LinuxBrew: issue with installing dependencies, glibc@2.13 and gcc@5 #3399

akhst7 · 2022-06-29T17:06:07Z

akhst7
Jun 29, 2022

I've been trying to install several packages that require glibc@2.13 and gcc@5 as dependencies in RHEL7 which is already loaded backward compatible glibc 2.17, and run into issue compiling glibc@2.13 as follows;

==> Upgrading libxml2
  2.9.13 -> 2.9.14_2 

==> Installing dependencies for libxml2: glibc@2.13, gcc@5 and icu4c
==> Installing libxml2 dependency: glibc@2.13
==> ../configure --disable-debug --disable-dependency-tracking --disable-silent-rules --prefix=/geode2/home/u010/aho
Last 15 lines from /N/u/me/Carbonate/.cache/Homebrew/Logs/glibc@2.13/01.configure:
../configure
--disable-debug
--disable-dependency-tracking
--disable-silent-rules
--prefix=/geode2/home/u010/me/Carbonate/.linuxbrew/Cellar/glibc@2.13/2.13
--enable-obsolete-rpc
--without-selinux
--with-headers=/geode2/home/u010/me/Carbonate/.linuxbrew/opt/linux-headers@4.4/include

checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking for suffix of object files... configure: error: in `/tmp/glibcA2.13-20220629-8492-va29e8/glibc-2.13/build':
configure: error: cannot compute suffix of object files: cannot compile

Any ways to tell brew to use glibc 2.17 instead of compiling glibc@2.13 ?

Thanks.

zc62 · 2022-06-29T21:10:24Z

zc62
Jun 29, 2022

I'm having a similar issue. I'm on CentOS 7. When upgrading, brew suddenly asks for glibc2.13 (brew has gcc-5 and glibc2.23), and the compilation failed at

{standard input}: Assembler messages:
{standard input}: Error: `_obstack@GLIBC_2.2.5' can't be versioned to common symbol '_obstack_compat'

In addition, brew deleted the links to older versions of the programs, whose new versions need glibc2.13, thus breaking a lot of things. (Pretty confused about why glibc2.13 is needed)

EDIT: packages in trouble were libxml2, curl, git and neovim. Running brew link restored those packages to older versions.

0 replies

carlocab · 2022-06-29T23:15:34Z

carlocab
Jun 29, 2022

@Homebrew/linux

0 replies

danielnachun · 2022-06-30T01:07:05Z

danielnachun
Jun 30, 2022

Only two packages have glibc@2.13 as a dependency - binutils and zlib. And both are relocatable and shouldn't need to be built from source by any user. I've just upgraded my own CentOS 7 install and this did not happen so I'm unsure how this would happen. Furthermore zlib didn't even get a revision bump so it shouldn't even be changed. binutils was revision bumped but it is should need glibc@2.13 just to install.

0 replies

danielnachun · 2022-06-30T01:07:31Z

danielnachun
Jun 30, 2022

Are these fresh installs or upgrades to existing ones? That will help us narrow down what's going wrong.

6 replies

akhst7 Jun 30, 2022
Author

Some of mine are fresh install.

danielnachun Jun 30, 2022

Okay, for the ones which are not fresh installs, can you try to do:

brew uninstall --ignore-dependencies zlib; brew install -v zlib
brew uninstall --ignore-dependencies binutils; brew install -v binutils

Neither of those should try to compile from source. After that is done, try to run your upgrades again.

zc62 Jun 30, 2022

It's complicated. My brew relies on brewed git and curl, uninstalling zlib breaks them, therefore I need to go back to compile git by myself. Also if I ignore those errors, I do still seem to see glibc2.13 is being compiled. Will update more after I compile my own git.

danielnachun Jun 30, 2022

It might be easier to use miniconda to get your own copy of git and curl, but that's up to you. The most important thing to know here is if brew install zlib or brew install binutils are falling back to building from source. glibc@2.13 is a build-only dependency that should be ignored when installing from a bottle, so either zlib or binutils are building from source even though they shouldn't, or brew is mistakenly trying to install a build-only dependency while installing from a bottle.

zc62 Jun 30, 2022

Oh, I was stupid. I have anaconda3 installed but never realized it ships git and curl. Never mind, I got my git compiled and ran those commands. zlib and binutils install fine without asking for glibc2.13, but when I upgrade again, the same thing happens.

Bo98 · 2022-06-30T02:30:09Z

Bo98
Jun 30, 2022
Maintainer

I've found the cause and am able to reproduce the issue. I'm working on a fix.

1 reply

Bo98 Jun 30, 2022
Maintainer

Homebrew/brew#13494

iMichka · 2022-06-30T20:27:56Z

iMichka
Jun 30, 2022

Homebrew/brew#13494 has been merged; you can now brew update and try again.

1 reply

zc62 Jun 30, 2022

I can confirm it works now.

akhst7 · 2022-07-01T22:18:16Z

akhst7
Jul 1, 2022
Author

It works now. Thanks.

2 replies

wscott Jul 31, 2022

I fixed the '_obstack_compat' failure with the following tweak.

diff --git a/Formula/glibc@2.13.rb b/Formula/glibc@2.13.rb
index 2aad2f76c19..a9dec355e7c 100644
--- a/Formula/glibc@2.13.rb
+++ b/Formula/glibc@2.13.rb
@@ -114,6 +114,8 @@ class GlibcAT213 < Formula
     # Use brewed ld.so.preload rather than the host's /etc/ld.so.preload
     inreplace "elf/rtld.c", '= "/etc/ld.so.preload";', "= \"#{prefix}/etc/ld.so.preload\";"
 
+    system "perl", "-i", "-lpe", "s/obstack_compat;/obstack_compat = 0;/", "malloc/obstack.c"
+
     mkdir "build" do
       args = [
         "--disable-debug",

But the after the recent 2.13_1 change my compiles are again failing:

Makefile:167: recipe for target '/tmp/glibcA2.13-20220731-13429-c4smf4/glibc-2.13/build/sunrpc/xbootparam_prot.stmp' failed
Inconsistency detected by ld.so: dynamic-link.h: 209: elf_get_dynamic_info: Assertion `info[15] == ((void *)0)' failed!
make[2]: *** [/tmp/glibcA2.13-20220731-13429-c4smf4/glibc-2.13/build/sunrpc/xbootparam_prot.stmp] Error 127
make[2]: *** Waiting for unfinished jobs....

Not sure how to fix that error. This is on SLES12

Bo98 Jul 31, 2022
Maintainer

You should never need to install glibc@2.13. Please provide more information, like brew config and the full output of the command you are running.

wscott · 2022-07-31T18:01:42Z

wscott
Jul 31, 2022

Huh. That's odd. A 'brew remove glibc@2.13' worked just fine without complaining about dependencies. Did that change recently? I am sure I had programs that required that package within the last month.

Thanks.

1 reply

Bo98 Jul 31, 2022
Maintainer

Yes, this was a bug which was fixed in Homebrew 3.5.4.

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LinuxBrew: issue with installing dependencies, glibc@2.13 and gcc@5 #3399

Replies: 8 comments · 11 replies

akhst7 Jun 30, 2022 Author

Bo98 Jun 30, 2022 Maintainer

Bo98 Jun 30, 2022 Maintainer

akhst7 Jul 1, 2022 Author

Bo98 Jul 31, 2022 Maintainer

Bo98 Jul 31, 2022 Maintainer

Replies: 8 comments 11 replies

akhst7 Jun 30, 2022
Author

Bo98
Jun 30, 2022
Maintainer

Bo98 Jun 30, 2022
Maintainer

akhst7
Jul 1, 2022
Author

Bo98 Jul 31, 2022
Maintainer

Bo98 Jul 31, 2022
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