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Building py-libxml2 fails (Ubuntu 22.04, unprivileged pkgsrc), because of the use of wrong headers (?) #150

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Building py-libxml2 fails (Ubuntu 22.04, unprivileged pkgsrc), because of the use of wrong headers (?)#150

Description

@algor512
algor512
opened on Sep 22, 2024

On Ubuntu 22.04, the installation crashes when the libxml2-dev package is installed. Removing it
makes the installation succeed. I noticed that in the former case the compilation log contains the
following lines:

cc -fno-strict-overflow -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/home/algor/tmp_pkg/include -DNCURSES_WIDECHAR=1 -I/home/algor/tmp_pkg/include/ncurses -I/home/algor/tmp_pkg/include/db4 -O2 -I/usr/include -I/home/algor/tmp_pkg/include -DNCURSES_WIDECHAR=1 -I/home/algor/tmp_pkg/include/ncurses -I/home/algor/tmp_pkg/include/db4 -O2 -I/usr/include -I/home/algor/tmp_pkg/include -DNCURSES_WIDECHAR=1 -I/home/algor/tmp_pkg/include/ncurses -I/home/algor/tmp_pkg/include/db4 -O2 -I/usr/include -I/home/algor/tmp_pkg/include/python3.12 -I/home/algor/tmp_pkg/include -I/usr/include -I/home/algor/tmp_pkg/include/python3.12 -I/home/algor/tmp_pkg/include -fPIC -D_REENTRANT=1 -I/usr/include/libxml2 -I/home/algor/tmp_pkg/include/python3.12 -c libxml.c -o build/temp.linux-x86_64-cpython-312/libxml.o
cc -fno-strict-overflow -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/home/algor/tmp_pkg/include -DNCURSES_WIDECHAR=1 -I/home/algor/tmp_pkg/include/ncurses -I/home/algor/tmp_pkg/include/db4 -O2 -I/usr/include -I/home/algor/tmp_pkg/include -DNCURSES_WIDECHAR=1 -I/home/algor/tmp_pkg/include/ncurses -I/home/algor/tmp_pkg/include/db4 -O2 -I/usr/include -I/home/algor/tmp_pkg/include -DNCURSES_WIDECHAR=1 -I/home/algor/tmp_pkg/include/ncurses -I/home/algor/tmp_pkg/include/db4 -O2 -I/usr/include -I/home/algor/tmp_pkg/include/python3.12 -I/home/algor/tmp_pkg/include -I/usr/include -I/home/algor/tmp_pkg/include/python3.12 -I/home/algor/tmp_pkg/include -fPIC -D_REENTRANT=1 -I/usr/include/libxml2 -I/home/algor/tmp_pkg/include/python3.12 -c libxml2-py.c -o build/temp.linux-x86_64-cpython-312/libxml2-py.o

While in the latter case it contains

cc -fno-strict-overflow -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/home/algor/tmp_pkg/include -DNCURSES_WIDECHAR=1 -I/home/algor/tmp_pkg/include/ncurses -I/home/algor/tmp_pkg/include/db4 -O2 -I/usr/include -I/home/algor/tmp_pkg/include -DNCURSES_WIDECHAR=1 -I/home/algor/tmp_pkg/include/ncurses -I/home/algor/tmp_pkg/include/db4 -O2 -I/usr/include -I/home/algor/tmp_pkg/include -DNCURSES_WIDECHAR=1 -I/home/algor/tmp_pkg/include/ncurses -I/home/algor/tmp_pkg/include/db4 -O2 -I/usr/include -I/home/algor/tmp_pkg/include/python3.12 -I/home/algor/tmp_pkg/include -I/usr/include -I/home/algor/tmp_pkg/include/python3.12 -I/home/algor/tmp_pkg/include -fPIC -D_REENTRANT=1 -I/home/algor/tmp_pkg/include/libxml2 -I/home/algor/tmp_pkg/include/python3.12 -c libxml.c -o build/temp.linux-x86_64-cpython-312/libxml.o
cc -fno-strict-overflow -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/home/algor/tmp_pkg/include -DNCURSES_WIDECHAR=1 -I/home/algor/tmp_pkg/include/ncurses -I/home/algor/tmp_pkg/include/db4 -O2 -I/usr/include -I/home/algor/tmp_pkg/include -DNCURSES_WIDECHAR=1 -I/home/algor/tmp_pkg/include/ncurses -I/home/algor/tmp_pkg/include/db4 -O2 -I/usr/include -I/home/algor/tmp_pkg/include -DNCURSES_WIDECHAR=1 -I/home/algor/tmp_pkg/include/ncurses -I/home/algor/tmp_pkg/include/db4 -O2 -I/usr/include -I/home/algor/tmp_pkg/include/python3.12 -I/home/algor/tmp_pkg/include -I/usr/include -I/home/algor/tmp_pkg/include/python3.12 -I/home/algor/tmp_pkg/include -fPIC -D_REENTRANT=1 -I/home/algor/tmp_pkg/include/libxml2 -I/home/algor/tmp_pkg/include/python3.12 -c libxml2-py.c -o build/temp.linux-x86_64-cpython-312/libxml2-py.o

As you can see, in the former case it contains -I/usr/include/libxml2 and it presumabely makes it
fail. I have the line PREFER_PKGSRC=yes in my mk.conf.

Activity

  1. sskras commented on Sep 23, 2024

    @sskras
    sskras
    on Sep 23, 2024

    @algor512, which commit is that, please?

  2. algor512 commented on Sep 23, 2024

    @algor512
    algor512
    on Sep 23, 2024
    Author

    @sskras sorry, I forgot to indicate that: I use the current trunk, so the commit c8e9012.

  3. netbsd-srcmastr
    added a commit that references this issue on Sep 23, 2024

    (sysutils/R-ps) Updated 1.7.7

    ea6e1c7
  4. netbsd-srcmastr
    added a commit that references this issue on Oct 18, 2024

    (devel/R-evaluate) Updated 0.23 to 1.0.1

    6d6c099
  5. msk
    added a commit that references this issue on Oct 18, 2024

    giflib[-util]: Update to 5.2.2. Libtoolize.

    df66c76
  6. netbsd-srcmastr
    added a commit that references this issue on Nov 6, 2024

    (math/R-nloptr) 2.0.3 to 2.1.1

    075eff9
  7. netbsd-srcmastr
    added 2 commits that reference this issue on Dec 2, 2024

    (geography/R-s2)% Updatd 1.0.6 to 1.1.7

    bd26696

    (geography/R-wk) Updated 0.6.0 to 0.9.4

    822e205
  8. netbsd-srcmastr
    added a commit that references this issue on Dec 11, 2024

    www/ruby-jekyll-archives: update to 2.3.0

    7bdd21a

  9. jperkin commented on Feb 13, 2025

    @jperkin
    jperkin
    on Feb 13, 2025
    Collaborator

    I ran into the same problem on my Ubuntu 22.04 CI system, and fixed it in drecklypkg@0bc50e3. I don't have the ability to test this properly in pkgsrc right now, so maybe someone else is interested in doing that.

  10. netbsd-srcmastr
    added a commit that references this issue on Feb 18, 2025

    py-serializable: update to 2.0.0.

    1a2f6d8
  11. netbsd-srcmastr
    added a commit that references this issue on May 4, 2025

    sysutils/upower: update to 1.90.9

    613abfa
  12. netbsd-srcmastr
    added a commit that references this issue on May 11, 2025

    py-snowballstemmer: update to 3.0.1.

    8332b72
  13. netbsd-srcmastr
    added a commit that references this issue on May 23, 2025

    shells/yash: update to 2.59

    98f23d8
  14. netbsd-srcmastr
    added a commit that references this issue on Jun 15, 2025

    www/ruby-jekyll-sass-converter: update to 3.1.0

    0df4f05

  15. 51 remaining items

  16. jakllsch
    added 6 commits that reference this issue on May 15, 2026

    shells/yash: update to 2.59

    c037b56

    www/ruby-jekyll-sass-converter: update to 3.1.0

    b8d05c4

    libsixel: update to 1.8.7.

    cb1d6f8

    www/ruby-uri: update to 1.1.1

    c7a95bf

    emulators/jgenesis: update to 0.11.2

    602eb37

    p5-XML-Parser: update to 2.48.

    271029e
  17. netbsd-srcmastr
    added 2 commits that reference this issue on May 21, 2026

    devel/serie: update to 0.7.2

    509d083

    p5-YAML-Syck: update to 1.45.

    245bc8e
  18. netbsd-srcmastr
    added a commit that references this issue on Jun 29, 2026

    ocaml-zarith: update to 1.14

    0fb741f
  19. netbsd-srcmastr
    added 2 commits that reference this issue on Aug 25, 2026

    lang/ruby-execjs: update to 2.10.2

    2866bc0

    confuse: update to 3.4.

    deb8816
  20. netbsd-srcmastr
    added a commit that references this issue on Sep 12, 2026

    p5-DateTime: update to 1.6700.

    e33c2d8
  21. netbsd-srcmastr
    closed this as completedin 14ceabeon Sep 29, 2026

  22. sskras commented on Sep 29, 2026

    @sskras
    sskras
    on Sep 29, 2026

    Well, something seems to be ridiculously wrong here.
    The commit 14ceabe that closed this issue says:

    • fix double-click not opening the file when the tree is scrolled - Fix #150

    ... which this issue seems to have no relation to.

    Pinging @0323pin: did you really want to refer to this issue in the commit above?

  23. jsonn commented on Sep 29, 2026

    @jsonn
    jsonn
    on Sep 29, 2026
    Member

    github is not the source of truth for there repositories. It is not possible to disable the commit message parser and it is constantly mistriggering.

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