[Bug 1810293] New: Review Request: seqan3 - The modern C++ library for sequence analysis
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
Bug ID: 1810293 Summary: Review Request: seqan3 - The modern C++ library for sequence analysis 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/seqan3/seqan3.spec SRPM URL: https://sagitter.fedorapeople.org/seqan3/seqan3-3.0.1-1.fc31.src.rpm
Description:
SeqAn3 is the new version of the popular SeqAn template library for the analysis of biological sequences.
Fedora Account System Username: sagitter
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
Antonio T. (sagitter) anto.trande@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Doc Type|--- |If docs needed, set a value Whiteboard| |NotReady
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
--- Comment #1 from Antonio T. (sagitter) anto.trande@gmail.com --- `gtest-1.10.0` is now available on Fedora 33. Unfortunately, this code is not ready for `GCC-10` yet.
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
Antonio T. sagitter trpost@rocketmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- CC| |trpost@rocketmail.com Whiteboard|NotReady |
--- Comment #2 from Antonio T. sagitter trpost@rocketmail.com --- seqan3 is ready for the review.
Spec URL: https://sagitter.fedorapeople.org/seqan3/seqan3.spec SRPM URL: https://sagitter.fedorapeople.org/seqan3/seqan3-3.0.2-1.fc32.src.rpm
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
--- Comment #3 from Antonio T. sagitter trpost@rocketmail.com --- Add Upstream patches for bug #2209 and #2210.
Spec URL: https://sagitter.fedorapeople.org/seqan3/seqan3.spec SRPM URL: https://sagitter.fedorapeople.org/seqan3/seqan3-3.0.2-2.fc32.src.rpm
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED CC| |sanjay.ankur@gmail.com Assignee|nobody@fedoraproject.org |sanjay.ankur@gmail.com Flags| |fedora-review?
--- Comment #4 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com --- Hi Antonio,
I'll review this. Putting it through fedora-review now.
Cheers,
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
--- Comment #5 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com --- The package cannot currently be installed in rawhide from the looks of it. Could you check this please Antonio?
fedora-review pointed this out and I verified it:
$ sudo dnf --releasever=34 install ./seqan3-devel-3.0.2-2.fc34.x86_64.rpm Problem: conflicting requests - nothing provides cereal-devel(x86-64) >= 1.2.3 needed by seqan3-devel-3.0.2-2.fc34.x86_64 - nothing provides range-v3-devel%{?_isa} >= 0.11.0 needed by seqan3-devel-3.0.2-2.fc34.x86_64
I see both cereal and range-v3-devel have the right versions, though, so not sure what's causing this.
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
--- Comment #6 from Antonio T. sagitter trpost@rocketmail.com --- Spec URL: https://sagitter.fedorapeople.org/seqan3/seqan3.spec SRPM URL: https://sagitter.fedorapeople.org/seqan3/seqan3-3.0.2-3.fc32.src.rpm
About range-v3-devel, it's a mine typo (double %%) (Requires: range-v3-devel%%{?_isa} >= 0.11.0). About cereal-devel package, it's unexpectedly not-arched
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
Antonio T. sagitter trpost@rocketmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Link ID| |Red Hat Bugzilla 1888969
--- Comment #7 from Antonio T. sagitter trpost@rocketmail.com --- cereal-devel is now fixed.
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
--- Comment #8 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com --- Thanks, this is the first round of review. A few points there to look into below:
Package Review ==============
Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated [ ] = Manual review needed
Issues: ======= - 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. Note: License file LICENSE.TXT is not marked as %license See: https://docs.fedoraproject.org/en-US/packaging- guidelines/LicensingGuidelines/#_license_text
===== MUST items =====
C/C++: [x]: Package does not contain kernel modules. [x]: Package contains no static executables. [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: [?]: Package is licensed with an open-source compatible license and meets other legal requirements as defined in the legal section of Packaging Guidelines. ^ See next point.
[?]: License field in the package spec file matches the actual license. Note: Checking patched sources after %prep for licenses. Licenses found: "Unknown or generated", "BSD 3-clause "New" or "Revised" License", "*No copyright* Expat License", "zlib/libpng license", "Expat License". 1028 files have unknown license. Detailed output of licensecheck in /home/asinha/dump/fedora- reviews/1810293-seqan3/licensecheck.txt ^ Please take a look at this to double check that all licenses are specified in the spec.
Do the subpackages need the License tag?
[?]: License file installed when any subpackage combination is installed. ^ Please see note above: I think it's one of the bundled sources.
[?]: If the package is under multiple licenses, the licensing breakdown must be documented in the spec. ^ Please see note above.
[x]: %build honors applicable compiler flags or justifies otherwise. [?]: Package contains no bundled libraries without FPC exception. ^ Is the package using the bundled range-v3 sources? There's a comment that seems to indicate so. If yes, it should be mentioned as bundled (and then you don't need it as a BR and Require?). https://docs.fedoraproject.org/en-US/packaging-guidelines/#bundling
[x]: Changelog in prescribed format. [x]: Sources contain only permissible code or content. [-]: Package contains desktop file if it is a GUI application. [x]: 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 does not generate any conflict. [x]: Package obeys FHS, except libexecdir and /usr/target. [x]: 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. [x]: Useful -debuginfo package or justification otherwise. [?]: Package is not known to require an ExcludeArch tag. ^ Is this upstream's restriction? Please make a note.
[x]: 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 ^ A few nitpicks above.
[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]: 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]: Macros in Summary, %description expandable at SRPM build time. [x]: Dist tag is present. [x]: Package does not contain duplicates in %files. [x]: 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. [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
===== SHOULD items =====
Generic: [!]: Uses parallel make %{?_smp_mflags} macro. ^ False positive: this is only for the docs.
[-]: 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). ^ See notes about bundling etc.
[-]: Fully versioned dependency in subpackages if applicable. Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in seqan3-devel ^ False positive.
[?]: Package functions as described. ^ I haven't been able to test this.
[x]: Latest version is packaged. [x]: Package does not include license text files separate from upstream. [?]: Patches link to upstream bugs/comments/lists or are otherwise justified. ^ Could you please include the links to the issues/bugs just for verbosity?
[-]: 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]: %check is present and all tests pass. [x]: Packages should try to preserve timestamps of original installed files. [?]: Spec use %global instead of %define unless justified. Note: %define requiring justification: %define _lto_cflags %{nil}, %define __cmake_in_source_build . ^ Any reason for using the in source build and then doing pushed/popd there instead of just using what the cmake macro now does automatically? https://docs.fedoraproject.org/en-US/packaging-guidelines/CMake/
[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. [x]: Package should compile and build into binary rpms on all supported architectures.
===== EXTRA items =====
Generic: [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: seqan3-devel-3.0.2-3.fc34.x86_64.rpm seqan3-doc-3.0.2-3.fc34.noarch.rpm seqan3-3.0.2-3.fc34.src.rpm seqan3-devel.x86_64: W: only-non-binary-in-usr-lib seqan3-devel.x86_64: E: version-control-internal-file /usr/include/sdsl/.gitignore 3 packages and 0 specfiles checked; 1 errors, 1 warnings.
^ We should remove that one.
Rpmlint (installed packages) ---------------------------- seqan3-devel.x86_64: W: invalid-url URL: http://www.seqan.de/ <urlopen error [Errno -3] Temporary failure in name resolution> seqan3-devel.x86_64: W: only-non-binary-in-usr-lib seqan3-devel.x86_64: E: version-control-internal-file /usr/include/sdsl/.gitignore seqan3-doc.noarch: W: invalid-url URL: http://www.seqan.de/ <urlopen error [Errno -3] Temporary failure in name resolution> 2 packages and 0 specfiles checked; 1 errors, 3 warnings.
Source checksums ---------------- https://github.com/seqan/seqan3/releases/download/3.0.2/seqan3-3.0.2-Source.... : CHECKSUM(SHA256) this package : bab1a9cd0c01fd486842e0fa7a5b41c1bf6d2c43fdadf4c543956923deb62ee9 CHECKSUM(SHA256) upstream package : bab1a9cd0c01fd486842e0fa7a5b41c1bf6d2c43fdadf4c543956923deb62ee9
Requires -------- seqan3-devel (rpmlib, GLIBC filtered): bzip2-devel(x86-64) cereal-devel cmake(x86-64) cmake-filesystem(x86-64) range-v3-devel(x86-64) zlib-devel(x86-64)
seqan3-doc (rpmlib, GLIBC filtered):
Provides -------- seqan3-devel: SDSL-devel(x86-64) cmake(seqan3) sdsl-devel(x86-64) sdsl-lite-devel(x86-64) seqan3-devel seqan3-devel(x86-64)
seqan3-doc: seqan3-doc
Generated by fedora-review 0.7.5 (5fa5b7e) last change: 2020-02-16 Command line :/usr/bin/fedora-review -b 1810293 Buildroot used: fedora-rawhide-x86_64 Active plugins: Generic, C/C++, Shell-api Disabled plugins: Ocaml, Python, Haskell, Java, Perl, fonts, SugarActivity, PHP, R Disabled flags: EPEL6, EPEL7, DISTTAG, BATCH, EXARCH
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
--- Comment #9 from Antonio T. sagitter trpost@rocketmail.com ---
Please take a look at this to double check that all licenses are specified in the spec.
Is the package using the bundled range-v3 sources? There's a comment that seems to indicate so. If yes, it should be mentioned as bundled (and then you don't need it as a BR and Require?). https://docs.fedoraproject.org/en-US/packaging-guidelines/#bundling
It's a legacy of old releases, erased it. CMake in-source-build macros should be more explicative, now.
Spec URL: https://sagitter.fedorapeople.org/seqan3/seqan3.spec SRPM URL: https://sagitter.fedorapeople.org/seqan3/seqan3-3.0.2-4.fc32.src.rpm
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
--- Comment #10 from Antonio T. sagitter trpost@rocketmail.com --- Rawhide build: https://koji.fedoraproject.org/koji/taskinfo?taskID=53660423
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
Antonio T. sagitter trpost@rocketmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Flags| |needinfo?(sanjay.ankur@gmai | |l.com)
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Flags|needinfo?(sanjay.ankur@gmai | |l.com) |
--- Comment #11 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com --- Sorry, missed the ping, will complete review later today
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
--- Comment #12 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com --- Looks pretty good:
- Please add comments about the upstream patches, with their URLs (without them, it's hard for a reader to see where these come from or what they do). - Please remove the License tag from the doc sub-package, - Please remove the /usr/include/sdsl/.gitignore file
You cannot include the sdsl-lite bits in this package and provide it in the -devel subpackage, each srpm/package should only provide one software, no? sdsl-lite needs to be either:
- packaged separately and included as a BR, - or bundled, but then it should not provide the publicly usable headers in this package,
Cheers!
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
--- Comment #13 from Antonio T. sagitter trpost@rocketmail.com --- Spec URL: https://sagitter.fedorapeople.org/seqan3/seqan3.spec SRPM URL: https://sagitter.fedorapeople.org/seqan3/seqan3-3.0.2-5.fc33.src.rpm
- Bundle sdsl header files
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |POST Flags|fedora-review? |fedora-review+
--- Comment #14 from Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com --- OK, looks good. XXX APPROVED XXX
Please keep in mind that whenever sddl is packaged, the headers bundled here (which aren't private) will conflict with the package.
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
--- Comment #15 from Antonio T. sagitter trpost@rocketmail.com --- Thank you Ankur.
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
Antonio T. sagitter trpost@rocketmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Flags| |needinfo?(sanjay.ankur@gmai | |l.com)
--- Comment #16 from Antonio T. sagitter trpost@rocketmail.com --- @Ankur,
i'm duplicating this review ticket because my FAS mail in changed since 2020 April 03 when i opened this review. I can't create a new repo: https://pagure.io/releng/fedora-scm-requests/issue/30242#comment-699630
New review for seqan3 will need to be approved.
Thank you again.
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
Antonio T. sagitter trpost@rocketmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Depends On| |1894895
Referenced Bugs:
https://bugzilla.redhat.com/show_bug.cgi?id=1894895 [Bug 1894895] Review Request: seqan3 - The modern C++ library for sequence analysis
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Flags|needinfo?(sanjay.ankur@gmai | |l.com) |
https://bugzilla.redhat.com/show_bug.cgi?id=1810293
Antonio T. sagitter trpost@rocketmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|POST |CLOSED Resolution|--- |DUPLICATE Last Closed| |2020-11-05 12:37:56
--- Comment #17 from Antonio T. sagitter trpost@rocketmail.com ---
*** This bug has been marked as a duplicate of bug 1894895 ***
https://bugzilla.redhat.com/show_bug.cgi?id=1810293 Bug 1810293 depends on bug 1894895, which changed state.
Bug 1894895 Summary: Review Request: seqan3 - The modern C++ library for sequence analysis https://bugzilla.redhat.com/show_bug.cgi?id=1894895
What |Removed |Added ---------------------------------------------------------------------------- Status|POST |CLOSED Resolution|--- |CURRENTRELEASE
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