Spec URL: https://sagitter.fedorapeople.org/percolator/percolator.spec SRPM URL: https://sagitter.fedorapeople.org/percolator/percolator-2.09.0-1.fc21.src.rpm Description: The first step in analyzing an mass spectrometry assay is to match the harvested spectra against a target database using database search engines such as Sequest and Mascot, a process that renders list of peptide-spectrum matches. However, it is not trivial to assess the accuracy of these identifications. Percolator uses a semi-supervised machine learning to discriminate correct from incorrect peptide-spectrum matches, and calculates accurate statistics such as q-value (FDR) and posterior error probabilities. Fedora Account System Username: sagitter
Why are you generating the xsd files manually? A different name of the xsd executable should not be any problem, as cmake/FindXsd.cmake already checks for both 'xsd' and 'xsdcxx'.
Nitpick: the cmake calls would look better--and would be easier to maintain too--if you defined the common arguments as a macro.
Package Review ============== Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated [ ] = Manual review needed ===== MUST items ===== Generic: [ ]: License field in the package spec file matches the actual license. Note: Checking patched sources after %prep for licenses. Licenses found: "Apache (v2.0)", "LGPL (v2.1 or later) (with incorrect FSF address)", "Unknown or generated". 84 files have unknown license. I assume that the LGPLv2+ sources are not used? [!]: If the package is under multiple licenses, the licensing breakdown must be documented in the spec. ===== EXTRA items ===== Generic: [!]: Large data in /usr/share should live in a noarch subpackage if package is arched. Note: Arch-ed rpms have a total of 11499520 bytes in /usr/share percolator-2.09.0-1.fc20.x86_64.rpm:11499520 See: http://fedoraproject.org/wiki/Packaging:ReviewGuidelines#Package_Review_Guidelines Rpmlint ------- Checking: percolator-2.09.0-1.fc20.x86_64.rpm percolator-2.09.0-1.fc20.src.rpm percolator.x86_64: W: spelling-error Summary(en_US) postprocessing -> post processing, post-processing, teleprocessing percolator.x86_64: W: spelling-error Summary(en_US) proteomics -> Proterozoic percolator.x86_64: W: spelling-error %description -l en_US spectrometry -> spectrometer, spectroscopy, spectroscope percolator.x86_64: W: spelling-error %description -l en_US peptide -> pep tide, pep-tide, peptic percolator.x86_64: E: description-line-too-long C The first step in analyzing an mass spectrometry assay is to match the harvested spectra percolator.x86_64: E: description-line-too-long C against a target database using database search engines such as Sequest and Mascot, percolator.x86_64: E: description-line-too-long C and calculates accurate statistics such as q-value (FDR) and posterior error probabilities. percolator.x86_64: E: script-without-shebang /usr/share/licenses/percolator/license.txt percolator.x86_64: W: spurious-executable-perm /usr/share/doc/percolator/ReadMe.txt percolator.x86_64: W: no-manual-page-for-binary tandem2pin percolator.x86_64: W: no-manual-page-for-binary msgf2pin percolator.x86_64: W: no-manual-page-for-binary percolator percolator.x86_64: W: no-manual-page-for-binary elude percolator.x86_64: W: no-manual-page-for-binary qvality percolator.x86_64: W: no-manual-page-for-binary sqt2pin percolator.src: W: spelling-error Summary(en_US) postprocessing -> post processing, post-processing, teleprocessing percolator.src: W: spelling-error Summary(en_US) proteomics -> Proterozoic percolator.src: W: spelling-error %description -l en_US spectrometry -> spectrometer, spectroscopy, spectroscope percolator.src: W: spelling-error %description -l en_US peptide -> pep tide, pep-tide, peptic percolator.src: E: description-line-too-long C The first step in analyzing an mass spectrometry assay is to match the harvested spectra percolator.src: E: description-line-too-long C against a target database using database search engines such as Sequest and Mascot, percolator.src: E: description-line-too-long C and calculates accurate statistics such as q-value (FDR) and posterior error probabilities. 2 packages and 0 specfiles checked; 7 errors, 15 warnings.
(In reply to David Tardon from comment #1) > Why are you generating the xsd files manually? A different name of the xsd > executable should not be any problem, as cmake/FindXsd.cmake already checks > for both 'xsd' and 'xsdcxx'. I had forget to comment: 'xsd' is not recognized in Fedora because is used 'xsdcxx'. I talked about with updstream https://github.com/percolator/percolator/issues/125#issuecomment-103890339.
(In reply to Antonio Trande from comment #4) > (In reply to David Tardon from comment #1) > > Why are you generating the xsd files manually? A different name of the xsd > > executable should not be any problem, as cmake/FindXsd.cmake already checks > > for both 'xsd' and 'xsdcxx'. > > I had forget to comment: 'xsd' is not recognized in Fedora because is used > 'xsdcxx'. I talked about with updstream > https://github.com/percolator/percolator/issues/125#issuecomment-103890339. So, the real problem is that /usr/bin/xsd is provided by another package, concretely mono-web. In that case, why don't you simply change the check in cmake/FindXsd.cmake to look for xsdcxx first? That would be a one-line patch (or sed expression).
(In reply to David Tardon from comment #5) > (In reply to Antonio Trande from comment #4) > > (In reply to David Tardon from comment #1) > > > Why are you generating the xsd files manually? A different name of the xsd > > > executable should not be any problem, as cmake/FindXsd.cmake already checks > > > for both 'xsd' and 'xsdcxx'. > > > > I had forget to comment: 'xsd' is not recognized in Fedora because is used > > 'xsdcxx'. I talked about with updstream > > https://github.com/percolator/percolator/issues/125#issuecomment-103890339. > > So, the real problem is that /usr/bin/xsd is provided by another package, > concretely mono-web. In that case, why don't you simply change the check in > cmake/FindXsd.cmake to look for xsdcxx first? That would be a one-line patch > (or sed expression). Maintainer replies to your question: >It might be a good idea to switch the order of these two around, so that it > will look for xsdcxx first, but this could potentially cause issues on other > systems. Spec URL: https://sagitter.fedorapeople.org/percolator/percolator.spec SRPM URL: https://sagitter.fedorapeople.org/percolator/percolator-2.09.0-2.fc21.src.rpm
(In reply to Antonio Trande from comment #6) > Maintainer replies to your question: > > >It might be a good idea to switch the order of these two around, so that it > > will look for xsdcxx first, but this could potentially cause issues on other > > systems. And why should we care about other systems in Fedora package?
[!]: If the package is under multiple licenses, the licensing breakdown must be documented in the spec. See examples in https://fedoraproject.org/wiki/Packaging:LicensingGuidelines .
There are still 2 text files with executable flag: RAMP-Readme.txt and RAMP.Readme.Mike.txt.
Spec URL: https://sagitter.fedorapeople.org/percolator/percolator.spec SRPM URL: https://sagitter.fedorapeople.org/percolator/percolator-2.09.0-3.fc21.src.rpm
[!]: If the package is under multiple licenses, the licensing breakdown must be documented in the spec. I think you should list concrete files/dirs. At least that is how I have always understood it. The ASL, which covers most of the code, can be handled by a blanket statement, something like: "All the code is licensed under ASL, except for ..." [!]: Package must own all directories that it creates. Note: Directories without known owners: /usr/share/xml, /usr/share/licenses Sorry, I missed this one previously... I think /usr/share/licenses should be owned by package filesystem, though. It is possible this is only shown because I am doing the review on F-20.
(In reply to David Tardon from comment #11) > [!]: If the package is under multiple licenses, the licensing breakdown must > be documented in the spec. > > I think you should list concrete files/dirs. At least that is how I have > always understood it. The ASL, which covers most of the code, can be handled > by a blanket statement, something like: "All the code is licensed under ASL, > except for ..." > > [!]: Package must own all directories that it creates. > Note: Directories without known owners: /usr/share/xml, > /usr/share/licenses > > Sorry, I missed this one previously... I think /usr/share/licenses should be > owned by package filesystem, though. Indeed. /usr/share/xml is now co-owned. I left the same release number: Spec URL: https://sagitter.fedorapeople.org/percolator/percolator.spec SRPM URL: https://sagitter.fedorapeople.org/percolator/percolator-2.09.0-3.fc21.src.rpm
(In reply to Antonio Trande from comment #12) > /usr/share/xml is now co-owned. I left the same release number: I think it would be better to depend on xml-common.
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 %doc. Note: Cannot find RAMP_license_lgpl-2.1.txt in rpm(s) See: http://fedoraproject.org/wiki/Packaging/LicensingGuidelines#License_Text ===== MUST items ===== C/C++: [x]: Package does not contain kernel modules. [x]: Package contains no static executables. [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: "Apache (v2.0)", "LGPL (v2.1 or later) (with incorrect FSF address)", "Unknown or generated". 84 files have unknown license. Detailed output of licensecheck in /home/dachjo/packaging/fedora/new/1224385-percolator/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. [x]: Package requires other packages for directories it uses. Note: No known owner of /usr/share/licenses [x]: Package must own all directories that it creates. Note: Directories without known owners: /usr/share/licenses [x]: Package does not own files or directories owned by other packages. Note: Dirs in package are owned also by: /usr/share/xml(xml-common) Maybe it would be better to require xml-common? [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. [-]: 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. [?]: 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. [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. [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 3 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]: All build dependencies are listed in BuildRequires, except for any that are listed in the exceptions section of Packaging Guidelines. [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 does not contain duplicates in %files. [x]: Permissions on files are set properly. [x]: Package use %makeinstall only when make install' ' DESTDIR=... doesn't work. [x]: Package is named using only allowed ASCII characters. [x]: Package do not use a name that already exist [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: [-]: 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). [-]: Fully versioned dependency in subpackages if applicable. Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in percolator- data [?]: Package functions as described. [x]: Latest version is packaged. [x]: Package does not include license text files separate from upstream. [-]: 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. [?]: Packages should try to preserve timestamps of original installed files. [x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file [x]: Sources can be downloaded from URI in Source: tag [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]: Dist tag is present (not strictly required in GL). [x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin. [x]: Uses parallel make %{?_smp_mflags} macro. [x]: SourceX is a working URL. [x]: Spec use %global instead of %define unless justified. ===== 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: percolator-2.09.0-3.fc20.x86_64.rpm percolator-data-2.09.0-3.fc20.noarch.rpm percolator-2.09.0-3.fc20.src.rpm percolator.x86_64: W: spelling-error Summary(en_US) postprocessing -> post processing, post-processing, teleprocessing percolator.x86_64: W: spelling-error Summary(en_US) proteomics -> Proterozoic percolator.x86_64: W: spelling-error %description -l en_US spectrometry -> spectrometer, spectroscopy, spectroscope percolator.x86_64: W: spelling-error %description -l en_US peptide -> pep tide, pep-tide, peptic percolator.x86_64: W: invalid-url URL: http://per-colator.com/ [Errno 104] Connection reset by peer percolator.x86_64: W: no-documentation percolator.x86_64: W: no-manual-page-for-binary tandem2pin percolator.x86_64: W: no-manual-page-for-binary msgf2pin percolator.x86_64: W: no-manual-page-for-binary percolator percolator.x86_64: W: no-manual-page-for-binary elude percolator.x86_64: W: no-manual-page-for-binary qvality percolator.x86_64: W: no-manual-page-for-binary sqt2pin percolator-data.noarch: W: summary-not-capitalized C percolator data files percolator.src: W: spelling-error Summary(en_US) postprocessing -> post processing, post-processing, teleprocessing percolator.src: W: spelling-error Summary(en_US) proteomics -> Proterozoic percolator.src: W: spelling-error %description -l en_US spectrometry -> spectrometer, spectroscopy, spectroscope percolator.src: W: spelling-error %description -l en_US peptide -> pep tide, pep-tide, peptic 3 packages and 0 specfiles checked; 0 errors, 17 warnings. Rpmlint (installed packages) ---------------------------- Cannot parse rpmlint output: Requires -------- percolator-data (rpmlib, GLIBC filtered): percolator (rpmlib, GLIBC filtered): libbz2.so.1()(64bit) libc.so.6()(64bit) libdl.so.2()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_4.0.0)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libm.so.6()(64bit) libpthread.so.0()(64bit) libsqlite3.so.0()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libtokyocabinet.so.9()(64bit) libxerces-c-3.1.so()(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.0)(64bit) percolator-data rtld(GNU_HASH) Provides -------- percolator-data: percolator-data percolator: percolator percolator(x86-64) Source checksums ---------------- https://github.com/percolator/percolator/tarball/master#/percolator-percolator-rel-2-09-0-g4e0d58a.tar.gz : CHECKSUM(SHA256) this package : cbbbcf768c02f8c72501f24238780caae3b1f93c46fe76ab5764ab8db94669e9 CHECKSUM(SHA256) upstream package : cbbbcf768c02f8c72501f24238780caae3b1f93c46fe76ab5764ab8db94669e9 http://noble.gs.washington.edu/proj/percolator/data/yeast-01.sqt.tar.gz : CHECKSUM(SHA256) this package : 6704da443434a1c6f15a24cccd4dbb5caeef5bc62e836a47f6fee351f911bf02 CHECKSUM(SHA256) upstream package : 6704da443434a1c6f15a24cccd4dbb5caeef5bc62e836a47f6fee351f911bf02 Generated by fedora-review 0.5.2 (63c24cb) last change: 2014-07-14 Command line :/usr/bin/fedora-review -b 1224385 Buildroot used: fedora-20-x86_64 Active plugins: Generic, Shell-api, C/C++ Disabled plugins: Java, Python, fonts, SugarActivity, Ocaml, Perl, Haskell, R, PHP, Ruby Disabled flags: EXARCH, EPEL5, BATCH, DISTTAG
Spec URL: https://sagitter.fedorapeople.org/percolator/percolator.spec SRPM URL: https://sagitter.fedorapeople.org/percolator/percolator-2.09.0-4.fc21.src.rpm
Thank you David. New Package SCM Request ======================= Package Name: percolator Short Description: Software for postprocessing of shotgun proteomics data Upstream URL: http://per-colator.com/ Owners: sagitter Branches: f22 f21
Git done (by process-git-requests).
percolator-2.09.0-4.fc21 has been submitted as an update for Fedora 21. https://admin.fedoraproject.org/updates/percolator-2.09.0-4.fc21
percolator-2.09.0-4.fc22 has been submitted as an update for Fedora 22. https://admin.fedoraproject.org/updates/percolator-2.09.0-4.fc22
percolator-2.09.0-4.fc21 has been pushed to the Fedora 21 testing repository.
percolator-2.09.0-4.fc22 has been pushed to the Fedora 22 stable repository.
percolator-2.09.0-4.fc21 has been pushed to the Fedora 21 stable repository.