[Bug 1821189] Package Review: Snakemake - Workflow management system to create reproducible and scalable data analyses

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

 



https://bugzilla.redhat.com/show_bug.cgi?id=1821189



--- Comment #2 from Hirotaka Wakabayashi <hiwkby@xxxxxxxxx> ---
Hello Aniket,

Thank you for submitting the package. As you say, this package needs no
"python" prefix because this package is not a library package. Please see:
https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/#_naming

Please check my review and ask if you have any questions. I checked this 
package but I couldn't install it because of dependency problem... rpmlint
is a very useful to detect common errors. Please see:
https://docs.fedoraproject.org/en-US/packaging-guidelines/#_use_rpmlint

Thanks in advance,
Hirotaka Wakabayashi

Package Review
==============

Legend:
[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
[ ] = Manual review needed


Issues:
=======
- Source0
  Please make sure the source code url is available.
  ```
  $ wget
https://github.com/aflc/snakemake/archive/v5.12.3/snakemake-5.12.3.tar.gz
  --2020-06-05 22:19:21-- 
https://github.com/aflc/snakemake/archive/v5.12.3/snakemake-5.12.3.tar.gz
  Resolving github.com (github.com)... 52.192.72.89
  Connecting to github.com (github.com)|52.192.72.89|:443... connected.
  HTTP request sent, awaiting response... 404 Not Found
  2020-06-05 22:19:21 ERROR 404: Not Found.
  ```
  You can use the %pypi_source macro. Please see:
 
https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/#_source_files_from_pypi
- Dependencies
  Please check dependent packages. Some packages don't seem to exist.
  ```
  $ sudo dnf install -y
~/rpmbuild/RPMS/x86_64/snakemake-5.12.3-1.fc33.x86_64.rpm 
  Last metadata expiration check: 0:49:45 ago on Fri 05 Jun 2020 10:06:39 PM
UTC.
  Error: 
   Problem: conflicting requests
    - nothing provides python3.9dist(datrie) needed by
snakemake-5.12.3-1.fc33.x86_64
    - nothing provides python3.9dist(ratelimiter) needed by
snakemake-5.12.3-1.fc33.x86_64
    - nothing provides python3.9dist(toposort) needed by
snakemake-5.12.3-1.fc33.x86_64
  ```
  You can see the list of dependencies:
  $ rpm -qp --requires  snakemake-5.12.3-1.fc33.x86_64.rpm 
- Version
  Please update the version if newer version exists.
- BuildRequires
  "gcc-c++" is not needed if you don't build c/c++ applications.
  "python-unversioned-command" is probably not needed because packages on
Fedora
  doesn't directly use /usr/bin/python.
- Package installs properly.
  Note: Installation errors (see attachment)
  See: https://docs.fedoraproject.org/en-US/packaging-guidelines/
- 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.
  Note: Unversionned Python dependency found.
  See: https://docs.fedoraproject.org/en-US/packaging-
  guidelines/Python/#_dependencies

===== MUST items =====

C/C++:
[x]: Package does not contain kernel modules.
[x]: Package contains no static executables.
[?]: 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.
[x]: License field in the package spec file matches the actual license.
     Note: Checking patched sources after %prep for licenses. Licenses
     found: "Unknown or generated", "Expat License", "*No copyright* Expat
     License". 682 files have unknown license. Detailed output of
     licensecheck in
     /home/vagrant/FedoraReview/1821189-snakemake/licensecheck.txt
[x]: %build honors applicable compiler flags or justifies otherwise.
[x]: Package contains no bundled libraries without FPC exception.
[x]: Changelog in prescribed format.
[x]: Sources contain only permissible code or content.
[x]: Macros in Summary, %description expandable at SRPM build time.
     Note: Macros in: snakemake (description)
[-]: Package contains desktop file if it is a GUI application.
[-]: Development files must be in a -devel package
[x]: Package uses nothing in %doc for runtime.
[x]: Package consistently uses macros (instead of hard-coded directory
     names).
[x]: Package is named according to the Package Naming Guidelines.

[x]: Package obeys FHS, except libexecdir and /usr/target.
[-]: If the package is a rename of another package, proper Obsoletes and
     Provides are present.
[x]: Requires correct, justified where necessary.
[x]: Spec file is legible and written in American English.
[-]: Package contains systemd file(s) if in need.
[-]: Useful -debuginfo package or justification otherwise.
[x]: 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 10240 bytes in 1 files.
[!]: Package complies to the Packaging Guidelines
[x]: Package successfully compiles and builds into binary rpms on at least
     one supported primary architecture.
[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 does not own files or directories owned by other packages.
[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]: Dist tag is present.
[x]: Package does not contain duplicates in %files.
[!]: Permissions on files are set properly.
[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 does not use a name that already exists.
[x]: Package is not relocatable.
[!]: 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:
[x]: Python eggs must not download any dependencies during the build
     process.
[x]: 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]: Python packages must not contain %{pythonX_site(lib|arch)}/* in %files
[x]: Binary eggs must be removed in %prep

===== SHOULD items =====

Generic:
[!]: Sources can be downloaded from URI in Source: tag
     Note: Could not download Source0:
     https://github.com/aflc/snakemake/archive/v5.12.3/snakemake-5.12.3.tar.gz
     See: https://docs.fedoraproject.org/en-US/packaging-
     guidelines/SourceURL/
[-]: If the source package does not include license text(s) as a separate
     file from upstream, the packager SHOULD query upstream to include it.
[x]: Final provides and requires are sane (see attachments).
[?]: Package functions as described.
[!]: Latest version is packaged.
[x]: Package does not include license text files separate from upstream.
[!]: SourceX tarball generation or download is documented.
     Note: Package contains tarball without URL, check comments
[?]: 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.
[x]: Package should compile and build into binary rpms on all supported
     architectures.
[x]: %check is present and all tests pass.
[?]: Packages should try to preserve timestamps of original installed
     files.
[!]: 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
[!]: SourceX is a working URL.
[x]: Spec use %global instead of %define unless justified.

===== EXTRA items =====

Generic:
[!]: Rpmlint is run on all installed packages.
     Note: Mock build failed
     See: https://docs.fedoraproject.org/en-US/packaging-
     guidelines/#_use_rpmlint
[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.


Installation errors
-------------------
INFO: mock.py version 2.3 starting (python version = 3.9.0)...
Start: init plugins
INFO: selinux enabled
Finish: init plugins
INFO: Signal handler active
Start: run
Start: chroot init
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 2.3
INFO: Mock Version: 2.3
Finish: chroot init
INFO: installing package(s):
/home/vagrant/FedoraReview/1821189-snakemake/results/snakemake-5.12.3-1.fc33.x86_64.rpm
ERROR: Command failed: 
 # /usr/bin/dnf --installroot /var/lib/mock/fedora-rawhide-x86_64/root/
--releasever 33 --setopt=deltarpm=False --allowerasing --disableplugin=local
--disableplugin=spacewalk install
/home/vagrant/FedoraReview/1821189-snakemake/results/snakemake-5.12.3-1.fc33.x86_64.rpm
--setopt=tsflags=nocontexts



Rpmlint
-------
Checking: snakemake-5.12.3-1.fc33.x86_64.rpm
          snakemake-5.12.3-1.fc33.src.rpm
snakemake.x86_64: W: spelling-error Summary(en_US) Workflow -> Work flow,
Work-flow, Workforce
snakemake.x86_64: W: unexpanded-macro %description -l C %python_provide
snakemake.x86_64: W: spelling-error %description -l en_US workflow -> work
flow, work-flow, workforce
snakemake.x86_64: W: spelling-error %description -l en_US Workflows -> Work
flows, Work-flows, Workloads
snakemake.x86_64: W: spelling-error %description -l en_US workflows -> work
flows, work-flows, workloads
snakemake.x86_64: E: no-binary
snakemake.x86_64: E: non-executable-script
/usr/lib/python3.9/site-packages/snakemake/jobscript.sh 644 /bin/sh 
snakemake.x86_64: W: no-manual-page-for-binary snakemake
snakemake.x86_64: W: no-manual-page-for-binary snakemake-bash-completion
snakemake.src: W: spelling-error Summary(en_US) Workflow -> Work flow,
Work-flow, Workforce
snakemake.src: W: spelling-error %description -l en_US workflow -> work flow,
work-flow, workforce
snakemake.src: W: spelling-error %description -l en_US Workflows -> Work flows,
Work-flows, Workloads
snakemake.src: W: spelling-error %description -l en_US workflows -> work flows,
work-flows, workloads
snakemake.src:68: W: mixed-use-of-spaces-and-tabs (spaces: line 14, tab: line
68)
snakemake.src: W: invalid-url Source0:
https://github.com/aflc/snakemake/archive/v5.12.3/snakemake-5.12.3.tar.gz HTTP
Error 404: Not Found
2 packages and 0 specfiles checked; 2 errors, 13 warnings.




Requires
--------
snakemake (rpmlib, GLIBC filtered):
    /usr/bin/python3
    python(abi)
    python3.9dist(appdirs)
    python3.9dist(configargparse)
    python3.9dist(datrie)
    python3.9dist(docutils)
    python3.9dist(gitpython)
    python3.9dist(jsonschema)
    python3.9dist(nbformat)
    python3.9dist(psutil)
    python3.9dist(pyyaml)
    python3.9dist(ratelimiter)
    python3.9dist(requests)
    python3.9dist(setuptools)
    python3.9dist(toposort)
    python3.9dist(wrapt)



Provides
--------
snakemake:
    python3.9dist(snakemake)
    python3dist(snakemake)
    snakemake
    snakemake(x86-64)



Generated by fedora-review 0.7.5 (cd5b7df) last change: 2020-03-19
Command line :try-fedora-review -b 1821189
Buildroot used: fedora-rawhide-x86_64
Active plugins: Python, C/C++, Generic, Shell-api
Disabled plugins: SugarActivity, Ocaml, Java, R, PHP, Perl, fonts, Ruby,
Haskell
Disabled flags: EPEL6, EPEL7, DISTTAG, BATCH, EXARCH


-- 
You are receiving this mail because:
You are on the CC list for the bug.
You are always notified about changes to this product and component
_______________________________________________
package-review mailing list -- package-review@xxxxxxxxxxxxxxxxxxxxxxx
To unsubscribe send an email to package-review-leave@xxxxxxxxxxxxxxxxxxxxxxx
Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/
List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines
List Archives: https://lists.fedoraproject.org/archives/list/package-review@xxxxxxxxxxxxxxxxxxxxxxx




[Index of Archives]     [Fedora Users]     [Fedora Desktop]     [Fedora SELinux]     [Yosemite Conditions]     [KDE Users]

  Powered by Linux