Bug 1226664

Summary: Review Request: fido-pi - Protein identification in MS/MS proteomics
Product: [Fedora] Fedora Reporter: Antonio T. (sagitter) <anto.trande>
Component: Package ReviewAssignee: Zbigniew Jędrzejewski-Szmek <zbyszek>
Status: CLOSED ERRATA QA Contact: Fedora Extras Quality Assurance <extras-qa>
Severity: medium Docs Contact:
Priority: medium    
Version: rawhideCC: package-review, zbyszek
Target Milestone: ---Flags: zbyszek: fedora-review+
gwync: fedora-cvs+
Target Release: ---   
Hardware: All   
OS: Linux   
Whiteboard:
Fixed In Version: fido-pi-0-0.1.20150209git281e4d.fc22 Doc Type: Bug Fix
Doc Text:
Story Points: ---
Clone Of: Environment:
Last Closed: 2015-06-21 00:02:36 UTC Type: ---
Regression: --- Mount Type: ---
Documentation: --- CRM:
Verified Versions: Category: ---
oVirt Team: --- RHEL 7.3 requirements from Atomic Host:
Cloudforms Team: --- Target Upstream Version:
Embargoed:

Description Antonio T. (sagitter) 2015-05-31 15:14:48 UTC
Spec URL: https://sagitter.fedorapeople.org/Fido/fido-pi.spec
SRPM URL: https://sagitter.fedorapeople.org/Fido/fido-pi-0-0.1.20150209git281e4d.fc22.src.rpm

Description: 
Fido is a tool used in the area of computational proteomics.
It calculates posterior probabilities for protein
identifications based on database searches of tandem mass spectra.

Fedora Account System Username: sagitter

Another package named Fido is already in Fedora, i chose 'fido-pi' as name of this package. There are not conflicts between binary executable names.

Comment 1 Zbigniew Jędrzejewski-Szmek 2015-06-08 16:19:39 UTC
===== 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.
MIT two-clause.

[x]: License field in the package spec file matches the actual license.
     Note: Checking patched sources after %prep for licenses. Licenses
     found: "BSD (2 clause) ISC", "Unknown or generated". 118 files have
     unknown license. Detailed output of licensecheck in /var/tmp/1226664
     -fido-pi/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.
[-]: 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.
[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 2 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]: 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]: 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]: Dist tag is present.
[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 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:
[-]: 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).
[x]: Package functions as described.
The binaries run. I didn't verify that they do useful things.

[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.
[x]: Package should compile and build into binary rpms on all supported
     architectures.
[-]: %check is present and all tests pass.
[x]: 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]: 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 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: fido-pi-0-0.1.20150209git281e4d.fc23.x86_64.rpm
          fido-pi-0-0.1.20150209git281e4d.fc23.src.rpm
fido-pi.x86_64: W: spelling-error Summary(en_US) proteomics -> Proterozoic
fido-pi.x86_64: W: spelling-error %description -l en_US proteomics -> Proterozoic
fido-pi.x86_64: W: no-manual-page-for-binary FidoChooseParameters
fido-pi.x86_64: W: no-manual-page-for-binary Fido
fido-pi.src: W: spelling-error Summary(en_US) proteomics -> Proterozoic
fido-pi.src: W: spelling-error %description -l en_US proteomics -> Proterozoic
2 packages and 0 specfiles checked; 0 errors, 6 warnings.




Rpmlint (debuginfo)
-------------------
Checking: fido-pi-debuginfo-0-0.1.20150209git281e4d.fc23.x86_64.rpm
1 packages and 0 specfiles checked; 0 errors, 0 warnings.





Rpmlint (installed packages)
----------------------------
fido-pi.x86_64: W: spelling-error Summary(en_US) proteomics -> Proterozoic
fido-pi.x86_64: W: spelling-error %description -l en_US proteomics -> Proterozoic
fido-pi.x86_64: W: no-manual-page-for-binary FidoChooseParameters
fido-pi.x86_64: W: no-manual-page-for-binary Fido
2 packages and 0 specfiles checked; 0 errors, 4 warnings.



Requires
--------
fido-pi (rpmlib, GLIBC filtered):
    libc.so.6()(64bit)
    libgcc_s.so.1()(64bit)
    libgcc_s.so.1(GCC_3.0)(64bit)
    libm.so.6()(64bit)
    libstdc++.so.6()(64bit)
    libstdc++.so.6(CXXABI_1.3)(64bit)
    rtld(GNU_HASH)



Provides
--------
fido-pi:
    fido-pi
    fido-pi(x86-64)



Source checksums
----------------
https://github.com/hendrikweisser/Fido/archive/281e4d1e85bc3d0f82f52dd04083d4dd2d1969b6.zip#/Fido-281e4d1e85bc3d0f82f52dd04083d4dd2d1969b6.zip :
  CHECKSUM(SHA256) this package     : fef8bcb6ae4f7e20d7a72dba5450bce92b1a00362da3a29ddf279d808c14e34d
  CHECKSUM(SHA256) upstream package : fef8bcb6ae4f7e20d7a72dba5450bce92b1a00362da3a29ddf279d808c14e34d


Generated by fedora-review 0.5.3 (bcf15e3) last change: 2015-05-04
Command line :/usr/bin/fedora-review -b 1226664
Buildroot used: fedora-rawhide-x86_64
Active plugins: Generic, Shell-api, C/C++
Disabled plugins: Java, Python, fonts, SugarActivity, Ocaml, Perl, Haskell, R, PHP, Ruby
Disabled flags: EXARCH, DISTTAG, EPEL5, BATCH, EPEL6

Package is APPROVED.

Comment 2 Antonio T. (sagitter) 2015-06-08 16:22:30 UTC
Thank you.

New Package SCM Request
=======================
Package Name: fido-pi
Short Description: Protein identification in MS/MS proteomics
Upstream URL: https://github.com/hendrikweisser/Fido
Owners: sagitter
Branches: f22

Comment 3 Gwyn Ciesla 2015-06-08 23:04:28 UTC
Git done (by process-git-requests).

Comment 4 Fedora Update System 2015-06-09 10:02:23 UTC
fido-pi-0-0.1.20150209git281e4d.fc22 has been submitted as an update for Fedora 22.
https://admin.fedoraproject.org/updates/fido-pi-0-0.1.20150209git281e4d.fc22

Comment 5 Fedora Update System 2015-06-10 19:15:38 UTC
Package fido-pi-0-0.1.20150209git281e4d.fc22:
* should fix your issue,
* was pushed to the Fedora 22 testing repository,
* should be available at your local mirror within two days.
Update it with:
# su -c 'yum update --enablerepo=updates-testing fido-pi-0-0.1.20150209git281e4d.fc22'
as soon as you are able to.
Please go to the following url:
https://admin.fedoraproject.org/updates/FEDORA-2015-9731/fido-pi-0-0.1.20150209git281e4d.fc22
then log in and leave karma (feedback).

Comment 6 Fedora Update System 2015-06-21 00:02:36 UTC
fido-pi-0-0.1.20150209git281e4d.fc22 has been pushed to the Fedora 22 stable repository.  If problems still persist, please make note of it in this bug report.