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Bacon" Date: Mon, 3 Aug 2020 15:45:22 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r544077 - in head/biology/kallisto: . files X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology/kallisto: . files X-SVN-Commit-Revision: 544077 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.33 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 03 Aug 2020 15:45:23 -0000 Author: jwb Date: Mon Aug 3 15:45:21 2020 New Revision: 544077 URL: https://svnweb.freebsd.org/changeset/ports/544077 Log: biology/kallisto: Revert to 0.46.1 0.46.2 has long-standing regressions that are not being addressed, including a seg fault when using --genomebam. Also revert to bundled htslib in preparation for biology/htslib upgrade to 1.10. Kallisto source contains modified bits of htslib 1.4.1 that are incompatible with htslib > 1.9. Added: head/biology/kallisto/files/patch-ext_htslib_configure.ac (contents, props changed) Deleted: head/biology/kallisto/files/patch-src_CMakeLists.txt Modified: head/biology/kallisto/Makefile head/biology/kallisto/distinfo head/biology/kallisto/files/patch-CMakeLists.txt Modified: head/biology/kallisto/Makefile ============================================================================== --- head/biology/kallisto/Makefile Mon Aug 3 15:30:38 2020 (r544076) +++ head/biology/kallisto/Makefile Mon Aug 3 15:45:21 2020 (r544077) @@ -2,8 +2,8 @@ PORTNAME= kallisto DISTVERSIONPREFIX= v -DISTVERSION= 0.46.2 -PORTREVISION= 1 +DISTVERSION= 0.46.1 +PORTEPOCH= 1 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -12,11 +12,11 @@ COMMENT= Quantify abundances of transcripts from RNA-S LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt +BUILD_DEPENDS= autoconf>=0:devel/autoconf LIB_DEPENDS= libhdf5.so:science/hdf5 \ - libsz.so:science/szip \ - libhts.so:biology/htslib + libsz.so:science/szip -USES= cmake:noninja compiler:c++11-lang localbase:ldflags +USES= cmake:noninja compiler:c++11-lang gmake localbase:ldflags USE_GITHUB= yes GH_ACCOUNT= pachterlab @@ -26,10 +26,11 @@ PORTEXAMPLES= * PLIST_FILES= bin/kallisto EXAMPLES_PLIST_FILES= bin/kallisto-test -# hdf5 is being phased out and is no longer build in by default, but is still -# required for Sleuth and other downstream tools. Remove this after Sleuth -# et all catch up. -CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON +# hdf5 is being phased out and is no longer built in by default, but is still +# required for Sleuth (requires kallisto bootstrap estimates) and other +# downstream tools. Remove this after Sleuth et all catch up. +CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON +MAKE_JOBS_UNSAFE= yes OPTIONS_DEFINE= EXAMPLES Modified: head/biology/kallisto/distinfo ============================================================================== --- head/biology/kallisto/distinfo Mon Aug 3 15:30:38 2020 (r544076) +++ head/biology/kallisto/distinfo Mon Aug 3 15:45:21 2020 (r544077) @@ -1,3 +1,3 @@ -TIMESTAMP = 1581611719 -SHA256 (pachterlab-kallisto-v0.46.2_GH0.tar.gz) = 10bab0c2929d8c345750e02735b305bbbfa89e8a48f42c4b9af44f3d44ff4c82 -SIZE (pachterlab-kallisto-v0.46.2_GH0.tar.gz) = 2693857 +TIMESTAMP = 1595454023 +SHA256 (pachterlab-kallisto-v0.46.1_GH0.tar.gz) = 492ef081395e8858fcd9832aceb8b61c79358f00afb45e6709146c0fb51dd231 +SIZE (pachterlab-kallisto-v0.46.1_GH0.tar.gz) = 2254560 Modified: head/biology/kallisto/files/patch-CMakeLists.txt ============================================================================== --- head/biology/kallisto/files/patch-CMakeLists.txt Mon Aug 3 15:30:38 2020 (r544076) +++ head/biology/kallisto/files/patch-CMakeLists.txt Mon Aug 3 15:45:21 2020 (r544077) @@ -1,25 +1,11 @@ ---- CMakeLists.txt.orig 2018-12-20 14:20:05 UTC +--- CMakeLists.txt.orig 2020-07-22 22:36:50 UTC +++ CMakeLists.txt -@@ -34,22 +34,6 @@ ELSE(LINK MATCHES shared) - message("shared build") - ENDIF(LINK MATCHES static) - -- --include(ExternalProject) --ExternalProject_Add(htslib -- PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib -- SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/htslib -- BUILD_IN_SOURCE 1 -- CONFIGURE_COMMAND autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure -- --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl +@@ -42,7 +42,7 @@ ExternalProject_Add(htslib + BUILD_IN_SOURCE 1 + CONFIGURE_COMMAND autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure + --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl - BUILD_COMMAND make lib-static -- INSTALL_COMMAND "" --) -- --include_directories(${htslib_PREFIX}/src/htslib) -- -- -- - # add_compile_options(-Wdeprecated-register) ++ BUILD_COMMAND gmake lib-static + INSTALL_COMMAND "" + ) - add_subdirectory(src) Added: head/biology/kallisto/files/patch-ext_htslib_configure.ac ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/kallisto/files/patch-ext_htslib_configure.ac Mon Aug 3 15:45:21 2020 (r544077) @@ -0,0 +1,11 @@ +--- ext/htslib/configure.ac.orig 2019-11-04 16:28:52 UTC ++++ ext/htslib/configure.ac +@@ -23,7 +23,7 @@ + # DEALINGS IN THE SOFTWARE. + + dnl Process this file with autoconf to produce a configure script +-AC_INIT([HTSlib], m4_esyscmd_s([make print-version]), ++AC_INIT([HTSlib], [1.4.1], + [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/]) + AC_PREREQ(2.63) dnl This version introduced 4-argument AC_CHECK_HEADER + AC_CONFIG_SRCDIR(hts.c)