diff options
13 files changed, 707 insertions, 49 deletions
diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py index 553c4ad05f..8fcc331482 100644 --- a/lib/spack/spack/stage.py +++ b/lib/spack/spack/stage.py @@ -321,15 +321,19 @@ class Stage(object): package_name = os.path.dirname(self.mirror_path) pkg = spack.repo.get(package_name) if pkg.list_url is not None and pkg.url is not None: - archive_version = spack.url.parse_version( - self.default_fetcher.url) - versions = pkg.fetch_remote_versions() try: - url_from_list = versions[Version(archive_version)] - fetchers.append(fs.URLFetchStrategy(url_from_list, digest)) - except KeyError: - tty.msg("Can not find version %s in url_list" % - archive_version) + archive_version = spack.url.parse_version( + self.default_fetcher.url) + versions = pkg.fetch_remote_versions() + try: + url_from_list = versions[Version(archive_version)] + fetchers.append(fs.URLFetchStrategy( + url_from_list, digest)) + except KeyError: + tty.msg("Can not find version %s in url_list" % + archive_version) + except: + tty.msg("Could not determine url from list_url.") for fetcher in fetchers: try: diff --git a/var/spack/repos/builtin/packages/bcftools/package.py b/var/spack/repos/builtin/packages/bcftools/package.py new file mode 100644 index 0000000000..a1b4a06dbb --- /dev/null +++ b/var/spack/repos/builtin/packages/bcftools/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Bcftools(Package): + """BCFtools is a set of utilities that manipulate variant calls in the + Variant Call Format (VCF) and its binary counterpart BCF. All + commands work transparently with both VCFs and BCFs, both + uncompressed and BGZF-compressed.""" + + homepage = "http://samtools.github.io/bcftools/" + url = "https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2" + + version('1.3.1', '575001e9fca37cab0c7a7287ad4b1cdb') + + depends_on('zlib') + + def install(self, spec, prefix): + make("prefix=%s" % prefix, "all") + make("prefix=%s" % prefix, "install") diff --git a/var/spack/repos/builtin/packages/fastx_toolkit/package.py b/var/spack/repos/builtin/packages/fastx_toolkit/package.py new file mode 100644 index 0000000000..04b4d24b39 --- /dev/null +++ b/var/spack/repos/builtin/packages/fastx_toolkit/package.py @@ -0,0 +1,43 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class FastxToolkit(Package): + """The FASTX-Toolkit is a collection of command line tools for + Short-Reads FASTA/FASTQ files preprocessing.""" + + homepage = "http://hannonlab.cshl.edu/fastx_toolkit/" + url = "https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2" + + version('0.0.14', 'bf1993c898626bb147de3d6695c20b40') + + depends_on('libgtextutils') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix)) + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/htslib/package.py b/var/spack/repos/builtin/packages/htslib/package.py new file mode 100644 index 0000000000..1a8b8fd2f5 --- /dev/null +++ b/var/spack/repos/builtin/packages/htslib/package.py @@ -0,0 +1,41 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Htslib(Package): + """C library for high-throughput sequencing data formats.""" + + homepage = "https://github.com/samtools/htslib" + url = "https://github.com/samtools/htslib/releases/download/1.3.1/htslib-1.3.1.tar.bz2" + + version('1.3.1', '16d78f90b72f29971b042e8da8be6843') + + depends_on('zlib') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix)) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/libgtextutils/package.py b/var/spack/repos/builtin/packages/libgtextutils/package.py new file mode 100644 index 0000000000..201e031869 --- /dev/null +++ b/var/spack/repos/builtin/packages/libgtextutils/package.py @@ -0,0 +1,40 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Libgtextutils(Package): + """Gordon's Text utils Library.""" + + homepage = "https://github.com/agordon/libgtextutils" + url = "https://github.com/agordon/libgtextutils/releases/download/0.7/libgtextutils-0.7.tar.gz" + + version('0.7', '593c7c62e3c76ec49f5736eed4f96806') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix)) + + make() + make('install') diff --git a/var/spack/repos/builtin/packages/lmod/package.py b/var/spack/repos/builtin/packages/lmod/package.py index 01911c1a30..a3ae4a7f51 100644 --- a/var/spack/repos/builtin/packages/lmod/package.py +++ b/var/spack/repos/builtin/packages/lmod/package.py @@ -38,6 +38,7 @@ class Lmod(Package): homepage = 'https://www.tacc.utexas.edu/research-development/tacc-projects/lmod' # NOQA: ignore=E501 url = 'https://github.com/TACC/Lmod/archive/6.4.1.tar.gz' + version('6.4.5', '14f6c58dbc0a5a75574d795eac2c1e3c') version('6.4.1', '7978ba777c8aa41a4d8c05fec5f780f4') version('6.3.7', '0fa4d5a24c41cae03776f781aa2dedc1') version('6.0.1', '91abf52fe5033bd419ffe2842ebe7af9') @@ -55,15 +56,16 @@ class Lmod(Package): spack_env.append_path('LUA_PATH', stage_lua_path.format( version=self.version), separator=';') - patch('fix_tclsh_paths.patch') + patch('fix_tclsh_paths.patch', when='@:6.4.3') def patch(self): """The tcl scripts should use the tclsh that was discovered by the configure script. Touch up their #! lines so that the sed in the Makefile's install step has something to work on. Requires the change in the associated patch file.fg""" - for tclscript in glob('src/*.tcl'): - filter_file(r'^#!.*tclsh', '#!@path_to_tclsh@', tclscript) + if self.spec.version <= Version('6.4.3'): + for tclscript in glob('src/*.tcl'): + filter_file(r'^#!.*tclsh', '#!@path_to_tclsh@', tclscript) def install(self, spec, prefix): configure('--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/pango/package.py b/var/spack/repos/builtin/packages/pango/package.py index 7ae90f1795..2da20e9dc2 100644 --- a/var/spack/repos/builtin/packages/pango/package.py +++ b/var/spack/repos/builtin/packages/pango/package.py @@ -32,6 +32,8 @@ class Pango(Package): far has been done in the context of the GTK+ widget toolkit.""" homepage = "http://www.pango.org" url = "http://ftp.gnome.org/pub/gnome/sources/pango/1.36/pango-1.36.8.tar.xz" + list_url = "http://ftp.gnome.org/pub/gnome/sources/pango/" + list_depth = 2 version('1.36.8', '217a9a753006275215fa9fa127760ece') version('1.40.1', '6fc88c6529890d6c8e03074d57a3eceb') diff --git a/var/spack/repos/builtin/packages/pdt/package.py b/var/spack/repos/builtin/packages/pdt/package.py index 60136fc0cd..32611a7b14 100644 --- a/var/spack/repos/builtin/packages/pdt/package.py +++ b/var/spack/repos/builtin/packages/pdt/package.py @@ -34,10 +34,12 @@ class Pdt(Package): class library supporting common PDB operations. """ homepage = "https://www.cs.uoregon.edu/research/pdt/home.php" - url = "https://www.cs.uoregon.edu/research/tau/pdt_releases/pdt-3.21.tar.gz" - version('3.21', '8df94298b71703decf680709a4ddf68f') - version('3.19', 'ba5591994998771fdab216699e362228') + version('3.21', '3092ca0d8833b69992c17e63ae66c263') + version('3.19', '5c5e1e6607086aa13bf4b1b9befc5864') + + def url_for_version(self, version): + return 'https://www.cs.uoregon.edu/research/tau/pdt_releases/pdtoolkit-%s.tar.gz' % (version) def install(self, spec, prefix): configure('-prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/pkg-config/g_date_strftime.patch b/var/spack/repos/builtin/packages/pkg-config/g_date_strftime.patch index 578cbf4d7c..9538f23875 100644 --- a/var/spack/repos/builtin/packages/pkg-config/g_date_strftime.patch +++ b/var/spack/repos/builtin/packages/pkg-config/g_date_strftime.patch @@ -20,14 +20,15 @@ index 4aece02..92c34d2 100644 +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wformat-nonliteral" + - gsize - g_date_strftime (gchar *s, - gsize slen, + gsize + g_date_strftime (gchar *s, + gsize slen, @@ -2549,3 +2552,5 @@ g_date_strftime (gchar *s, return retval; #endif } + +#pragma GCC diagnostic pop --- +-- 2.7.1 + diff --git a/var/spack/repos/builtin/packages/samtools/package.py b/var/spack/repos/builtin/packages/samtools/package.py index f5c7f4431f..6b0b224785 100644 --- a/var/spack/repos/builtin/packages/samtools/package.py +++ b/var/spack/repos/builtin/packages/samtools/package.py @@ -24,19 +24,27 @@ ############################################################################## from spack import * + class Samtools(Package): - """SAM Tools provide various utilities for manipulating alignments in the SAM format, - including sorting, merging, indexing and generating + """SAM Tools provide various utilities for manipulating alignments in + the SAM format, including sorting, merging, indexing and generating alignments in a per-position format""" homepage = "www.htslib.org" - version('1.2','988ec4c3058a6ceda36503eebecd4122',url = "https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2") + url = "https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2" - depends_on("zlib") - depends_on("mpc") - parallel=False - patch("samtools1.2.patch",level=0) + version('1.3.1', 'a7471aa5a1eb7fc9cc4c6491d73c2d88') + version('1.2', '988ec4c3058a6ceda36503eebecd4122') - def install(self, spec, prefix): - make("prefix=%s" % prefix, "install") + depends_on("ncurses") + depends_on("htslib", when='@1.3.1:') # htslib became standalone + depends_on('zlib', when='@1.2') # needed for builtin htslib + def install(self, spec, prefix): + if self.spec.version >= Version('1.3.1'): + configure('--prefix={0}'.format(prefix), '--with-ncurses') + make() + make('install') + else: + make("prefix=%s" % prefix) + make("prefix=%s" % prefix, "install") diff --git a/var/spack/repos/builtin/packages/samtools/samtools1.2.patch b/var/spack/repos/builtin/packages/samtools/samtools1.2.patch deleted file mode 100644 index ead3ab4e2c..0000000000 --- a/var/spack/repos/builtin/packages/samtools/samtools1.2.patch +++ /dev/null @@ -1,20 +0,0 @@ ---- Makefile 2015-02-03 08:27:34.000000000 -0800 -+++ Makefile.new 2015-07-21 10:38:27.881406892 -0700 -@@ -26,7 +26,7 @@ - CFLAGS = -g -Wall -O2 - LDFLAGS = - LDLIBS = --DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -+DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 - LOBJS= bam_aux.o bam.o bam_import.o sam.o \ - sam_header.o bam_plbuf.o - AOBJS= bam_index.o bam_plcmd.o sam_view.o \ -@@ -37,7 +37,7 @@ - faidx.o stats.o stats_isize.o bam_flags.o bam_split.o \ - bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o - INCLUDES= -I. -I$(HTSDIR) --LIBCURSES= -lcurses # -lXCurses -+#LIBCURSES= -lcurses # -lXCurses - - prefix = /usr/local - exec_prefix = $(prefix) diff --git a/var/spack/repos/builtin/packages/tar/gnutar-configure-xattrs.patch b/var/spack/repos/builtin/packages/tar/gnutar-configure-xattrs.patch new file mode 100644 index 0000000000..e5c183b720 --- /dev/null +++ b/var/spack/repos/builtin/packages/tar/gnutar-configure-xattrs.patch @@ -0,0 +1,482 @@ +diff --git a/Makefile.in b/Makefile.in +index f9f1d1d..b403e46 100644 +--- a/Makefile.in ++++ b/Makefile.in +@@ -1,4 +1,4 @@ +-# Makefile.in generated by automake 1.14 from Makefile.am. ++# Makefile.in generated by automake 1.14.1 from Makefile.am. + # @configure_input@ + + # Copyright (C) 1994-2013 Free Software Foundation, Inc. +@@ -1583,9 +1583,10 @@ distcheck: dist + && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \ + && am__cwd=`pwd` \ + && $(am__cd) $(distdir)/_build \ +- && ../configure --srcdir=.. --prefix="$$dc_install_base" \ ++ && ../configure \ + $(AM_DISTCHECK_CONFIGURE_FLAGS) \ + $(DISTCHECK_CONFIGURE_FLAGS) \ ++ --srcdir=.. --prefix="$$dc_install_base" \ + && $(MAKE) $(AM_MAKEFLAGS) \ + && $(MAKE) $(AM_MAKEFLAGS) dvi \ + && $(MAKE) $(AM_MAKEFLAGS) check \ +diff --git a/aclocal.m4 b/aclocal.m4 +index 0e09589..804c0b3 100644 +--- a/aclocal.m4 ++++ b/aclocal.m4 +@@ -1,4 +1,4 @@ +-# generated automatically by aclocal 1.14 -*- Autoconf -*- ++# generated automatically by aclocal 1.14.1 -*- Autoconf -*- + + # Copyright (C) 1996-2013 Free Software Foundation, Inc. + +@@ -35,7 +35,7 @@ AC_DEFUN([AM_AUTOMAKE_VERSION], + [am__api_version='1.14' + dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to + dnl require some minimum version. Point them to the right macro. +-m4_if([$1], [1.14], [], ++m4_if([$1], [1.14.1], [], + [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl + ]) + +@@ -51,7 +51,7 @@ m4_define([_AM_AUTOCONF_VERSION], []) + # Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced. + # This function is AC_REQUIREd by AM_INIT_AUTOMAKE. + AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION], +-[AM_AUTOMAKE_VERSION([1.14])dnl ++[AM_AUTOMAKE_VERSION([1.14.1])dnl + m4_ifndef([AC_AUTOCONF_VERSION], + [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl + _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))]) +diff --git a/config.h.in b/config.h.in +index 6646ea5..8571ef4 100644 +--- a/config.h.in ++++ b/config.h.in +@@ -617,7 +617,7 @@ + */ + #undef HAVE_ALLOCA_H + +-/* define to 1 if we have <attr/xattr.h> header */ ++/* Define to 1 if you have the <attr/xattr.h> header file. */ + #undef HAVE_ATTR_XATTR_H + + /* Define to 1 if you have the <bp-sym.h> header file. */ +@@ -924,21 +924,12 @@ + /* Define to 1 if you have the <features.h> header file. */ + #undef HAVE_FEATURES_H + +-/* Define to 1 if you have the `fgetxattr' function. */ +-#undef HAVE_FGETXATTR +- +-/* Define to 1 if you have the `flistxattr' function. */ +-#undef HAVE_FLISTXATTR +- + /* Define to 1 if you have the `flockfile' function. */ + #undef HAVE_FLOCKFILE + + /* Define to 1 if fseeko (and presumably ftello) exists and is declared. */ + #undef HAVE_FSEEKO + +-/* Define to 1 if you have the `fsetxattr' function. */ +-#undef HAVE_FSETXATTR +- + /* Define to 1 if you have the `fstatat' function. */ + #undef HAVE_FSTATAT + +@@ -990,9 +981,6 @@ + /* Define to 1 if you have the `gettimeofday' function. */ + #undef HAVE_GETTIMEOFDAY + +-/* Define to 1 if you have the `getxattr' function. */ +-#undef HAVE_GETXATTR +- + /* Define to 1 if you have the `grantpt' function. */ + #undef HAVE_GRANTPT + +@@ -1045,12 +1033,6 @@ + /* Define to 1 if you have the `lchown' function. */ + #undef HAVE_LCHOWN + +-/* Define to 1 if you have the `lgetxattr' function. */ +-#undef HAVE_LGETXATTR +- +-/* Define to 1 if you have the `attr' library (-lattr). */ +-#undef HAVE_LIBATTR +- + /* Define to 1 if you have the <libgen.h> header file. */ + #undef HAVE_LIBGEN_H + +@@ -1069,12 +1051,6 @@ + /* Define to 1 if you have the <linux/fd.h> header file. */ + #undef HAVE_LINUX_FD_H + +-/* Define to 1 if you have the `listxattr' function. */ +-#undef HAVE_LISTXATTR +- +-/* Define to 1 if you have the `llistxattr' function. */ +-#undef HAVE_LLISTXATTR +- + /* Define to 1 if you have the <locale.h> header file. */ + #undef HAVE_LOCALE_H + +@@ -1087,9 +1063,6 @@ + /* Define to 1 if the system has the type 'long long int'. */ + #undef HAVE_LONG_LONG_INT + +-/* Define to 1 if you have the `lsetxattr' function. */ +-#undef HAVE_LSETXATTR +- + /* Define to 1 if you have the `lstat' function. */ + #undef HAVE_LSTAT + +@@ -1867,9 +1840,6 @@ + /* Define to 1 if you have the `setlocale' function. */ + #undef HAVE_SETLOCALE + +-/* Define to 1 if you have the `setxattr' function. */ +-#undef HAVE_SETXATTR +- + /* Define to 1 if you have the <sgtty.h> header file. */ + #undef HAVE_SGTTY_H + +@@ -2074,7 +2044,7 @@ + /* Define to 1 if you have the <sys/wait.h> header file. */ + #undef HAVE_SYS_WAIT_H + +-/* define to 1 if we have <sys/xattr.h> header */ ++/* Define to 1 if you have the <sys/xattr.h> header file. */ + #undef HAVE_SYS_XATTR_H + + /* Define if struct tm has the tm_gmtoff member. */ +diff --git a/configure b/configure +index cfdd721..8cf6e91 100755 +--- a/configure ++++ b/configure +@@ -663,8 +663,6 @@ RSH + LIBOBJS + TAR_COND_GRANTPT_FALSE + TAR_COND_GRANTPT_TRUE +-TAR_LIB_ATTR_FALSE +-TAR_LIB_ATTR_TRUE + TAR_COND_XATTR_H_FALSE + TAR_COND_XATTR_H_TRUE + GNULIB_TEST_WARN_CFLAGS +@@ -34994,41 +34992,6 @@ else + TAR_COND_XATTR_H_FALSE= + fi + +- if false; then +- TAR_LIB_ATTR_TRUE= +- TAR_LIB_ATTR_FALSE='#' +-else +- TAR_LIB_ATTR_TRUE='#' +- TAR_LIB_ATTR_FALSE= +-fi +- +- if test "$ac_cv_header_sys_xattr_h" = yes; then +- for ac_func in getxattr fgetxattr lgetxattr \ +- setxattr fsetxattr lsetxattr \ +- listxattr flistxattr llistxattr +-do : +- as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh` +-ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var" +-if eval test \"x\$"$as_ac_var"\" = x"yes"; then : +- cat >>confdefs.h <<_ACEOF +-#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1 +-_ACEOF +- # only when functions are present +- +-$as_echo "#define HAVE_SYS_XATTR_H 1" >>confdefs.h +- +- if test "$with_xattrs" != no; then +- +-$as_echo "#define HAVE_XATTRS /**/" >>confdefs.h +- +- fi +- +-fi +-done +- +- fi +- +- # If <sys/xattr.h> is not found, then check for <attr/xattr.h> + if test "$ac_cv_header_sys_xattr_h" != yes; then + for ac_header in attr/xattr.h + do : +@@ -35050,13 +35013,20 @@ else + TAR_COND_XATTR_H_FALSE= + fi + +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for fgetxattr in -lattr" >&5 +-$as_echo_n "checking for fgetxattr in -lattr... " >&6; } +-if ${ac_cv_lib_attr_fgetxattr+:} false; then : ++ fi ++ ++ if test "$with_xattrs" != no; then ++ for i in getxattr fgetxattr lgetxattr \ ++ setxattr fsetxattr lsetxattr \ ++ listxattr flistxattr llistxattr ++ do ++ as_ac_Search=`$as_echo "ac_cv_search_$i" | $as_tr_sh` ++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing $i" >&5 ++$as_echo_n "checking for library containing $i... " >&6; } ++if eval \${$as_ac_Search+:} false; then : + $as_echo_n "(cached) " >&6 + else +- ac_check_lib_save_LIBS=$LIBS +-LIBS="-lattr $LIBS" ++ ac_func_search_save_LIBS=$LIBS + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + +@@ -35066,67 +35036,56 @@ cat confdefs.h - <<_ACEOF >conftest.$ac_ext + #ifdef __cplusplus + extern "C" + #endif +-char fgetxattr (); ++char $i (); + int + main () + { +-return fgetxattr (); ++return $i (); + ; + return 0; + } + _ACEOF +-if ac_fn_c_try_link "$LINENO"; then : +- ac_cv_lib_attr_fgetxattr=yes +-else +- ac_cv_lib_attr_fgetxattr=no ++for ac_lib in '' attr; do ++ if test -z "$ac_lib"; then ++ ac_res="none required" ++ else ++ ac_res=-l$ac_lib ++ LIBS="-l$ac_lib $ac_func_search_save_LIBS" ++ fi ++ if ac_fn_c_try_link "$LINENO"; then : ++ eval "$as_ac_Search=\$ac_res" + fi + rm -f core conftest.err conftest.$ac_objext \ +- conftest$ac_exeext conftest.$ac_ext +-LIBS=$ac_check_lib_save_LIBS +-fi +-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_attr_fgetxattr" >&5 +-$as_echo "$ac_cv_lib_attr_fgetxattr" >&6; } +-if test "x$ac_cv_lib_attr_fgetxattr" = xyes; then : +- cat >>confdefs.h <<_ACEOF +-#define HAVE_LIBATTR 1 +-_ACEOF +- +- LIBS="-lattr $LIBS" +- ++ conftest$ac_exeext ++ if eval \${$as_ac_Search+:} false; then : ++ break + fi ++done ++if eval \${$as_ac_Search+:} false; then : + +- if test "$ac_cv_lib_attr_fgetxattr" = yes; then +- TAR_LIB_ATTR_TRUE= +- TAR_LIB_ATTR_FALSE='#' + else +- TAR_LIB_ATTR_TRUE='#' +- TAR_LIB_ATTR_FALSE= ++ eval "$as_ac_Search=no" ++fi ++rm conftest.$ac_ext ++LIBS=$ac_func_search_save_LIBS + fi ++eval ac_res=\$$as_ac_Search ++ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5 ++$as_echo "$ac_res" >&6; } ++eval ac_res=\$$as_ac_Search ++if test "$ac_res" != no; then : ++ test "$ac_res" = "none required" || LIBS="$ac_res $LIBS" + +- if test "$ac_cv_header_attr_xattr_h" = yes; then +- for ac_func in getxattr fgetxattr lgetxattr \ +- setxattr fsetxattr lsetxattr \ +- listxattr flistxattr llistxattr +-do : +- as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh` +-ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var" +-if eval test \"x\$"$as_ac_var"\" = x"yes"; then : +- cat >>confdefs.h <<_ACEOF +-#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1 +-_ACEOF +- # only when functions are present ++fi + +-$as_echo "#define HAVE_ATTR_XATTR_H 1" >>confdefs.h ++ eval found=\$ac_cv_search_$i ++ test "$found" = "no" && break ++ done + +- if test "$with_xattrs" != no; then ++ if test "$found" != no; then + + $as_echo "#define HAVE_XATTRS /**/" >>confdefs.h + +- fi +- +-fi +-done +- + fi + fi + +@@ -38187,18 +38146,10 @@ if test -z "${TAR_COND_XATTR_H_TRUE}" && test -z "${TAR_COND_XATTR_H_FALSE}"; th + as_fn_error $? "conditional \"TAR_COND_XATTR_H\" was never defined. + Usually this means the macro was only invoked conditionally." "$LINENO" 5 + fi +-if test -z "${TAR_LIB_ATTR_TRUE}" && test -z "${TAR_LIB_ATTR_FALSE}"; then +- as_fn_error $? "conditional \"TAR_LIB_ATTR\" was never defined. +-Usually this means the macro was only invoked conditionally." "$LINENO" 5 +-fi + if test -z "${TAR_COND_XATTR_H_TRUE}" && test -z "${TAR_COND_XATTR_H_FALSE}"; then + as_fn_error $? "conditional \"TAR_COND_XATTR_H\" was never defined. + Usually this means the macro was only invoked conditionally." "$LINENO" 5 + fi +-if test -z "${TAR_LIB_ATTR_TRUE}" && test -z "${TAR_LIB_ATTR_FALSE}"; then +- as_fn_error $? "conditional \"TAR_LIB_ATTR\" was never defined. +-Usually this means the macro was only invoked conditionally." "$LINENO" 5 +-fi + if test -z "${TAR_COND_GRANTPT_TRUE}" && test -z "${TAR_COND_GRANTPT_FALSE}"; then + as_fn_error $? "conditional \"TAR_COND_GRANTPT\" was never defined. + Usually this means the macro was only invoked conditionally." "$LINENO" 5 +diff --git a/doc/Makefile.in b/doc/Makefile.in +index ca44f1a..42a06b3 100644 +--- a/doc/Makefile.in ++++ b/doc/Makefile.in +@@ -1,4 +1,4 @@ +-# Makefile.in generated by automake 1.14 from Makefile.am. ++# Makefile.in generated by automake 1.14.1 from Makefile.am. + # @configure_input@ + + # Copyright (C) 1994-2013 Free Software Foundation, Inc. +diff --git a/gnu/Makefile.in b/gnu/Makefile.in +index 03eed58..d908a03 100644 +--- a/gnu/Makefile.in ++++ b/gnu/Makefile.in +@@ -1,4 +1,4 @@ +-# Makefile.in generated by automake 1.14 from Makefile.am. ++# Makefile.in generated by automake 1.14.1 from Makefile.am. + # @configure_input@ + + # Copyright (C) 1994-2013 Free Software Foundation, Inc. +diff --git a/lib/Makefile.in b/lib/Makefile.in +index 41a9aca..1254b8f 100644 +--- a/lib/Makefile.in ++++ b/lib/Makefile.in +@@ -1,4 +1,4 @@ +-# Makefile.in generated by automake 1.14 from Makefile.am. ++# Makefile.in generated by automake 1.14.1 from Makefile.am. + # @configure_input@ + + # Copyright (C) 1994-2013 Free Software Foundation, Inc. +diff --git a/rmt/Makefile.in b/rmt/Makefile.in +index c3f2509..0f3dca4 100644 +--- a/rmt/Makefile.in ++++ b/rmt/Makefile.in +@@ -1,4 +1,4 @@ +-# Makefile.in generated by automake 1.14 from Makefile.am. ++# Makefile.in generated by automake 1.14.1 from Makefile.am. + # @configure_input@ + + # Copyright (C) 1994-2013 Free Software Foundation, Inc. +diff --git a/scripts/Makefile.in b/scripts/Makefile.in +index 57c0d0d..bf344ed 100644 +--- a/scripts/Makefile.in ++++ b/scripts/Makefile.in +@@ -1,4 +1,4 @@ +-# Makefile.in generated by automake 1.14 from Makefile.am. ++# Makefile.in generated by automake 1.14.1 from Makefile.am. + # @configure_input@ + + # Copyright (C) 1994-2013 Free Software Foundation, Inc. +diff --git a/src/Makefile.in b/src/Makefile.in +index 6f9a592..fc6fc87 100644 +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -1,4 +1,4 @@ +-# Makefile.in generated by automake 1.14 from Makefile.am. ++# Makefile.in generated by automake 1.14.1 from Makefile.am. + # @configure_input@ + + # Copyright (C) 1994-2013 Free Software Foundation, Inc. +@@ -99,7 +99,6 @@ POST_UNINSTALL = : + build_triplet = @build@ + host_triplet = @host@ + bin_PROGRAMS = tar$(EXEEXT) +-@TAR_LIB_ATTR_TRUE@am__append_1 = -lattr + subdir = src + DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \ + $(top_srcdir)/build-aux/depcomp $(noinst_HEADERS) +@@ -254,7 +253,7 @@ am__DEPENDENCIES_2 = ../lib/libtar.a ../gnu/libgnu.a \ + $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) + tar_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_2) \ + $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \ +- $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) ++ $(am__DEPENDENCIES_1) + AM_V_P = $(am__v_P_@AM_V@) + am__v_P_ = $(am__v_P_@AM_DEFAULT_V@) + am__v_P_0 = false +@@ -1225,8 +1224,7 @@ tar_SOURCES = \ + AM_CPPFLAGS = -I$(top_srcdir)/gnu -I../ -I../gnu -I$(top_srcdir)/lib -I../lib + AM_CFLAGS = $(WARN_CFLAGS) $(WERROR_CFLAGS) + LDADD = ../lib/libtar.a ../gnu/libgnu.a $(LIBINTL) $(LIBICONV) +-tar_LDADD = $(LIBS) $(LDADD) $(LIB_CLOCK_GETTIME) $(LIB_EACCESS) \ +- $(LIB_SELINUX) $(am__append_1) ++tar_LDADD = $(LIBS) $(LDADD) $(LIB_CLOCK_GETTIME) $(LIB_EACCESS) $(LIB_SELINUX) + all: all-am + + .SUFFIXES: +diff --git a/tests/Makefile.in b/tests/Makefile.in +index 6807509..50d7689 100644 +--- a/tests/Makefile.in ++++ b/tests/Makefile.in +@@ -1,4 +1,4 @@ +-# Makefile.in generated by automake 1.14 from Makefile.am. ++# Makefile.in generated by automake 1.14.1 from Makefile.am. + # @configure_input@ + + # Copyright (C) 1994-2013 Free Software Foundation, Inc. +diff --git a/lib/xattr-at.c b/lib/xattr-at.c +index 443ccae..009bde5 100644 +--- a/lib/xattr-at.c ++++ b/lib/xattr-at.c +@@ -18,6 +18,11 @@ + + #include <config.h> + ++/* Temporarily don't build. We are unable to build on (probably not only) ++ darwin due to lack of l*xattr callbacks (XATTR_NOFOLLOW is alternative) and ++ different function definitions. */ ++#ifdef HAVE_XATTRS ++ + #include "xattr-at.h" + #include "openat.h" + +@@ -108,3 +113,5 @@ + #undef AT_FUNC_RESULT + #undef AT_FUNC_POST_FILE_PARAM_DECLS + #undef AT_FUNC_POST_FILE_ARGS ++ ++#endif +diff --git a/src/Makefile.am b/src/Makefile.am +index 82b2d46..42daaef 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -52,7 +52,3 @@ AM_CFLAGS = $(WARN_CFLAGS) $(WERROR_CFLAGS) + LDADD = ../lib/libtar.a ../gnu/libgnu.a $(LIBINTL) $(LIBICONV) + + tar_LDADD = $(LIBS) $(LDADD) $(LIB_CLOCK_GETTIME) $(LIB_EACCESS) $(LIB_SELINUX) +- +-if TAR_LIB_ATTR +-tar_LDADD += -lattr +-endif +-- +1.9.3
\ No newline at end of file diff --git a/var/spack/repos/builtin/packages/tar/package.py b/var/spack/repos/builtin/packages/tar/package.py index c55b5165bf..4dce0e5be1 100644 --- a/var/spack/repos/builtin/packages/tar/package.py +++ b/var/spack/repos/builtin/packages/tar/package.py @@ -23,14 +23,24 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * +import sys +import os + class Tar(Package): - """GNU Tar provides the ability to create tar archives, as well as various other kinds of manipulation.""" + """GNU Tar provides the ability to create tar archives, as well as various + other kinds of manipulation.""" homepage = "https://www.gnu.org/software/tar/" - url = "http://ftp.gnu.org/gnu/tar/tar-1.28.tar.gz" + url = "https://ftp.gnu.org/gnu/tar/tar-1.28.tar.gz" + version('1.29', 'cae466e6e58c7292355e7080248f244db3a4cf755f33f4fa25ca7f9a7ed09af0') version('1.28', '6ea3dbea1f2b0409b234048e021a9fd7') + # see http://lists.gnu.org/archive/html/bug-tar/2014-08/msg00001.html and + # https://github.com/Homebrew/homebrew-core/commit/aef9a1792de4648d0322b4b04d32287532f046bb # NOQA: ignore=E501 + # TODO: when=sys.platform=='darwin' ? + patch('gnutar-configure-xattrs.patch', when='@1.28') + def install(self, spec, prefix): configure("--prefix=%s" % prefix) make() |