo/plugins/builtin/functions/eval.php
-share/ganglia/dwoo/plugins/builtin/functions/extends.php
-share/ganglia/dwoo/plugins/builtin/functions/extendsCheck.php
-share/ganglia/dwoo/plugins/builtin/functions/fetch.php
-share/ganglia/dwoo/plugins/builtin/functions/include.php
-share/ganglia/dwoo/plugins/builtin/functions/indent.php
-share/ganglia/dwoo/plugins/builtin/functions/isset.php
-share/ganglia/dwoo/plugins/builtin/functions/load_templates.php
-share/ganglia/dwoo/plugins/builtin/functions/lower.php
-share/ganglia/dwoo/plugins/builtin/functions/mailto.php
-share/ganglia/dwoo/plugins/builtin/functions/math.php
-share/ganglia/dwoo/plugins/builtin/functions/nl2br.php
-share/ganglia/dwoo/plugins/builtin/functions/optional.php
-share/ganglia/dwoo/plugins/builtin/functions/regex_replace.php
-share/ganglia/dwoo/plugins/builtin/functions/replace.php
-share/ganglia/dwoo/plugins/builtin/functions/return.php
-share/ganglia/dwoo/plugins/builtin/functions/reverse.php
-share/ganglia/dwoo/plugins/builtin/functions/safe.php
-share/ganglia/dwoo/plugins/builtin/functions/spacify.php
-share/ganglia/dwoo/plugins/builtin/functions/string_format.php
-share/ganglia/dwoo/plugins/builtin/functions/strip_tags.php
-share/ganglia/dwoo/plugins/builtin/functions/tif.php
-share/ganglia/dwoo/plugins/builtin/functions/truncate.php
-share/ganglia/dwoo/plugins/builtin/functions/upper.php
-share/ganglia/dwoo/plugins/builtin/functions/whitespace.php
-share/ganglia/dwoo/plugins/builtin/functions/wordwrap.php
-share/ganglia/dwoo/plugins/builtin/helper.array.php
-share/ganglia/dwoo/plugins/builtin/processors/pre.smarty_compat.php
-share/ganglia/edit_optional_graphs.php
-share/ganglia/eval_conf.php
-share/ganglia/events.php
-share/ganglia/footer.php
-share/ganglia/functions.php
-share/ganglia/ganglia.php
-share/ganglia/get_context.php
-share/ganglia/get_ganglia.php
-share/ganglia/get_overlay_events.php
-share/ganglia/global.php
-share/ganglia/graph.d/apache_report.json
-share/ganglia/graph.d/apache_response_report.json
-share/ganglia/graph.d/cpu_report.json
-share/ganglia/graph.d/cpu_report.php
-share/ganglia/graph.d/disk_report.json
-share/ganglia/graph.d/disk_report.php
-share/ganglia/graph.d/io_report.json
-share/ganglia/graph.d/load_all_report.json
-share/ganglia/graph.d/load_report.json
-share/ganglia/graph.d/mem_report.json
-share/ganglia/graph.d/mem_report.php
-share/ganglia/graph.d/metric.php
-share/ganglia/graph.d/moab_cores_report.json
-share/ganglia/graph.d/moab_jobs_report.json
-share/ganglia/graph.d/moab_nodes_report.json
-share/ganglia/graph.d/network_report.json
-share/ganglia/graph.d/nfs_v3_client_report.json
-share/ganglia/graph.d/packet_report.json
-share/ganglia/graph.d/sample_report.php
-share/ganglia/graph.d/varnish_report.php
-share/ganglia/graph.php
-share/ganglia/graph_all_periods.php
-share/ganglia/grid_tree.php
-share/ganglia/header.php
-share/ganglia/host_overview.php
-share/ganglia/host_view.php
-share/ganglia/img/access-denied.jpg
-share/ganglia/img/calendar.gif
-share/ganglia/img/red-pointer.png
-share/ganglia/img/spin-night.gif
-share/ganglia/img/spin.gif
-share/ganglia/img/spinner.gif
-share/ganglia/img/toggle-night.png
-share/ganglia/img/toggle-number.png
-share/ganglia/index.php
-share/ganglia/inspect_graph.php
-share/ganglia/js/chosen.jquery.js
-share/ganglia/js/chosen.jquery.min.js
-share/ganglia/js/combobox.js
-share/ganglia/js/create-flot-graphs.js
-share/ganglia/js/excanvas.js
-share/ganglia/js/excanvas.min.js
-share/ganglia/js/flot_graph.js
-share/ganglia/js/fullcalendar.js
-share/ganglia/js/ganglia.js
-share/ganglia/js/jquery-ui-timepicker-addon.js
-share/ganglia/js/jquery-ui.min.js
-share/ganglia/js/jquery.ba-bbq.js
-share/ganglia/js/jquery.ba-bbq.min.js
-share/ganglia/js/jquery.cookie.js
-share/ganglia/js/jquery.flot.dashes.js
-share/ganglia/js/jquery.flot.events.js
-share/ganglia/js/jquery.flot.ganglia-time.js
-share/ganglia/js/jquery.flot.js
-share/ganglia/js/jquery.gangZoom.js
-share/ganglia/js/jquery.livesearch.js
-share/ganglia/js/jquery.livesearch.min.js
-share/ganglia/js/jquery.multiselect.filter.css
-share/ganglia/js/jquery.multiselect.filter.js
-share/ganglia/js/jquery.multiselect.js
-share/ganglia/js/jquery.qtip.min.js
-share/ganglia/js/jquery.scrollTo-1.4.2.js
-share/ganglia/js/jquery.scrollTo-1.4.3.1-min.js
-share/ganglia/js/tasseo.js
-share/ganglia/lib/Cache/Driver_Json.php
-share/ganglia/lib/Cache/Driver_Memcache.php
-share/ganglia/lib/Events/Driver_Json.php
-share/ganglia/lib/Events/Driver_Mdb2.php
-share/ganglia/lib/Events/Driver_Pdo.php
-share/ganglia/lib/GangliaAcl.php
-share/ganglia/lib/GangliaAuth.php
-share/ganglia/lib/Services/JSON.php
-share/ganglia/lib/Zend/Acl.php
-share/ganglia/lib/Zend/Acl/Assert/Interface.php
-share/ganglia/lib/Zend/Acl/Exception.php
-share/ganglia/lib/Zend/Acl/Resource.php
-share/ganglia/lib/Zend/Acl/Resource/Interface.php
-share/ganglia/lib/Zend/Acl/Role.php
-share/ganglia/lib/Zend/Acl/Role/Interface.php
-share/ganglia/lib/Zend/Acl/Role/Registry.php
-share/ganglia/lib/Zend/Acl/Role/Registry/Exception.php
-share/ganglia/lib/Zend/Exception.php
-share/ganglia/lib/cache.php
-share/ganglia/lib/common_api.php
-share/ganglia/lib/json.php
-share/ganglia/login.php
-share/ganglia/logout.php
-share/ganglia/meta_view.php
-share/ganglia/metric_group_view.php
-share/ganglia/mobile.php
-share/ganglia/mobile_helper.php
-share/ganglia/nagios/check_for_stuck_gmonds.php
-share/ganglia/nagios/check_for_stuck_gmonds.sh
-share/ganglia/nagios/check_ganglia_metric.sh
-share/ganglia/nagios/check_heartbeat.php
-share/ganglia/nagios/check_heartbeat.sh
-share/ganglia/nagios/check_host_regex.php
-share/ganglia/nagios/check_host_regex.sh
-share/ganglia/nagios/check_metric.php
-share/ganglia/nagios/check_metric_regex.php
-share/ganglia/nagios/check_metric_regex.sh
-share/ganglia/nagios/check_multiple_metrics.php
-share/ganglia/nagios/check_multiple_metrics.sh
-share/ganglia/nagios/check_multiple_metrics_warn.php
-share/ganglia/nagios/check_multiple_metrics_warn.sh
-share/ganglia/nagios/check_value_same_everywhere.php
-share/ganglia/nagios/check_value_same_everywhere.sh
-share/ganglia/nagios/warmup_ganglia_cache.php
-share/ganglia/nagios/warmup_metric_cache.php
-share/ganglia/nagios/warmup_metric_cache.sh
-share/ganglia/node_legend.html
-share/ganglia/physical_view.php
-share/ganglia/pie.php
-share/ganglia/search.php
-share/ganglia/show_node.php
-share/ganglia/stacked.php
-share/ganglia/styles.css
-share/ganglia/tasseo.php
-share/ganglia/tattle_autocomplete.php
-share/ganglia/templates/default/cluster_extra.tpl
-share/ganglia/templates/default/cluster_host_metric_graphs.tpl
-share/ganglia/templates/default/cluster_overview.tpl
-share/ganglia/templates/default/cluster_refresh.tpl
-share/ganglia/templates/default/cluster_view.tpl
-share/ganglia/templates/default/compare_hosts.tpl
-share/ganglia/templates/default/decompose_graph.tpl
-share/ganglia/templates/default/footer.tpl
-share/ganglia/templates/default/graph_all_periods.tpl
-share/ganglia/templates/default/grid_tree.tpl
-share/ganglia/templates/default/header-nobanner.tpl
-share/ganglia/templates/default/header.tpl
-share/ganglia/templates/default/host_extra.tpl
-share/ganglia/templates/default/host_overview.tpl
-share/ganglia/templates/default/host_view.tpl
-share/ganglia/templates/default/images/cluster_0-24.jpg
-share/ganglia/templates/default/images/cluster_25-49.jpg
-share/ganglia/templates/default/images/cluster_50-74.jpg
-share/ganglia/templates/default/images/cluster_75-100.jpg
-share/ganglia/templates/default/images/cluster_overloaded.jpg
-share/ganglia/templates/default/images/cluster_private.jpg
-share/ganglia/templates/default/images/grid_0-24.jpg
-share/ganglia/templates/default/images/grid_25-49.jpg
-share/ganglia/templates/default/images/grid_50-74.jpg
-share/ganglia/templates/default/images/grid_75-100.jpg
-share/ganglia/templates/default/images/grid_overloaded.jpg
-share/ganglia/templates/default/images/grid_private.jpg
-share/ganglia/templates/default/images/logo.jpg
-share/ganglia/templates/default/images/node_0-24.jpg
-share/ganglia/templates/default/images/node_25-49.jpg
-share/ganglia/templates/default/images/node_50-74.jpg
-share/ganglia/templates/default/images/node_75-100.jpg
-share/ganglia/templates/default/images/node_dead.jpg
-share/ganglia/templates/default/images/node_overloaded.jpg
-share/ganglia/templates/default/meta_view.tpl
-share/ganglia/templates/default/metric_group_view.tpl
-share/ganglia/templates/default/node_extra.tpl
-share/ganglia/templates/default/physical_view.tpl
-share/ganglia/templates/default/scripts.tpl
-share/ganglia/templates/default/show_node.tpl
-share/ganglia/templates/default/view_content.tpl
-share/ganglia/templates/default/views_view.tpl
-share/ganglia/test/GangliaAclTest.php
-share/ganglia/test/GangliaAuthTest.php
-share/ganglia/test/TestCase.php
-share/ganglia/test/phpcs-ganglia-web.xml
-share/ganglia/trend_navigation.php
-share/ganglia/version.php
-share/ganglia/view_content.php
-share/ganglia/views_view.php
diff --git a/ganglia-webfrontend/distinfo b/ganglia-webfrontend/distinfo
deleted file mode 100644
index 89b46a5c71..0000000000
--- a/ganglia-webfrontend/distinfo
+++ /dev/null
@@ -1,8 +0,0 @@
-$NetBSD$
-
-RMD160 (3.7.4.tar.gz) = 5f4371b3b255ef7751255badcc928d38a2ffb356
-SHA512 (3.7.4.tar.gz) = bcec0d7388c7055b79c356901302d934555a5a61ad41a3e97ba6bcb9f7afb89798c497abf4b7d57f76d93fe82ab2f4b7c4a02fa8c19126d151e44ab4e8016765
-Size (3.7.4.tar.gz) = 709630 bytes
-SHA1 (patch-Makefile) = 72fd912c847da6620006d7e8bf97c318ca480d68
-SHA1 (patch-conf__default.php.in) = 0d5d9417d20f74bd1b1e3ab4e83738779a19fda1
-SHA1 (patch-eval__conf.php) = ce40cbee4c9867f86a67009074d0d46308dcb561
diff --git a/ganglia-webfrontend/files/apache.conf b/ganglia-webfrontend/files/apache.conf
deleted file mode 100644
index 8ad9c5d44c..0000000000
--- a/ganglia-webfrontend/files/apache.conf
+++ /dev/null
@@ -1,23 +0,0 @@
-# $NetBSD: apache.conf,v 1.1 2016/02/16 13:05:23 fhajny Exp $
-#
-# Ganglia Web configuration file fragment for Apache
-# Add to your existing httpd.conf configuration file.
-
-Alias /ganglia/ "@PREFIX@/@DOCROOT@/"
-
-<Directory "@PREFIX@/@DOCROOT@/">
- Options Indexes FollowSymlinks MultiViews
- AllowOverride None
- <IfModule authn_core_module>
- # Apache 2.4
- Require all granted
- </IfModule>
- <IfModule !authn_core_module>
- # Apache 2.2
- Order allow,deny
- Allow from all
- </IfModule>
- <IfModule dir_module>
- DirectoryIndex index.php
- </IfModule>
-</Directory>
diff --git a/ganglia-webfrontend/files/conf.php b/ganglia-webfrontend/files/conf.php
deleted file mode 100644
index ae29bd72c2..0000000000
--- a/ganglia-webfrontend/files/conf.php
+++ /dev/null
@@ -1,9 +0,0 @@
-<?php
-
-/* $NetBSD: conf.php,v 1.1 2016/02/16 13:05:23 fhajny Exp $
-
- Use this file to override defaults in @PREFIX@/DOCROOT@/conf_default.php
-
-*/
-
-?>
diff --git a/ganglia-webfrontend/files/nginx.conf b/ganglia-webfrontend/files/nginx.conf
deleted file mode 100644
index be12fc2591..0000000000
--- a/ganglia-webfrontend/files/nginx.conf
+++ /dev/null
@@ -1,15 +0,0 @@
-# $NetBSD: nginx.conf,v 1.1 2016/02/16 13:05:23 fhajny Exp $
-#
-# Ganglia Web configuration file fragment for nginx
-# Add to your existing server{} definition.
-
- location /ganglia {
- alias @PREFIX@/@DOCROOT@;
- index index.php;
- location ~ \.php$ {
- include @PKG_SYSCONFBASE@/nginx/fastcgi_params;
- fastcgi_pass unix:@VARBASE@/run/php-fpm.sock;
- fastcgi_param SCRIPT_FILENAME $request_filename;
- fastcgi_index index.php;
- }
- }
diff --git a/ganglia-webfrontend/options.mk b/ganglia-webfrontend/options.mk
deleted file mode 100644
index 7a7dc7d0c2..0000000000
--- a/ganglia-webfrontend/options.mk
+++ /dev/null
@@ -1,34 +0,0 @@
-# $NetBSD: options.mk,v 1.1 2016/02/16 13:05:23 fhajny Exp $
-
-PKG_OPTIONS_VAR= PKG_OPTIONS.ganglia-webfrontend
-
-PKG_OPTIONS_REQUIRED_GROUPS= webserver
-PKG_OPTIONS_GROUP.webserver= apache nginx
-
-PKG_SUPPORTED_OPTIONS= #
-PKG_SUGGESTED_OPTIONS= apache
-
-.include "../../mk/bsd.options.mk"
-
-###
-### Use apache web server
-###
-.if !empty(PKG_OPTIONS:Mapache)
-DEPENDS+= ${APACHE_PKG_PREFIX}-${PHP_PKG_PREFIX}>=4.1:../../www/ap-php
-WWW_USER?= ${APACHE_USER}
-WWW_GROUP?= ${APACHE_GROUP}
-BUILD_DEFS+= APACHE_USER APACHE_GROUP
-.include "../../mk/apache.mk"
-.endif
-
-###
-### Use nginx web server
-###
-.if !empty(PKG_OPTIONS:Mnginx)
-DEPENDS+= nginx-[0-9]*:../../www/nginx
-NGINX_USER?= nginx
-NGINX_GROUP?= nginx
-WWW_USER?= ${NGINX_USER}
-WWW_GROUP?= ${NGINX_USER}
-BUILD_DEFS+= NGINX_USER NGINX_GROUP
-.endif
diff --git a/ganglia-webfrontend/patches/patch-Makefile b/ganglia-webfrontend/patches/patch-Makefile
deleted file mode 100644
index 57fa644572..0000000000
--- a/ganglia-webfrontend/patches/patch-Makefile
+++ /dev/null
@@ -1,28 +0,0 @@
-$NetBSD$
-
-# Assert proper paths
-
---- Makefile.orig 2018-03-13 20:37:09.000000000 +0000
-+++ Makefile
-@@ -66,7 +66,7 @@ clean:
- rm -rf $(TARGETS) $(DIST_DIR) $(DIST_TARBALL) rpmbuild
-
- conf_default.php: conf_default.php.in
-- sed -e "s|@vargmetadir@|$(GMETAD_ROOTDIR)|" -e "s|@vargwebstatedir@|$(GWEB_STATEDIR)|g" conf_default.php.in > conf_default.php
-+ sed -e "s|@etcdir@|$(GCONFDIR)|" -e "s|@vargmetadir@|$(GMETAD_ROOTDIR)|" -e "s|@vargwebstatedir@|$(GWEB_STATEDIR)|g" conf_default.php.in > conf_default.php
-
- ganglia-web.spec: ganglia-web.spec.in
- sed -e s/@GWEB_VERSION@/$(GWEB_VERSION)/ -e "s|@vargwebdir@|$(GWEB_STATEDIR)|" -e "s|@varapacheuser@|$(APACHE_USER)|g" -e "s|@etcdir@|$(GCONFDIR)|g" ganglia-web.spec.in > ganglia-web.spec
-@@ -84,10 +84,9 @@ install: dist-dir
- mkdir -p $(DESTDIR)/$(GWEB_STATEDIR)/dwoo/compiled && \
- mkdir -p $(DESTDIR)/$(GWEB_STATEDIR)/dwoo/cache && \
- mkdir -p $(DESTDIR)/$(GWEB_STATEDIR) && \
-- rsync -a $(DIST_DIR)/conf $(DESTDIR)/$(GWEB_STATEDIR) && \
-+ rsync -a $(DIST_DIR)/conf $(DESTDIR)/$(GCONFDIR) && \
- mkdir -p $(DESTDIR)/$(GDESTDIR) && \
-- rsync --exclude "conf" -a $(DIST_DIR)/* $(DESTDIR)/$(GDESTDIR) && \
-- chown -R $(APACHE_USER):$(APACHE_GROUP) $(DESTDIR)/$(GWEB_STATEDIR)
-+ rsync --exclude "conf" -a $(DIST_DIR)/* $(DESTDIR)/$(GDESTDIR)
-
- dist-gzip: dist-dir
- if [ -f $(DIST_TARBALL) ]; then \
diff --git a/ganglia-webfrontend/patches/patch-conf__default.php.in b/ganglia-webfrontend/patches/patch-conf__default.php.in
deleted file mode 100644
index 8599f84817..0000000000
--- a/ganglia-webfrontend/patches/patch-conf__default.php.in
+++ /dev/null
@@ -1,35 +0,0 @@
-$NetBSD: patch-conf__default.php.in,v 1.1 2016/02/16 13:05:23 fhajny Exp $
-
-Assert proper paths.
-
---- conf_default.php.in.orig 2015-10-01 15:47:41.000000000 +0000
-+++ conf_default.php.in
-@@ -11,6 +11,7 @@
- #
- $conf['gweb_root'] = dirname(__FILE__);
- $conf['gweb_confdir'] = "@vargwebstatedir@";
-+$conf['gweb_sysconfdir'] = "@etcdir@";
-
- include_once $conf['gweb_root'] . "/version.php";
-
-@@ -42,16 +43,16 @@ $conf['dwoo_compiled_dir'] = "${conf['gw
- $conf['dwoo_cache_dir'] = "${conf['gweb_confdir']}/dwoo/cache";
-
- # Where to store web-based configuration
--$conf['views_dir'] = $conf['gweb_confdir'] . '/conf';
--$conf['conf_dir'] = $conf['gweb_confdir'] . '/conf';
-+$conf['views_dir'] = $conf['gweb_sysconfdir'];
-+$conf['conf_dir'] = $conf['gweb_sysconfdir'];
-
- # Where to find filter configuration files, if not set filtering
- # will be disabled
--#$conf['filter_dir'] = "${conf['gweb_confdir']}/filters";
-+#$conf['filter_dir'] = "${conf['gweb_sysconfdir']}/filters";
-
- # Leave this alone if rrdtool is installed in $conf['gmetad_root'],
- # otherwise, change it if it is installed elsewhere (like /usr/bin)
--$conf['rrdtool'] = "/usr/bin/rrdtool";
-+$conf['rrdtool'] = "@PREFIX@/bin/rrdtool";
-
- # Render graphs with rrdtool's --slope-mode option
- $conf['rrdtool_slope_mode'] = true;
diff --git a/ganglia-webfrontend/patches/patch-eval__conf.php b/ganglia-webfrontend/patches/patch-eval__conf.php
deleted file mode 100644
index 33527082d0..0000000000
--- a/ganglia-webfrontend/patches/patch-eval__conf.php
+++ /dev/null
@@ -1,17 +0,0 @@
-$NetBSD: patch-eval__conf.php,v 1.1 2016/02/16 13:05:23 fhajny Exp $
-
-Assert proper paths.
-
---- eval_conf.php.orig 2015-04-12 00:04:33.000000000 +0000
-+++ eval_conf.php
-@@ -13,8 +13,8 @@ require_once 'lib/GangliaAcl.php';
- require_once 'lib/GangliaAuth.php';
-
- # Include user-defined overrides if they exist.
--if( file_exists( $base_dir . "/conf.php" ) ) {
-- include_once $base_dir . "/conf.php";
-+if( file_exists( "@PKG_SYSCONFDIR@/conf.php" ) ) {
-+ include_once "@PKG_SYSCONFDIR@/conf.php";
- }
-
- $errors = array();
diff --git a/libbacon/DESCR b/libbacon/DESCR
deleted file mode 100644
index f9ff4ac390..0000000000
--- a/libbacon/DESCR
+++ /dev/null
@@ -1,5 +0,0 @@
-Libbacon is a collection of miscellaneous C functions that I felt were
-generally useful enough that they should be made available in a library.
-My hope is that many of them will someday be added to the existing C
-libraries, such as libc, libm, etc. ( A few, such as strlcpy(), and
-strlcat() already have on some systems. )
diff --git a/libbacon/Makefile b/libbacon/Makefile
deleted file mode 100644
index 5450879d56..0000000000
--- a/libbacon/Makefile
+++ /dev/null
@@ -1,18 +0,0 @@
-# $NetBSD: Makefile,v 1.3 2013/12/16 14:06:40 outpaddling Exp $
-#
-
-DISTNAME= libbacon-1.2.2.1
-CATEGORIES= devel
-MASTER_SITES= ${MASTER_SITE_GITHUB:=outpaddling/}
-GITHUB_TAG= 2e181aa1d6f39d0b767453b7e5e6bc7b0f301dc3
-
-MAINTAINER= bacon%NetBSD.org@localhost
-HOMEPAGE= https://github.com/outpaddling/libbacon
-COMMENT= Miscellaneous experimental functions
-LICENSE= 2-clause-bsd
-
-PKG_DESTDIR_SUPPORT= user-destdir
-
-INSTALL_MAKE_FLAGS+= PREFIX=${DESTDIR}${PREFIX}
-
-.include "../../mk/bsd.pkg.mk"
diff --git a/libbacon/PLIST b/libbacon/PLIST
deleted file mode 100644
index f14d03c913..0000000000
--- a/libbacon/PLIST
+++ /dev/null
@@ -1,3 +0,0 @@
-@comment $NetBSD$
-include/bacon.h
-lib/libbacon.a
diff --git a/libbacon/buildlink3.mk b/libbacon/buildlink3.mk
deleted file mode 100644
index 691a6c1051..0000000000
--- a/libbacon/buildlink3.mk
+++ /dev/null
@@ -1,13 +0,0 @@
-# $NetBSD: buildlink3.mk,v 1.2 2013/08/14 01:33:35 outpaddling Exp $
-
-BUILDLINK_TREE+= libbacon
-
-.if !defined(LIBBACON_BUILDLINK3_MK)
-LIBBACON_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.libbacon+= libbacon>=1.2.2
-BUILDLINK_PKGSRCDIR.libbacon?= ../../wip/libbacon
-BUILDLINK_DEPMETHOD.libbacon?= build
-.endif # LIBBACON_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -libbacon
diff --git a/libbacon/distinfo b/libbacon/distinfo
deleted file mode 100644
index 8abb886c62..0000000000
--- a/libbacon/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD$
-
-RMD160 (libbacon-1.2.2.1-2e181aa1d6f39d0b767453b7e5e6bc7b0f301dc3.tar.gz) = c086f8a8ce7dba4dddabbc8813b49722b82b0856
-SHA512 (libbacon-1.2.2.1-2e181aa1d6f39d0b767453b7e5e6bc7b0f301dc3.tar.gz) = ed182db4d2557664045b018785ed44617ea65701cdbacea1f91a75e7f7636398466ce2f85b24058262e9746647ecc6ea2a4cd8b8f90ca6ad0623638df031103f
-Size (libbacon-1.2.2.1-2e181aa1d6f39d0b767453b7e5e6bc7b0f301dc3.tar.gz) = 51612 bytes
diff --git a/pbbam/DESCR b/pbbam/DESCR
deleted file mode 100644
index 53da43f078..0000000000
--- a/pbbam/DESCR
+++ /dev/null
@@ -1 +0,0 @@
-PacBio BAM C++ library, with SWIG bindings
diff --git a/pbbam/Makefile b/pbbam/Makefile
deleted file mode 100644
index 4b392278e1..0000000000
--- a/pbbam/Makefile
+++ /dev/null
@@ -1,52 +0,0 @@
-# $NetBSD$
-#
-###########################################################
-# Generated by fbsd2pkg #
-# Mon Sep 12 17:24:02 CDT 2016 #
-###########################################################
-
-DISTNAME= pbbam-${PORTVERSION}
-CATEGORIES= biology
-MASTER_SITES= ${MASTER_SITE_GITHUB:=PacificBiosciences/}
-GITHUB_PROJECT= pbbam
-GITHUB_TAG= e46654e0e0b816230c16f4a6132c1feff633a62a
-
-MAINTAINER= bacon%NetBSD.org@localhost
-HOMEPAGE= https://github.com/PacificBiosciences/pbbam
-COMMENT= PacBio BAM C++ library, with SWIG bindings
-LICENSE= modified-bsd
-
-MAKE_JOBS_SAFE= yes
-
-USE_LANGUAGES= c c++
-USE_TOOLS+= pax
-USE_CMAKE= yes
-# FIXME: Disable tests for now. Bound to bundled googletest.
-CMAKE_ARGS= -DHTSLIB_INCLUDE_DIRS:STRING=${PREFIX}/include/htslib \
- -DHTSLIB_LIBRARIES:STRING="-L${PREFIX}/lib" \
- -DPacBioBAM_build_tests:BOOL=OFF \
- -DPacBioBAM_build_docs:BOOL=OFF
-GCC_REQD= 4.9 # pbcopper requires 4.9 due to use of json
-
-CXXFLAGS+= -O2
-
-WRKSRC= ${WRKDIR}/pbbam-${GITHUB_TAG}
-
-PORTVERSION= 2016.09.13
-
-INSTALLATION_DIRS= bin lib ${PKGMANDIR}/man1 share/doc share/examples
-
-MAKE_FLAGS+= VERBOSE=1
-# FIXME: Shouldn't buildlink provide this?
-LDFLAGS+= -L${PREFIX}/lib -lhts -lssl
-
-do-install:
- ${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${DESTDIR}${PREFIX}/bin
- ${INSTALL_DATA} ${WRKSRC}/lib/* ${DESTDIR}${PREFIX}/lib
- cd ${WRKSRC}/include && pax -rw * ${DESTDIR}${PREFIX}/include
-
-.include "../../devel/boost-libs/buildlink3.mk"
-.include "../../biology/htslib/buildlink3.mk"
-.include "../../security/openssl/buildlink3.mk"
-.include "../../devel/zlib/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/pbbam/PLIST b/pbbam/PLIST
deleted file mode 100644
index 15d64068af..0000000000
--- a/pbbam/PLIST
+++ /dev/null
@@ -1,111 +0,0 @@
-@comment $NetBSD$
-bin/bam2sam
-bin/pbindex
-bin/pbindexdump
-bin/pbmerge
-include/pbbam/Accuracy.h
-include/pbbam/AlignmentPrinter.h
-include/pbbam/BaiIndexedBamReader.h
-include/pbbam/BamFile.h
-include/pbbam/BamHeader.h
-include/pbbam/BamReader.h
-include/pbbam/BamRecord.h
-include/pbbam/BamRecordBuilder.h
-include/pbbam/BamRecordImpl.h
-include/pbbam/BamTagCodec.h
-include/pbbam/BamWriter.h
-include/pbbam/BarcodeQuery.h
-include/pbbam/Cigar.h
-include/pbbam/CigarOperation.h
-include/pbbam/Compare.h
-include/pbbam/CompositeBamReader.h
-include/pbbam/Config.h
-include/pbbam/DataSet.h
-include/pbbam/DataSetTypes.h
-include/pbbam/DataSetXsd.h
-include/pbbam/EntireFileQuery.h
-include/pbbam/Frames.h
-include/pbbam/GenomicInterval.h
-include/pbbam/GenomicIntervalQuery.h
-include/pbbam/IndexedFastaReader.h
-include/pbbam/Interval.h
-include/pbbam/LocalContextFlags.h
-include/pbbam/MD5.h
-include/pbbam/Orientation.h
-include/pbbam/PbiBasicTypes.h
-include/pbbam/PbiBuilder.h
-include/pbbam/PbiFile.h
-include/pbbam/PbiFilter.h
-include/pbbam/PbiFilterQuery.h
-include/pbbam/PbiFilterTypes.h
-include/pbbam/PbiIndex.h
-include/pbbam/PbiIndexedBamReader.h
-include/pbbam/PbiLookupData.h
-include/pbbam/PbiRawData.h
-include/pbbam/Position.h
-include/pbbam/ProgramInfo.h
-include/pbbam/QNameQuery.h
-include/pbbam/QualityValue.h
-include/pbbam/QualityValues.h
-include/pbbam/ReadAccuracyQuery.h
-include/pbbam/ReadGroupInfo.h
-include/pbbam/SamTagCodec.h
-include/pbbam/SequenceInfo.h
-include/pbbam/Strand.h
-include/pbbam/SubreadLengthQuery.h
-include/pbbam/Tag.h
-include/pbbam/TagCollection.h
-include/pbbam/UnmappedReadsQuery.h
-include/pbbam/Validator.h
-include/pbbam/ZmwGroupQuery.h
-include/pbbam/ZmwQuery.h
-include/pbbam/ZmwType.h
-include/pbbam/ZmwTypeMap.h
-include/pbbam/exception/InvalidSequencingChemistryException.h
-include/pbbam/exception/ValidationException.h
-include/pbbam/internal/Accuracy.inl
-include/pbbam/internal/BamHeader.inl
-include/pbbam/internal/BamRecord.inl
-include/pbbam/internal/BamRecordBuilder.inl
-include/pbbam/internal/BamRecordImpl.inl
-include/pbbam/internal/Cigar.inl
-include/pbbam/internal/CigarOperation.inl
-include/pbbam/internal/Compare.inl
-include/pbbam/internal/CompositeBamReader.inl
-include/pbbam/internal/DataSet.inl
-include/pbbam/internal/DataSetBaseTypes.h
-include/pbbam/internal/DataSetBaseTypes.inl
-include/pbbam/internal/DataSetElement.h
-include/pbbam/internal/DataSetElement.inl
-include/pbbam/internal/DataSetListElement.h
-include/pbbam/internal/DataSetListElement.inl
-include/pbbam/internal/DataSetTypes.inl
-include/pbbam/internal/Frames.inl
-include/pbbam/internal/GenomicInterval.inl
-include/pbbam/internal/Interval.inl
-include/pbbam/internal/PbiBasicTypes.inl
-include/pbbam/internal/PbiFilter.inl
-include/pbbam/internal/PbiFilterTypes.inl
-include/pbbam/internal/PbiIndex.inl
-include/pbbam/internal/PbiLookupData.inl
-include/pbbam/internal/PbiRawData.inl
-include/pbbam/internal/ProgramInfo.inl
-include/pbbam/internal/QualityValue.inl
-include/pbbam/internal/QualityValues.inl
-include/pbbam/internal/QueryBase.h
-include/pbbam/internal/QueryBase.inl
-include/pbbam/internal/ReadGroupInfo.inl
-include/pbbam/internal/SequenceInfo.inl
-include/pbbam/internal/Tag.inl
-include/pbbam/internal/Validator.inl
-include/pbbam/virtual/VirtualPolymeraseBamRecord.h
-include/pbbam/virtual/VirtualPolymeraseCompositeReader.h
-include/pbbam/virtual/VirtualPolymeraseReader.h
-include/pbbam/virtual/VirtualRegion.h
-include/pbbam/virtual/VirtualRegionType.h
-include/pbbam/virtual/VirtualRegionTypeMap.h
-include/pbbam/virtual/VirtualZmwBamRecord.h
-include/pbbam/virtual/WhitelistedZmwReadStitcher.h
-include/pbbam/virtual/ZmwReadStitcher.h
-include/pbbam/virtual/ZmwWhitelistVirtualReader.h
-lib/libpbbam.a
diff --git a/pbbam/TODO b/pbbam/TODO
deleted file mode 100644
index b687356e6b..0000000000
--- a/pbbam/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test
diff --git a/pbbam/buildlink3.mk b/pbbam/buildlink3.mk
deleted file mode 100644
index b2a64711ef..0000000000
--- a/pbbam/buildlink3.mk
+++ /dev/null
@@ -1,24 +0,0 @@
-# $NetBSD$
-
-BUILDLINK_TREE+= pbbam
-
-.if !defined(PBBAM_BUILDLINK3_MK)
-PBBAM_BUILDLINK3_MK:=
-
-BUILDLINK_DEPMETHOD.pbbam?= build
-
-BUILDLINK_API_DEPENDS.pbbam+= pbbam>=2016.09.13
-BUILDLINK_PKGSRCDIR.pbbam?= ../../wip/pbbam
-
-# XXX
-# XXX Uncomment and keep only the buildlink3 lines below which are directly
-# XXX needed for dependencies to compile, link, and run. If this package
-# XXX provides a wrappered API or otherwise does not expose the APIs of the
-# XXX buildlink3 lines below to dependencies, remove them.
-# XXX
-#.include "../../devel/boost-libs/buildlink3.mk"
-#.include "../../biology/htslib/buildlink3.mk"
-#.include "../../security/openssl/buildlink3.mk"
-.endif # PBBAM_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -pbbam
diff --git a/pbbam/distinfo b/pbbam/distinfo
deleted file mode 100644
index 506288d296..0000000000
--- a/pbbam/distinfo
+++ /dev/null
@@ -1,6 +0,0 @@
-$NetBSD$
-
-RMD160 (pbbam-2016.09.13-e46654e0e0b816230c16f4a6132c1feff633a62a.tar.gz) = 010dd296d08a46ffc5aa74681338c5b6a90a6442
-SHA512 (pbbam-2016.09.13-e46654e0e0b816230c16f4a6132c1feff633a62a.tar.gz) = 2c7ea6187ebb057951e70773905ce6dc971cbb59864c861e55b51d45253fe5c4b7c1547344eba171f69ab7fd71beb7dd4b74c4947054c7befe23f702f2805f84
-Size (pbbam-2016.09.13-e46654e0e0b816230c16f4a6132c1feff633a62a.tar.gz) = 5394101 bytes
-SHA1 (patch-src_MD5.cpp) = cc7f845a08678b87075142e92f479cc5ac876037
diff --git a/pbbam/patches/patch-src_MD5.cpp b/pbbam/patches/patch-src_MD5.cpp
deleted file mode 100644
index 1891a6f423..0000000000
--- a/pbbam/patches/patch-src_MD5.cpp
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD$
-
-# Use external ssl
-
---- src/MD5.cpp.orig 2016-07-12 16:00:45 UTC
-+++ src/MD5.cpp
-@@ -40,7 +40,7 @@
- // Author: Brett Bowman
-
- #include "pbbam/MD5.h"
--#include <cram/md5.h>
-+#include <openssl/md5.h>
-
- namespace PacBio {
- namespace BAM {
diff --git a/pbcopper/DESCR b/pbcopper/DESCR
deleted file mode 100644
index 845dbab1b0..0000000000
--- a/pbcopper/DESCR
+++ /dev/null
@@ -1 +0,0 @@
-[description of the port]
diff --git a/pbcopper/Makefile b/pbcopper/Makefile
deleted file mode 100644
index 2e0774eb98..0000000000
--- a/pbcopper/Makefile
+++ /dev/null
@@ -1,39 +0,0 @@
-# $NetBSD$
-#
-###########################################################
-# Generated by fbsd2pkg #
-# Tue Sep 13 11:08:59 CDT 2016 #
-###########################################################
-
-DISTNAME= pbcopper-${PORTVERSION}
-CATEGORIES= biology
-MASTER_SITES= ${MASTER_SITE_GITHUB:=PacificBiosciences/}
-GITHUB_PROJECT= pbcopper
-GITHUB_TAG= ce9a4b6d836d53997d7acce6b5dceaa8bb8f7c22
-
-MAINTAINER= bacon%NetBSD.org@localhost
-HOMEPAGE= https://github.com/PacificBiosciences/pbcopper
-COMMENT= Core C++ library for data structures, algorithms, and utilities
-LICENSE= modified-bsd
-
-USE_LANGUAGES= c c++
-USE_TOOLS+= pax
-USE_CMAKE= yes
-GCC_REQD= 4.9 # pbcopper requires 4.9 due to use of json
-
-MAKE_JOBS_SAFE= yes
-
-CXXFLAGS+= -O2
-
-WRKSRC= ${WRKDIR}/pbcopper-${GITHUB_TAG}
-
-PORTVERSION= 2016.09.13
-
-INSTALLATION_DIRS= include lib
-
-do-install:
- ${INSTALL_DATA} ${WRKSRC}/lib/*.a ${DESTDIR}${PREFIX}/lib
- cd ${WRKSRC}/include && pax -rw . ${DESTDIR}${PREFIX}/include
-
-.include "../../devel/boost-libs/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/pbcopper/PLIST b/pbcopper/PLIST
deleted file mode 100644
index 40da3be0fa..0000000000
--- a/pbcopper/PLIST
+++ /dev/null
@@ -1,57 +0,0 @@
-@comment $NetBSD$
-include/pbcopper/Config.h
-include/pbcopper/cli/BuiltInOption.h
-include/pbcopper/cli/CLI.h
-include/pbcopper/cli/HelpPrinter.h
-include/pbcopper/cli/Interface.h
-include/pbcopper/cli/Option.h
-include/pbcopper/cli/Parser.h
-include/pbcopper/cli/PositionalArg.h
-include/pbcopper/cli/Results.h
-include/pbcopper/cli/SingleDashMode.h
-include/pbcopper/cli/VersionPrinter.h
-include/pbcopper/cli/internal/Option-inl.h
-include/pbcopper/cli/internal/Results-inl.h
-include/pbcopper/cli/toolcontract/Config.h
-include/pbcopper/cli/toolcontract/Driver.h
-include/pbcopper/cli/toolcontract/InputFileType.h
-include/pbcopper/cli/toolcontract/JsonPrinter.h
-include/pbcopper/cli/toolcontract/OutputFileType.h
-include/pbcopper/cli/toolcontract/ResolvedToolContract.h
-include/pbcopper/cli/toolcontract/ResourceType.h
-include/pbcopper/cli/toolcontract/Task.h
-include/pbcopper/cli/toolcontract/TaskType.h
-include/pbcopper/cli/toolcontract/internal/Config-inl.h
-include/pbcopper/cli/toolcontract/internal/Driver-inl.h
-include/pbcopper/cli/toolcontract/internal/InputFileType-inl.h
-include/pbcopper/cli/toolcontract/internal/OutputFileType-inl.h
-include/pbcopper/cli/toolcontract/internal/Task-inl.h
-include/pbcopper/data/CCSTag.h
-include/pbcopper/data/Interval.h
-include/pbcopper/data/MovieName.h
-include/pbcopper/data/Position.h
-include/pbcopper/data/RSMovieName.h
-include/pbcopper/data/RSReadName.h
-include/pbcopper/data/ReadName.h
-include/pbcopper/data/Zmw.h
-include/pbcopper/data/internal/Interval-inl.h
-include/pbcopper/data/internal/MovieName-inl.h
-include/pbcopper/data/internal/RSMovieName-inl.h
-include/pbcopper/data/internal/ReadNameBase-inl.h
-include/pbcopper/data/internal/ReadNameBase.h
-include/pbcopper/json/JSON.h
-include/pbcopper/json/internal/json.hpp
-include/pbcopper/logging/Logging.h
-include/pbcopper/logging/internal/Logging-inl.h
-include/pbcopper/stream/Stream.h
-include/pbcopper/utility/CallbackTimer.h
-include/pbcopper/utility/EnumClassHash.h
-include/pbcopper/utility/Stopwatch.h
-include/pbcopper/utility/StringUtils.h
-include/pbcopper/utility/SystemInfo.h
-include/pbcopper/utility/Version.h.in
-include/pbcopper/utility/internal/CallbackTimer-inl.h
-include/pbcopper/utility/internal/Stopwatch-inl.h
-include/pbcopper/utility/internal/StringUtils-inl.h
-include/pbcopper/utility/internal/SystemInfo-inl.h
-lib/libpbcopper.a
diff --git a/pbcopper/TODO b/pbcopper/TODO
deleted file mode 100644
index d7a5d11ff7..0000000000
--- a/pbcopper/TODO
+++ /dev/null
@@ -1,3 +0,0 @@
-Clean up and test
-
-Fails if git is not installed. Patch to eliminate the check.
diff --git a/pbcopper/buildlink3.mk b/pbcopper/buildlink3.mk
deleted file mode 100644
index 99fc0ce144..0000000000
--- a/pbcopper/buildlink3.mk
+++ /dev/null
@@ -1,22 +0,0 @@
-# $NetBSD$
-
-BUILDLINK_TREE+= pbcopper
-
-.if !defined(PBCOPPER_BUILDLINK3_MK)
-PBCOPPER_BUILDLINK3_MK:=
-
-BUILDLINK_DEPMETHOD.pbcopper?= build
-
-BUILDLINK_API_DEPENDS.pbcopper+= pbcopper>=2016.09.13
-BUILDLINK_PKGSRCDIR.pbcopper?= ../../wip/pbcopper
-
-# XXX
-# XXX Uncomment and keep only the buildlink3 lines below which are directly
-# XXX needed for dependencies to compile, link, and run. If this package
-# XXX provides a wrappered API or otherwise does not expose the APIs of the
-# XXX buildlink3 lines below to dependencies, remove them.
-# XXX
-#.include "../../devel/boost-libs/buildlink3.mk"
-.endif # PBCOPPER_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -pbcopper
diff --git a/pbcopper/distinfo b/pbcopper/distinfo
deleted file mode 100644
index c8a616795c..0000000000
--- a/pbcopper/distinfo
+++ /dev/null
@@ -1,6 +0,0 @@
-$NetBSD$
-
-RMD160 (pbcopper-2016.09.13-ce9a4b6d836d53997d7acce6b5dceaa8bb8f7c22.tar.gz) = 314e5637aec372e9dbf3457a58d3f4cb9506cd45
-SHA512 (pbcopper-2016.09.13-ce9a4b6d836d53997d7acce6b5dceaa8bb8f7c22.tar.gz) = db1521dfb5c31f42aead50934cd614b61514e78ebfd70a5e54ff6736a872e23dfd8cc1c1eaa48012dc482d104331c7179de8c260e904112fe9ff7957447700b6
-Size (pbcopper-2016.09.13-ce9a4b6d836d53997d7acce6b5dceaa8bb8f7c22.tar.gz) = 448047 bytes
-SHA1 (patch-cmake_pbcopper-gitsha1.cmake) = 5331e4a27dd5268e31e142a25b158100fa0711a7
diff --git a/pbcopper/patches/patch-cmake_pbcopper-gitsha1.cmake b/pbcopper/patches/patch-cmake_pbcopper-gitsha1.cmake
deleted file mode 100644
index 8da728a375..0000000000
--- a/pbcopper/patches/patch-cmake_pbcopper-gitsha1.cmake
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD$
-
-# wrksrc is not a git repo
-
---- cmake/pbcopper-gitsha1.cmake.orig 2016-09-13 09:43:00.051959348 -0500
-+++ cmake/pbcopper-gitsha1.cmake 2016-09-13 09:43:10.461246575 -0500
-@@ -7,7 +7,7 @@ set(__find_git_sha1 YES)
- function(find_git_sha1 _GIT_SHA1)
- find_package(Git QUIET REQUIRED)
- execute_process(COMMAND
-- "${GIT_EXECUTABLE}" "describe" "--always" "--dirty=*"
-+ echo ce9a4b6
- WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
- RESULT_VARIABLE res
- OUTPUT_VARIABLE out
diff --git a/pbseqan/DESCR b/pbseqan/DESCR
deleted file mode 100644
index 311be65bc7..0000000000
--- a/pbseqan/DESCR
+++ /dev/null
@@ -1,3 +0,0 @@
-Slimmed copy of the seqan repo from 2.0.0 with PacBio-specific changes.
-Will hopefully be eliminated in the future when patches are pulled into
-the standard seqan project.
diff --git a/pbseqan/Makefile b/pbseqan/Makefile
deleted file mode 100644
index 8ea74e01e6..0000000000
--- a/pbseqan/Makefile
+++ /dev/null
@@ -1,33 +0,0 @@
-# $NetBSD$
-#
-###########################################################
-# Generated by fbsd2pkg #
-# Tue Sep 13 11:04:45 CDT 2016 #
-###########################################################
-
-DISTNAME= pbseqan-${PORTVERSION}
-CATEGORIES= biology
-MASTER_SITES= ${MASTER_SITE_GITHUB:=PacificBiosciences/}
-GITHUB_PROJECT= seqan
-GITHUB_TAG= a1fa79fd98923d2a017a792082e2e1252d05e9e3
-
-MAINTAINER= bacon%NetBSD.org@localhost
-HOMEPAGE= https://github.com/PacificBiosciences/seqan
-COMMENT= PacBio patched and stripped down seqan
-LICENSE= modified-bsd
-
-USE_LANGUAGES= c c++
-USE_TOOLS+= pax
-NO_BUILD= yes
-
-MAKE_JOBS_SAFE= yes
-
-PORTVERSION= 2016.09.13
-
-INSTALLATION_DIRS= include/PacBio
-
-do-install:
- cd ${WRKSRC}/include/seqan && \
- pax -rw . ${DESTDIR}${PREFIX}/include/PacBio/seqan
-
-.include "../../mk/bsd.pkg.mk"
diff --git a/pbseqan/PLIST b/pbseqan/PLIST
deleted file mode 100644
index da5d2b95ec..0000000000
--- a/pbseqan/PLIST
+++ /dev/null
@@ -1,658 +0,0 @@
-@comment $NetBSD$
-include/PacBio/seqan/LICENSE
-include/PacBio/seqan/align.h
-include/PacBio/seqan/align/align_base.h
-include/PacBio/seqan/align/align_cols.h
-include/PacBio/seqan/align/align_config.h
-include/PacBio/seqan/align/align_iterator_base.h
-include/PacBio/seqan/align/align_metafunctions.h
-include/PacBio/seqan/align/align_traceback.h
-include/PacBio/seqan/align/alignment_algorithm_tags.h
-include/PacBio/seqan/align/alignment_operations.h
-include/PacBio/seqan/align/dp_algorithm_impl.h
-include/PacBio/seqan/align/dp_band.h
-include/PacBio/seqan/align/dp_cell.h
-include/PacBio/seqan/align/dp_cell_affine.h
-include/PacBio/seqan/align/dp_cell_dynamic.h
-include/PacBio/seqan/align/dp_cell_linear.h
-include/PacBio/seqan/align/dp_context.h
-include/PacBio/seqan/align/dp_formula.h
-include/PacBio/seqan/align/dp_formula_affine.h
-include/PacBio/seqan/align/dp_formula_dynamic.h
-include/PacBio/seqan/align/dp_formula_linear.h
-include/PacBio/seqan/align/dp_matrix.h
-include/PacBio/seqan/align/dp_matrix_navigator.h
-include/PacBio/seqan/align/dp_matrix_navigator_score_matrix.h
-include/PacBio/seqan/align/dp_matrix_navigator_score_matrix_sparse.h
-include/PacBio/seqan/align/dp_matrix_navigator_trace_matrix.h
-include/PacBio/seqan/align/dp_matrix_sparse.h
-include/PacBio/seqan/align/dp_meta_info.h
-include/PacBio/seqan/align/dp_profile.h
-include/PacBio/seqan/align/dp_scout.h
-include/PacBio/seqan/align/dp_setup.h
-include/PacBio/seqan/align/dp_trace_segment.h
-include/PacBio/seqan/align/dp_traceback_adaptor.h
-include/PacBio/seqan/align/dp_traceback_impl.h
-include/PacBio/seqan/align/evaluate_alignment.h
-include/PacBio/seqan/align/fragment.h
-include/PacBio/seqan/align/gap_anchor.h
-include/PacBio/seqan/align/gapped_value_type.h
-include/PacBio/seqan/align/gaps_anchor.h
-include/PacBio/seqan/align/gaps_array.h
-include/PacBio/seqan/align/gaps_base.h
-include/PacBio/seqan/align/gaps_iterator_anchor.h
-include/PacBio/seqan/align/gaps_iterator_array.h
-include/PacBio/seqan/align/gaps_iterator_base.h
-include/PacBio/seqan/align/global_alignment_banded.h
-include/PacBio/seqan/align/global_alignment_hirschberg_impl.h
-include/PacBio/seqan/align/global_alignment_myers_hirschberg_impl.h
-include/PacBio/seqan/align/global_alignment_myers_impl.h
-include/PacBio/seqan/align/global_alignment_specialized.h
-include/PacBio/seqan/align/global_alignment_unbanded.h
-include/PacBio/seqan/align/local_alignment_banded.h
-include/PacBio/seqan/align/local_alignment_banded_waterman_eggert_impl.h
-include/PacBio/seqan/align/local_alignment_enumeration.h
-include/PacBio/seqan/align/local_alignment_enumeration_banded.h
-include/PacBio/seqan/align/local_alignment_enumeration_unbanded.h
-include/PacBio/seqan/align/local_alignment_unbanded.h
-include/PacBio/seqan/align/local_alignment_waterman_eggert_impl.h
-include/PacBio/seqan/align/matrix_base.h
-include/PacBio/seqan/align_extend.h
-include/PacBio/seqan/align_extend/align_extend.h
-include/PacBio/seqan/align_extend/align_extend_base.h
-include/PacBio/seqan/align_extend/dp_scout_xdrop.h
-include/PacBio/seqan/align_profile.h
-include/PacBio/seqan/align_profile/add_to_profile.h
-include/PacBio/seqan/align_profile/score_profile_seq.h
-include/PacBio/seqan/align_split.h
-include/PacBio/seqan/align_split/align_split_interface.h
-include/PacBio/seqan/align_split/dp_scout_split.h
-include/PacBio/seqan/alignment_free.h
-include/PacBio/seqan/alignment_free/af_d2.h
-include/PacBio/seqan/alignment_free/af_d2star.h
-include/PacBio/seqan/alignment_free/af_d2z.h
-include/PacBio/seqan/alignment_free/af_n2.h
-include/PacBio/seqan/alignment_free/alignment_free_base.h
-include/PacBio/seqan/alignment_free/alignment_free_comparison.h
-include/PacBio/seqan/alignment_free/kmer_functions.h
-include/PacBio/seqan/arg_parse.h
-include/PacBio/seqan/arg_parse/arg_parse_argument.h
-include/PacBio/seqan/arg_parse/arg_parse_ctd_support.h
-include/PacBio/seqan/arg_parse/arg_parse_doc.h
-include/PacBio/seqan/arg_parse/arg_parse_exceptions.h
-include/PacBio/seqan/arg_parse/arg_parse_option.h
-include/PacBio/seqan/arg_parse/arg_parse_parse.h
-include/PacBio/seqan/arg_parse/arg_parse_type_support.h
-include/PacBio/seqan/arg_parse/argument_parser.h
-include/PacBio/seqan/arg_parse/tool_doc.h
-include/PacBio/seqan/arg_parse/xml_support.h
-include/PacBio/seqan/bam_io.h
-include/PacBio/seqan/bam_io/bam_alignment_record.h
-include/PacBio/seqan/bam_io/bam_alignment_record_util.h
-include/PacBio/seqan/bam_io/bam_file.h
-include/PacBio/seqan/bam_io/bam_header_record.h
-include/PacBio/seqan/bam_io/bam_index_bai.h
-include/PacBio/seqan/bam_io/bam_io_context.h
-include/PacBio/seqan/bam_io/bam_sam_conversion.h
-include/PacBio/seqan/bam_io/bam_scanner_cache.h
-include/PacBio/seqan/bam_io/bam_tags_dict.h
-include/PacBio/seqan/bam_io/cigar.h
-include/PacBio/seqan/bam_io/read_bam.h
-include/PacBio/seqan/bam_io/read_sam.h
-include/PacBio/seqan/bam_io/write_bam.h
-include/PacBio/seqan/bam_io/write_sam.h
-include/PacBio/seqan/basic.h
-include/PacBio/seqan/basic/aggregate_concept.h
-include/PacBio/seqan/basic/allocator_chunkpool.h
-include/PacBio/seqan/basic/allocator_interface.h
-include/PacBio/seqan/basic/allocator_multipool.h
-include/PacBio/seqan/basic/allocator_simple.h
-include/PacBio/seqan/basic/allocator_singlepool.h
-include/PacBio/seqan/basic/allocator_to_std.h
-include/PacBio/seqan/basic/alphabet_adapt_builtins.h
-include/PacBio/seqan/basic/alphabet_bio.h
-include/PacBio/seqan/basic/alphabet_concept.h
-include/PacBio/seqan/basic/alphabet_math.h
-include/PacBio/seqan/basic/alphabet_profile.h
-include/PacBio/seqan/basic/alphabet_qualities.h
-include/PacBio/seqan/basic/alphabet_residue.h
-include/PacBio/seqan/basic/alphabet_residue_funcs.h
-include/PacBio/seqan/basic/alphabet_residue_tabs.h
-include/PacBio/seqan/basic/alphabet_simple_type.h
-include/PacBio/seqan/basic/alphabet_storage.h
-include/PacBio/seqan/basic/array_construct_destruct.h
-include/PacBio/seqan/basic/basic_aggregate.h
-include/PacBio/seqan/basic/basic_allocator.h
-include/PacBio/seqan/basic/basic_alphabet.h
-include/PacBio/seqan/basic/basic_concept.h
-include/PacBio/seqan/basic/basic_container.h
-include/PacBio/seqan/basic/basic_debug.h
-include/PacBio/seqan/basic/basic_device.h
-include/PacBio/seqan/basic/basic_exception.h
-include/PacBio/seqan/basic/basic_functors.h
-include/PacBio/seqan/basic/basic_fundamental.h
-include/PacBio/seqan/basic/basic_iterator.h
-include/PacBio/seqan/basic/basic_math.h
-include/PacBio/seqan/basic/basic_metaprogramming.h
-include/PacBio/seqan/basic/basic_parallelism.h
-include/PacBio/seqan/basic/basic_proxy.h
-include/PacBio/seqan/basic/basic_simd_vector.h
-include/PacBio/seqan/basic/basic_smart_pointer.h
-include/PacBio/seqan/basic/basic_stream.h
-include/PacBio/seqan/basic/basic_tangle.h
-include/PacBio/seqan/basic/basic_type.h
-include/PacBio/seqan/basic/basic_view.h
-include/PacBio/seqan/basic/boost_preprocessor_subset.h
-include/PacBio/seqan/basic/builtin_functions.h
-include/PacBio/seqan/basic/concept_checking.h
-include/PacBio/seqan/basic/container_concept.h
-include/PacBio/seqan/basic/debug_helper.h
-include/PacBio/seqan/basic/debug_test_system.h
-include/PacBio/seqan/basic/fundamental_chunking.h
-include/PacBio/seqan/basic/fundamental_comparison.h
-include/PacBio/seqan/basic/fundamental_concepts.h
-include/PacBio/seqan/basic/fundamental_conversion.h
-include/PacBio/seqan/basic/fundamental_metafunctions.h
-include/PacBio/seqan/basic/fundamental_tags.h
-include/PacBio/seqan/basic/fundamental_transport.h
-include/PacBio/seqan/basic/holder_base.h
-include/PacBio/seqan/basic/holder_simple.h
-include/PacBio/seqan/basic/holder_tristate.h
-include/PacBio/seqan/basic/hosted_type_interface.h
-include/PacBio/seqan/basic/iterator_adapt_pointer.h
-include/PacBio/seqan/basic/iterator_adapt_std.h
-include/PacBio/seqan/basic/iterator_adaptor.h
-include/PacBio/seqan/basic/iterator_base.h
-include/PacBio/seqan/basic/iterator_concept.h
-include/PacBio/seqan/basic/iterator_counting.h
-include/PacBio/seqan/basic/iterator_interface.h
-include/PacBio/seqan/basic/iterator_position.h
-include/PacBio/seqan/basic/iterator_range.h
-include/PacBio/seqan/basic/macro_deprecated.h
-include/PacBio/seqan/basic/math_functions.h
-include/PacBio/seqan/basic/math_log_space_value.h
-include/PacBio/seqan/basic/metaprogramming_control.h
-include/PacBio/seqan/basic/metaprogramming_enable_if.h
-include/PacBio/seqan/basic/metaprogramming_logic.h
-include/PacBio/seqan/basic/metaprogramming_math.h
-include/PacBio/seqan/basic/metaprogramming_type.h
-include/PacBio/seqan/basic/metaprogramming_type_algebra.h
-include/PacBio/seqan/basic/pair_base.h
-include/PacBio/seqan/basic/pair_bit_compressed.h
-include/PacBio/seqan/basic/pair_packed.h
-include/PacBio/seqan/basic/profiling.h
-include/PacBio/seqan/basic/property_map_concept.h
-include/PacBio/seqan/basic/proxy_base.h
-include/PacBio/seqan/basic/proxy_iterator.h
-include/PacBio/seqan/basic/test_system.h
-include/PacBio/seqan/basic/triple_base.h
-include/PacBio/seqan/basic/triple_packed.h
-include/PacBio/seqan/basic/tuple_base.h
-include/PacBio/seqan/basic/tuple_bit_compressed.h
-include/PacBio/seqan/basic/volatile_ptr.h
-include/PacBio/seqan/bed_io.h
-include/PacBio/seqan/bed_io/bed_file.h
-include/PacBio/seqan/bed_io/bed_record.h
-include/PacBio/seqan/bed_io/read_bed.h
-include/PacBio/seqan/bed_io/write_bed.h
-include/PacBio/seqan/consensus.h
-include/PacBio/seqan/consensus/consensus_aligner.h
-include/PacBio/seqan/consensus/consensus_aligner_interface.h
-include/PacBio/seqan/consensus/consensus_alignment_options.h
-include/PacBio/seqan/consensus/consensus_base.h
-include/PacBio/seqan/consensus/consensus_builder.h
-include/PacBio/seqan/consensus/consensus_library.h
-include/PacBio/seqan/consensus/consensus_realign.h
-include/PacBio/seqan/consensus/consensus_score.h
-include/PacBio/seqan/consensus/overlap_info_computation.h
-include/PacBio/seqan/consensus/overlapper.h
-include/PacBio/seqan/file.h
-include/PacBio/seqan/file/file_base.h
-include/PacBio/seqan/file/file_cstyle.h
-include/PacBio/seqan/file/file_forwards.h
-include/PacBio/seqan/file/file_interface.h
-include/PacBio/seqan/file/file_mapping.h
-include/PacBio/seqan/file/file_page.h
-include/PacBio/seqan/file/string_external.h
-include/PacBio/seqan/file/string_mmap.h
-include/PacBio/seqan/find.h
-include/PacBio/seqan/find/find_abndm.h
-include/PacBio/seqan/find/find_ahocorasick.h
-include/PacBio/seqan/find/find_base.h
-include/PacBio/seqan/find/find_begin.h
-include/PacBio/seqan/find/find_bndm.h
-include/PacBio/seqan/find/find_bom.h
-include/PacBio/seqan/find/find_hamming_simple.h
-include/PacBio/seqan/find/find_horspool.h
-include/PacBio/seqan/find/find_lambda.h
-include/PacBio/seqan/find/find_multi.h
-include/PacBio/seqan/find/find_multiple_bfam.h
-include/PacBio/seqan/find/find_multiple_shiftand.h
-include/PacBio/seqan/find/find_myers_ukkonen.h
-include/PacBio/seqan/find/find_pattern_base.h
-include/PacBio/seqan/find/find_pex.h
-include/PacBio/seqan/find/find_score.h
-include/PacBio/seqan/find/find_set_horspool.h
-include/PacBio/seqan/find/find_shiftand.h
-include/PacBio/seqan/find/find_shiftor.h
-include/PacBio/seqan/find/find_simple.h
-include/PacBio/seqan/find/find_wild_shiftand.h
-include/PacBio/seqan/find/find_wumanber.h
-include/PacBio/seqan/gff_io.h
-include/PacBio/seqan/gff_io/gff_file.h
-include/PacBio/seqan/gff_io/gff_io_base.h
-include/PacBio/seqan/graph_algorithms.h
-include/PacBio/seqan/graph_algorithms/all_pairs_shortest_path.h
-include/PacBio/seqan/graph_algorithms/bellman_ford.h
-include/PacBio/seqan/graph_algorithms/bipartite_matching.h
-include/PacBio/seqan/graph_algorithms/breadth_first_search.h
-include/PacBio/seqan/graph_algorithms/connected_components.h
-include/PacBio/seqan/graph_algorithms/depth_first_search.h
-include/PacBio/seqan/graph_algorithms/dijkstra.h
-include/PacBio/seqan/graph_algorithms/floyd_warshall.h
-include/PacBio/seqan/graph_algorithms/ford_fulkerson.h
-include/PacBio/seqan/graph_algorithms/graph_algorithm_heap_tree.h
-include/PacBio/seqan/graph_algorithms/graph_algorithm_hmm.h
-include/PacBio/seqan/graph_algorithms/graph_algorithm_lis_his.h
-include/PacBio/seqan/graph_algorithms/kruskal.h
-include/PacBio/seqan/graph_algorithms/path_growing.h
-include/PacBio/seqan/graph_algorithms/prim.h
-include/PacBio/seqan/graph_algorithms/single_source_shortest_path.h
-include/PacBio/seqan/graph_algorithms/strongly_connected_compnents.h
-include/PacBio/seqan/graph_algorithms/topological_sort.h
-include/PacBio/seqan/graph_algorithms/transitive_closure.h
-include/PacBio/seqan/graph_algorithms/weakly_connected_components.h
-include/PacBio/seqan/graph_algorithms/weighted_bipartite_matching.h
-include/PacBio/seqan/graph_align.h
-include/PacBio/seqan/graph_align/graph_algorithm_refine_align.h
-include/PacBio/seqan/graph_align/graph_algorithm_refine_aligngraph.h
-include/PacBio/seqan/graph_align/graph_algorithm_refine_annotation.h
-include/PacBio/seqan/graph_align/graph_algorithm_refine_exact.h
-include/PacBio/seqan/graph_align/graph_algorithm_refine_exact_iterative.h
-include/PacBio/seqan/graph_align/graph_algorithm_refine_fragment.h
-include/PacBio/seqan/graph_align/graph_algorithm_refine_inexact.h
-include/PacBio/seqan/graph_align/graph_algorithm_refine_scoring.h
-include/PacBio/seqan/graph_align/graph_impl_align.h
-include/PacBio/seqan/graph_align/graph_impl_align_adapt.h
-include/PacBio/seqan/graph_msa.h
-include/PacBio/seqan/graph_msa/graph_align_tcoffee_base.h
-include/PacBio/seqan/graph_msa/graph_align_tcoffee_distance.h
-include/PacBio/seqan/graph_msa/graph_align_tcoffee_guidetree.h
-include/PacBio/seqan/graph_msa/graph_align_tcoffee_io.h
-include/PacBio/seqan/graph_msa/graph_align_tcoffee_kmer.h
-include/PacBio/seqan/graph_msa/graph_align_tcoffee_library.h
-include/PacBio/seqan/graph_msa/graph_align_tcoffee_msa.h
-include/PacBio/seqan/graph_msa/graph_align_tcoffee_progressive.h
-include/PacBio/seqan/graph_msa/graph_align_tcoffee_refinement.h
-include/PacBio/seqan/graph_types.h
-include/PacBio/seqan/graph_types/graph_base.h
-include/PacBio/seqan/graph_types/graph_drawing.h
-include/PacBio/seqan/graph_types/graph_edgestump.h
-include/PacBio/seqan/graph_types/graph_idmanager.h
-include/PacBio/seqan/graph_types/graph_impl_automaton.h
-include/PacBio/seqan/graph_types/graph_impl_directed.h
-include/PacBio/seqan/graph_types/graph_impl_hmm.h
-include/PacBio/seqan/graph_types/graph_impl_oracle.h
-include/PacBio/seqan/graph_types/graph_impl_tree.h
-include/PacBio/seqan/graph_types/graph_impl_trie.h
-include/PacBio/seqan/graph_types/graph_impl_undirected.h
-include/PacBio/seqan/graph_types/graph_impl_wordgraph.h
-include/PacBio/seqan/graph_types/graph_interface.h
-include/PacBio/seqan/graph_types/graph_iterator.h
-include/PacBio/seqan/graph_types/graph_iterator_adjacency.h
-include/PacBio/seqan/graph_types/graph_iterator_bfs.h
-include/PacBio/seqan/graph_types/graph_iterator_dfs.h
-include/PacBio/seqan/graph_types/graph_iterator_edge.h
-include/PacBio/seqan/graph_types/graph_iterator_outedge.h
-include/PacBio/seqan/graph_types/graph_iterator_vertex.h
-include/PacBio/seqan/graph_types/graph_utility_parsing.h
-include/PacBio/seqan/graph_types/property_map_generic.h
-include/PacBio/seqan/graph_types/property_map_internal.h
-include/PacBio/seqan/graph_types/property_map_internal_pointer.h
-include/PacBio/seqan/index.h
-include/PacBio/seqan/index/find2_backtracking.h
-include/PacBio/seqan/index/find2_base.h
-include/PacBio/seqan/index/find2_functors.h
-include/PacBio/seqan/index/find2_index.h
-include/PacBio/seqan/index/find2_index_multi.h
-include/PacBio/seqan/index/find2_vstree_factory.h
-include/PacBio/seqan/index/find_backtracking.h
-include/PacBio/seqan/index/find_index.h
-include/PacBio/seqan/index/find_index_approx.h
-include/PacBio/seqan/index/find_index_esa.h
-include/PacBio/seqan/index/find_index_lambda.h
-include/PacBio/seqan/index/find_index_qgram.h
-include/PacBio/seqan/index/find_pigeonhole.h
-include/PacBio/seqan/index/find_quasar.h
-include/PacBio/seqan/index/find_swift.h
-include/PacBio/seqan/index/index_base.h
-include/PacBio/seqan/index/index_bwt.h
-include/PacBio/seqan/index/index_childtab.h
-include/PacBio/seqan/index/index_device.h
-include/PacBio/seqan/index/index_dfi.h
-include/PacBio/seqan/index/index_esa_algs.h
-include/PacBio/seqan/index/index_esa_algs_multi.h
-include/PacBio/seqan/index/index_esa_base.h
-include/PacBio/seqan/index/index_esa_drawing.h
-include/PacBio/seqan/index/index_esa_stree.h
-include/PacBio/seqan/index/index_fm.h
-include/PacBio/seqan/index/index_fm_compressed_sa.h
-include/PacBio/seqan/index/index_fm_compressed_sa_iterator.h
-include/PacBio/seqan/index/index_fm_device.h
-include/PacBio/seqan/index/index_fm_dox.h
-include/PacBio/seqan/index/index_fm_lf_table.h
-include/PacBio/seqan/index/index_fm_rank_dictionary_base.h
-include/PacBio/seqan/index/index_fm_rank_dictionary_levels.h
-include/PacBio/seqan/index/index_fm_rank_dictionary_naive.h
-include/PacBio/seqan/index/index_fm_rank_dictionary_wt.h
-include/PacBio/seqan/index/index_fm_right_array_binary_tree.h
-include/PacBio/seqan/index/index_fm_right_array_binary_tree_iterator.h
-include/PacBio/seqan/index/index_fm_sparse_string.h
-include/PacBio/seqan/index/index_fm_stree.h
-include/PacBio/seqan/index/index_forwards.h
-include/PacBio/seqan/index/index_lcp.h
-include/PacBio/seqan/index/index_lcp_tree.h
-include/PacBio/seqan/index/index_pizzachili.h
-include/PacBio/seqan/index/index_pizzachili_find.h
-include/PacBio/seqan/index/index_pizzachili_string.h
-include/PacBio/seqan/index/index_qgram.h
-include/PacBio/seqan/index/index_qgram_bucketrefinement.h
-include/PacBio/seqan/index/index_qgram_openaddressing.h
-include/PacBio/seqan/index/index_qgram_stree.h
-include/PacBio/seqan/index/index_sa_btree.h
-include/PacBio/seqan/index/index_sa_bwtwalk.h
-include/PacBio/seqan/index/index_sa_lss.h
-include/PacBio/seqan/index/index_sa_mm.h
-include/PacBio/seqan/index/index_sa_qsort.h
-include/PacBio/seqan/index/index_sa_stree.h
-include/PacBio/seqan/index/index_sa_truncated.h
-include/PacBio/seqan/index/index_shawarma.h
-include/PacBio/seqan/index/index_shims.h
-include/PacBio/seqan/index/index_skew3.h
-include/PacBio/seqan/index/index_skew7.h
-include/PacBio/seqan/index/index_skew7_multi.h
-include/PacBio/seqan/index/index_view.h
-include/PacBio/seqan/index/index_wotd.h
-include/PacBio/seqan/index/pipe_merger3.h
-include/PacBio/seqan/index/pipe_merger7.h
-include/PacBio/seqan/index/pizzachili_api.h
-include/PacBio/seqan/index/pump_extender3.h
-include/PacBio/seqan/index/pump_extender7.h
-include/PacBio/seqan/index/pump_lcp_core.h
-include/PacBio/seqan/index/pump_separator7.h
-include/PacBio/seqan/index/radix.h
-include/PacBio/seqan/index/repeat_base.h
-include/PacBio/seqan/index/shape_base.h
-include/PacBio/seqan/index/shape_gapped.h
-include/PacBio/seqan/index/shape_onegapped.h
-include/PacBio/seqan/index/shape_predefined.h
-include/PacBio/seqan/index/shape_threshold.h
-include/PacBio/seqan/journaled_set.h
-include/PacBio/seqan/journaled_set/journal_alignment_interface.h
-include/PacBio/seqan/journaled_set/journal_alignment_traceback_adaptor.h
-include/PacBio/seqan/journaled_set/journaled_set_base.h
-include/PacBio/seqan/journaled_set/journaled_set_impl.h
-include/PacBio/seqan/journaled_set/journaled_set_join.h
-include/PacBio/seqan/journaled_set/journaled_set_join_config.h
-include/PacBio/seqan/journaled_set/journaled_set_join_global_align_compact.h
-include/PacBio/seqan/journaled_set/journaled_set_join_global_align_manhatten.h
-include/PacBio/seqan/journaled_set/journaled_set_journal_trace_descriptor.h
-include/PacBio/seqan/journaled_set/score_biaffine.h
-include/PacBio/seqan/map.h
-include/PacBio/seqan/map/map_adapter_stl.h
-include/PacBio/seqan/map/map_base.h
-include/PacBio/seqan/map/map_chooser.h
-include/PacBio/seqan/map/map_skiplist.h
-include/PacBio/seqan/map/map_vector.h
-include/PacBio/seqan/map/sumlist.h
-include/PacBio/seqan/map/sumlist_mini.h
-include/PacBio/seqan/map/sumlist_skip.h
-include/PacBio/seqan/math.h
-include/PacBio/seqan/math/math_common_factor.h
-include/PacBio/seqan/math/math_operators.h
-include/PacBio/seqan/math/math_rational.h
-include/PacBio/seqan/misc/accumulators.h
-include/PacBio/seqan/misc/base.h
-include/PacBio/seqan/misc/bit_twiddling.h
-include/PacBio/seqan/misc/bit_twiddling_functors.h
-include/PacBio/seqan/misc/cuda.h
-include/PacBio/seqan/misc/dequeue.h
-include/PacBio/seqan/misc/edit_environment.h
-include/PacBio/seqan/misc/interval_tree.h
-include/PacBio/seqan/misc/map.h
-include/PacBio/seqan/misc/memset.h
-include/PacBio/seqan/misc/name_store_cache.h
-include/PacBio/seqan/misc/priority_type_base.h
-include/PacBio/seqan/misc/priority_type_heap.h
-include/PacBio/seqan/misc/set.h
-include/PacBio/seqan/misc/sse2.h
-include/PacBio/seqan/misc/svg.h
-include/PacBio/seqan/misc/terminal.h
-include/PacBio/seqan/misc/union_find.h
-include/PacBio/seqan/modifier.h
-include/PacBio/seqan/modifier/cyclic_shape.h
-include/PacBio/seqan/modifier/modifier_alphabet.h
-include/PacBio/seqan/modifier/modifier_alphabet_expansion.h
-include/PacBio/seqan/modifier/modifier_cyclic_shape.h
-include/PacBio/seqan/modifier/modifier_functors.h
-include/PacBio/seqan/modifier/modifier_iterator.h
-include/PacBio/seqan/modifier/modifier_reverse.h
-include/PacBio/seqan/modifier/modifier_shortcuts.h
-include/PacBio/seqan/modifier/modifier_string.h
-include/PacBio/seqan/modifier/modifier_view.h
-include/PacBio/seqan/parallel.h
-include/PacBio/seqan/parallel/parallel_algorithms.h
-include/PacBio/seqan/parallel/parallel_atomic_misc.h
-include/PacBio/seqan/parallel/parallel_atomic_primitives.h
-include/PacBio/seqan/parallel/parallel_lock.h
-include/PacBio/seqan/parallel/parallel_macros.h
-include/PacBio/seqan/parallel/parallel_queue.h
-include/PacBio/seqan/parallel/parallel_queue_suspendable.h
-include/PacBio/seqan/parallel/parallel_resource_pool.h
-include/PacBio/seqan/parallel/parallel_sequence.h
-include/PacBio/seqan/parallel/parallel_serializer.h
-include/PacBio/seqan/parallel/parallel_splitting.h
-include/PacBio/seqan/parallel/parallel_tags.h
-include/PacBio/seqan/parse_lm.h
-include/PacBio/seqan/parse_lm/local_match_store.h
-include/PacBio/seqan/parse_lm/parse_blastn_tabular.h
-include/PacBio/seqan/parse_lm/parse_lastz_general.h
-include/PacBio/seqan/parse_lm/parse_stellar_gff.h
-include/PacBio/seqan/pipe.h
-include/PacBio/seqan/pipe/pipe_base.h
-include/PacBio/seqan/pipe/pipe_caster.h
-include/PacBio/seqan/pipe/pipe_counter.h
-include/PacBio/seqan/pipe/pipe_echoer.h
-include/PacBio/seqan/pipe/pipe_edit_environment.h
-include/PacBio/seqan/pipe/pipe_filter.h
-include/PacBio/seqan/pipe/pipe_iterator.h
-include/PacBio/seqan/pipe/pipe_joiner.h
-include/PacBio/seqan/pipe/pipe_namer.h
-include/PacBio/seqan/pipe/pipe_sampler.h
-include/PacBio/seqan/pipe/pipe_shifter.h
-include/PacBio/seqan/pipe/pipe_source.h
-include/PacBio/seqan/pipe/pipe_tupler.h
-include/PacBio/seqan/pipe/pool_base.h
-include/PacBio/seqan/pipe/pool_mapper.h
-include/PacBio/seqan/pipe/pool_sorter.h
-include/PacBio/seqan/platform.h
-include/PacBio/seqan/platform/platform_gcc.h
-include/PacBio/seqan/platform/platform_icc.h
-include/PacBio/seqan/platform/platform_mingw.h
-include/PacBio/seqan/platform/platform_nvcc.h
-include/PacBio/seqan/platform/platform_pgi.h
-include/PacBio/seqan/platform/platform_solaris.h
-include/PacBio/seqan/platform/platform_windows.h
-include/PacBio/seqan/platform/windows_stdint.h
-include/PacBio/seqan/random.h
-include/PacBio/seqan/random/ext_MersenneTwister.h
-include/PacBio/seqan/random/random_base.h
-include/PacBio/seqan/random/random_beta.h
-include/PacBio/seqan/random/random_beta_kfunc.h
-include/PacBio/seqan/random/random_geometric.h
-include/PacBio/seqan/random/random_lognormal.h
-include/PacBio/seqan/random/random_mt19937.h
-include/PacBio/seqan/random/random_normal.h
-include/PacBio/seqan/random/random_rng_functor.h
-include/PacBio/seqan/random/random_shuffle.h
-include/PacBio/seqan/random/random_uniform.h
-include/PacBio/seqan/realign.h
-include/PacBio/seqan/realign/realign_base.h
-include/PacBio/seqan/realign/realign_helper_functions.h
-include/PacBio/seqan/reduced_aminoacid.h
-include/PacBio/seqan/reduced_aminoacid/reduced_aminoacid_base.h
-include/PacBio/seqan/reduced_aminoacid/reduced_aminoacid_base_late.h
-include/PacBio/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_base.h
-include/PacBio/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h
-include/PacBio/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h
-include/PacBio/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h
-include/PacBio/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h
-include/PacBio/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_tables.h
-include/PacBio/seqan/roi_io.h
-include/PacBio/seqan/roi_io/read_roi.h
-include/PacBio/seqan/roi_io/roi_file.h
-include/PacBio/seqan/roi_io/roi_io_context.h
-include/PacBio/seqan/roi_io/roi_record.h
-include/PacBio/seqan/roi_io/write_roi.h
-include/PacBio/seqan/score.h
-include/PacBio/seqan/score/score_base.h
-include/PacBio/seqan/score/score_edit.h
-include/PacBio/seqan/score/score_matrix.h
-include/PacBio/seqan/score/score_matrix_data.h
-include/PacBio/seqan/score/score_matrix_io.h
-include/PacBio/seqan/score/score_simple.h
-include/PacBio/seqan/seeds.h
-include/PacBio/seqan/seeds/banded_chain_alignment.h
-include/PacBio/seqan/seeds/banded_chain_alignment_impl.h
-include/PacBio/seqan/seeds/banded_chain_alignment_profile.h
-include/PacBio/seqan/seeds/banded_chain_alignment_scout.h
-include/PacBio/seqan/seeds/banded_chain_alignment_traceback.h
-include/PacBio/seqan/seeds/basic_iter_indirect.h
-include/PacBio/seqan/seeds/seeds_base.h
-include/PacBio/seqan/seeds/seeds_combination.h
-include/PacBio/seqan/seeds/seeds_extension.h
-include/PacBio/seqan/seeds/seeds_global_chaining.h
-include/PacBio/seqan/seeds/seeds_global_chaining_base.h
-include/PacBio/seqan/seeds/seeds_global_chaining_gusfield.h
-include/PacBio/seqan/seeds/seeds_seed_base.h
-include/PacBio/seqan/seeds/seeds_seed_chained.h
-include/PacBio/seqan/seeds/seeds_seed_diagonal.h
-include/PacBio/seqan/seeds/seeds_seed_set_base.h
-include/PacBio/seqan/seeds/seeds_seed_set_non_scored.h
-include/PacBio/seqan/seeds/seeds_seed_set_scored.h
-include/PacBio/seqan/seeds/seeds_seed_set_unordered.h
-include/PacBio/seqan/seeds/seeds_seed_simple.h
-include/PacBio/seqan/seq_io.h
-include/PacBio/seqan/seq_io/fai_index.h
-include/PacBio/seqan/seq_io/fasta_fastq.h
-include/PacBio/seqan/seq_io/genomic_region.h
-include/PacBio/seqan/seq_io/read_embl.h
-include/PacBio/seqan/seq_io/read_genbank.h
-include/PacBio/seqan/seq_io/sequence_file.h
-include/PacBio/seqan/sequence.h
-include/PacBio/seqan/sequence/adapt_array_pointer.h
-include/PacBio/seqan/sequence/adapt_std_list.h
-include/PacBio/seqan/sequence/adapt_std_string.h
-include/PacBio/seqan/sequence/adapt_std_vector.h
-include/PacBio/seqan/sequence/adapt_thrust_vector.h
-include/PacBio/seqan/sequence/container_view.h
-include/PacBio/seqan/sequence/iter_concat_virtual.h
-include/PacBio/seqan/sequence/segment_base.h
-include/PacBio/seqan/sequence/segment_infix.h
-include/PacBio/seqan/sequence/segment_prefix.h
-include/PacBio/seqan/sequence/segment_suffix.h
-include/PacBio/seqan/sequence/segment_utils.h
-include/PacBio/seqan/sequence/sequence_concatenator.h
-include/PacBio/seqan/sequence/sequence_forwards.h
-include/PacBio/seqan/sequence/sequence_interface.h
-include/PacBio/seqan/sequence/sequence_lexical.h
-include/PacBio/seqan/sequence/sequence_shortcuts.h
-include/PacBio/seqan/sequence/string_alloc.h
-include/PacBio/seqan/sequence/string_array.h
-include/PacBio/seqan/sequence/string_base.h
-include/PacBio/seqan/sequence/string_block.h
-include/PacBio/seqan/sequence/string_cstyle.h
-include/PacBio/seqan/sequence/string_packed.h
-include/PacBio/seqan/sequence/string_packed_old.h
-include/PacBio/seqan/sequence/string_set_base.h
-include/PacBio/seqan/sequence/string_set_concat_direct.h
-include/PacBio/seqan/sequence/string_set_dependent_generous.h
-include/PacBio/seqan/sequence/string_set_dependent_tight.h
-include/PacBio/seqan/sequence/string_set_device.h
-include/PacBio/seqan/sequence/string_set_owner.h
-include/PacBio/seqan/sequence/string_set_segment.h
-include/PacBio/seqan/sequence/string_set_view.h
-include/PacBio/seqan/sequence_journaled.h
-include/PacBio/seqan/sequence_journaled/journal_entries_sorted_array.h
-include/PacBio/seqan/sequence_journaled/journal_entry.h
-include/PacBio/seqan/sequence_journaled/sequence_journaled.h
-include/PacBio/seqan/sequence_journaled/sequence_journaled_iterator.h
-include/PacBio/seqan/sequence_journaled/sequence_journaled_iterator_fast.h
-include/PacBio/seqan/simple_intervals_io.h
-include/PacBio/seqan/simple_intervals_io/simple_intervals_file.h
-include/PacBio/seqan/simple_intervals_io/simple_intervals_io.h
-include/PacBio/seqan/statistics.h
-include/PacBio/seqan/statistics/statistics_base.h
-include/PacBio/seqan/statistics/statistics_markov_model.h
-include/PacBio/seqan/store.h
-include/PacBio/seqan/store/store_align.h
-include/PacBio/seqan/store/store_align_intervals.h
-include/PacBio/seqan/store/store_all.h
-include/PacBio/seqan/store/store_annotation.h
-include/PacBio/seqan/store/store_base.h
-include/PacBio/seqan/store/store_contig.h
-include/PacBio/seqan/store/store_intervaltree.h
-include/PacBio/seqan/store/store_io.h
-include/PacBio/seqan/store/store_io_gff.h
-include/PacBio/seqan/store/store_io_sam.h
-include/PacBio/seqan/store/store_io_ucsc.h
-include/PacBio/seqan/store/store_library.h
-include/PacBio/seqan/store/store_matepair.h
-include/PacBio/seqan/store/store_read.h
-include/PacBio/seqan/stream.h
-include/PacBio/seqan/stream/adapt_ios.h
-include/PacBio/seqan/stream/buffered_stream.h
-include/PacBio/seqan/stream/file_stream.h
-include/PacBio/seqan/stream/formatted_file.h
-include/PacBio/seqan/stream/guess_format.h
-include/PacBio/seqan/stream/iostream_bgzf.h
-include/PacBio/seqan/stream/iostream_bgzf_impl.h
-include/PacBio/seqan/stream/iostream_bzip2.h
-include/PacBio/seqan/stream/iostream_bzip2_impl.h
-include/PacBio/seqan/stream/iostream_zip.h
-include/PacBio/seqan/stream/iostream_zip_impl.h
-include/PacBio/seqan/stream/iostream_zutil.h
-include/PacBio/seqan/stream/iter_stream.h
-include/PacBio/seqan/stream/lexical_cast.h
-include/PacBio/seqan/stream/stream_base.h
-include/PacBio/seqan/stream/stream_compressor.h
-include/PacBio/seqan/stream/tokenization.h
-include/PacBio/seqan/stream/virtual_stream.h
-include/PacBio/seqan/system.h
-include/PacBio/seqan/system/file_async.h
-include/PacBio/seqan/system/file_directory.h
-include/PacBio/seqan/system/file_forwards.h
-include/PacBio/seqan/system/file_sync.h
-include/PacBio/seqan/system/system_base.h
-include/PacBio/seqan/system/system_condition.h
-include/PacBio/seqan/system/system_critical_section.h
-include/PacBio/seqan/system/system_event.h
-include/PacBio/seqan/system/system_forwards.h
-include/PacBio/seqan/system/system_mutex.h
-include/PacBio/seqan/system/system_thread.h
-include/PacBio/seqan/translation.h
-include/PacBio/seqan/translation/translation.h
-include/PacBio/seqan/translation/translation_tables.h
-include/PacBio/seqan/ucsc_io.h
-include/PacBio/seqan/ucsc_io/ucsc_file.h
-include/PacBio/seqan/ucsc_io/ucsc_io.h
-include/PacBio/seqan/ucsc_io/ucsc_record.h
-include/PacBio/seqan/vcf_io.h
-include/PacBio/seqan/vcf_io/read_vcf.h
-include/PacBio/seqan/vcf_io/vcf_file.h
-include/PacBio/seqan/vcf_io/vcf_header.h
-include/PacBio/seqan/vcf_io/vcf_header_record.h
-include/PacBio/seqan/vcf_io/vcf_io_context.h
-include/PacBio/seqan/vcf_io/vcf_record.h
-include/PacBio/seqan/vcf_io/write_vcf.h
-include/PacBio/seqan/version.h
diff --git a/pbseqan/TODO b/pbseqan/TODO
deleted file mode 100644
index b687356e6b..0000000000
--- a/pbseqan/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test
diff --git a/pbseqan/buildlink3.mk b/pbseqan/buildlink3.mk
deleted file mode 100644
index d5276c894a..0000000000
--- a/pbseqan/buildlink3.mk
+++ /dev/null
@@ -1,14 +0,0 @@
-# $NetBSD$
-
-BUILDLINK_TREE+= pbseqan
-
-.if !defined(PBSEQAN_BUILDLINK3_MK)
-PBSEQAN_BUILDLINK3_MK:=
-
-BUILDLINK_DEPMETHOD.pbseqan?= build
-
-BUILDLINK_API_DEPENDS.pbseqan+= pbseqan>=2016.09.13
-BUILDLINK_PKGSRCDIR.pbseqan?= ../../wip/pbseqan
-.endif # PBSEQAN_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -pbseqan
diff --git a/pbseqan/distinfo b/pbseqan/distinfo
deleted file mode 100644
index fedb75e540..0000000000
--- a/pbseqan/distinfo
+++ /dev/null
@@ -1,5 +0,0 @@
-$NetBSD$
-
-RMD160 (pbseqan-2016.09.13-a1fa79fd98923d2a017a792082e2e1252d05e9e3.tar.gz) = 55fbbd70ce7f3dc1b3c89a1d604d8bf90a1fe479
-SHA512 (pbseqan-2016.09.13-a1fa79fd98923d2a017a792082e2e1252d05e9e3.tar.gz) = d2294a4e0736672e6211f9e370ad38d0472e67e66986009e4c9857545843069c233f6fe5501225e775b5b17732b81e8dca8823c6d74fda845bc18d366c9afa14
-Size (pbseqan-2016.09.13-a1fa79fd98923d2a017a792082e2e1252d05e9e3.tar.gz) = 1526537 bytes
diff --git a/suitesparse/Makefile b/suitesparse/Makefile
index c40fe4ad7e..07ea36cf5f 100644
--- a/suitesparse/Makefile
+++ b/suitesparse/Makefile
@@ -6,7 +6,7 @@ PKGREVISION= 2
CATEGORIES= math
MASTER_SITES= http://faculty.cse.tamu.edu/davis/SuiteSparse/
-MAINTAINER= bacon%NetBSD.org@localhost
+MAINTAINER= pkgsrc-users%NetBSD.org@localhost
HOMEPAGE= http://www.cise.ufl.edu/research/sparse/SuiteSparse/
COMMENT= SuiteSparse is a set of packages for sparse matrices calculation
LICENSE= gnu-gpl-v2 AND gnu-lgpl-v2
diff --git a/unanimity/DESCR b/unanimity/DESCR
deleted file mode 100644
index bcd2f881fe..0000000000
--- a/unanimity/DESCR
+++ /dev/null
@@ -1 +0,0 @@
-Pacific Biosciences Consensus library and applications.
diff --git a/unanimity/Makefile b/unanimity/Makefile
deleted file mode 100644
index bc120ae5c3..0000000000
--- a/unanimity/Makefile
+++ /dev/null
@@ -1,52 +0,0 @@
-# $NetBSD$
-#
-###########################################################
-# Generated by fbsd2pkg #
-# Tue Sep 13 12:49:29 CDT 2016 #
-###########################################################
-
-# FIXME: Searches /usr/local/include before /usr/local/include/PacBio
-# so it will pick up the wrong seqan headers if biology/seqan is installed.
-# Hopefully PacBio's seqan patches will be in the next seqan release.
-
-DISTNAME= unanimity-${PORTVERSION}
-CATEGORIES= biology
-MASTER_SITES= ${MASTER_SITE_GITHUB:=PacificBiosciences/}
-GITHUB_PROJECT= unanimity
-GITHUB_TAG= 054c59530f7ee7c3ce0adde4524f367e8d0244cd
-
-MAINTAINER= bacon%NetBSD.org@localhost
-HOMEPAGE= https://github.com/PacificBiosciences/unanimity
-COMMENT= Consensus library and applications
-LICENSE= modified-bsd
-
-MAKE_JOBS_SAFE= yes
-
-USE_LANGUAGES= c c++
-USE_CMAKE= yes
-GCC_REQD= 4.9 # 4.8 would do, but pbcopper requires 4.9 for json
-CMAKE_ARGS= -DHTSLIB_INCLUDE_DIRS:STRING=${PREFIX}/include/htslib \
- -DHTSLIB_LIBRARIES:STRING="-L${PREFIX}/lib -lhts" \
- -DPacBioBAM_INCLUDE_DIRS:STRING=${PREFIX}/include/pbbam \
- -DPacBioBAM_LIBRARIES:STRING="-L${PREFIX}/lib -lpbbam" \
- -DSEQAN_INCLUDE_DIRS:STRING=${PREFIX}/include/PacBio \
- -Dpbcopper_INCLUDE_DIRS=${PREFIX}/include \
- -Dpbcopper_LIBRARIES="-L${PREFIX}/lib -lpbcopper"
-
-CXXFLAGS+= -O2
-
-# Why is this needed with openssl/buildlink3.mk?
-LDFLAGS+= -lssl
-
-WRKSRC= ${WRKDIR}/unanimity-${GITHUB_TAG}
-
-PORTVERSION= 2016.09.13
-
-.include "../../wip/pbseqan/buildlink3.mk"
-.include "../../wip/pbbam/buildlink3.mk"
-.include "../../wip/pbcopper/buildlink3.mk"
-.include "../../biology/htslib/buildlink3.mk"
-.include "../../devel/boost-libs/buildlink3.mk"
-.include "../../security/openssl/buildlink3.mk"
-.include "../../lang/python/application.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/unanimity/PLIST b/unanimity/PLIST
deleted file mode 100644
index e486b5d47e..0000000000
--- a/unanimity/PLIST
+++ /dev/null
@@ -1,2 +0,0 @@
-@comment $NetBSD$
-bin/ccs
diff --git a/unanimity/TODO b/unanimity/TODO
deleted file mode 100644
index b687356e6b..0000000000
--- a/unanimity/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test
diff --git a/unanimity/distinfo b/unanimity/distinfo
deleted file mode 100644
index e71def7487..0000000000
--- a/unanimity/distinfo
+++ /dev/null
@@ -1,9 +0,0 @@
-$NetBSD$
-
-RMD160 (unanimity-2016.09.13-054c59530f7ee7c3ce0adde4524f367e8d0244cd.tar.gz) = eebee01595e399d80967923d3533f126e7e9a512
-SHA512 (unanimity-2016.09.13-054c59530f7ee7c3ce0adde4524f367e8d0244cd.tar.gz) = af65bc699af545141496e996900d7fae8a65b1060907fc0c1070109c46eca2fbf787ea085905e7344ebf0f2a3fde7de9901a8dd0796eb3ecd01f03e06c8b15f9
-Size (unanimity-2016.09.13-054c59530f7ee7c3ce0adde4524f367e8d0244cd.tar.gz) = 5423410 bytes
-SHA1 (patch-cmake_uny-gitsha1.cmake) = 0323b8dda91693bd02af715efe9b4f6bc2837263
-SHA1 (patch-src_align_AffineAlignment.cpp) = 019c0029b9fdacdbb72b4e7c8c1d861be7904a9f
-SHA1 (patch-src_align_LinearAlignment.cpp) = 568aaded0adbf7d36df9ee4ec07c725b3b764d0e
-SHA1 (patch-src_align_PairwiseAlignment.cpp) = 8a1809e9942fffa2d77ef28cfc97b804dc13f9a3
diff --git a/unanimity/patches/patch-cmake_uny-gitsha1.cmake b/unanimity/patches/patch-cmake_uny-gitsha1.cmake
deleted file mode 100644
index e915360510..0000000000
--- a/unanimity/patches/patch-cmake_uny-gitsha1.cmake
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD$
-
-# Not using git to fetch.
-
---- cmake/uny-gitsha1.cmake.orig 2016-08-12 12:47:37 UTC
-+++ cmake/uny-gitsha1.cmake
-@@ -7,7 +7,7 @@ set(__find_git_sha1 YES)
- function(find_git_sha1 _GIT_SHA1)
- find_package(Git QUIET REQUIRED)
- execute_process(COMMAND
-- "${GIT_EXECUTABLE}" "describe" "--always" "--dirty=*"
-+ echo 054c595
- WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
- RESULT_VARIABLE res
- OUTPUT_VARIABLE out
diff --git a/unanimity/patches/patch-src_align_AffineAlignment.cpp b/unanimity/patches/patch-src_align_AffineAlignment.cpp
deleted file mode 100644
index 65bb463678..0000000000
--- a/unanimity/patches/patch-src_align_AffineAlignment.cpp
+++ /dev/null
@@ -1,16 +0,0 @@
-$NetBSD$
-
-# Work around a boost ublas heade bug
-
---- src/align/AffineAlignment.cpp.orig 2016-09-12 19:55:43.000000000 +0000
-+++ src/align/AffineAlignment.cpp
-@@ -41,6 +41,9 @@
- #include <string>
- #include <vector>
-
-+// Bug workaround: https://stackoverflow.com/questions/44534516/error-make-array-is-not-a-member-of-boostserialization
-+#include <boost/serialization/array_wrapper.hpp>
-+
- #include <boost/numeric/ublas/matrix.hpp>
- #include <boost/numeric/ublas/matrix_proxy.hpp>
-
diff --git a/unanimity/patches/patch-src_align_LinearAlignment.cpp b/unanimity/patches/patch-src_align_LinearAlignment.cpp
deleted file mode 100644
index 5f8f15f55c..0000000000
--- a/unanimity/patches/patch-src_align_LinearAlignment.cpp
+++ /dev/null
@@ -1,16 +0,0 @@
-$NetBSD$
-
-# Work around a boost ublas heade bug
-
---- src/align/LinearAlignment.cpp.orig 2016-09-12 19:55:43.000000000 +0000
-+++ src/align/LinearAlignment.cpp
-@@ -53,6 +53,9 @@
- #include <string>
- #include <vector>
-
-+// Bug workaround: https://stackoverflow.com/questions/44534516/error-make-array-is-not-a-member-of-boostserialization
-+#include <boost/serialization/array_wrapper.hpp>
-+
- #include <boost/numeric/ublas/io.hpp>
- #include <boost/numeric/ublas/matrix.hpp>
- #include <boost/numeric/ublas/vector.hpp>
diff --git a/unanimity/patches/patch-src_align_PairwiseAlignment.cpp b/unanimity/patches/patch-src_align_PairwiseAlignment.cpp
deleted file mode 100644
index ca9df7f7fa..0000000000
--- a/unanimity/patches/patch-src_align_PairwiseAlignment.cpp
+++ /dev/null
@@ -1,16 +0,0 @@
-$NetBSD$
-
-# Work around a boost ublas heade bug
-
---- src/align/PairwiseAlignment.cpp.orig 2016-09-12 19:55:43.000000000 +0000
-+++ src/align/PairwiseAlignment.cpp
-@@ -39,6 +39,9 @@
- #include <string>
- #include <vector>
-
-+// Bug workaround: https://stackoverflow.com/questions/44534516/error-make-array-is-not-a-member-of-boostserialization
-+#include <boost/serialization/array_wrapper.hpp>
-+
- #include <boost/numeric/ublas/matrix.hpp>
-
- #include <pacbio/align/PairwiseAlignment.h>
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