coot How to install on fedora 39?

Dear @pemsley ... Are there any recipes to install coot 1.x on a Fedora box?

Thanks

Feb 28 '24 15:02 mysecondnameisdanger

@mysecondnameisdanger

How much time do you have to tinker with it?

You can try the build-it-3-3 script on the main branch. My experience on Redhat/Fedora is that there are (usually/always) problems with installing Python and PyGObject.

If you can get that to work, then the chances are good.

Some years ago Coot was (briefly) part of Fedora thanks to the work of Tim Fenn.

Feb 29 '24 05:02 pemsley

Trying build-it-3-3

mysecondnameisdanger@fedora:~/Repos/coot$ bash build-it-3-3 
==================================================== add test for SWIG version
==================================================== add test for CMake version
this is script version 6.16
PATH is now: /home/mysecondnameisdanger/autobuild/Linux-fedora-pre-release-gtk4/bin:/home/mysecondnameisdanger/GPhL/autoPROC_snapshot_20240123/autoPROC/bin/linux64:/home/mysecondnameisdanger/xstl/phenix-dev-5240/build/bin:/home/mysecondnameisdanger/xstl/arp_warp_8.0/bin/bin-x86_64-Linux:/home/mysecondnameisdanger/xstl/ccp4-8.0/etc:/home/mysecondnameisdanger/xstl/ccp4-8.0/bin:/home/mysecondnameisdanger/GPhL/autoPROC_snapshot_20240123/autoPROC/bin/linux64:/home/mysecondnameisdanger/.local/bin:/home/mysecondnameisdanger/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/usr/local/texlive/2023/bin/x86_64-linux:/home/mysecondnameisdanger/bin/linux_bin:/usr/local/texlive/2023/bin/x86_64-linux:/home/mysecondnameisdanger/bin/linux_bin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc
LOGS is /home/mysecondnameisdanger/public_html/build-logs/Linux-fedora
AUTOBUILD_SOURCES is /home/mysecondnameisdanger/autobuild/building/sources
AUTOBUILD_BUILD is /home/mysecondnameisdanger/autobuild/building
AUTOBUILD_INSTALLED is /home/mysecondnameisdanger/autobuild/Linux-fedora
GITHUB_ENV
GITHUB_WORKSPACE
mkdir -p /home/mysecondnameisdanger/public_html/build-logs/Linux-fedora
INFO:: redirecting std output to /home/mysecondnameisdanger/public_html/build-logs/Linux-fedora/build-gtk4.log
build-it-3-3: line 1500: cmake: command not found
mysecondnameisdanger@fedora:~/Repos/coot$ vim /home/mysecondnameisdanger/public_html/build-logs/Linux-fedora/build-gtk4.log
mysecondnameisdanger@fedora:~/Repos/coot$ sudo dnf install cmake
[sudo] password for mysecondnameisdanger: 
Last metadata expiration check: 1:21:17 ago on Thu 29 Feb 2024 09:32:14 AM CST.
Dependencies resolved.
==================================================================================================================================================
 Package                                 Architecture                  Version                                Repository                     Size
==================================================================================================================================================
Installing:
 cmake                                   x86_64                        3.27.7-1.fc39                          fedora                        8.0 M
Installing dependencies:
 cmake-data                              noarch                        3.27.7-1.fc39                          fedora                        2.2 M
 cmake-rpm-macros                        noarch                        3.27.7-1.fc39                          fedora                         18 k
 jsoncpp                                 x86_64                        1.9.5-5.fc39                           fedora                         99 k
 rhash                                   x86_64                        1.4.3-3.fc39                           fedora                        194 k

Transaction Summary
==================================================================================================================================================
Install  5 Packages

Total download size: 11 M
Installed size: 39 M
Is this ok [y/N]: y
Downloading Packages:
(1/5): cmake-rpm-macros-3.27.7-1.fc39.noarch.rpm                                                                   37 kB/s |  18 kB     00:00    
(2/5): jsoncpp-1.9.5-5.fc39.x86_64.rpm                                                                            361 kB/s |  99 kB     00:00    
(3/5): rhash-1.4.3-3.fc39.x86_64.rpm                                                                              574 kB/s | 194 kB     00:00    
(4/5): cmake-data-3.27.7-1.fc39.noarch.rpm                                                                        798 kB/s | 2.2 MB     00:02    
(5/5): cmake-3.27.7-1.fc39.x86_64.rpm                                                                             911 kB/s | 8.0 MB     00:09    
--------------------------------------------------------------------------------------------------------------------------------------------------
Total                                                                                                             1.1 MB/s |  11 MB     00:09     
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Preparing        :                                                                                                                          1/1 
  Installing       : cmake-rpm-macros-3.27.7-1.fc39.noarch                                                                                    1/5 
  Installing       : rhash-1.4.3-3.fc39.x86_64                                                                                                2/5 
  Installing       : jsoncpp-1.9.5-5.fc39.x86_64                                                                                              3/5 
  Installing       : cmake-data-3.27.7-1.fc39.noarch                                                                                          4/5 
  Installing       : cmake-3.27.7-1.fc39.x86_64                                                                                               5/5 
  Running scriptlet: cmake-3.27.7-1.fc39.x86_64                                                                                               5/5 
  Verifying        : cmake-3.27.7-1.fc39.x86_64                                                                                               1/5 
  Verifying        : cmake-data-3.27.7-1.fc39.noarch                                                                                          2/5 
  Verifying        : cmake-rpm-macros-3.27.7-1.fc39.noarch                                                                                    3/5 
  Verifying        : jsoncpp-1.9.5-5.fc39.x86_64                                                                                              4/5 
  Verifying        : rhash-1.4.3-3.fc39.x86_64                                                                                                5/5 

Installed:
  cmake-3.27.7-1.fc39.x86_64      cmake-data-3.27.7-1.fc39.noarch      cmake-rpm-macros-3.27.7-1.fc39.noarch      jsoncpp-1.9.5-5.fc39.x86_64     
  rhash-1.4.3-3.fc39.x86_64      

Complete!
mysecondnameisdanger@fedora:~/Repos/coot$ bash build-it-3-3 
==================================================== add test for SWIG version
==================================================== add test for CMake version
this is script version 6.16
PATH is now: /home/mysecondnameisdanger/autobuild/Linux-fedora-pre-release-gtk4/bin:/home/mysecondnameisdanger/GPhL/autoPROC_snapshot_20240123/autoPROC/bin/linux64:/home/mysecondnameisdanger/xstl/phenix-dev-5240/build/bin:/home/mysecondnameisdanger/xstl/arp_warp_8.0/bin/bin-x86_64-Linux:/home/mysecondnameisdanger/xstl/ccp4-8.0/etc:/home/mysecondnameisdanger/xstl/ccp4-8.0/bin:/home/mysecondnameisdanger/GPhL/autoPROC_snapshot_20240123/autoPROC/bin/linux64:/home/mysecondnameisdanger/.local/bin:/home/mysecondnameisdanger/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/usr/local/texlive/2023/bin/x86_64-linux:/home/mysecondnameisdanger/bin/linux_bin:/usr/local/texlive/2023/bin/x86_64-linux:/home/mysecondnameisdanger/bin/linux_bin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc
LOGS is /home/mysecondnameisdanger/public_html/build-logs/Linux-fedora
AUTOBUILD_SOURCES is /home/mysecondnameisdanger/autobuild/building/sources
AUTOBUILD_BUILD is /home/mysecondnameisdanger/autobuild/building
AUTOBUILD_INSTALLED is /home/mysecondnameisdanger/autobuild/Linux-fedora
GITHUB_ENV
GITHUB_WORKSPACE
mkdir -p /home/mysecondnameisdanger/public_html/build-logs/Linux-fedora
INFO:: redirecting std output to /home/mysecondnameisdanger/public_html/build-logs/Linux-fedora/build-gtk4.log
ls: cannot access '/home/mysecondnameisdanger/autobuild/Linux-fedora-gtk4/include/ltdl.h': No such file or directory
build-it-3-3: line 2149: /home/mysecondnameisdanger/autobuild/Linux-fedora-gtk4/bin/gsl-config: No such file or directory
2024-02-29 10:54:08 URL:http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/libccp4-6.5.1.tar.gz [947521/947521] -> "/home/mysecondnameisdanger/autobuild/building/sources/libccp4-6.5.1.tar.gz" [1]
BUILDING libccp4 6.5.1
done libccp4 6.5.1
2024-02-29 10:54:15 URL:http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/mmdb2-2.0.22.tar.gz [737837/737837] -> "/home/mysecondnameisdanger/autobuild/building/sources/mmdb2-2.0.22.tar.gz" [1]
BUILDING mmdb 2.0.22
done mmdb 2.0.22
BUILDING SSM
2024-02-29 10:54:24 URL:http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/ssm-1.4.tar.gz [426685/426685] -> "/home/mysecondnameisdanger/autobuild/building/sources/ssm-1.4.tar.gz" [1]
done SSM 1.4
BUILDING fftw 2.1.5:
2024-02-29 10:54:32 URL:http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/fftw-2.1.5.tar.gz [1256888/1256888] -> "/home/mysecondnameisdanger/autobuild/building/sources/fftw-2.1.5.tar.gz" [1]
done fftw
2024-02-29 10:54:54 URL:http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/clipper-2.1.20180802.tar.gz [4238748/4238748] -> "/home/mysecondnameisdanger/autobuild/building/sources/clipper-2.1.20180802.tar.gz" [1]
2024-02-29 10:54:55 URL:http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/clipper-configure-2.patch [5888/5888] -> "/home/mysecondnameisdanger/autobuild/building/sources/clipper-configure-2.patch" [1]
BUILDING clipper 2.1.20180802
done clipper
BUILDING gemmi from git repo (and installing GEMMI)
/home/mysecondnameisdanger/autobuild/building/fedora_2024-02-29__T16_54_01
BUILDING readline:
2024-02-29 10:56:35 URL:https://ftp.gnu.org/gnu/readline/readline-8.2.tar.gz [3043952/3043952] -> "/home/mysecondnameisdanger/autobuild/building/sources/readline-8.2.tar.gz" [1]
2024-02-29 10:56:36 URL:http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/readline-5.1.patch [1665/1665] -> "/home/mysecondnameisdanger/autobuild/building/sources/readline-5.1.patch" [1]
BUILDING libffi 3.2.1:
post libffi with LD_LIBRARY_PATH /home/mysecondnameisdanger/autobuild/Linux-fedora-gtk4/lib
BUILDING Python 3.11.4:
2024-02-29 10:56:55 URL:https://www.python.org/ftp/python/3.11.4/Python-3.11.4.tgz [26526163/26526163] -> "/home/mysecondnameisdanger/autobuild/building/sources/Python-3.11.4.tgz" [1]
BUILDING Python 3.11.4 done
Pip update done
BUILDING meson 1.2.3:
2024-02-29 10:58:39 URL:http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/libtool/libtool-2.4.6.tar.gz [1806697/1806697] -> "/home/mysecondnameisdanger/autobuild/building/sources/libtool-2.4.6.tar.gz" [1]
BUILDING libidn:
BUILDING curl: 7.65.3
donecurl:
BUILDING gsl 2.7
2024-02-29 10:59:42 URL:http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/gsl/gsl-2.7.tar.gz [7508761/7508761] -> "/home/mysecondnameisdanger/autobuild/building/sources/gsl-2.7.tar.gz" [1]
done gsl:
BUILDING boost 1_83_0
2024-02-29 11:01:10 URL:https://jfrog-prod-usw2-shared-oregon-main.s3.amazonaws.com/aol-boostorg/filestore/eb/eb5e17350b5ccd5926fd6bad9f09385c742a3352?X-Artifactory-username=anonymous&X-Artifactory-repoType=local&X-Artifactory-repositoryKey=main&X-Artifactory-packageType=generic&X-Artifactory-artifactPath=release%2F1.83.0%2Fsource%2Fboost_1_83_0.tar.gz&X-Artifactory-projectKey=default&x-jf-traceId=cba4a57b34ebf59&response-content-disposition=attachment%3Bfilename%3D%22boost_1_83_0.tar.gz%22&response-content-type=application%2Fx-gzip&X-Amz-Security-Token=IQoJb3JpZ2luX2VjECEaCXVzLXdlc3QtMiJIMEYCIQDJaoiI9QbCW95UhdAVIqywWN%2FArbGDb1THPFn52c%2B24QIhAO9LgYYoa%2F02GJwcO1Qfx94sXKwcSIp5fA7%2Fj7iZEDB1KoYFCBoQABoMNzIxODgyNjEzMDM3IgxORnPUowvlqgm%2FrHYq4wRJja7fSzt2ME0Kv1ok9Zr6CJ1ga%2F7d%2ByVSH7EmnalaV%2F5z9A%2FkE%2Fc9poknExD01V5XEDDf6jjZFWya3zoVH5SF6jANRqepiy0N1qG4xTLpNapZAbwomxacmZ6KFzYd9NYDAVUvkUWvKeRsDDA3K4QMTSHrEA65pnmhs%2FLmlEUemWJd7Ip0XR4W3iOmaLaHg%2Bp2r0W5SP%2B45tr4KJ6HniZgGMTSeYrZrXBrDfd5rVVWz1lDgeFZ8rSuPPGL4dmIhJWa81WnCSGfs4oTvqFTKQ9avf4vAS5A6OYQIhALgXkkMqb7Hgn0riSUMIwcimoQ4pGFiXFGLjoF2boOITcb0%2BvKgzg9SgzR2Gi2ui%2BF2iwAX550tQzy%2FD%2Fy5ikHD7ZVsMq3Ty90ecv2kC%2FekcFcPh2nYUWTmBtGrZC%2BxMjUxQYTFc8QbVMYR7AMcoSp62elaev8P0t3RxACMs8NEUN4FmFOEaFC%2Bc66ItKH%2FqRBebJrXatTGGKt4ikiVNhdt1IPHl4DEcWHcxIeLKhkTXZya3bvU1gCu3AoK8elioxENh0RBG03NqQyItbhYpxV8Tru4YSVqWsqcs2kr8ET%2FVkXzqRMJJZ09ma3MrA06FTFqYWIB6FvdgODY0oVdlHJl5jNBJYqNBY0eeSkXhWO15%2BnyuXBzVazjJ0RLuymuygDblMS1XwG4rNtj4I2tJkTqVq8qENwvh684vcL%2FmdxbmsM0E%2FotgkaH6%2BAFhTd0OJPfYawO25A8exfr50jDuqGmgkHVoyMyOlEu8v%2BVpJ8kDe9pUcbesbwrOmosEcXT0z00%2BQyl5RJSjCx4YKvBjqZAWbsBe2Nd7U540XQQVWmqT6dPLI3E%2B7QUThMOV31d94%2BhC3dryvO7Ug85fc6ycumLaNU2ojyVuH2%2FN1goYDoBaayHOPmwaGNhC5PNBvagdJ%2F5IdcBiT2GmtZCg6L%2BGxUCEIdSWbf9AzYY%2FuP3Lt3cyWpXSz2UTMOfGvd20nxfDnU2fWhR5CZ8ZY%2F8tMpx8r173a6NuZLbwUqDg%3D%3D&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Date=20240229T170051Z&X-Amz-SignedHeaders=host&X-Amz-Expires=30&X-Amz-Credential=ASIA2QE4OQUWSUBX4C6H%2F20240229%2Fus-west-2%2Fs3%2Faws4_request&X-Amz-Signature=fbe3f0b6db2f0fceddf41fa0a7df02fe7d1ae08f7c664b8fcfb418af656f374c [144645738/144645738] -> "/home/mysecondnameisdanger/autobuild/building/sources/boost_1_83_0.tar.gz" [1]
done boost 1_83_0
BUILDING glm:
fetching https://github.com/g-truc/glm/archive/refs/tags/1.0.0.tar.gz
Last-modified header missing -- time-stamps turned off.
2024-02-29 11:02:30 URL:https://codeload.github.com/g-truc/glm/tar.gz/refs/tags/1.0.0 [4523789] -> "/home/mysecondnameisdanger/autobuild/building/sources/1.0.0.tar.gz" [1]
done glm:
/home/mysecondnameisdanger/autobuild/Linux-fedora-gtk4/lib/python3.11/site-packages/pip/_internal/metadata/importlib/_envs.py:111: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  from pip._vendor.pkg_resources import find_distributions
DEPRECATION: Loading egg at /home/mysecondnameisdanger/autobuild/Linux-fedora-gtk4/lib/python3.11/site-packages/meson-1.2.3-py3.11.egg is deprecated. pip 24.3 will enforce this behaviour change. A possible replacement is to use pip for package installation.. Discussion can be found at https://github.com/pypa/pip/issues/12330
/home/mysecondnameisdanger/autobuild/Linux-fedora-gtk4/lib/python3.11/site-packages/pip/_internal/metadata/importlib/_envs.py:111: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  from pip._vendor.pkg_resources import find_distributions
DEPRECATION: Loading egg at /home/mysecondnameisdanger/autobuild/Linux-fedora-gtk4/lib/python3.11/site-packages/meson-1.2.3-py3.11.egg is deprecated. pip 24.3 will enforce this behaviour change. A possible replacement is to use pip for package installation.. Discussion can be found at https://github.com/pypa/pip/issues/12330
pip3 install nanobind
/home/mysecondnameisdanger/autobuild/Linux-fedora-gtk4/lib/python3.11/site-packages/pip/_internal/metadata/importlib/_envs.py:111: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  from pip._vendor.pkg_resources import find_distributions
DEPRECATION: Loading egg at /home/mysecondnameisdanger/autobuild/Linux-fedora-gtk4/lib/python3.11/site-packages/meson-1.2.3-py3.11.egg is deprecated. pip 24.3 will enforce this behaviour change. A possible replacement is to use pip for package installation.. Discussion can be found at https://github.com/pypa/pip/issues/12330
pip3 install nanobind done
ls: cannot access '/home/mysecondnameisdanger/autobuild/Linux-fedora-gtk4/lib/python3.11/site-packages/numpy/lib/_version.py': No such file or directory
BUILDING numpy 1.26.3
BUILDING numpy 1.26.3 finished
BUILDING eigen 3.3.9
BUILDING eigen finished
Last-modified header missing -- time-stamps turned off.
2024-02-29 11:03:52 URL:https://codeload.github.com/catchorg/Catch2/tar.gz/refs/tags/v3.5.2 [1159985] -> "/home/mysecondnameisdanger/autobuild/building/sources/v3.5.2.tar.gz" [1]
BUILDING RDKit 2023_09_4
installing python requests
/home/mysecondnameisdanger/autobuild/Linux-fedora-gtk4/lib/python3.11/site-packages/pip/_internal/metadata/importlib/_envs.py:111: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  from pip._vendor.pkg_resources import find_distributions
DEPRECATION: Loading egg at /home/mysecondnameisdanger/autobuild/Linux-fedora-gtk4/lib/python3.11/site-packages/meson-1.2.3-py3.11.egg is deprecated. pip 24.3 will enforce this behaviour change. A possible replacement is to use pip for package installation.. Discussion can be found at https://github.com/pypa/pip/issues/12330
BUILDING gmp 6.1.2
2024-02-29 11:04:35 URL:http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/gmp/gmp-6.1.2.tar.bz2 [2386766/2386766] -> "/home/mysecondnameisdanger/autobuild/building/sources/gmp-6.1.2.tar.bz2" [1]
done gmp 6.1.2
BUILDING gobject-introspection:
done gobject-introspection:
BUILDING pygobject 3.42.1:
done pygobject 3.42.1:
2024-02-29 11:05:34 URL:http://skuld.bmsc.washington.edu/raster3d/Raster3D_3.0-7.tar.gz [1729798/1729798] -> "/home/mysecondnameisdanger/autobuild/building/sources/Raster3D_3.0-7.tar.gz" [1]
BUILDING raster3d 3.0-7
done raster3d 3.0-7
installing pygobject with pip3
done install pygobject with pip3
BUILDING libunistring 0.9.10
done libunistring 0.9.10
done libatomic-ops:
BUILDING gc 7.6.12
done gc 7.6.12
BUILDING guile 2.2.7
BUILDING g-wrap:
BUILDING g-wrap finished
BUILDING guile-cairo
BUILDING guile-cairo finished
build-it-3-3: line 4374: guile-config: command not found
BUILDING gnome-gnome-platform
Now Coot.....
Thu Feb 29 11:07:01 AM CST 2024
/home/mysecondnameisdanger/Repos/coot
CASE 2 coot directory not exists in /home/mysecondnameisdanger/Repos/coot
BUILDING coot

Feb 29 '24 17:02 mysecondnameisdanger

@mysecondnameisdanger OK! So what have you got in ~/autobuild/Linux-hostname/bin ? Do you have package build failures in ~/public_html/build-logs/hostname/compiler-version?

Feb 29 '24 18:02 pemsley

Ok... Now I have time and a fresh Fedora and a couple of questions.

First... I am making a comparison to know the stuff needed to run build-it-3-3 ... The first column is the name of the program/library in ubuntu (Am I missing something?) and the second column is the corresponding name in fedora (third column is the version).

patch                   patch                   2.7.6
m4                      m4                      1.4.19
g++                     gcc-c++                 13.2.1
libxext-dev             libXext-devel           1.3.5
libxt-dev               libXt-devel             1.2.1
libc6-dev               glibc-devel             2.38
libglu1-mesa-dev        mesa-libGLU-devel       9.0.3
mesa-common-dev         ?
swig                    swig                    4.1.1
libgtk2.0-dev           gtk2-devel              2.24.33
libgnomecanvas2-dev     libgnomecanvas-devel    2.30.3
git                     git                     2.44.0
cmake                   cmake                   3.27.7
flex                    flex                    2.6.4
bison                   bison                   3.8.2
gfortran                gcc-gfortran            13.2.1
libglfw3-dev            glfw-devel              3.3.8
libssl-dev              openssl-devel           3.1.1
libblas-dev             blas-devel              3.11.0
liblapack-dev           lapack-devel            3.11.0
libncurses5-dev         ncurses-devel           6.4
libgtk-4-dev            gtk4-devel              4.12.5

The only one that I am missing is mesa-common-dev. Do you know by chance the name of that library in fedora?

msnid@fedora:~$ dnf search *mesa*devel
Last metadata expiration check: 0:16:04 ago on Fri 08 Mar 2024 08:46:35 AM CST.
========================================== Name Matched: *mesa*devel ===========================================
mesa-libEGL-devel.i686 : Mesa libEGL development package
mesa-libEGL-devel.x86_64 : Mesa libEGL development package
mesa-libGL-devel.i686 : Mesa libGL development package
mesa-libGL-devel.x86_64 : Mesa libGL development package
mesa-libGLU-devel.i686 : Development files for mesa-libGLU
mesa-libGLU-devel.x86_64 : Development files for mesa-libGLU
mesa-libGLw-devel.i686 : Mesa libGLw development package
mesa-libGLw-devel.x86_64 : Mesa libGLw development package
mesa-libOSMesa-devel.i686 : Mesa offscreen rendering development package
mesa-libOSMesa-devel.x86_64 : Mesa offscreen rendering development package
mesa-libOpenCL-devel.i686 : Mesa OpenCL development package
mesa-libOpenCL-devel.x86_64 : Mesa OpenCL development package
mesa-libd3d-devel.i686 : Mesa Direct3D9 state tracker development package
mesa-libd3d-devel.x86_64 : Mesa Direct3D9 state tracker development package
mesa-libgbm-devel.i686 : Mesa libgbm development package
mesa-libgbm-devel.x86_64 : Mesa libgbm development package
mesa-libxatracker-devel.i686 : Mesa XA state tracker development package
mesa-libxatracker-devel.x86_64 : Mesa XA state tracker development package
rust-osmesa-sys+default-devel.noarch : OSMesa library bindings for Rust
rust-osmesa-sys-devel.noarch : OSMesa library bindings for Rust

I am also pasting what is in "C Development Tools and Libraries"... those should be installed?

msnid@fedora:~$ dnf group info "C Development Tools and Libraries"
Last metadata expiration check: 0:24:35 ago on Fri 08 Mar 2024 08:46:35 AM CST.
Group: C Development Tools and Libraries
 Description: These tools include core development tools such as automake, gcc and debuggers.
 Mandatory Packages:
   autoconf
   automake
   binutils
   bison
   flex
   gcc
   gcc-c++
   gdb
   glibc-devel
   libtool
   make
   pkgconf
   strace
 Default Packages:
   byacc
   ccache
   cscope
   ctags
   elfutils
   indent
   ltrace
   perf
   valgrind
 Optional Packages:
   ElectricFence
   astyle
   cbmc
   check
   cmake
   coan
   cproto
   insight
   nasm
   pscan
   python3-scons
   remake
   scorep
   splint
   yasm
   zzuf

Thanks again.

Mar 08 '24 16:03 mysecondnameisdanger

Ps.. Also found this https://gnome.pages.gitlab.gnome.org/pygobject/devguide/dev_environ.html ...

Mar 08 '24 17:03 mysecondnameisdanger

mesa-common-dev provides the OpenGL headers - at least that's what Coot uses it for, so mesa-libGL-devel.x86_64 I imagine.
I have changed the script so that gettext is not compiled for non-macOS.
At the top of the script it tells me to write a test for swig and cmake - I guess that I should get around to doing that.
glm version has been pushed back a bit.
You will need these:
autoconf automake binutils bison flex gcc gcc-c++ gdb glibc-devel elfutils libtool make cmake I don't think you will need the others - but I could be wrong.

Mar 08 '24 20:03 pemsley

Seems like patch is also needed.

msnid@fedora:~/autobuild/Linux-fedora-gtk4/bin$ ls
2to3       curl-config  gsl-histogram  idle3.11  libtoolize  pydoc3.11  python3.11
2to3-3.11  gemmi        gsl-randist    idn2      ninja       python     python3.11-config
curl       gsl-config   idle3          libtool   pydoc3      python3    python3-config
msnid@fedora:~/public_html/build-logs/Linux-fedora/gtk4-gcc-13_and_g++-13$ tail -n 40 2*.txt
==> 20-libatomic-ops.txt <==
 /usr/bin/install -c -m 644  atomic_ops/ao_version.h atomic_ops/generalize.h atomic_ops/generalize-arithm.h atomic_ops/generalize-small.h '/home/msnid/autobuild/Linux-fedora-gtk4/include//atomic_ops'
 /usr/bin/mkdir -p '/home/msnid/autobuild/Linux-fedora-gtk4/include//atomic_ops/sysdeps/loadstore'
 /usr/bin/install -c -m 644  atomic_ops/sysdeps/loadstore/acquire_release_volatile.h atomic_ops/sysdeps/loadstore/atomic_load.h atomic_ops/sysdeps/loadstore/atomic_store.h atomic_ops/sysdeps/loadstore/char_acquire_release_volatile.h atomic_ops/sysdeps/loadstore/char_atomic_load.h atomic_ops/sysdeps/loadstore/char_atomic_store.h atomic_ops/sysdeps/loadstore/int_acquire_release_volatile.h atomic_ops/sysdeps/loadstore/int_atomic_load.h atomic_ops/sysdeps/loadstore/int_atomic_store.h atomic_ops/sysdeps/loadstore/ordered_loads_only.h atomic_ops/sysdeps/loadstore/ordered_stores_only.h atomic_ops/sysdeps/loadstore/short_acquire_release_volatile.h atomic_ops/sysdeps/loadstore/short_atomic_load.h atomic_ops/sysdeps/loadstore/short_atomic_store.h atomic_ops/sysdeps/loadstore/double_atomic_load_store.h '/home/msnid/autobuild/Linux-fedora-gtk4/include//atomic_ops/sysdeps/loadstore'
 /usr/bin/mkdir -p '/home/msnid/autobuild/Linux-fedora-gtk4/include//atomic_ops/sysdeps/sunc'
 /usr/bin/install -c -m 644  atomic_ops/sysdeps/sunc/sparc.h atomic_ops/sysdeps/sunc/x86.h '/home/msnid/autobuild/Linux-fedora-gtk4/include//atomic_ops/sysdeps/sunc'
 /usr/bin/mkdir -p '/home/msnid/autobuild/Linux-fedora-gtk4/include//atomic_ops/sysdeps/icc'
 /usr/bin/install -c -m 644  atomic_ops/sysdeps/icc/ia64.h '/home/msnid/autobuild/Linux-fedora-gtk4/include//atomic_ops/sysdeps/icc'
 /usr/bin/mkdir -p '/home/msnid/autobuild/Linux-fedora-gtk4/include//atomic_ops/sysdeps/armcc'
 /usr/bin/install -c -m 644  atomic_ops/sysdeps/armcc/arm_v6.h '/home/msnid/autobuild/Linux-fedora-gtk4/include//atomic_ops/sysdeps/armcc'
make[3]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T20_44_30/libatomic_ops-7.6.12/src'
make[2]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T20_44_30/libatomic_ops-7.6.12/src'
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T20_44_30/libatomic_ops-7.6.12/src'
Making install in doc
make[1]: Entering directory '/home/msnid/autobuild/building/fedora_2024-03-08__T20_44_30/libatomic_ops-7.6.12/doc'
make[2]: Entering directory '/home/msnid/autobuild/building/fedora_2024-03-08__T20_44_30/libatomic_ops-7.6.12/doc'
make[2]: Nothing to be done for 'install-exec-am'.
 /usr/bin/mkdir -p '/home/msnid/autobuild/Linux-fedora-gtk4/share/doc/libatomic_ops'
 /usr/bin/install -c -m 644 LICENSING.txt README_details.txt README_stack.txt README_malloc.txt README_win32.txt '/home/msnid/autobuild/Linux-fedora-gtk4/share/doc/libatomic_ops'
make[2]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T20_44_30/libatomic_ops-7.6.12/doc'
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T20_44_30/libatomic_ops-7.6.12/doc'
Making install in tests
make[1]: Entering directory '/home/msnid/autobuild/building/fedora_2024-03-08__T20_44_30/libatomic_ops-7.6.12/tests'
make  install-am
make[2]: Entering directory '/home/msnid/autobuild/building/fedora_2024-03-08__T20_44_30/libatomic_ops-7.6.12/tests'
make[3]: Entering directory '/home/msnid/autobuild/building/fedora_2024-03-08__T20_44_30/libatomic_ops-7.6.12/tests'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T20_44_30/libatomic_ops-7.6.12/tests'
make[2]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T20_44_30/libatomic_ops-7.6.12/tests'
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T20_44_30/libatomic_ops-7.6.12/tests'
make[1]: Entering directory '/home/msnid/autobuild/building/fedora_2024-03-08__T20_44_30/libatomic_ops-7.6.12'
make[2]: Entering directory '/home/msnid/autobuild/building/fedora_2024-03-08__T20_44_30/libatomic_ops-7.6.12'
make[2]: Nothing to be done for 'install-exec-am'.
 /usr/bin/mkdir -p '/home/msnid/autobuild/Linux-fedora-gtk4/share/doc/libatomic_ops'
 /usr/bin/install -c -m 644 COPYING README.md '/home/msnid/autobuild/Linux-fedora-gtk4/share/doc/libatomic_ops'
 /usr/bin/mkdir -p '/home/msnid/autobuild/Linux-fedora-gtk4/lib/pkgconfig'
 /usr/bin/install -c -m 644 pkgconfig/atomic_ops.pc '/home/msnid/autobuild/Linux-fedora-gtk4/lib/pkgconfig'
make[2]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T20_44_30/libatomic_ops-7.6.12'
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T20_44_30/libatomic_ops-7.6.12'
/home/msnid/autobuild/building/fedora_2024-03-08__T20_44_30

==> 21-gc.txt <==
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) awk: symbol lookup error: /home/msnid/autobuild/Linux-fedora-gtk4/lib/libreadline.so.8: undefined symbol: UP
GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for thread model used by GCC... posix
checking for inline... inline
checking for pthread_self in -lpthread... yes
configure: WARNING: "Explicit GC_INIT() calls may be required."
checking whether compiler supports -Wextra... yes
checking whether compiler supports -Wpedantic... yes
checking for xlc... no
checking whether compiler supports -fno-strict-aliasing... yes
checking for getcontext... yes
checking for dl_iterate_phdr... yes
checking for dlopen in -ldl... yes
checking execinfo.h usability... yes
checking execinfo.h presence... yes
checking for execinfo.h... yes
checking whether to build shared libraries... yes
checking which machine-dependent code should be used... 
checking whether Solaris gcc optimization fix is necessary... no
checking for dladdr... yes
checking sys/dg_sys_info.h usability... no
checking sys/dg_sys_info.h presence... no
checking for sys/dg_sys_info.h... no
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for atomic_ops... yes
checking which libatomic_ops to use... external
checking for lock-free AO_or primitive... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
gawk: symbol lookup error: /home/msnid/autobuild/Linux-fedora-gtk4/lib/libreadline.so.8: undefined symbol: UP
config.status: error: could not create Makefile
/home/msnid/autobuild/building/fedora_2024-03-08__T20_44_30

==> 24-guile.txt <==
checking whether sockaddr_in6 has sin6_scope_id... yes
checking for struct sockaddr_in6.sin6_len... no
checking whether localtime caches TZ... no
checking for strerror... yes
checking for memmove... yes
checking for asinh... yes
checking for acosh... yes
checking for atanh... yes
checking for copysign... yes
checking for finite... yes
checking for sincos... yes
checking for __sincos... no
checking for trunc... yes
checking for isinf... yes
checking for isnan... yes
checking for struct stat.st_rdev... yes
checking for struct stat.st_blksize... yes
checking for struct stat.st_blocks... yes
checking for struct stat.st_atim... yes
checking for struct stat.st_mtim... yes
checking for struct stat.st_ctim... yes
checking for struct tm.tm_zone... (cached) yes
checking for struct tm.tm_gmtoff... (cached) yes
checking whether we need POSIX to get struct utimbuf... no
checking the value of `iconveh_error'... 0
checking the value of `iconveh_question_mark'... 1
checking the value of `iconveh_escape_sequence'... 2
checking for which bdw-gc pkg-config file to use... bdw-gc
checking for bdw-gc >= 7.2... no
configure: error: Package requirements (bdw-gc >= 7.2) were not met:

Package 'bdw-gc', required by 'virtual:world', not found

Consider adjusting the PKG_CONFIG_PATH environment variable if you
installed software in a non-standard prefix.

Alternatively, you may set the environment variables BDW_GC_CFLAGS
and BDW_GC_LIBS to avoid the need to call pkg-config.
See the pkg-config man page for more details.
/home/msnid/autobuild/building/fedora_2024-03-08__T20_44_30

==> 25-g-wrap.txt <==
========================= build g-wrap =================================
2024-03-08 14:55:40 URL:http://nongnu.askapache.com/g-wrap/g-wrap-1.9.15.tar.gz [701601/701601] -> "/home/msnid/autobuild/building/sources/g-wrap-1.9.15.tar.gz" [1]
no guile

==> 26-guile-cairo.txt <==
========================= build guile-cairo =================================
fetching file /home/msnid/autobuild/building/sources/guile-cairo-1.9.91.tar.gz
2024-03-08 14:55:41 URL:http://download-mirror.savannah.gnu.org/releases/guile-cairo/guile-cairo-1.9.91.tar.gz [578928/578928] -> "/home/msnid/autobuild/building/sources/guile-cairo-1.9.91.tar.gz" [1]
no guile

==> 27-gemmi.txt <==
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/cellred.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/neutron92.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/mmcif_impl.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/interop.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/atof.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/mmread.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/fstream.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/riding_h.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/resinfo.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/elem.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/pdb_id.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/binner.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/sprintf.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/sfcalc.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/fail.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/blob.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/topo.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/calculate.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/linkhunt.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/fprime.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/numb.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/levmar.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/twin.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/bessel.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/to_chemcomp.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/modify.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/xds_ascii.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/intensit.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/cif2mtz.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/eig3.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/gz.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/dencalc.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/floodfill.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/fourier.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/small.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/lib64/libgemmi_cpp.so
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/lib64/cmake/gemmi/gemmi-targets.cmake
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/lib64/cmake/gemmi/gemmi-targets-release.cmake
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/lib64/cmake/gemmi/gemmi-config.cmake
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/lib64/cmake/gemmi/gemmi-config-version.cmake

==> 28-guile-gnome-platform.txt <==
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... awk: symbol lookup error: /home/msnid/autobuild/Linux-fedora-gtk4/lib/libreadline.so.8: undefined symbol: UP
awk: symbol lookup error: /home/msnid/autobuild/Linux-fedora-gtk4/lib/libreadline.so.8: undefined symbol: UP
awk: symbol lookup error: /home/msnid/autobuild/Linux-fedora-gtk4/lib/libreadline.so.8: undefined symbol: UP
GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
configure: checking for guile 2.2
configure: checking for guile 2.0
configure: error: 
No Guile development packages were found.

Please verify that you have Guile installed.  If you installed Guile
from a binary distribution, please verify that you have also installed
the development packages.  If you installed it yourself, you might need
to adjust your PKG_CONFIG_PATH; see the pkg-config man page for more.

and something with guile

Mar 08 '24 21:03 mysecondnameisdanger

msnid@fedora:~/public_html/build-logs/Linux-fedora/gtk4-gcc-13_and_g++-13$ dnf search "*guile*"
Last metadata expiration check: 6:22:18 ago on Fri 08 Mar 2024 08:46:31 AM CST.
============================================================================== Name & Summary Matched: *guile* ===============================================================================
compat-guile18-devel.i686 : Libraries and header files for the GUILE extensibility library
compat-guile18-devel.x86_64 : Libraries and header files for the GUILE extensibility library
graphviz-guile.x86_64 : Guile extension for graphviz
guile-NLopt.x86_64 : Guile bindings for NLopt
guile-devel.i686 : Libraries and header files for the GUILE extensibility library
guile-devel.x86_64 : Libraries and header files for the GUILE extensibility library
guile-gnutls.x86_64 : Guile bindings for the GNUTLS library
guile-reader.i686 : A simple framework for building readers for GNU Guile
guile-reader.x86_64 : A simple framework for building readers for GNU Guile
guile-reader-devel.i686 : Development files for guile-reader
guile-reader-devel.x86_64 : Development files for guile-reader
guile22-devel.i686 : Libraries and header files for the GUILE extensibility library
guile22-devel.x86_64 : Libraries and header files for the GUILE extensibility library
guile30-devel.i686 : Libraries and header files for the GUILE extensibility library
guile30-devel.x86_64 : Libraries and header files for the GUILE extensibility library
maildir-utils-guile.x86_64 : Guile bindings for mu (maildir-utils)
=================================================================================== Name Matched: *guile* ====================================================================================
compat-guile18.i686 : A GNU implementation of Scheme for application extensibility
compat-guile18.x86_64 : A GNU implementation of Scheme for application extensibility
guile.i686 : A GNU implementation of Scheme for application extensibility
guile.x86_64 : A GNU implementation of Scheme for application extensibility
guile22.x86_64 : A GNU implementation of Scheme for application extensibility
guile22.i686 : A GNU implementation of Scheme for application extensibility
guile30.i686 : A GNU implementation of Scheme for application extensibility
guile30.x86_64 : A GNU implementation of Scheme for application extensibility

Probably also need to install guile-devel?

Mar 08 '24 21:03 mysecondnameisdanger

After installing gcc-gfortran and guile-devel got this.

msnid@fedora:~/public_html/build-logs/Linux-fedora/gtk4-gcc-13_and_g++-13$ tail *txt
==> 01-libccp4.txt <==
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[2]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libccp4-6.5.1'
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libccp4-6.5.1'

==> 02-mmdb.txt <==
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/mmdb2-2.0.22'

==> 02-ssm.txt <==
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/ssm-1.4'

==> 03-fftw.txt <==
/bin/sh ../mkinstalldirs /home/msnid/autobuild/Linux-fedora-gtk4/lib
/bin/sh ../mkinstalldirs /home/msnid/autobuild/Linux-fedora-gtk4/include
make[2]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/fftw-2.1.5/mpi'
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/fftw-2.1.5/mpi'
make[1]: Entering directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/fftw-2.1.5'
make[2]: Entering directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/fftw-2.1.5'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/fftw-2.1.5'
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/fftw-2.1.5'

==> 04-clipper.txt <==
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/clipper-2.1/examples'
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/clipper-2.1/examples'
make[1]: Entering directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/clipper-2.1'
make[2]: Entering directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/clipper-2.1'
make[2]: Nothing to be done for 'install-exec-am'.
 /usr/bin/mkdir -p '/home/msnid/autobuild/Linux-fedora-gtk4/lib/pkgconfig'
 /usr/bin/install -c -m 644 clipper.pc '/home/msnid/autobuild/Linux-fedora-gtk4/lib/pkgconfig'
make[2]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/clipper-2.1'
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/clipper-2.1'

==> 07a-pip-upgrade.txt <==
which: no pip3 in (/home/msnid/autobuild/Linux-fedora-gtk4/bin:/home/msnid/autobuild/Linux-fedora-gtk4/bin:/home/msnid/autobuild/Linux-fedora-pre-release-gtk4/bin:/home/msnid/.local/bin:/home/msnid/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc)
build-it-3-3: line 2869: pip3: command not found

==> 07b-meson.txt <==
ModuleNotFoundError: No module named 'setuptools'
Traceback (most recent call last):
  File "/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/meson-1.2.3/setup.py", line 23, in <module>
    from setuptools import setup
ModuleNotFoundError: No module named 'setuptools'
/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36
which meson
which: no meson in (/home/msnid/autobuild/Linux-fedora-gtk4/bin:/home/msnid/autobuild/Linux-fedora-gtk4/bin:/home/msnid/autobuild/Linux-fedora-pre-release-gtk4/bin:/home/msnid/.local/bin:/home/msnid/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc)
meson --version
build-it-3-3: line 2937: meson: command not found

==> 07c1-ninja.txt <==
[25/29] CXX build/manifest_parser.o
[26/29] CXX build/build.o
[27/29] AR build/libninja.a
[28/29] CXX build/ninja.o
[29/29] LINK ninja
bootstrapping ninja...
warning: A compatible version of re2c (>= 0.11.3) was not found; changes to src/*.in.cc will not affect your build.
wrote build.ninja.
bootstrap complete.  rebuilding...
/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36

==> 07e-libffi.txt <==
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /usr/bin/mkdir -p '/home/msnid/autobuild/Linux-fedora-gtk4/share/info'
 /usr/bin/install -c -m 644 ../doc/libffi.info '/home/msnid/autobuild/Linux-fedora-gtk4/share/info'
 /usr/bin/mkdir -p '/home/msnid/autobuild/Linux-fedora-gtk4/lib/pkgconfig'
 /usr/bin/install -c -m 644 libffi.pc '/home/msnid/autobuild/Linux-fedora-gtk4/lib/pkgconfig'
make[3]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libffi-3.2.1/x86_64-unknown-linux-gnu'
make[2]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libffi-3.2.1/x86_64-unknown-linux-gnu'
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libffi-3.2.1/x86_64-unknown-linux-gnu'

==> 07g-pygobject.txt <==
:::: PKG_CONFIG_PATH is /home/msnid/autobuild/Linux-fedora-gtk4/lib64/pkgconfig:/home/msnid/autobuild/Linux-fedora-gtk4/lib/pkgconfig:/home/msnid/autobuild/Linux-fedora-gtk4/lib/x86_64-linux-gnu/pkgconfig:/lib/pkgconfig
2024-03-08 15:43:58 URL:http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/PyGObject-3.42.1.tar.gz [718402/718402] -> "/home/msnid/autobuild/building/sources/PyGObject-3.42.1.tar.gz" [1]
::: trying to untar /home/msnid/autobuild/building/sources/PyGObject-3.42.1.tar.gz
::: which python3
/home/msnid/autobuild/Linux-fedora-gtk4/bin/python3
ld_library_path /home/msnid/autobuild/Linux-fedora-gtk4/lib
:::: in directory /home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/PyGObject-3.42.1
:::: building using meson -Dprefix=/home/msnid/autobuild/Linux-fedora-gtk4 build
build-it-3-3: line 3931: meson: command not found
:::: meson failed

==> 07-python.txt <==
  File "/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/Python-3.11.4/Lib/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/Python-3.11.4/python', '-W', 'ignore::DeprecationWarning', '-c', '\nimport runpy\nimport sys\nsys.path = [\'/tmp/tmpmwlasruh/setuptools-65.5.0-py3-none-any.whl\', \'/tmp/tmpmwlasruh/pip-23.1.2-py3-none-any.whl\'] + sys.path\nsys.argv[1:] = [\'install\', \'--no-cache-dir\', \'--no-index\', \'--find-links\', \'/tmp/tmpmwlasruh\', \'--root\', \'/\', \'setuptools\', \'pip\']\nrunpy.run_module("pip", run_name="__main__", alter_sys=True)\n']' returned non-zero exit status 1.
make: *** [Makefile:1860: install] Error 1
test cypes in the new python
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/msnid/autobuild/Linux-fedora-gtk4/lib/python3.11/ctypes/__init__.py", line 8, in <module>
    from _ctypes import Union, Structure, Array
ModuleNotFoundError: No module named '_ctypes'

==> 08-pre-gmp.txt <==
     during linking
   - use the '-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to '/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[3]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/gmp-6.1.2'
make[2]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/gmp-6.1.2'
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/gmp-6.1.2'

==> 09-pre-libtool.txt <==
 /usr/bin/install -c -m 644 './libltdl/lt_dlloader.c' '/home/msnid/autobuild/Linux-fedora-gtk4/share/libtool/lt_dlloader.c'
 /usr/bin/install -c -m 644 './libltdl/lt_error.c' '/home/msnid/autobuild/Linux-fedora-gtk4/share/libtool/lt_error.c'
 /usr/bin/install -c -m 644 './libltdl/ltdl.c' '/home/msnid/autobuild/Linux-fedora-gtk4/share/libtool/ltdl.c'
 /usr/bin/install -c -m 644 './libltdl/ltdl.h' '/home/msnid/autobuild/Linux-fedora-gtk4/share/libtool/ltdl.h'
 /usr/bin/install -c -m 644 './libltdl/ltdl.mk' '/home/msnid/autobuild/Linux-fedora-gtk4/share/libtool/ltdl.mk'
 /usr/bin/install -c -m 644 './libltdl/slist.c' '/home/msnid/autobuild/Linux-fedora-gtk4/share/libtool/slist.c'
chmod a+x '/home/msnid/autobuild/Linux-fedora-gtk4/share/libtool/configure'
make[3]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libtool-2.4.6'
make[2]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libtool-2.4.6'
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libtool-2.4.6'

==> 10-pre-readline.txt <==
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/readline-8.2/shlib'
( cd shlib ; make  DESTDIR= install )
make[1]: Entering directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/readline-8.2/shlib'
/bin/sh ../support/mkdirs /home/msnid/autobuild/Linux-fedora-gtk4/lib
/bin/sh ../support/mkdirs /home/msnid/autobuild/Linux-fedora-gtk4/bin
/bin/sh ../support/shlib-install -O linux-gnu -V pc -d /home/msnid/autobuild/Linux-fedora-gtk4/lib -b /home/msnid/autobuild/Linux-fedora-gtk4/bin -i "/usr/bin/install -c -m 644" libhistory.so.8.2
/bin/sh ../support/shlib-install -O linux-gnu -V pc -d /home/msnid/autobuild/Linux-fedora-gtk4/lib -b /home/msnid/autobuild/Linux-fedora-gtk4/bin -i "/usr/bin/install -c -m 644" libreadline.so.8.2
install: you may need to run ldconfig
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/readline-8.2/shlib'

==> 15-a-libidn2.txt <==
make[3]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libidn2-2.2.0/doc'
make[2]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libidn2-2.2.0/doc'
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libidn2-2.2.0/doc'
make[1]: Entering directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libidn2-2.2.0'
make[2]: Entering directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libidn2-2.2.0'
make[2]: Nothing to be done for 'install-exec-am'.
 /usr/bin/mkdir -p '/home/msnid/autobuild/Linux-fedora-gtk4/lib/pkgconfig'
 /usr/bin/install -c -m 644 libidn2.pc '/home/msnid/autobuild/Linux-fedora-gtk4/lib/pkgconfig'
make[2]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libidn2-2.2.0'
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libidn2-2.2.0'

==> 15-b-curl.txt <==
 /usr/bin/mkdir -p '/home/msnid/autobuild/Linux-fedora-gtk4/share/man/man3'
 /usr/bin/install -c -m 644 libcurl.m4 '/home/msnid/autobuild/Linux-fedora-gtk4/share/aclocal'
 /usr/bin/install -c -m 644 curl_easy_cleanup.3 curl_easy_duphandle.3 curl_easy_escape.3 curl_easy_getinfo.3 curl_easy_init.3 curl_easy_pause.3 curl_easy_perform.3 curl_easy_recv.3 curl_easy_reset.3 curl_easy_send.3 curl_easy_setopt.3 curl_easy_strerror.3 curl_easy_unescape.3 curl_easy_upkeep.3 curl_escape.3 curl_formadd.3 curl_formfree.3 curl_formget.3 curl_free.3 curl_getdate.3 curl_getenv.3 curl_global_cleanup.3 curl_global_init.3 curl_global_init_mem.3 curl_global_sslset.3 curl_mime_addpart.3 curl_mime_data.3 curl_mime_data_cb.3 curl_mime_encoder.3 curl_mime_filedata.3 curl_mime_filename.3 curl_mime_free.3 curl_mime_headers.3 curl_mime_init.3 curl_mime_name.3 curl_mime_subparts.3 curl_mime_type.3 curl_mprintf.3 curl_multi_add_handle.3 curl_multi_assign.3 '/home/msnid/autobuild/Linux-fedora-gtk4/share/man/man3'
 /usr/bin/install -c -m 644 curl_multi_cleanup.3 curl_multi_fdset.3 curl_multi_info_read.3 curl_multi_init.3 curl_multi_perform.3 curl_multi_remove_handle.3 curl_multi_setopt.3 curl_multi_socket.3 curl_multi_socket_action.3 curl_multi_socket_all.3 curl_multi_strerror.3 curl_multi_timeout.3 curl_multi_wait.3 curl_share_cleanup.3 curl_share_init.3 curl_share_setopt.3 curl_share_strerror.3 curl_slist_append.3 curl_slist_free_all.3 curl_strequal.3 curl_strnequal.3 curl_unescape.3 curl_url.3 curl_url_cleanup.3 curl_url_dup.3 curl_url_get.3 curl_url_set.3 curl_version.3 curl_version_info.3 libcurl-easy.3 libcurl-env.3 libcurl-errors.3 libcurl-multi.3 libcurl-security.3 libcurl-share.3 libcurl-symbols.3 libcurl-thread.3 libcurl-tutorial.3 libcurl-url.3 libcurl.3 '/home/msnid/autobuild/Linux-fedora-gtk4/share/man/man3'
make[6]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/curl-7.65.3/docs/libcurl'
make[5]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/curl-7.65.3/docs/libcurl'
make[4]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/curl-7.65.3/docs/libcurl'
make[3]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/curl-7.65.3'
make[2]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/curl-7.65.3'
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/curl-7.65.3'

==> 15-gsl.txt <==

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /usr/bin/mkdir -p '/home/msnid/autobuild/Linux-fedora-gtk4/bin'
  /bin/sh ./libtool   --mode=install /usr/bin/install -c gsl-randist gsl-histogram '/home/msnid/autobuild/Linux-fedora-gtk4/bin'
libtool: install: /usr/bin/install -c .libs/gsl-randist /home/msnid/autobuild/Linux-fedora-gtk4/bin/gsl-randist
libtool: install: /usr/bin/install -c .libs/gsl-histogram /home/msnid/autobuild/Linux-fedora-gtk4/bin/gsl-histogram
make[2]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/gsl-2.7'
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/gsl-2.7'

==> 15-libgd.txt <==
   Support for Fontconfig library:   no
   Support for Xpm library:          no
   Support for pthreads:             yes

configure: creating ./config.status
config.status: creating Makefile
gawk: symbol lookup error: /home/msnid/autobuild/Linux-fedora-gtk4/lib/libreadline.so.8: undefined symbol: UP
config.status: error: could not create Makefile
make: *** No targets specified and no makefile found.  Stop.
/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36

==> 15-raster3d.txt <==
make render
gfortran -std=legacy -g -w -O3 -Wno-tabs -ffixed-line-length-132  -c -o render.o render.f
gcc -g -Wall -Dgfortran -I/usr/include -I/usr/local/include -DGUNZIP   -DGD_SUPPORT -I/home/msnid/autobuild/Linux-fedora-gtk4/include  -DLINUX -DNETWORKBYTEORDER -c local.c
local.c:63:10: fatal error: gd.h: No such file or directory
   63 | #include "gd.h"
      |          ^~~~~~
compilation terminated.
make: *** [Makefile:207: local.o] Error 1
make render failed
/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36

==> 16-boost.txt <==
common.copy /home/msnid/autobuild/Linux-fedora-gtk4/lib/cmake/boost_python-1.83.0/libboost_python-variant-shared-py3.11.cmake
gcc.compile.c++ bin.v2/libs/regex/build/gcc-13/release/threading-multi/visibility-hidden/posix_api.o
gcc.compile.c++ bin.v2/libs/regex/build/gcc-13/release/threading-multi/visibility-hidden/wide_posix_api.o
gcc.link.dll bin.v2/libs/regex/build/gcc-13/release/threading-multi/visibility-hidden/libboost_regex.so.1.83.0
boost-install.generate-cmake-variant- bin.v2/libs/regex/build/gcc-13/release/threading-multi/visibility-hidden/libboost_regex-variant-shared.cmake
common.copy /home/msnid/autobuild/Linux-fedora-gtk4/lib/libboost_regex.so.1.83.0
ln-UNIX /home/msnid/autobuild/Linux-fedora-gtk4/lib/libboost_regex.so
common.copy /home/msnid/autobuild/Linux-fedora-gtk4/lib/cmake/boost_regex-1.83.0/libboost_regex-variant-shared.cmake
...updated 17323 targets...
/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36

==> 17-a-numpy.txt <==
  For more details, see:
    https://numpy.org/devdocs/reference/distutils_status_migration.html 


  import numpy.distutils.command.sdist
Traceback (most recent call last):
  File "/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/numpy-1.26.3/setup.py", line 76, in <module>
    import setuptools
ModuleNotFoundError: No module named 'setuptools'
/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36

==> 17-b-eigen.txt <==
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/eigen3/unsupported/Eigen/CXX11/src/ThreadPool/ThreadYield.h
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/eigen3/unsupported/Eigen/CXX11/src/ThreadPool/SimpleThreadPool.h
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/eigen3/unsupported/Eigen/CXX11/src/ThreadPool/EventCount.h
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/eigen3/unsupported/Eigen/CXX11/src/util
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/eigen3/unsupported/Eigen/CXX11/src/util/CXX11Workarounds.h
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/eigen3/unsupported/Eigen/CXX11/src/util/EmulateCXX11Meta.h
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/eigen3/unsupported/Eigen/CXX11/src/util/CXX11Meta.h
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/eigen3/unsupported/Eigen/CXX11/src/util/EmulateArray.h
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/eigen3/unsupported/Eigen/CXX11/src/util/MaxSizeVector.h
/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36

==> 17-c-catch2.txt <==
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/catch2/matchers/catch_matchers_vector.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/catch2/matchers/catch_matchers_quantifiers.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/catch2/matchers/catch_matchers_exception.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/catch2/matchers/catch_matchers_predicate.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/catch2/matchers/catch_matchers.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/catch2/matchers/catch_matchers_string.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/catch2/matchers/catch_matchers_range_equals.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/catch2/catch_assertion_result.hpp
-- Up-to-date: /home/msnid/autobuild/Linux-fedora-gtk4/include/catch2
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/catch2/catch_user_config.hpp

==> 17-glm.txt <==
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/glm/detail/type_mat2x4.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/glm/detail/type_vec2.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/glm/detail/_swizzle_func.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/glm/detail/type_half.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/glm/glm.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/glm/vec4.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/lib64/cmake/glm/glmConfig.cmake
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/lib64/cmake/glm/glmConfigVersion.cmake
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/lib64/cmake/glm/glmTargets.cmake
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/lib64/pkgconfig/glm.pc

==> 17-pip-wheel-pygobject.txt <==
installing pygobject
PKG_CONFIG_PATH /home/msnid/autobuild/Linux-fedora-gtk4/lib64/pkgconfig:/home/msnid/autobuild/Linux-fedora-gtk4/lib/pkgconfig:/home/msnid/autobuild/Linux-fedora-gtk4/lib/x86_64-linux-gnu/pkgconfig:/lib/pkgconfig
which: no pip3 in (/home/msnid/cmake/bin:/home/msnid/autobuild/Linux-fedora-gtk4/bin:/home/msnid/autobuild/Linux-fedora-gtk4/bin:/home/msnid/autobuild/Linux-fedora-pre-release-gtk4/bin:/home/msnid/.local/bin:/home/msnid/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc)
build-it-3-3: line 4076: pip3: command not found
build-it-3-3: line 4077: pip3: command not found

==> 18-rdkit.txt <==
  The md5 checksum for
  /home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/rdkit-Release_2023_09_4/External/CoordGen/maeparser-v1.3.1.tar.gz
  is incorrect; expected: cfa40e29366f4b413e4ec15f959ee139, found:
  d41d8cd98f00b204e9800998ecf8427e
Call Stack (most recent call first):
  External/CoordGen/CMakeLists.txt:19 (downloadAndCheckMD5)


-- Configuring incomplete, errors occurred!
problem configuring the RDKit.

==> 19-gobject-introspection.txt <==
Perhaps you should add the directory containing `glib-2.0.pc'
to the PKG_CONFIG_PATH environment variable
Package 'glib-2.0', required by 'virtual:world', not found
building in:
/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/gobject-introspection-1.72.0
which meson
which: no meson in (/home/msnid/cmake/bin:/home/msnid/autobuild/Linux-fedora-gtk4/bin:/home/msnid/autobuild/Linux-fedora-gtk4/bin:/home/msnid/autobuild/Linux-fedora-pre-release-gtk4/bin:/home/msnid/.local/bin:/home/msnid/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc)
build-it-3-3: line 3830: meson: command not found
build-it-3-3: line 3840: meson: command not found
meson failed

==> 19-libubunistring.txt <==
make[3]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libunistring-0.9.10/tests'
make[2]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libunistring-0.9.10/tests'
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libunistring-0.9.10/tests'
make[1]: Entering directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libunistring-0.9.10'
make[2]: Entering directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libunistring-0.9.10'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libunistring-0.9.10'
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libunistring-0.9.10'
/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36

==> 20-libatomic-ops.txt <==
make[1]: Entering directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libatomic_ops-7.6.12'
make[2]: Entering directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libatomic_ops-7.6.12'
make[2]: Nothing to be done for 'install-exec-am'.
 /usr/bin/mkdir -p '/home/msnid/autobuild/Linux-fedora-gtk4/share/doc/libatomic_ops'
 /usr/bin/install -c -m 644 COPYING README.md '/home/msnid/autobuild/Linux-fedora-gtk4/share/doc/libatomic_ops'
 /usr/bin/mkdir -p '/home/msnid/autobuild/Linux-fedora-gtk4/lib/pkgconfig'
 /usr/bin/install -c -m 644 pkgconfig/atomic_ops.pc '/home/msnid/autobuild/Linux-fedora-gtk4/lib/pkgconfig'
make[2]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libatomic_ops-7.6.12'
make[1]: Leaving directory '/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36/libatomic_ops-7.6.12'
/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36

==> 21-gc.txt <==
checking pkg-config is at least version 0.9.0... yes
checking for atomic_ops... yes
checking which libatomic_ops to use... external
checking for lock-free AO_or primitive... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
gawk: symbol lookup error: /home/msnid/autobuild/Linux-fedora-gtk4/lib/libreadline.so.8: undefined symbol: UP
config.status: error: could not create Makefile
/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36

==> 24-guile.txt <==
checking for rl_getc_function pointer in readline... no
configure: WARNING: *** GNU Readline is too old on your system.
configure: WARNING: *** You need readline version 2.1 or later.
checking for strdup... (cached) yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating libguile/gen-scmconfig.h
gawk: symbol lookup error: /home/msnid/autobuild/Linux-fedora-gtk4/lib/libreadline.so.8: undefined symbol: UP
config.status: error: could not create libguile/gen-scmconfig.h
/home/msnid/autobuild/building/fedora_2024-03-08__T21_34_36

==> 25-g-wrap.txt <==
========================= build g-wrap =================================
2024-03-08 15:45:52 URL:http://nongnu.askapache.com/g-wrap/g-wrap-1.9.15.tar.gz [701601/701601] -> "/home/msnid/autobuild/building/sources/g-wrap-1.9.15.tar.gz" [1]
no guile

==> 26-guile-cairo.txt <==
========================= build guile-cairo =================================
fetching file /home/msnid/autobuild/building/sources/guile-cairo-1.9.91.tar.gz
2024-03-08 15:45:53 URL:http://mirrors.ocf.berkeley.edu/nongnu/guile-cairo/guile-cairo-1.9.91.tar.gz [578928/578928] -> "/home/msnid/autobuild/building/sources/guile-cairo-1.9.91.tar.gz" [1]
no guile

==> 27-gemmi.txt <==
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/gz.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/dencalc.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/floodfill.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/fourier.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/include/gemmi/small.hpp
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/lib64/libgemmi_cpp.so
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/lib64/cmake/gemmi/gemmi-targets.cmake
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/lib64/cmake/gemmi/gemmi-targets-release.cmake
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/lib64/cmake/gemmi/gemmi-config.cmake
-- Installing: /home/msnid/autobuild/Linux-fedora-gtk4/lib64/cmake/gemmi/gemmi-config-version.cmake

==> 28-guile-gnome-platform.txt <==
configure: error: Package requirements (g-wrap-2.0-guile >= 1.9.15) were not met:

Package 'g-wrap-2.0-guile', required by 'virtual:world', not found

Consider adjusting the PKG_CONFIG_PATH environment variable if you
installed software in a non-standard prefix.

Alternatively, you may set the environment variables G_WRAP_CFLAGS
and G_WRAP_LIBS to avoid the need to call pkg-config.
See the pkg-config man page for more details.

==> 30-clone-autogen.txt <==
libtoolize: copying file 'macros/ltsugar.m4'
libtoolize: copying file 'macros/ltversion.m4'
libtoolize: copying file 'macros/lt~obsolete.m4'
aclocal -I macros -I /home/msnid/autobuild/Linux-fedora-gtk4/share/aclocal
autoconf
automake --add-missing --copy
configure.ac:41: installing './compile'
configure.ac:41: installing './config.guess'
configure.ac:41: installing './config.sub'
api/Makefile.am:92: installing './py-compile'

==> 30-coot.txt <==
Consider adjusting the PKG_CONFIG_PATH environment variable if you
installed software in a non-standard prefix.

Alternatively, you may set the environment variables GLIB_CFLAGS
and GLIB_LIBS to avoid the need to call pkg-config.
See the pkg-config man page for more details.
make: *** No targets specified and no makefile found.  Stop.
=== make again ===
make: *** No targets specified and no makefile found.  Stop.
make failed.

Probably need meson and python3-pip?

Mar 08 '24 22:03 mysecondnameisdanger

Python is frustratingly finickety to compile correctly (notice that your Python does have ctypes (and ctypes are vital for the Python gui part of Coot)). Maybe you can fix it "by hand"? The directory where you can find the Python code and build is written at the top of 07-python.txt

Maybe related:? https://stackoverflow.com/questions/27022373/python3-importerror-no-module-named-ctypes-when-using-value-from-module-mul

build-it-3-3 is supposed to build guile and meson and python3 and (hence) pip3.

Coot doesn't require guile but it is better if it has it.

Have added a fix for the gc build and the guile build - I hope.

Perhaps the build script should just stop if Python fails to build. That would be less confusing.

Mar 09 '24 04:03 pemsley

after installing libffi-devel still get the ctypes error... in 07-python.txt. Maybe need to execute ldconfig? as in comment by @Ben-xue on given url ... *ldconfig needs sudo

Do we need to compile python in fedora? I do not find a lot of information on this...except maybe this https://devguide.python.org/getting-started/setup-building/index.html#build-dependencies and https://www.youtube.com/watch?v=bz_dpRHmoZM

Yes...It would be nice to check if something is not found/built and stop right there :P

Mar 10 '24 01:03 mysecondnameisdanger

Maybe need to execute ldconfig?

I'd be surprised.

Do we need to compile python in fedora?

Coot needs Python to use RDKit and to use with its own GUI code and Pyrogen (and Layla, I think).

If you can make a stand-alone script for your system that compiles Python 3.10.13 and it has working ctypes and ssl that would be great. (Using self-installed libffi and OpenSSL would be the best, but even using the system libs would be a step forward).

Mar 11 '24 01:03 pemsley

The python that comes with Fedora 39 says

Python 3.12.2 (main, Feb 21 2024, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import ssl
>>> import ctypes
>>>

After installing some dependencies in a fresh fedora 39

  sudo dnf update
  sudo dnf install dnf-plugins-core # to get builddep
  sudo dnf builddep python3 # to get the deps to build python3
  sudo dnf install perl-FindBin perl-IPC-Cmd # also required

and then running this

#!/bin/bash
# I am not an expert writing bash code :P
# Set paths (this can be asked and/or tested)
DIRECTORIES=("$HOME/libs-for-python" "$HOME/building-python")

# Function to create directory or remove and create if it exists
create_directory() {
    if [ -d "$1" ]; then
        rm -rf "$1"
    fi
    mkdir -p "$1"
}

# Create directories
for DIR in "${DIRECTORIES[@]}"; do
    create_directory "$DIR"
done

# Download and install openssl
cd "$HOME/libs-for-python"
wget https://openssl.org/source/openssl-3.2.1.tar.gz
tar -xvzf openssl*.tar.gz 
rm openssl*.tar.gz
mv openssl-3.2.1 ssl
cd "$HOME/libs-for-python/ssl"
./config --prefix="$HOME/libs-for-python/ssl" --openssldir="$HOME/libs-for-python/ssl"
make
# make test  # Uncomment if you want to run tests
make install

# Download and install libffi
cd "$HOME/libs-for-python"
wget https://github.com/libffi/libffi/archive/refs/heads/master.zip
unzip master.zip
mv master ffi
cd "$HOME/libs-for-python/ffi"
./configure --prefix="$HOME/libs-for-python/ffi"
make
make install

# Download Python source
cd "$HOME/building-python"
wget https://www.python.org/ftp/python/3.10.13/Python-3.10.13.tgz
tar -xvzf Python-3.10.13.tgz
cd Python-3.10.13
# Configure and compile Python with self-installed OpenSSL and libffi
./configure --prefix="$HOME/building-python" --with-openssl="$HOME/libs-for-python/ssl" --with-system-ffi="$HOME/libs-for-python/ffi" LDFLAGS="-L$HOME/libs-for-python/ssl/lib"
make
make altinstall

# Test Python installation
echo "Open $HOME/building-python/bin/python3.10 and do `import ssl` and `import ctypes`"

I also get no errors for ctypes and ssl

msnid@fedora:~/building-python/bin$ ./python3.10
Python 3.10.13 (main, Mar 11 2024, 19:36:55) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import ctypes
>>> import ssl
>>>

Mar 12 '24 02:03 mysecondnameisdanger

OK, that looks great. I will pick it over and maybe add some of it to build-it-3-3.

Now, if you install that compiled python3 into the directory where build-it-3-3 is installing components, then when you run build-it-3-3 again, it should detect your python3 and not build "its own."

Hopefully that will be progress...

Mar 13 '24 05:03 pemsley

What if the built python is added to the $PATH, before the system's python? Names are not the same

msnid@fedora:~/building-python/bin$ which python
/usr/bin/python
msnid@fedora:~/building-python/bin$ export PATH=/home/msnid/building-python/bin:$PATH
msnid@fedora:~/building-python/bin$ echo $PATH
/home/msnid/building-python/bin:/home/msnid/.local/bin:/home/msnid/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin
msnid@fedora:~/building-python/bin$ ls -lrt
total 16280
-rwxr-xr-x. 1 msnid msnid 16647008 Mar 11 19:37 python3.10
-rwxr-xr-x. 1 msnid msnid      102 Mar 11 19:38 pydoc3.10
-rwxr-xr-x. 1 msnid msnid      117 Mar 11 19:38 idle3.10
-rwxr-xr-x. 1 msnid msnid      119 Mar 11 19:38 2to3-3.10
-rwxr-xr-x. 1 msnid msnid     3073 Mar 11 19:38 python3.10-config
-rwxr-xr-x. 1 msnid msnid      247 Mar 11 19:38 pip3.10
msnid@fedora:~/building-python/bin$ which python3.10
~/building-python/bin/python3.10

.... I guess it's easier your way...

Mar 13 '24 16:03 mysecondnameisdanger

PS.... stopping if python is not built, works :)

BUILDING Python 3.11.4:
2024-03-13 10:56:21 URL:http://www.python.org/ftp/python/3.11.4/Python-3.11.4.tgz [26526163/26526163] -> "/home/msnid/autobuild/building/sources/Python-3.11.4.tgz" [1]
BUILDING Python 3.11.4 done
Pip update done
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/msnid/autobuild/Linux-fedora-gtk4/lib/python3.11/ctypes/__init__.py", line 8, in <module>
    from _ctypes import Union, Structure, Array
ModuleNotFoundError: No module named '_ctypes'

Mar 13 '24 17:03 mysecondnameisdanger

When I said "python" I meant "python3" - sorry for the confusion.

Mar 13 '24 22:03 pemsley

What if the built python is added to the $PATH, before the system's python?

The build script does that (python3).

I think you are hitting this line:

     echo wrong version of Python - needs rebuild

build-it-3-3 wants Python 3.11.4 and you have installed 3.10.13, so I think you need to run your script above changed to install Python 3.11.4.

Mar 13 '24 22:03 pemsley

@mysecondnameisdanger I've got it working on Fedora 40. Maybe it will also work on Fedora 39. Clear out your installation directory and give it another bash.

Apr 27 '24 23:04 pemsley

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How to install on fedora 39?

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