[Linux] [perl] perl 5.36.1 fails to build

[jacktose]

Additional Info

❌ I am using Windows Subsystem for Linux
❌ My "brew doctor output" says Your system is ready to brew. and am still able to reproduce my issue.
✔️ I ran brew update and am still able to reproduce my issue.
❌ I have resolved all warnings from brew doctor and that did not fix my problem.
✔️ I searched for recent similar issues at https://github.com/Homebrew/homebrew-core/issues?q=is%3Aissue and found no duplicates.
This is an unsupported configuration because I don't have root (and it's CentOS 7).

Output of brew config

https://gist.github.com/jacktose/eb2d067ce37b055725d34af3d76f74d5#file-00-config-out

Output of brew doctor

https://gist.github.com/jacktose/eb2d067ce37b055725d34af3d76f74d5#file-00-doctor-out

Description of issue

What were you trying to do (and why)?

Upgrade perl because it's a dependency of vim and I want to upgrade vim.

What happened (include all command output)?

$ brew upgrade perl
==> Upgrading 1 outdated package:
perl 5.36.0 -> 5.36.1
==> Fetching perl
Warning: Building perl from source as the bottle needs:
- HOMEBREW_CELLAR: /home/linuxbrew/.linuxbrew/Cellar (yours is /data/shared/lusers/jacktose/.linuxbrew/Cellar)
- HOMEBREW_PREFIX: /home/linuxbrew/.linuxbrew (yours is /data/shared/lusers/jacktose/.linuxbrew)
==> Downloading https://github.com/Perl/perl5/commit/7e19816aa8661ce0e984742e2df11dd20dcdff18.patch?full_index=
Already downloaded: /usr/lusers/jacktose/.cache/Homebrew/downloads/7f32311b27d50333920999cd093f656926711401ab1fb378a60622e1e6d84b49--7e19816aa8661ce0e984742e2df11dd20dcdff18.patch
==> Downloading https://www.cpan.org/src/5.0/perl-5.36.1.tar.xz
Already downloaded: /usr/lusers/jacktose/.cache/Homebrew/downloads/0c3623eef02b5d10e6d80df0336d5d5e2a8b5bca762ba34c87f42b3327043f18--perl-5.36.1.tar.xz
==> Upgrading perl
  5.36.0 -> 5.36.1 

==> Patching
==> Applying 7e19816aa8661ce0e984742e2df11dd20dcdff18.patch
File Configure is read-only; trying to patch anyway
patching file Configure
Hunk #1 succeeded at 1503 (offset -2 lines).
==> ./Configure -des -Dinstallstyle=lib/perl5 -Dinstallprefix=/data/shared/lusers/jacktose/.linuxbrew/Cellar/pe
==> make
Last 15 lines from /usr/lusers/jacktose/.cache/Homebrew/Logs/perl/02.make:
Processing IndicSyllabicCategory.txt
Processing BidiBrackets.txt
Processing IndicPositionalCategory.txt
Processing VerticalOrientation.txt
Processing EquivalentUnifiedIdeograph.txt
Processing emoji/emoji.txt
Processing IdStatus.txt
Processing IdType.txt
Finishing processing Unicode properties
Compiling Perl properties
Creating Perl synonyms
Writing tables
Making pod file
Making test script
Updating 'mktables.lst'

READ THIS: https://docs.brew.sh/Troubleshooting

What did you expect to happen?

Brew to build the new version of perl from source. (Not bottle because I don't have root.)

[jacktose]

This is still a problem for me, and I'm still trying to figure it out, but I don't understand the buildchain at all.

Here's a recent gist-log. The farthest back I can trace the error is in 02.make lines 461–499, notably a bunch of errors like this:

/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /tmp/perl-20230626-4176-pzvvmp/perl-5.36.1/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /tmp/perl-20230626-4176-pzvvmp/perl-5.36.1/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /tmp/perl-20230626-4176-pzvvmp/perl-5.36.1/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /data/shared/lusers/jacktose/.linuxbrew/opt/libxcrypt/lib/libcrypt.so.2)

I have brew's glibc 2.35 installed, but I don't know if all these requirements for other versions are really a problem. Or am I missing something else?

[osalbahr]

It’s hard to tell without knowing your system’s configuration, but I guess your issue is the same as this one:

• [linuxbrew] gcc-13 doesn't work on an Ubuntu distribution which targets glibc 2.31 homebrew-core#135068

[porelli]

$ brew config
HOMEBREW_VERSION: 4.0.29
ORIGIN: https://github.com/Homebrew/brew
HEAD: a2a05f96ef6215643f599e7bfeaacd4f34e7cd9a
Last commit: 18 hours ago
Core tap origin: https://github.com/Homebrew/homebrew-core
Core tap HEAD: f1ce780e60ca3f729908257a9b30deb2fb8662c5
Core tap last commit: 9 minutes ago
Core tap branch: master
Core tap JSON: 27 Mar 15:58 UTC
HOMEBREW_PREFIX: /local/home/linuxbrew/.linuxbrew
HOMEBREW_REPOSITORY: /local/home/linuxbrew/.linuxbrew/Homebrew
HOMEBREW_CELLAR: /local/home/linuxbrew/.linuxbrew/Cellar
HOMEBREW_CASK_OPTS: []
HOMEBREW_EDITOR: vim
HOMEBREW_MAKE_JOBS: 40
HOMEBREW_NO_INSTALL_FROM_API: set
Homebrew Ruby: 2.6.10 => /local/home/linuxbrew/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/2.6.10_1/bin/ruby
CPU: 40-core 64-bit haswell
Clang: N/A
Git: 2.40.1 => /bin/git
Curl: 8.0.1 => /bin/curl
Kernel: Linux 5.4.247-169.350.x86_64 x86_64 GNU/Linux
OS: Unknown
Host glibc: 2.26
/usr/bin/gcc: 10.4.1
/usr/bin/ruby: 2.0.0
glibc: 2.35_1
gcc@11: N/A
gcc: 13.1.0
xorg: N/A

$ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: You have unlinked kegs in your Cellar.
Leaving kegs unlinked can lead to build-trouble and cause formulae that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
  curl

The command I run to get the snippet was just inspecting the make log file (/home/user/.cache/Homebrew/Logs/perl/02.make)

For the moment I resolved using the bottle (brew reinstall --force-bottle perl) and everything seems working ok:

perl -v

This is perl 5, version 36, subversion 1 (v5.36.1) built for x86_64-linux-thread-multi

Copyright 1987-2023, Larry Wall

Perl may be copied only under the terms of either the Artistic License or the
GNU General Public License, which may be found in the Perl 5 source kit.

Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl".  If you have access to the
Internet, point your browser at https://www.perl.org/, the Perl Home Page.

To your point, yes it does look like the same problem. Indeed I had to use the gcc bottle as well (brew reinstall --force-bottle gcc)

[osalbahr]

Interesting, glad you figured it out!

I assumed you’d probably have to also force linking binutils. But maybe it happened indirectly already via one of the other commands you ran. You can check via which -a ld, I expect Homebrew’s ld to appear as the first line.

If brew doctor no longer complains then you’re all set.

[osalbahr]

Side note: I noticed that you have OS: Unknown as part of your brew config. I’ve noticed that before. I think it’s because not all systems have the lsb_release command, but you’ll probably see a PRETTY_NAME field in cat /etc/os-release. That’s a fallback I plan to implement at some point (Homebrew/brew#15689 (comment)).

If the lsb_release command can’t be found, but echo "$(source /etc/os-release && echo "${PRETTY_NAME}")" does show your OS, then that confirms it as a viable fallback that might help with future bug reports.

[jacktose]

I just tried building again (5.38.2 now) with similar results: gist.

I get a lot of those same errors.

...
sh: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /data/shared/lusers/jacktose/.linuxbrew/opt/libxcrypt/lib/libcrypt.so.2)
sh: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /data/shared/lusers/jacktose/.linuxbrew/opt/libxcrypt/lib/libcrypt.so.2)
sh: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /data/shared/lusers/jacktose/.linuxbrew/opt/libxcrypt/lib/libcrypt.so.2)
sh: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /data/shared/lusers/jacktose/.linuxbrew/opt/libxcrypt/lib/libcrypt.so.2)
sh: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /data/shared/lusers/jacktose/.linuxbrew/opt/libxcrypt/lib/libcrypt.so.2)
sh: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /data/shared/lusers/jacktose/.linuxbrew/opt/libxcrypt/lib/libcrypt.so.2)
sh: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /data/shared/lusers/jacktose/.linuxbrew/opt/libxcrypt/lib/libcrypt.so.2)
Generating a Unix-style Makefile
Writing Makefile for attributes
sh: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /data/shared/lusers/jacktose/.linuxbrew/opt/libxcrypt/lib/libcrypt.so.2)
sh: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
sh: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /data/shared/lusers/jacktose/.linuxbrew/opt/libxcrypt/lib/libcrypt.so.2)
/usr/bin/make: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /data/shared/lusers/jacktose/.linuxbrew/opt/libxcrypt/lib/libcrypt.so.2)
/usr/bin/make: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /data/shared/lusers/jacktose/.linuxbrew/opt/libxcrypt/lib/libcrypt.so.2)
Unsuccessful make(ext/attributes): code=256 at make_ext.pl line 584.
make: *** [lib/auto/attributes/attributes.so] Error 25
make: *** Waiting for unfinished jobs....
Generating a Unix-style Makefile
Writing Makefile for B
/usr/bin/make: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /data/shared/lusers/jacktose/.linuxbrew/opt/libxcrypt/lib/libcrypt.so.2)
/usr/bin/make: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /data/shared/lusers/jacktose/.linuxbrew/opt/libxcrypt/lib/libcrypt.so.2)
Unsuccessful make(ext/B): code=256 at make_ext.pl line 584.
make: *** [lib/auto/B/B.so] Error 25
Generating a Unix-style Makefile
Writing Makefile for Compress::Raw::Bzip2
/usr/bin/make: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /data/shared/lusers/jacktose/.linuxbrew/opt/libxcrypt/lib/libcrypt.so.2)
/usr/bin/make: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /tmp/perl-20231205-2759-cifu17/perl-5.38.2/libperl.so)
/usr/bin/make: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /data/shared/lusers/jacktose/.linuxbrew/opt/libxcrypt/lib/libcrypt.so.2)
Unsuccessful make(cpan/Compress-Raw-Bzip2): code=256 at make_ext.pl line 584.
make: *** [lib/auto/Compress/Raw/Bzip2/Bzip2.so] Error 25
...

I hadn't thought to try --force-bottle; I assumed that brew had good reason to build. But it seems to have worked.

[osalbahr]

I'm not sure what your errors mean, but I had generally good experience with Spack on CentOS 7. After installing spack you should be able to spack install vim && spack load vim.