libxml2: 2.12.7 → 2.13.2

[jtojnar]

Description of changes

Supersedes #319982, #324629

Things done

• Built on platform(s)
  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin
• For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)
  • sandbox = relaxed
  • sandbox = true
• Tested, as applicable:
  • NixOS test(s) (look inside nixos/tests)
  • and/or package tests
  • or, for functions and "core" functionality, tests in lib/tests or pkgs/test
  • made sure NixOS tests are linked to the relevant packages
• Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
• Tested basic functionality of all binary files (usually in ./result/bin/)
• 24.11 Release Notes (or backporting 23.11 and 24.05 Release notes)
  • (Package updates) Added a release notes entry if the change is major or breaking
  • (Module updates) Added a release notes entry if the change is significant
  • (Module addition) Added a release notes entry if adding a new NixOS module
• Fits CONTRIBUTING.md.

---

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[trofi]

Bisect says 25bc618 libxml2: 2.12.7 → 2.13.2 broke colord build in staging as:

ERROR: Error in gtkdoc helper script:

ERROR: ['/nix/store/3bjl4a6x553igz8av394afjlb9r85p9z-gtk-doc-1.34.0/bin/gtkdoc-mkhtml', '--path=/build/colord-1.4.6/doc/api:/build/colord-1.4.6/build/doc/api', 'colord', '../colord-docs.xml'] failed with status 6
warning: failed to load external entity "../../../COPYING"

[jtojnar]

@trofi that sounds like an issue with the build system. Looking at the code, the path refers to build/copying since Meson does out-of-tree builds:

https://github.com/hughsie/colord/blob/4a5a8ac167f940d74b4ac6e3f588bd50b8b777ea/doc/api/colord-docs.xml#L107

The following appears to fix it:

substituteInPlace doc/api/colord-docs.xml --replace-fail "../../COPYING" "../../../COPYING"

But that is not upstreamable since build directory location is configurable.

Also for some reason, the warning actually shows correct relative path (one higher than used).

And it is not clear to me why it fails when there is a xinclude fallback.

[jtojnar]

Actually, might be the same as https://gitlab.gnome.org/GNOME/libxml2/-/issues/733 that affected systemd docs. We should probably backport that. Edit: Those are part of 2.13.2.

[jtojnar]

Opened new upstream issue: https://gitlab.gnome.org/GNOME/libxml2/-/issues/772

[trofi]

Looks like librdf_raptor2 is also affected by the same 25bc618 libxml2: 2.12.7 → 2.13.2 on staging:

$ nix build --no-link -f. -L librdf_raptor2
...
raptor2-unstable> /build/source/src/raptor_www_libxml.c: In function 'raptor_www_libxml_init':
raptor2-unstable> /build/source/src/raptor_www_libxml.c:43:3: warning: implicit declaration of function 'xmlNanoHTTPInit' [8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wimplicit-function-declaration-Wimplicit-function-declaration8;;]
raptor2-unstable>    43 |   xmlNanoHTTPInit();
raptor2-unstable>       |   ^~~~~~~~~~~~~~~
...
raptor2-unstable> /nix/store/2qnz8ch0m3vjgjmjy8g66ik1rrm560ki-binutils-2.42/bin/ld: libraptor2.so: undefined reference to `xmlNanoHTTPScanProxy'
raptor2-unstable> /nix/store/2qnz8ch0m3vjgjmjy8g66ik1rrm560ki-binutils-2.42/bin/ld: libraptor2.so: undefined reference to `xmlNanoHTTPClose'
raptor2-unstable> /nix/store/2qnz8ch0m3vjgjmjy8g66ik1rrm560ki-binutils-2.42/bin/ld: libraptor2.so: undefined reference to `xmlNanoHTTPReturnCode'
raptor2-unstable> /nix/store/2qnz8ch0m3vjgjmjy8g66ik1rrm560ki-binutils-2.42/bin/ld: libraptor2.so: undefined reference to `xmlNanoHTTPRead'
raptor2-unstable> /nix/store/2qnz8ch0m3vjgjmjy8g66ik1rrm560ki-binutils-2.42/bin/ld: libraptor2.so: undefined reference to `xmlNanoHTTPCleanup'
raptor2-unstable> /nix/store/2qnz8ch0m3vjgjmjy8g66ik1rrm560ki-binutils-2.42/bin/ld: libraptor2.so: undefined reference to `xmlNanoHTTPMethod'
raptor2-unstable> /nix/store/2qnz8ch0m3vjgjmjy8g66ik1rrm560ki-binutils-2.42/bin/ld: libraptor2.so: undefined reference to `xmlNanoHTTPInit'
raptor2-unstable> collect2: error: ld returned 1 exit status
raptor2-unstable> make[2]: *** [src/CMakeFiles/raptor_uri_test.dir/build.make:100: src/raptor_uri_test] Error 1

[nwellnhof]

raptor2-unstable> /build/source/src/raptor_www_libxml.c:43:3: warning: implicit declaration of function 'xmlNanoHTTPInit' [8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wimplicit-function-declaration-Wimplicit-function-declaration8;;]
raptor2-unstable>    43 |   xmlNanoHTTPInit();

You either have to build libxml2 with HTTP or legacy support or build raptor without "www" support.

[jtojnar]

Fixing libraptor in #328243

Tried to apply the patch with libxml2 fix but that breaks tests: https://gitlab.gnome.org/GNOME/libxml2/-/issues/772#note_2171538

[trofi]

postgresql is also affected by 25bc618 libxml2: 2.12.7 → 2.13.2 in staging:

$ nix build --no-link -f. -L postgresql
...
postgresql>      xml                          ... FAILED      179 ms
...
postgresql> make: *** [GNUmakefile:69: check] Error 2
error: builder for '/nix/store/gvx4dp3zzq14ra5cxkfr0bh6j8jaaqax-postgresql-15.7.drv' failed with exit code 2;

[jtojnar]

That might be fixed by postgres/postgres@e719248
Possibly also postgres/postgres@896cd26 for future proofing.

[nwellnhof]

For Postgres, you might also need this libxml2 commit from the 2.13 branch: https://gitlab.gnome.org/GNOME/libxml2/-/commit/e30cb632e734394ddbd7bd62b57cee3586424352

There will be a 2.13.3 release next week.

[vcunat]

• libspatialite: it's missing zlib right now but mainly it's missing the libxml2 http API.

  [...]/libspatialite.so: undefined reference to `xmlNanoHTTPCleanup'
  

  /cc maintainers (subset for now): @dotlambda, @imincik
  [staging-next] Fix libspatialite build #330337

[imincik]

• libspatialite: it's missing zlib right now but mainly it's missing the libxml2 http API.

  [...]/libspatialite.so: undefined reference to `xmlNanoHTTPCleanup'
  

  /cc maintainers (subset for now): @dotlambda, @imincik
  [staging-next] Fix libspatialite build #330337

Sorry, just returned from vacation. Thanks for fix.

[kirillrdy]

there is also postgis failure

#331166

[jtojnar]

For some reason 25bc618 is the first bad commit causing runtime issues in mysqlnd PHP extensions:

$ nix-build --expr 'let pkgs = import ./. {}; in pkgs.php.withExtensions ({ all, ... }: [ all.mysqlnd ])' && result/bin/php -i | grep Warning
/nix/store/m8s2xh98lx9n30jx256qw79hfpdnx2sk-php-with-extensions-8.2.21
Warning: PHP Startup: Unable to load dynamic library '/nix/store/4gz4xg5g4j2i7yq1qsnq4sp63dmyl5s0-php-mysqlnd-8.2.21/lib/php/extensions/mysqlnd.so' (tried: /nix/store/4gz4xg5g4j2i7yq1qsnq4sp63dmyl5s0-php-mysqlnd-8.2.21/lib/php/extensions/mysqlnd.so (/nix/store/4gz4xg5g4j2i7yq1qsnq4sp63dmyl5s0-php-mysqlnd-8.2.21/lib/php/extensions/mysqlnd.so: undefined symbol: compress), /nix/store/qh0311v3hwbbd8mf15kv3zmz91hq4d1c-php-8.2.21/lib/php/extensions//nix/store/4gz4xg5g4j2i7yq1qsnq4sp63dmyl5s0-php-mysqlnd-8.2.21/lib/php/extensions/mysqlnd.so.so (/nix/store/qh0311v3hwbbd8mf15kv3zmz91hq4d1c-php-8.2.21/lib/php/extensions//nix/store/4gz4xg5g4j2i7yq1qsnq4sp63dmyl5s0-php-mysqlnd-8.2.21/lib/php/extensions/mysqlnd.so.so: cannot open shared object file: No such file or directory)) in Unknown on line 0

$ nix-build --expr 'let pkgs = import ./. {}; in pkgs.php.withExtensions ({ all, ... }: [ all.mysqli ])' && result/bin/php -i | grep Warning
/nix/store/78nn66mdmvqry6x3nv960w4rjaz6rf19-php-with-extensions-8.2.21
Warning: PHP Startup: Unable to load dynamic library '/nix/store/4gz4xg5g4j2i7yq1qsnq4sp63dmyl5s0-php-mysqlnd-8.2.21/lib/php/extensions/mysqlnd.so' (tried: /nix/store/4gz4xg5g4j2i7yq1qsnq4sp63dmyl5s0-php-mysqlnd-8.2.21/lib/php/extensions/mysqlnd.so (/nix/store/4gz4xg5g4j2i7yq1qsnq4sp63dmyl5s0-php-mysqlnd-8.2.21/lib/php/extensions/mysqlnd.so: undefined symbol: compress), /nix/store/qh0311v3hwbbd8mf15kv3zmz91hq4d1c-php-8.2.21/lib/php/extensions//nix/store/4gz4xg5g4j2i7yq1qsnq4sp63dmyl5s0-php-mysqlnd-8.2.21/lib/php/extensions/mysqlnd.so.so (/nix/store/qh0311v3hwbbd8mf15kv3zmz91hq4d1c-php-8.2.21/lib/php/extensions//nix/store/4gz4xg5g4j2i7yq1qsnq4sp63dmyl5s0-php-mysqlnd-8.2.21/lib/php/extensions/mysqlnd.so.so: cannot open shared object file: No such file or directory)) in Unknown on line 0
Warning: PHP Startup: Unable to load dynamic library '/nix/store/47v522nby5yhg5dm70qb1dld0jwv29xg-php-mysqli-8.2.21/lib/php/extensions/mysqli.so' (tried: /nix/store/47v522nby5yhg5dm70qb1dld0jwv29xg-php-mysqli-8.2.21/lib/php/extensions/mysqli.so (/nix/store/47v522nby5yhg5dm70qb1dld0jwv29xg-php-mysqli-8.2.21/lib/php/extensions/mysqli.so: undefined symbol: mysqlnd_global_stats), /nix/store/qh0311v3hwbbd8mf15kv3zmz91hq4d1c-php-8.2.21/lib/php/extensions//nix/store/47v522nby5yhg5dm70qb1dld0jwv29xg-php-mysqli-8.2.21/lib/php/extensions/mysqli.so.so (/nix/store/qh0311v3hwbbd8mf15kv3zmz91hq4d1c-php-8.2.21/lib/php/extensions//nix/store/47v522nby5yhg5dm70qb1dld0jwv29xg-php-mysqli-8.2.21/lib/php/extensions/mysqli.so.so: cannot open shared object file: No such file or directory)) in Unknown on line 0

cc @NixOS/php

Edit: Tried to re-add the propagation of zlib in case it was the issue but no luck:

$ nix-build --expr 'let pkgs = import ./. { overlays = [ (final: prev: { libxml2 = prev.libxml2.overrideAttrs (attrs: { propagatedBuildInputs = [prev.zlib]; }); }) ]; }; in pkgs.php.withExtensions ({ all, ... }: [ all.mysqlnd ])' && result/bin/php -i | grep Warning
/nix/store/xp8f9fgd1159wdi20fwwkznlz7z8lb77-php-with-extensions-8.2.21
Warning: PHP Startup: Unable to load dynamic library '/nix/store/z7jda5b5269wy85n2x2hjr35alc0jz4f-php-mysqlnd-8.2.21/lib/php/extensions/mysqlnd.so' (tried: /nix/store/z7jda5b5269wy85n2x2hjr35alc0jz4f-php-mysqlnd-8.2.21/lib/php/extensions/mysqlnd.so (/nix/store/z7jda5b5269wy85n2x2hjr35alc0jz4f-php-mysqlnd-8.2.21/lib/php/extensions/mysqlnd.so: undefined symbol: compress), /nix/store/sxw3pmri2vbl9kfdh0772kfwjpz2kchv-php-8.2.21/lib/php/extensions//nix/store/z7jda5b5269wy85n2x2hjr35alc0jz4f-php-mysqlnd-8.2.21/lib/php/extensions/mysqlnd.so.so (/nix/store/sxw3pmri2vbl9kfdh0772kfwjpz2kchv-php-8.2.21/lib/php/extensions//nix/store/z7jda5b5269wy85n2x2hjr35alc0jz4f-php-mysqlnd-8.2.21/lib/php/extensions/mysqlnd.so.so: cannot open shared object file: No such file or directory)) in Unknown on line 0

Edit: I forgot symbols use a single namespace, resolved in #337380.