Spec URL: https://raw.githubusercontent.com/junaruga/fedora-bowtie2/master/bowtie2.spec SRPM URL: https://github.com/junaruga/fedora-bowtie2/raw/master/bowtie2-2.4.1-1.fc33.src.rpm Description: An ultrafast and memory-efficient read aligner for genome sequencing. Fedora Account System Username: jaruga
This is a package for the genome sequencing. I tested following things. * Check by `rpmlint`: ok * Check the binary RPMs installation: ok * Scratch build: ok https://koji.fedoraproject.org/koji/taskinfo?taskID=43448945
>Requires: perl Requiring the "perl" metapackage pulls in a lot of dependencies, many of which will probably be unused. The Perl Packaging Guidelines say that there's a generator that will automatically generate "Requires:" for appropriate Perl modules. https://docs.fedoraproject.org/en-US/packaging-guidelines/Perl/#_perl_requires_and_provides >sed -i '1s|/usr/bin/env perl|/usr/bin/perl|' bowtie2 You might want to use %{_bindir}/perl here instead writing /usr/bin/perl. >%make_install PREFIX="%{_usr}" DESTDIR="%{buildroot}" 1. Use %{_prefix} instead of %{_usr} here. 2. %make_install already sets up DESTDIR.
Hi Artur, thanks for your review! Okay. I fixed every items you mentioned above, and updated the files for Spec URL and SRPM URL. I confirmed that the bowite2 has the generated Perl modules "Requires:" by `rpm -q -R bowtie2`. I also checked binary RPM installation, and scratch build here again. https://koji.fedoraproject.org/koji/taskinfo?taskID=43511628 Could you review again?
*** Bug 1824347 has been marked as a duplicate of this bug. ***
1. May be change it %ifnarch x86_64 BuildRequires: simde-devel %endif %ifarch x86_64 BuildRequires: tbb-devel %endif to %ifarch x86_64 BuildRequires: tbb-devel %else BuildRequires: simde-devel %endif 2. Change %setup -q to %autosetup 3. Change sed -i 's/“/"/g' processor_support.h sed -i 's/”/"/g' processor_support.h to sed -e 's/“/"/g' -e 's/”/"/g' -i processor_support.h
Thanks for your review! I fixed every items you mentioned, and update the Spec and SRPM URL, and checked the rpmlint and installation and scratch build here again. https://koji.fedoraproject.org/koji/taskinfo?taskID=43660524 Sorry for the 2. %autosetup. You mentioned it for my last simde package's review. And now you had to say repeatedly it for this review too.
Package Review ============== Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated [ ] = Manual review needed Issues: ======= Is there a good reason to not use the tar.gz from github as source0? It would contain the source and the tests. The way I understand [1] combined with [2] is that the not-downloadable source is only acceptable if the source is not allowed in fedora. Are there any items in release that are not allowed? [1] https://fedoraproject.org/wiki/Packaging:ReviewGuidelines#Things_To_Check_On_Review [2] https://fedoraproject.org/wiki/Packaging:SourceURL?rd=Packaging/SourceURL#When_Upstream_uses_Prohibited_Code Typos: 'ultrafast' should be 'ultra fast'. Rest seems to be false-positives. As configure isn't run, the compiler flags are not set. Manuals for the binaries would be nice. ===== 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]: Header files in -devel subpackage, if present. [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", "*No copyright* GNU General Public License (v3)", "GPL (v3 or later)", "zlib/libpng license". 40 files have unknown license. Detailed output of licensecheck in /home/dave/rpmbuild/review/1824348-bowtie2/licensecheck.txt [x]: License file installed when any subpackage combination is installed. [x]: If the package is under multiple licenses, the licensing breakdown must be documented in the spec. [!]: %build honors applicable compiler flags or justifies otherwise. [-]: Package contains no bundled libraries without FPC exception. [x]: Changelog in prescribed format. [x]: Sources contain only permissible code or content. [-]: 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 does not generate any conflict. [x]: 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. The explicit require on python3 doesn't seem to be needed. This way python3 is listed twice as requirement. [x]: 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. [x]: Large documentation must go in a -doc subpackage. Large could be size (~1MB) or number of files. Note: Documentation size is 245760 bytes in 5 files. [x]: 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 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 Perl: [-]: Package contains the mandatory BuildRequires and Requires:. Note: Requires: perl(:MODULE_COMPAT_%(eval "`%{__perl} -V:version`"; echo $version)) missing? 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]: 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. [x]: Final provides and requires are sane (see attachments). [?]: Package functions as described. [x]: Latest version is packaged. [x]: Package does not include license text files separate from upstream. [-]: 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. [x]: %check is present and all tests pass. [x]: Packages should try to preserve timestamps of original installed files. [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]: Fully versioned dependency in subpackages if applicable. [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]: Spec use %global instead of %define unless justified. ===== 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: bowtie2-2.4.1-1.fc33.x86_64.rpm bowtie2-debuginfo-2.4.1-1.fc33.x86_64.rpm bowtie2-debugsource-2.4.1-1.fc33.x86_64.rpm bowtie2-2.4.1-1.fc33.src.rpm bowtie2.x86_64: W: spelling-error Summary(en_US) ultrafast -> ultra fast, ultra-fast, ultrasound bowtie2.x86_64: W: spelling-error %description -l en_US Bowtie -> Bowie, Bow tie, Bow-tie bowtie2.x86_64: W: spelling-error %description -l en_US ultrafast -> ultra fast, ultra-fast, ultrasound bowtie2.x86_64: W: spelling-error %description -l en_US gapped -> gaped, gasped, sapped bowtie2.x86_64: W: no-manual-page-for-binary bowtie2 bowtie2.x86_64: W: no-manual-page-for-binary bowtie2-align-l bowtie2.x86_64: W: no-manual-page-for-binary bowtie2-align-s bowtie2.x86_64: W: no-manual-page-for-binary bowtie2-build bowtie2.x86_64: W: no-manual-page-for-binary bowtie2-build-l bowtie2.x86_64: W: no-manual-page-for-binary bowtie2-build-s bowtie2.x86_64: W: no-manual-page-for-binary bowtie2-inspect bowtie2.x86_64: W: no-manual-page-for-binary bowtie2-inspect-l bowtie2.x86_64: W: no-manual-page-for-binary bowtie2-inspect-s bowtie2.src: W: spelling-error Summary(en_US) ultrafast -> ultra fast, ultra-fast, ultrasound bowtie2.src: W: spelling-error %description -l en_US Bowtie -> Bowie, Bow tie, Bow-tie bowtie2.src: W: spelling-error %description -l en_US ultrafast -> ultra fast, ultra-fast, ultrasound bowtie2.src: W: spelling-error %description -l en_US gapped -> gaped, gasped, sapped bowtie2.src: W: invalid-url Source1: bowtie2-2.4.1-tests.tgz 4 packages and 0 specfiles checked; 0 errors, 18 warnings.
Add %set_build_flags at top of build section.
Hi David and Vasily. I appreciate your review and help. Every point you mentioned makes sense. I am working on it now.
Hi I fixed every point you mentioned upsating Spec and SRPM URLs. Here is the modification. https://github.com/junaruga/fedora-bowtie2/commit/a09cc9aa542dd190ff0a4a54ca1ad8ae1a31947a I checked rpmlint, the binary RPM installation and scratch build here. https://koji.fedoraproject.org/koji/taskinfo?taskID=44066815 Could you review again?
There is still an explicit 'Requires: python3' in line 16. This isn't needed, rpm automagically adds a requirement for /usr/bin/python3. Sorry, I should have copied it to the beginning. However, this is only a minor issue, so package is approved. Don't forget to open bugz for the excluded arches, thanks.
Hi David, Thanks for your review! I removed the 'Requires: python3', and update above Spec and SRPM URLs, and confirmed the /usr/bin/python3 requirement is still exists. ``` <mock-chroot> sh-5.0# rpm -qR bowtie2 /usr/bin/perl /usr/bin/python3 ``` You might have to change this ticket's status from NEW to POST or ASSIGNED for the repository to be created. Now I am requesting bowtie2 dist-git repository. And we will see the result. ``` $ fedpkg request-repo bowtie2 1824348 https://pagure.io/releng/fedora-scm-requests/issue/24782 ```
(fedscm-admin): The Pagure repository was created at https://src.fedoraproject.org/rpms/bowtie2
FEDORA-EPEL-2020-c2a178362b has been submitted as an update to Fedora EPEL 8. https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2020-c2a178362b
FEDORA-2020-a2ce0fa73b has been submitted as an update to Fedora 32. https://bodhi.fedoraproject.org/updates/FEDORA-2020-a2ce0fa73b
FEDORA-2020-c540172327 has been submitted as an update to Fedora 30. https://bodhi.fedoraproject.org/updates/FEDORA-2020-c540172327
FEDORA-EPEL-2020-bd011d5c00 has been submitted as an update to Fedora EPEL 7. https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2020-bd011d5c00
FEDORA-2020-a2ce0fa73b has been pushed to the Fedora 32 testing repository. In short time you'll be able to install the update with the following command: `sudo dnf install --enablerepo=updates-testing --advisory=FEDORA-2020-a2ce0fa73b \*` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2020-a2ce0fa73b See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
FEDORA-2020-c540172327 has been pushed to the Fedora 30 testing repository. In short time you'll be able to install the update with the following command: `sudo dnf install --enablerepo=updates-testing --advisory=FEDORA-2020-c540172327 \*` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2020-c540172327 See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
FEDORA-2020-fbd101aa06 has been pushed to the Fedora 31 testing repository. In short time you'll be able to install the update with the following command: `sudo dnf install --enablerepo=updates-testing --advisory=FEDORA-2020-fbd101aa06 \*` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2020-fbd101aa06 See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
FEDORA-EPEL-2020-c2a178362b has been pushed to the Fedora EPEL 8 testing repository. You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2020-c2a178362b See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
FEDORA-EPEL-2020-bd011d5c00 has been pushed to the Fedora EPEL 7 testing repository. You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2020-bd011d5c00 See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
FEDORA-2020-fbd101aa06 has been pushed to the Fedora 31 stable repository. If problem still persists, please make note of it in this bug report.
FEDORA-2020-a2ce0fa73b has been pushed to the Fedora 32 stable repository. If problem still persists, please make note of it in this bug report.
FEDORA-2020-c540172327 has been pushed to the Fedora 30 stable repository. If problem still persists, please make note of it in this bug report.
FEDORA-EPEL-2020-c2a178362b has been pushed to the Fedora EPEL 8 stable repository. If problem still persists, please make note of it in this bug report.
FEDORA-EPEL-2020-bd011d5c00 has been pushed to the Fedora EPEL 7 stable repository. If problem still persists, please make note of it in this bug report.