https://bugzilla.redhat.com/show_bug.cgi?id=1780849
Bug ID: 1780849 Summary: Review Request: pymol - PyMOL Molecular Graphics System Product: Fedora Version: rawhide Hardware: All OS: Linux Status: NEW Component: Package Review Severity: medium Priority: medium Assignee: nobody@fedoraproject.org Reporter: anto.trande@gmail.com QA Contact: extras-qa@fedoraproject.org CC: package-review@lists.fedoraproject.org Target Milestone: --- Classification: Fedora
Spec URL: https://sagitter.fedorapeople.org/pymol/pymol.spec SRPM URL: https://sagitter.fedorapeople.org/pymol/pymol-2.3.0-1.fc31.src.rpm
Description: New release of PyMOL software; re-review to resume this package.
Fedora Account System Username: sagitter
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
Antonio anto.trande@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Depends On| |1780848
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=1780848 [Bug 1780848] Review Request: mmtf-cpp - The Macromolecular Transmission Format (MMTF) header only files
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
Antonio anto.trande@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Blocks| |1754678 Doc Type|--- |If docs needed, set a value
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=1754678 [Bug 1754678] Pymol is absent from Fedora 31
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
Antonio anto.trande@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Blocks| |1597205
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=1597205 [Bug 1597205] pymol-2.1.0 is available
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
Miro Hrončok mhroncok@redhat.com changed:
What |Removed |Added ---------------------------------------------------------------------------- CC| |mhroncok@redhat.com
--- Comment #1 from Miro Hrončok mhroncok@redhat.com ---
# Turn off the brp-python-bytecompile script
1. why is this neeeded 2. there is a newer way to do this described at https://docs.fedoraproject.org/en-US/packaging-guidelines/#_brp_buildroot_po...
License: MIT and BSD and ZPLv2.0 and Bitstream Vera and OFL
This needs an explanation in comment.
Patch0: pymol-setup.py.patch Patch1: pymol-wmclass-main.patch Patch2: pymol-wmclass-pmgapp.patch Patch3: pymol-mmtf.patch
So do those.
# Fix shebang in individual files to ensure Python 3 dependence sed -i '1s=^#!/usr/bin/(python|env python)[0-9.]*=#!%{__python3}=' test/cyg test/run test/show
Consider using pathfix.py from python3-devel.
echo "%{__python3} %{python3_sitearch}/pymol/__init__.py "$@"" >> pymol
Consider using `exec` here.
%{python3_sitearch}/*.egg-info
Consider adding trailing slash to ensure this remains a directory (if it is a directory).
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
--- Comment #2 from Antonio anto.trande@gmail.com --- New release:
Spec URL: https://copr-be.cloud.fedoraproject.org/results/sagitter/ForTesting/fedora-r... SRPM URL: https://copr-be.cloud.fedoraproject.org/results/sagitter/ForTesting/fedora-r...
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
--- Comment #3 from Antonio anto.trande@gmail.com --- New release:
Spec URL: https://copr-be.cloud.fedoraproject.org/results/sagitter/ForTesting/fedora-r... SRPM URL: https://copr-be.cloud.fedoraproject.org/results/sagitter/ForTesting/fedora-r...
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
Sergio Monteiro Basto sergio@serjux.com changed:
What |Removed |Added ---------------------------------------------------------------------------- CC| |sergio@serjux.com
--- Comment #4 from Sergio Monteiro Basto sergio@serjux.com --- fedora-review 0.7.4 says: No matching package to install: 'mmtf-cpp-devel' DEBUG util.py:596: Not all dependencies satisfied
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
--- Comment #5 from Antonio anto.trande@gmail.com --- (In reply to Sergio Monteiro Basto from comment #4)
fedora-review 0.7.4 says: No matching package to install: 'mmtf-cpp-devel' DEBUG util.py:596: Not all dependencies satisfied
You can't build pymol without mmtf-cpp In fact, this ticket depends by rhbz #1780848
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
--- Comment #6 from Antonio anto.trande@gmail.com --- pymol can be built on Rawhide now.
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
Robert-André Mauchin zebob.m@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- CC| |zebob.m@gmail.com
--- Comment #7 from Robert-André Mauchin zebob.m@gmail.com --- There's some shenanigans with python-pyside2 which break the build in Rawhide.
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
Sergio Monteiro Basto sergio@serjux.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED Assignee|nobody@fedoraproject.org |sergio@serjux.com Flags| |fedora-review?
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
--- Comment #8 from Sergio Monteiro Basto sergio@serjux.com --- Package Review ==============
Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated [ ] = Manual review needed
Issues: ======= - Permissions on files are set properly. Note: See rpmlint output See: https://docs.fedoraproject.org/en-US/packaging- guidelines/#_file_permissions
===== MUST items =====
C/C++: [ ]: Package does not contain kernel modules. [ ]: Package contains no static executables. [ ]: Development (unversioned) .so files in -devel subpackage, if present. Note: Unversioned so-files in private %_libdir subdirectory (see attachment). Verify they are not in ld path. [x]: If your application is a C or C++ application you must list a BuildRequires against gcc, gcc-c++ or clang. [x]: Package does not contain any libtool archives (.la) [x]: Rpath absent or only used for internal libs.
Generic: [x]: Package is licensed with an open-source compatible license and meets other legal requirements as defined in the legal section of Packaging Guidelines. []: License field in the package spec file matches the actual license. Note: Checking patched sources after %prep for licenses. Licenses found: "Unknown or generated", "Python Software Foundation License", "SIL Open Font License (v1.0)", "Apache License (v2.0)", "BSD 2-clause "Simplified" License", "BSD 3-clause "New" or "Revised" License", "Expat License". 1260 files have unknown license. Detailed output of licensecheck in /home/sergio/fedora-scm/1780849-pymol/licensecheck.txt [ ]: Package does not own files or directories owned by other packages. Note: Dirs in package are owned also by: /usr/lib64/python3.8/site- packages/chempy(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/chempy/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/chempy/bmin(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/chempy/bmin/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/chempy/champ(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/chempy/champ/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/chempy/fast(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/chempy/fast/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/chempy/fragments(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/chempy/fragments/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/chempy/mmtf(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/chempy/mmtf/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/chempy/tinker(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/chempy/tinker/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pmg_qt(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pmg_qt/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pmg_qt/forms(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pmg_qt/forms/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pmg_qt/syntax(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pmg_qt/syntax/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pmg_tk(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pmg_tk/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pmg_tk/skins(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pmg_tk/skins/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pmg_tk/skins/demo(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pmg_tk/skins/demo/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pmg_tk/skins/normal(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pmg_tk/skins/normal/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pmg_tk/startup(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pmg_tk/startup/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pymol/Qt(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/Qt/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pymol/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/contrib(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pymol/contrib/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/data(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pymol/data/chempy(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/data/chempy/fragments(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/data/chempy/sidechains(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/data/chempy/tinker(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/data/demo(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pymol/data/pmg_qt(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/data/pmg_qt/icons(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/data/pmg_qt/styles(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/data/pmg_tk(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pymol/data/pmg_tk/bitmaps(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/data/pmg_tk/bitmaps/builder(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/data/pymol(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pymol/data/pymol/icons(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/data/pymol/matrices(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/data/shaders(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pymol/data/startup(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/data/startup/lightingsettings_gui(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/data/test(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pymol/data/tut(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/embed(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pymol/embed/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/embed/epymol(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/embed/epymol/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/embed/wxpymol(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/embed/wxpymol/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/examples(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pymol/examples/chempy(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/examples/cookbook(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pymol/examples/devel(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/examples/launching(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/opengl(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pymol/opengl/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/opengl/gl(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/opengl/gl/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/opengl/glu(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/opengl/glu/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/opengl/glut(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/opengl/glut/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/plugins(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pymol/plugins/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/scripts(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pymol/scripts/metaphorics(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/stereochemistry(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/stereochemistry/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pymol/test(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/test/dat(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pymol/test/inp(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/test/ref(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pymol/wizard(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol/wizard/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site-packages/pymol2(locale,, to, Failed, set, defaulting, C), /usr/lib64/python3.8/site- packages/pymol2/__pycache__(locale,, to, Failed, set, defaulting, C), /usr/share/doc/pymol(locale,, to, Failed, set, defaulting, C), /usr/share/licenses/pymol(locale,, to, Failed, set, defaulting, C) [ ]: %build honors applicable compiler flags or justifies otherwise. [x]: Package contains no bundled libraries without FPC exception. [x]: Changelog in prescribed format. [ ]: Sources contain only permissible code or content. [ ]: Development files must be in a -devel package [ ]: Package uses nothing in %doc for runtime. [ ]: Package consistently uses macros (instead of hard-coded directory names). [ ]: Package is named according to the Package Naming Guidelines. [ ]: Package does not generate any conflict. [ ]: Package obeys FHS, except libexecdir and /usr/target. [ ]: If the package is a rename of another package, proper Obsoletes and Provides are present. [ ]: Requires correct, justified where necessary. [ ]: Spec file is legible and written in American English. [ ]: Package contains systemd file(s) if in need. [ ]: Useful -debuginfo package or justification otherwise. [ ]: Package is not known to require an ExcludeArch tag. [ ]: Large documentation must go in a -doc subpackage. Large could be size (~1MB) or number of files. Note: Documentation size is 20480 bytes in 3 files. [ ]: Package complies to the Packaging Guidelines [x]: Package successfully compiles and builds into binary rpms on at least one supported primary architecture. [x]: Package installs properly. [x]: Rpmlint is run on all rpms the build produces. Note: There are rpmlint messages (see attachment). [x]: If (and only if) the source package includes the text of the license(s) in its own file, then that file, containing the text of the license(s) for the package is included in %license. [x]: Package requires other packages for directories it uses. [x]: Package must own all directories that it creates. [x]: Package uses either %{buildroot} or $RPM_BUILD_ROOT [x]: Package does not run rm -rf %{buildroot} (or $RPM_BUILD_ROOT) at the beginning of %install. [x]: Macros in Summary, %description expandable at SRPM build time. [x]: Package contains desktop file if it is a GUI application. [x]: Package installs a %{name}.desktop using desktop-file-install or desktop-file-validate if there is such a file. [x]: Dist tag is present. [x]: Package does not contain duplicates in %files. [x]: Package must not depend on deprecated() packages. [x]: Package use %makeinstall only when make install DESTDIR=... doesn't work. [x]: Package is named using only allowed ASCII characters. [x]: Package is not relocatable. [x]: Sources used to build the package match the upstream source, as provided in the spec URL. [x]: Spec file name must match the spec package %{name}, in the format %{name}.spec. [x]: File names are valid UTF-8. [x]: Packages must not store files under /srv, /opt or /usr/local
Python: [ ]: Python eggs must not download any dependencies during the build process. [ ]: A package which is used by another package via an egg interface should provide egg info. [ ]: Package meets the Packaging Guidelines::Python [x]: Package contains BR: python2-devel or python3-devel [x]: Packages MUST NOT have dependencies (either build-time or runtime) on packages named with the unversioned python- prefix unless no properly versioned package exists. Dependencies on Python packages instead MUST use names beginning with python2- or python3- as appropriate. [x]: Python packages must not contain %{pythonX_site(lib|arch)}/* in %files [x]: Binary eggs must be removed in %prep
===== SHOULD items =====
Generic: [ ]: If the source package does not include license text(s) as a separate file from upstream, the packager SHOULD query upstream to include it. [ ]: Final provides and requires are sane (see attachments). [ ]: Package functions as described. [ ]: Latest version is packaged. [ ]: Package does not include license text files separate from upstream. [ ]: Patches link to upstream bugs/comments/lists or are otherwise justified. [ ]: Sources are verified with gpgverify first in %prep if upstream publishes signatures. Note: gpgverify is not used. [ ]: Description and summary sections in the package spec file contains translations for supported Non-English languages, if available. [ ]: Package should compile and build into binary rpms on all supported architectures. [ ]: %check is present and all tests pass. [ ]: Packages should try to preserve timestamps of original installed files. [ ]: Spec use %global instead of %define unless justified. Note: %define requiring justification: %define __brp_python_bytecompile %{nil} [x]: Reviewer should test that the package builds in mock. [x]: Buildroot is not present [x]: Package has no %clean section with rm -rf %{buildroot} (or $RPM_BUILD_ROOT) [x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin. [x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file [x]: Sources can be downloaded from URI in Source: tag [x]: SourceX is a working URL.
===== EXTRA items =====
Generic: [x]: Rpmlint is run on debuginfo package(s). Note: No rpmlint messages. [x]: Rpmlint is run on all installed packages. Note: There are rpmlint messages (see attachment). [x]: Large data in /usr/share should live in a noarch subpackage if package is arched. [x]: Spec file according to URL is the same as in SRPM.
Rpmlint ------- Checking: pymol-2.3.0-3.fc32.x86_64.rpm pymol-2.3.0-3.fc32.src.rpm pymol.x86_64: W: name-repeated-in-summary C PyMOL pymol.x86_64: E: non-standard-executable-perm /usr/lib64/python3.8/site-packages/chempy/champ/_champ.cpython-38-x86_64-linux-gnu.so 775 pymol.x86_64: E: non-standard-executable-perm /usr/lib64/python3.8/site-packages/pymol/_cmd.cpython-38-x86_64-linux-gnu.so 775 pymol.x86_64: W: no-manual-page-for-binary pymol pymol.src: W: name-repeated-in-summary C PyMOL 2 packages and 0 specfiles checked; 2 errors, 3 warnings.
Rpmlint (debuginfo) ------------------- Checking: pymol-debuginfo-2.3.0-3.fc32.x86_64.rpm 1 packages and 0 specfiles checked; 0 errors, 0 warnings.
Rpmlint (installed packages) ---------------------------- pymol.x86_64: W: name-repeated-in-summary C PyMOL pymol.x86_64: E: non-standard-executable-perm /usr/lib64/python3.8/site-packages/chempy/champ/_champ.cpython-38-x86_64-linux-gnu.so 775 pymol.x86_64: E: non-standard-executable-perm /usr/lib64/python3.8/site-packages/pymol/_cmd.cpython-38-x86_64-linux-gnu.so 775 pymol.x86_64: W: no-manual-page-for-binary pymol 2 packages and 0 specfiles checked; 2 errors, 2 warnings.
Unversioned so-files -------------------- pymol: /usr/lib64/python3.8/site-packages/chempy/champ/_champ.cpython-38-x86_64-linux-gnu.so pymol: /usr/lib64/python3.8/site-packages/pymol/_cmd.cpython-38-x86_64-linux-gnu.so
Source checksums ---------------- https://github.com/schrodinger/pymol-open-source/archive/v2.3.0/pymol-open-s... : CHECKSUM(SHA256) this package : 62aa21fafd1db805c876f89466e47513809f8198395e1f00a5f5cc40d6f40ed0 CHECKSUM(SHA256) upstream package : 62aa21fafd1db805c876f89466e47513809f8198395e1f00a5f5cc40d6f40ed0
Requires -------- pymol (rpmlib, GLIBC filtered): /usr/bin/csh /usr/bin/python3 /usr/bin/sh apbs(x86-64) chemical-mime-data libGL.so.1()(64bit) libGLEW.so.2.1()(64bit) libc.so.6()(64bit) libfreetype.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libglut.so.3()(64bit) libm.so.6()(64bit) libpng16.so.16()(64bit) libpng16.so.16(PNG16_0)(64bit) libpthread.so.0()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.3)(64bit) python(abi) python3-PyQt4(x86-64) python3-mmtf python3-numpy(x86-64) python3-pmw python3-tkinter(x86-64) rtld(GNU_HASH)
Provides -------- pymol: PyMOL(x86-64) application() application(pymol.desktop) metainfo() metainfo(pymol.appdata.xml) pymol pymol(x86-64) python3.8dist(pymol) python3dist(pymol)
Generated by fedora-review 0.7.4 (54fa030) last change: 2019-12-07 Command line :/usr/bin/fedora-review -b 1780849 Buildroot used: fedora-rawhide-x86_64 Active plugins: Python, C/C++, Generic, Shell-api Disabled plugins: Java, fonts, SugarActivity, Perl, Ruby, Ocaml, PHP, R, Haskell Disabled flags: EPEL6, EPEL7, DISTTAG, BATCH, EXARCH
Development files must be in a -devel package , I don't know if we need one pymol-devel package but I don't know is unversioned so-files are needed and the non-standard-executable-perm are only thing that I see that needs to be review .
https://bugzilla.redhat.com/show_bug.cgi?id=1780849 Bug 1780849 depends on bug 1780848, which changed state.
Bug 1780848 Summary: Review Request: mmtf-cpp - The Macromolecular Transmission Format (MMTF) header only files https://bugzilla.redhat.com/show_bug.cgi?id=1780848
What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |CLOSED Resolution|--- |RAWHIDE
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
--- Comment #9 from Antonio anto.trande@gmail.com --- The package needs manual review []
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
--- Comment #10 from Robert-André Mauchin zebob.m@gmail.com ---
pymol.x86_64: E: non-standard-executable-perm /usr/lib64/python3.8/site-packages/chempy/champ/_champ.cpython-38-x86_64-linux-gnu.so 775 pymol.x86_64: E: non-standard-executable-perm /usr/lib64/python3.8/site-packages/pymol/_cmd.cpython-38-x86_64-linux-gnu.so 775
It's a bug with fedora-review/Mock or rpmlint. If you extract the rpm, it has correct 0755 perms.
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
--- Comment #11 from Sergio Monteiro Basto sergio@serjux.com --- https://sagitter.fedorapeople.org/pymol/pymol.spec is not available anymore
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
--- Comment #12 from Antonio anto.trande@gmail.com --- (In reply to Sergio Monteiro Basto from comment #11)
https://sagitter.fedorapeople.org/pymol/pymol.spec is not available anymore
Last release is on Copr:
Spec URL: https://copr-be.cloud.fedoraproject.org/results/sagitter/ForTesting/fedora-r... SRPM URL: https://copr-be.cloud.fedoraproject.org/results/sagitter/ForTesting/fedora-r...
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
--- Comment #13 from Sergio Monteiro Basto sergio@serjux.com --- Rawhide is broken again , please add me on https://src.fedoraproject.org/rpms/mmtf-cpp and or build mmtf-ccp on Fedora 31 , I want bring pymol to F31 anyway I guess .
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
Sergio Monteiro Basto sergio@serjux.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Flags|fedora-review? |fedora-review+
--- Comment #14 from Sergio Monteiro Basto sergio@serjux.com --- I'd would propose all patches be -p1 instead -p0 [1] and use %py3_build and %py3_install [2].
Also I'd remove "%define __brp_python_bytecompile %{nil}" with next patch in attachment .
Other questions raised on my previous comment one are replied (bug in other place) and Development files must be in a -devel package , for now we can keep it on main package.
Package APPROVED !
Please add me as maintainer and I could do the changes myself
[1] %autosetup -n pymol-open-source-%{version} -p1
[2]
%build %py3_build -- --use-msgpackc=c++11 --glut
%install %py3_install -- --use-msgpackc=c++11 --glut --pymol-path=%{python3_sitearch}/pymol
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
--- Comment #15 from Sergio Monteiro Basto sergio@serjux.com --- Created attachment 1648700 --> https://bugzilla.redhat.com/attachment.cgi?id=1648700&action=edit pymol-python3.patch
Applying this patch, fixes brp-python-bytecompile script, i.e. we can remove %define __brp_python_bytecompile %{nil}
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
--- Comment #16 from Antonio anto.trande@gmail.com --- Thank you Sergio.
https://bugzilla.redhat.com/show_bug.cgi?id=1780849
Sergio Monteiro Basto sergio@serjux.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |CLOSED Resolution|--- |RAWHIDE Last Closed| |2020-01-05 04:02:20
package-review@lists.fedoraproject.org
-
bugzilla＠redhat.com