如何将补丁应用于 spack 包？

问：

spack install gzip失败。

> 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

我找到了有问题的文件：.../spack-stage-gzip-1.12-hjaryhgrkevrdht64fqblm3pnyyd26ep/spack-src/spack-build/lib/string.h

我可以注释掉有问题的代码块：

# 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

我可以diff -u string.h string.h.modified > gzip.patch

然后我可以摆弄补丁的前 2 行以获得：

> 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)

现在我可以摆弄 /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')

...并将 gzip.patch 复制到同一文件夹中。

但是当我跑步时，我得到：spack install gzip

> 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: 

...我只是不知道下一步该怎么做。

也许我只能从下载的 .gzip 中修补 SOURCE 文件？

我尝试下载并解压缩 https://ftp.gnu.org/gnu/gzip/gzip-1.12.tar.gz 并检查 gzip-1.12/lib/string.in.h（我想它会转换为有问题的 string.h）

那么我应该尝试对这个 .in.h 文件应用补丁吗？

如果是这样，补丁上的文件夹路径应该是什么样子的？

不知何故，在 spack 安装程序下载 .gzip 并将 .in.h 文件编译为 .h 文件后，我需要调整这个 string.h 文件。但在它尝试构建包之前。

我真的被困在这里。我可以在 spack 上提交问题，但 spack 有超过 2k 的未解决问题。

编辑：

我能够通过注释来解决我最初的引导 spack 问题（使用 ）：spack install spack

    # patch('gzip.patch')

...从我的 /path/to/spack/var/spack/repos/builtin/packages/gzip/package.py，然后在集群上使用 NATIVE 编译器进行构建：gzip

> spack clean -a
> spack install gzip %[email protected]

..., modifying ~/.spack/packages.yaml:

包： 都： 编译器： [[email protected]] gzip： 外部： - 规格：[email protected] 前缀：[FOO] buildable：假

(where [FOO] is the output of `spack location -i [email protected]`), and running:

spack 安装 spack

Now:

spack 查找 --explicit -- linux-centos7-cascadelake / [email protected] ----------------------- [email protected] [email protected]

-- linux-centos7-haswell / [email protected] ---------------------------- [email protected]

-- linux-centos7-sandybridge / [电子邮件保护] ------------------------ [电子邮件保护]

I won't post this as an answer as it's a workaround.