CVS commit: pkgsrc/biology/bedtools

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Mon Feb  8 01:49:25 UTC 2021

Modified Files:
        pkgsrc/biology/bedtools: Makefile PLIST distinfo
        pkgsrc/biology/bedtools/patches: patch-Makefile
            patch-src_utils_htslib_Makefile
Added Files:
        pkgsrc/biology/bedtools/patches:
            patch-src_utils_BamTools_include_SamHeader.hpp patch-test_test.sh

Log Message:
biology/bedtools: Update to 2.30.0

Some major performance improvements
Numerous minor bug fixes and enhancements
Added a do-test target to the pkgsrc Makefile


To generate a diff of this commit:
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/bedtools/Makefile \
    pkgsrc/biology/bedtools/PLIST pkgsrc/biology/bedtools/distinfo
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/bedtools/patches/patch-Makefile \
    pkgsrc/biology/bedtools/patches/patch-src_utils_htslib_Makefile
cvs rdiff -u -r0 -r1.1 \
    pkgsrc/biology/bedtools/patches/patch-src_utils_BamTools_include_SamHeader.hpp \
    pkgsrc/biology/bedtools/patches/patch-test_test.sh

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/bedtools/Makefile
diff -u pkgsrc/biology/bedtools/Makefile:1.1 pkgsrc/biology/bedtools/Makefile:1.2
--- pkgsrc/biology/bedtools/Makefile:1.1        Fri Jan 22 17:07:50 2021
+++ pkgsrc/biology/bedtools/Makefile    Mon Feb  8 01:49:25 2021
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.1 2021/01/22 17:07:50 bacon Exp $
+# $NetBSD: Makefile,v 1.2 2021/02/08 01:49:25 bacon Exp $
 
-DISTNAME=      bedtools-2.29.2
+DISTNAME=      bedtools-2.30.0
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=arq5x/}
 GITHUB_PROJECT=        bedtools2
@@ -12,7 +12,7 @@ COMMENT=      Swiss army knife for genome ari
 LICENSE=       mit
 
 USE_LANGUAGES= c c++
-USE_TOOLS+=    gmake
+USE_TOOLS+=    bash:test gmake
 REPLACE_SH+=   scripts/vcfsort.sh
 REPLACE_PYTHON=        scripts/makeBashScripts.py
 
@@ -21,10 +21,8 @@ SUBST_STAGE.pybin=   pre-configure
 SUBST_SED.pybin=       -e 's|python|${PYTHONBIN}|g'
 SUBST_FILES.pybin=     Makefile
 
-# Avoid conflict with C++20 <version> by adding .txt suffix
-post-extract:
-       ${MV} ${WRKSRC}/src/utils/gzstream/version \
-               ${WRKSRC}/src/utils/gzstream/version.txt
+do-test:
+       cd ${WRKSRC}/test && bash test.sh
 
 .include "../../devel/zlib/buildlink3.mk"
 .include "../../archivers/bzip2/buildlink3.mk"
Index: pkgsrc/biology/bedtools/PLIST
diff -u pkgsrc/biology/bedtools/PLIST:1.1 pkgsrc/biology/bedtools/PLIST:1.2
--- pkgsrc/biology/bedtools/PLIST:1.1   Fri Jan 22 17:07:50 2021
+++ pkgsrc/biology/bedtools/PLIST       Mon Feb  8 01:49:25 2021
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.1 2021/01/22 17:07:50 bacon Exp $
+@comment $NetBSD: PLIST,v 1.2 2021/02/08 01:49:25 bacon Exp $
 bin/annotateBed
 bin/bamToBed
 bin/bamToFastq
Index: pkgsrc/biology/bedtools/distinfo
diff -u pkgsrc/biology/bedtools/distinfo:1.1 pkgsrc/biology/bedtools/distinfo:1.2
--- pkgsrc/biology/bedtools/distinfo:1.1        Fri Jan 22 17:07:50 2021
+++ pkgsrc/biology/bedtools/distinfo    Mon Feb  8 01:49:25 2021
@@ -1,8 +1,10 @@
-$NetBSD: distinfo,v 1.1 2021/01/22 17:07:50 bacon Exp $
+$NetBSD: distinfo,v 1.2 2021/02/08 01:49:25 bacon Exp $
 
-SHA1 (bedtools-2.29.2.tar.gz) = 51f03e1cac60f99c062d9babb6385800c89c78f6
-RMD160 (bedtools-2.29.2.tar.gz) = 08ea14501ddfc85f2d4a5a756a10512a61ec93f2
-SHA512 (bedtools-2.29.2.tar.gz) = 06b0016674acb08fd85b80fe1a8ff1ebce5c54c0a30ff7f4e52e63fe5b3f3841413f49df3c51088454d79048ca267fde8c23d9ed51f309ee6916d9b49610be41
-Size (bedtools-2.29.2.tar.gz) = 20638840 bytes
-SHA1 (patch-Makefile) = d6a76cb23e623842d6d5c60d67eff928b45b091c
-SHA1 (patch-src_utils_htslib_Makefile) = ba513efa59eed05321c176185fb576f4892ea7a5
+SHA1 (bedtools-2.30.0.tar.gz) = b3bae21434f261818e15875727b4a3c5c7366bc7
+RMD160 (bedtools-2.30.0.tar.gz) = 1cc30e5bc3df12f38d8f1e055ff2f939d7608395
+SHA512 (bedtools-2.30.0.tar.gz) = 3d69d6a53d3e5d15597dfefa26f7895231adbf3c1fe3b16ee4213e497ef01a20698add2f0e6f03d8eb7cd7c70709955f0ebdf897a025a83d31ef17e2c91f9856
+Size (bedtools-2.30.0.tar.gz) = 20639858 bytes
+SHA1 (patch-Makefile) = d21b4a69ce18eac7de59d277a03d0a5f5e2e1cb5
+SHA1 (patch-src_utils_BamTools_include_SamHeader.hpp) = 7ab168b247b5edf7f3eccd9ef7329a5e1605c787
+SHA1 (patch-src_utils_htslib_Makefile) = 8785ff3110f8df26e0cc5b2fdf1e2e02d6cdc836
+SHA1 (patch-test_test.sh) = e3a17815d6a30c17db7134613d25f08c6be3494e

Index: pkgsrc/biology/bedtools/patches/patch-Makefile
diff -u pkgsrc/biology/bedtools/patches/patch-Makefile:1.1 pkgsrc/biology/bedtools/patches/patch-Makefile:1.2
--- pkgsrc/biology/bedtools/patches/patch-Makefile:1.1  Fri Jan 22 17:07:50 2021
+++ pkgsrc/biology/bedtools/patches/patch-Makefile      Mon Feb  8 01:49:25 2021
@@ -1,8 +1,8 @@
-$NetBSD: patch-Makefile,v 1.1 2021/01/22 17:07:50 bacon Exp $
+$NetBSD: patch-Makefile,v 1.2 2021/02/08 01:49:25 bacon Exp $
 
 # Respect pkgsrc env, drop bash dep
 
---- Makefile.orig      2019-12-17 20:12:15.000000000 +0000
+--- Makefile.orig      2021-02-05 21:42:03.926301547 +0000
 +++ Makefile
 @@ -4,7 +4,7 @@
  # (c) 2009 Aaron Quinlan
@@ -31,7 +31,16 @@ $NetBSD: patch-Makefile,v 1.1 2021/01/22
  
  SUBDIRS = $(SRC_DIR)/annotateBed \
                  $(SRC_DIR)/bamToBed \
-@@ -191,9 +191,9 @@ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
+@@ -155,7 +155,7 @@ $(CCPREFIX) $(CC_WRAPPER) $(CXX) $(ALL_C
+ @mv -f $*.Td $*.d
+ endef
+ 
+-$(OBJ_DIR)/%.d: ;
++$(OBJ_DIR)/%.d: $(OBJ_DIR) ;
+ .PRECIOUS: $(OBJ_DIR)/%.d
+ 
+ -include $(patsubst %.o,%.d,$(BUILT_OBJECTS))
+@@ -197,9 +197,9 @@ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
  .PHONY: all
  
  install: all
Index: pkgsrc/biology/bedtools/patches/patch-src_utils_htslib_Makefile
diff -u pkgsrc/biology/bedtools/patches/patch-src_utils_htslib_Makefile:1.1 pkgsrc/biology/bedtools/patches/patch-src_utils_htslib_Makefile:1.2
--- pkgsrc/biology/bedtools/patches/patch-src_utils_htslib_Makefile:1.1 Fri Jan 22 17:07:50 2021
+++ pkgsrc/biology/bedtools/patches/patch-src_utils_htslib_Makefile     Mon Feb  8 01:49:25 2021
@@ -1,8 +1,8 @@
-$NetBSD: patch-src_utils_htslib_Makefile,v 1.1 2021/01/22 17:07:50 bacon Exp $
+$NetBSD: patch-src_utils_htslib_Makefile,v 1.2 2021/02/08 01:49:25 bacon Exp $
 
 # Respect pkgsrc env
 
---- src/utils/htslib/Makefile.orig     2021-01-21 22:49:18.823750624 +0000
+--- src/utils/htslib/Makefile.orig     2021-01-23 19:33:26.000000000 +0000
 +++ src/utils/htslib/Makefile
 @@ -22,7 +22,7 @@
  # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER

Added files:

Index: pkgsrc/biology/bedtools/patches/patch-src_utils_BamTools_include_SamHeader.hpp
diff -u /dev/null pkgsrc/biology/bedtools/patches/patch-src_utils_BamTools_include_SamHeader.hpp:1.1
--- /dev/null   Mon Feb  8 01:49:26 2021
+++ pkgsrc/biology/bedtools/patches/patch-src_utils_BamTools_include_SamHeader.hpp      Mon Feb  8 01:49:25 2021
@@ -0,0 +1,27 @@
+$NetBSD: patch-src_utils_BamTools_include_SamHeader.hpp,v 1.1 2021/02/08 01:49:25 bacon Exp $
+
+# Silence compiler warnings
+
+--- src/utils/BamTools/include/SamHeader.hpp.orig      2021-01-24 16:15:06 UTC
++++ src/utils/BamTools/include/SamHeader.hpp
+@@ -7,6 +7,7 @@
+ #include <string.h>
+ #include <api/BamAux.h>
+ #include <stdlib.h>
++#include <sysexits.h>
+ 
+ 
+ #ifdef WITH_HTS_CB_API
+@@ -29,7 +30,11 @@ namespace htslib_future {
+               ops.cb_data = buffer;
+               samFile* fp = hts_open_callback(NULL, &ops, "w");
+ 
+-              sam_hdr_write(fp, hdr);
++              if ( sam_hdr_write(fp, hdr) != 0 )
++              {
++                      fputs("sam_hdr_rebuild: Error: sam_hdr_write() failed.\n", stderr);
++                      exit(EX_IOERR);
++              }
+ 
+               hts_close(fp);
+ 
Index: pkgsrc/biology/bedtools/patches/patch-test_test.sh
diff -u /dev/null pkgsrc/biology/bedtools/patches/patch-test_test.sh:1.1
--- /dev/null   Mon Feb  8 01:49:26 2021
+++ pkgsrc/biology/bedtools/patches/patch-test_test.sh  Mon Feb  8 01:49:25 2021
@@ -0,0 +1,20 @@
+$NetBSD: patch-test_test.sh,v 1.1 2021/02/08 01:49:25 bacon Exp $
+
+# Warning for impending failed tests
+
+--- test/test.sh.orig  2021-02-07 19:54:21.793084552 +0000
++++ test/test.sh
+@@ -1,5 +1,13 @@
+ set -e; # Alert user to any uncaught error
+ 
++if [ $(uname) = FreeBSD ] || [ $(uname) = NetBSD ]; then
++    if ! df | fgrep -q fdesc; then
++        echo "fdesc FS must be mounted in order to run $0."
++        echo "It uses bash process substitutions, e.g. <(ls)."
++        exit 1
++    fi
++fi
++
+ ulimit -c unlimited
+ 
+ STARTWD=$(pwd);