From bb1632c99d908cccb66f0fae4788753d66f5090e Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Mon, 18 Jul 2022 02:37:21 -0500 Subject: Fixes for kallisto package (#31617) This PR contains several fixes for the kallisto package. - create hdf5 variant as hdf5 is optional beginning with 0.46.2 - provide patch for 0.43 to link against libz - provide patch for older versions to build again gcc-11 and up - patch and code to use autoconf-2.70 and up --- .../packages/kallisto/htslib_configure.patch | 12 ++++++++++ .../repos/builtin/packages/kallisto/limits.patch | 9 ++++++++ .../builtin/packages/kallisto/link_zlib.patch | 10 +++++++++ .../repos/builtin/packages/kallisto/package.py | 26 ++++++++++++++++++++-- 4 files changed, 55 insertions(+), 2 deletions(-) create mode 100644 var/spack/repos/builtin/packages/kallisto/htslib_configure.patch create mode 100644 var/spack/repos/builtin/packages/kallisto/limits.patch create mode 100644 var/spack/repos/builtin/packages/kallisto/link_zlib.patch (limited to 'var') diff --git a/var/spack/repos/builtin/packages/kallisto/htslib_configure.patch b/var/spack/repos/builtin/packages/kallisto/htslib_configure.patch new file mode 100644 index 0000000000..df14a118cb --- /dev/null +++ b/var/spack/repos/builtin/packages/kallisto/htslib_configure.patch @@ -0,0 +1,12 @@ +--- a/ext/htslib/configure.ac 2022-01-16 23:02:18.000000000 -0600 ++++ b/ext/htslib/configure.ac 2022-07-16 18:45:33.283586367 -0500 +@@ -46,7 +46,9 @@ + the PACKAGE_* defines are unused and are overridden by the more + accurate PACKAGE_VERSION as computed by the Makefile. */]) + ++AC_CANONICAL_HOST + AC_PROG_CC ++AC_PROG_INSTALL + AC_PROG_RANLIB + + dnl Avoid chicken-and-egg problem where pkg-config supplies the diff --git a/var/spack/repos/builtin/packages/kallisto/limits.patch b/var/spack/repos/builtin/packages/kallisto/limits.patch new file mode 100644 index 0000000000..57825634c9 --- /dev/null +++ b/var/spack/repos/builtin/packages/kallisto/limits.patch @@ -0,0 +1,9 @@ +--- a/src/MinCollector.cpp 2020-02-16 16:27:33.000000000 -0600 ++++ b/src/MinCollector.cpp 2022-07-17 13:09:47.698229720 -0500 +@@ -1,5 +1,6 @@ + #include "MinCollector.h" + #include ++#include + + // utility functions + diff --git a/var/spack/repos/builtin/packages/kallisto/link_zlib.patch b/var/spack/repos/builtin/packages/kallisto/link_zlib.patch new file mode 100644 index 0000000000..65d07d4918 --- /dev/null +++ b/var/spack/repos/builtin/packages/kallisto/link_zlib.patch @@ -0,0 +1,10 @@ +--- a/src/CMakeLists.txt 2017-03-20 05:38:35.000000000 -0500 ++++ b/src/CMakeLists.txt 2022-07-17 12:56:04.456804708 -0500 +@@ -32,6 +32,7 @@ + + if ( ZLIB_FOUND ) + include_directories( ${ZLIB_INCLUDE_DIRS} ) ++ target_link_libraries(kallisto kallisto_core ${ZLIB_LIBRARIES}) + else() + message(FATAL_ERROR "zlib not found. Required for to output files" ) + endif( ZLIB_FOUND ) diff --git a/var/spack/repos/builtin/packages/kallisto/package.py b/var/spack/repos/builtin/packages/kallisto/package.py index 8a47df16d3..75a4e601d1 100644 --- a/var/spack/repos/builtin/packages/kallisto/package.py +++ b/var/spack/repos/builtin/packages/kallisto/package.py @@ -17,8 +17,15 @@ class Kallisto(CMakePackage): version('0.46.2', sha256='c447ca8ddc40fcbd7d877d7c868bc8b72807aa8823a8a8d659e19bdd515baaf2') version('0.43.1', sha256='7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400') + # HDF5 support is optional beginning with version 0.46.2. + variant('hdf5', + when='@0.46.2:', + default=False, + description='Build with HDF5 support') + depends_on('zlib') - depends_on('hdf5') + depends_on('hdf5', when='@:0.43') + depends_on('hdf5', when='+hdf5') # htslib isn't built in time to be used.... parallel = False @@ -30,6 +37,19 @@ class Kallisto(CMakePackage): depends_on('libtool', type='build', when='@0.44.0:') depends_on('m4', type='build', when='@0.44.0:') + patch('link_zlib.patch', when='@:0.43') + patch('limits.patch', when='@:0.46') + patch('htslib_configure.patch', when='@0.44.0:^autoconf@2.70:') + + @run_before('cmake') + def autoreconf(self): + # Versions of autoconf greater than 2.69 need config.guess and + # config.sub in the tree. + if self.spec.satisfies('@0.44.0:^autoconf@2.70:'): + with working_dir(join_path(self.stage.source_path, 'ext', 'htslib')): + autoreconf = which('autoreconf') + autoreconf('--install') + # Including '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' in the cmake args # causes bits of cmake's output to end up in the autoconf-generated # configure script. @@ -41,8 +61,10 @@ class Kallisto(CMakePackage): setting. """ a = super(Kallisto, self).std_cmake_args - if (self.spec.version >= Version('0.44.0')): + if self.spec.satisfies('@0.44.0:'): args = [i for i in a if i != '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON'] + if self.spec.satisfies('@0.46.2:'): + args.append(self.define_from_variant('USE_HDF5', 'hdf5')) else: args = a -- cgit v1.2.3-70-g09d2