spack install gzip fails.
> spack install gzip
==> Installing gzip-1.12-hjaryhgrkevrdht64fqblm3pnyyd26ep [1/1]
==> No binary for gzip-1.12-hjaryhgrkevrdht64fqblm3pnyyd26ep found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/5b/5b4fb14d38314e09f2fc8a1c510e7cd540a3ea0e3eb9b0420046b82c3bf41085.tar.gz
==> No patches needed for gzip
==> gzip: Executing phase: 'autoreconf'
==> gzip: Executing phase: 'configure'
==> gzip: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
'make' '-j16' 'V=1'
13 errors found in build log:
1634 /umbc/rs/iharp/common/chhaya/spack/lib/spack/env/gcc/gcc -DHAVE_CONFIG_H -I. -I/tmp/ckulkar1/spack-stage/spack-stage-gzip-1.12-hjaryhgrkevrdht64fqblm3pnyyd26ep/spack-src/
lib -Wno-cast-qual -Wno-conversion -Wno-float-equal -Wno-sign-compare -Wno-undef -Wno-unused-function -Wno-unused-parameter -Wno-float-conversion -Wimplicit-fallthro
ugh -Wno-pedantic -Wno-sign-conversion -Wno-type-limits -Wno-unsuffixed-float-constants -g -O2 -MT libgzip_a-fflush.o -MD -MP -MF .deps/libgzip_a-fflush.Tpo -c -o libgzip
_a-fflush.o `test -f 'fflush.c' || echo '/tmp/ckulkar1/spack-stage/spack-stage-gzip-1.12-hjaryhgrkevrdht64fqblm3pnyyd26ep/spack-src/lib/'`fflush.c
1635 In file included from /usr/include/string.h:633,
1636 from ./string.h:41,
1637 from /tmp/ckulkar1/spack-stage/spack-stage-gzip-1.12-hjaryhgrkevrdht64fqblm3pnyyd26ep/spack-src/lib/filename.h:24,
1638 from /tmp/ckulkar1/spack-stage/spack-stage-gzip-1.12-hjaryhgrkevrdht64fqblm3pnyyd26ep/spack-src/lib/dirname.h:24,
1639 from /tmp/ckulkar1/spack-stage/spack-stage-gzip-1.12-hjaryhgrkevrdht64fqblm3pnyyd26ep/spack-src/lib/stripslash.c:21:
>> 1640 ./string.h:1091:1: error: expected identifier or '(' before '__extension__'
1641 1091 | _GL_FUNCDECL_SYS (strndup, char *,
1642 | ^~~~~~~~~~~~~~~~
>> 1643 make[3]: *** [libgzip_a-stripslash.o] Error 1
1644 make[3]: *** Waiting for unfinished jobs....
1645 In file included from /usr/include/string.h:633,
1646 from ./string.h:41,
1647 from /tmp/ckulkar1/spack-stage/spack-stage-gzip-1.12-hjaryhgrkevrdht64fqblm3pnyyd26ep/spack-src/lib/filename.h:24,
1648 from /tmp/ckulkar1/spack-stage/spack-stage-gzip-1.12-hjaryhgrkevrdht64fqblm3pnyyd26ep/spack-src/lib/dirname.h:24,
1649 from /tmp/ckulkar1/spack-stage/spack-stage-gzip-1.12-hjaryhgrkevrdht64fqblm3pnyyd26ep/spack-src/lib/dirname-lgpl.c:21:
>> 1650 ./string.h:1091:1: error: expected identifier or '(' before '__extension__'
1651 1091 | _GL_FUNCDECL_SYS (strndup, char *,
1652 | ^~~~~~~~~~~~~~~~
1653 mv -f .deps/libgzip_a-open-safer.Tpo .deps/libgzip_a-open-safer.Po
1654 In file included from /usr/include/string.h:633,
1655 from ./string.h:41,
1656 from /tmp/ckulkar1/spack-stage/spack-stage-gzip-1.12-hjaryhgrkevrdht64fqblm3pnyyd26ep/spack-src/lib/basename-lgpl.c:25:
>> 1657 ./string.h:1091:1: error: expected identifier or '(' before '__extension__'
1658 1091 | _GL_FUNCDECL_SYS (strndup, char *,
1659 | ^~~~~~~~~~~~~~~~
>> 1660 make[3]: *** [libgzip_a-dirname-lgpl.o] Error 1
1661 mv -f .deps/libgzip_a-exitfail.Tpo .deps/libgzip_a-exitfail.Po
>> 1662 make[3]: *** [libgzip_a-basename-lgpl.o] Error 1
1663 mv -f .deps/libgzip_a-fd-hook.Tpo .deps/libgzip_a-fd-hook.Po
1664 mv -f .deps/libgzip_a-creat-safer.Tpo .deps/libgzip_a-creat-safer.Po
1665 mv -f .deps/libgzip_a-dup-safer-flag.Tpo .deps/libgzip_a-dup-safer-flag.Po
1666 In file included from /usr/include/string.h:633,
1667 from ./string.h:41,
1668 from /tmp/ckulkar1/spack-stage/spack-stage-gzip-1.12-hjaryhgrkevrdht64fqblm3pnyyd26ep/spack-src/lib/chdir-long.c:27:
>> 1669 ./string.h:1091:1: error: expected identifier or '(' before '__extension__'
1670 1091 | _GL_FUNCDECL_SYS (strndup, char *,
1671 | ^~~~~~~~~~~~~~~~
1672 mv -f .deps/libgzip_a-fclose.Tpo .deps/libgzip_a-fclose.Po
1673 mv -f .deps/libgzip_a-cloexec.Tpo .deps/libgzip_a-cloexec.Po
1674 In file included from /usr/include/string.h:633,
1675 from ./string.h:41,
1676 from /tmp/ckulkar1/spack-stage/spack-stage-gzip-1.12-hjaryhgrkevrdht64fqblm3pnyyd26ep/spack-src/lib/openat-proc.c:30:
>> 1677 ./string.h:1091:1: error: expected identifier or '(' before '__extension__'
1678 1091 | _GL_FUNCDECL_SYS (strndup, char *,
1679 | ^~~~~~~~~~~~~~~~
1680 mv -f .deps/libgzip_a-fcntl.Tpo .deps/libgzip_a-fcntl.Po
1681 mv -f .deps/libgzip_a-fd-safer-flag.Tpo .deps/libgzip_a-fd-safer-flag.Po
1682 mv -f .deps/libgzip_a-opendir-safer.Tpo .deps/libgzip_a-opendir-safer.Po
>> 1683 make[3]: *** [libgzip_a-openat-proc.o] Error 1
>> 1684 make[3]: *** [libgzip_a-chdir-long.o] Error 1
1685 mv -f .deps/libgzip_a-fflush.Tpo .deps/libgzip_a-fflush.Po
1686 make[3]: Leaving directory `/tmp/ckulkar1/spack-stage/spack-stage-gzip-1.12-hjaryhgrkevrdht64fqblm3pnyyd26ep/spack-src/spack-build/lib'
>> 1687 make[2]: *** [all] Error 2
1688 make[2]: Leaving directory `/tmp/ckulkar1/spack-stage/spack-stage-gzip-1.12-hjaryhgrkevrdht64fqblm3pnyyd26ep/spack-src/spack-build/lib'
>> 1689 make[1]: *** [all-recursive] Error 1
1690 make[1]: Leaving directory `/tmp/ckulkar1/spack-stage/spack-stage-gzip-1.12-hjaryhgrkevrdht64fqblm3pnyyd26ep/spack-src/spack-build'
>> 1691 make: *** [all] Error 2
See build log for details:
/tmp/ckulkar1/spack-stage/spack-stage-gzip-1.12-hjaryhgrkevrdht64fqblm3pnyyd26ep/spack-build-out.txt
I've located the offending file: .../spack-stage-gzip-1.12-hjaryhgrkevrdht64fqblm3pnyyd26ep/spack-src/spack-build/lib/string.h
I can comment out the offending codeblock:
# if 0 // __GNUC__ >= 11
/* For -Wmismatched-dealloc: Associate strndup with free or rpl_free. */
_GL_FUNCDECL_SYS (strndup, char *,
(char const *__s, size_t __n)
_GL_ARG_NONNULL ((1))
_GL_ATTRIBUTE_MALLOC _GL_ATTRIBUTE_DEALLOC_FREE);
# endif
I can diff -u string.h string.h.modified > gzip.patch
Then I can fiddle the first 2 lines of the patch to get:
> cat patch
--- string.h 2023-10-31 21:07:57.752141778 -0400
+++ string.h 2023-10-31 21:13:39.283715230 -0400
@@ -1086,7 +1086,7 @@
# endif
_GL_CXXALIASWARN (strndup);
#else
-# if __GNUC__ >= 11
+# if 0 // __GNUC__ >= 11
/* For -Wmismatched-dealloc: Associate strndup with free or rpl_free. */
_GL_FUNCDECL_SYS (strndup, char *,
(char const *__s, size_t __n)
Now I can fiddle /home/ckulkar1/iharp_common/chhaya/spack/var/spack/repos/builtin/packages/gzip/package.py
class Gzip(AutotoolsPackage):
"""GNU Gzip is a popular data compression program originally written by
Jean-loup Gailly for the GNU project."""
homepage = "https://www.gnu.org/software/gzip/"
url = "https://ftp.gnu.org/gnu/gzip/gzip-1.10.tar.gz"
version("1.12", sha256="5b4fb14d38314e09f2fc8a1c510e7cd540a3ea0e3eb9b0420046b82c3bf41085")
version("1.11", sha256="3e8a0e0c45bad3009341dce17d71536c4c655d9313039021ce7554a26cd50ed9")
version("1.10", sha256="c91f74430bf7bc20402e1f657d0b252cb80aa66ba333a25704512af346633c68")
# Gzip makes a recursive symlink if built in-source
build_directory = "spack-build"
patch('gzip.patch')
... and copy the gzip.patch into the same folder.
But when I run spack install gzip I get:
> spack install gzip
==> Installing gzip-1.12-zalk3vqblkxwfrgkyol4msfelfme64qw [1/1]
==> No binary for gzip-1.12-zalk3vqblkxwfrgkyol4msfelfme64qw found: installing from source
==> Using cached archive: /umbc/rs/iharp/common/chhaya/spack/var/spack/cache/_source-cache/archive/5b/5b4fb14d38314e09f2fc8a1c510e7cd540a3ea0e3eb9b0420046b82c3bf41085.tar.gz
The text leading up to this was:
--------------------------
|--- lib/string.h 2023-10-31 21:07:57.752141778 -0400
|+++ lib/string.h 2023-10-31 21:13:39.283715230 -0400
--------------------------
File to patch:
... and I just don't know what to do next.
Maybe I can only patch over the SOURCE files from the downloaded .gzip?
I've tried downloading and unpacking https://ftp.gnu.org/gnu/gzip/gzip-1.12.tar.gz and inspecting gzip-1.12/lib/string.in.h (which I suppose gets converted into the offending string.h)
So should I be trying to apply a patch to this .in.h file?
And if so what should the folder-paths on the patch look like?
Somehow I need to tweak this string.h file after the spack installer has downloaded the .gzip and compiled the .in.h files to .h files. but before it tries to build the package.
I'm really stuck here. I could file an issue on spack, but spack has over 2k open issues.
Edit:
I was able to solve my original problem of bootstrapping spack (with spack install spack) by commenting out:
# patch('gzip.patch')
... from my
/path/to/spack/var/spack/repos/builtin/packages/gzip/package.py, then building gzip with the NATIVE compiler on the cluster:
> spack clean -a
> spack install gzip %[email protected]
..., modifying ~/.spack/packages.yaml:
packages:
all:
compiler: [[email protected]]
gzip:
externals:
- spec: [email protected]
prefix: [FOO]
buildable: False
(where [FOO] is the output of spack location -i [email protected]), and running:
spack install spack
Now:
> spack find --explicit
-- linux-centos7-cascadelake / [email protected] -----------------------
[email protected] [email protected]
-- linux-centos7-haswell / [email protected] ----------------------------
[email protected]
-- linux-centos7-sandybridge / [email protected] ------------------------
[email protected]
I won't post this as an answer as it's a workaround.
You just needed to supply the full path from spack-src:
Alternatively, you could supply a working directory argument to the patch() function.