[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730 Dominik 'Rathann' Mierzejewski domi...@greysector.net changed: What|Removed |Added Blocks|505154 (FE-SCITECH) | Referenced Bugs: https://bugzilla.redhat.com/show_bug.cgi?id=505154 [Bug 505154] Tracker: Review Requests for Science and Technology related packages -- 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@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730 Fedora Update System upda...@fedoraproject.org changed: What|Removed |Added Status|ON_QA |CLOSED Fixed In Version||seqan-1.4.1-2.fc20 Resolution|--- |ERRATA Last Closed||2014-06-30 06:31:54 --- Comment #21 from Fedora Update System upda...@fedoraproject.org --- seqan-1.4.1-2.fc20 has been pushed to the Fedora 20 stable repository. -- 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@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730 Fedora Update System upda...@fedoraproject.org changed: What|Removed |Added Status|MODIFIED|ON_QA --- Comment #20 from Fedora Update System upda...@fedoraproject.org --- seqan-1.4.1-2.fc20 has been pushed to the Fedora 20 testing repository. -- 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@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730 Fedora Update System upda...@fedoraproject.org changed: What|Removed |Added Status|ASSIGNED|MODIFIED -- 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@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730 --- Comment #19 from Fedora Update System upda...@fedoraproject.org --- seqan-1.4.1-2.fc20 has been submitted as an update for Fedora 20. https://admin.fedoraproject.org/updates/seqan-1.4.1-2.fc20 -- 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@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730 --- Comment #18 from Kevin Fenzi ke...@scrye.com --- Git done (by process-git-requests). -- 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@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730 Kevin Fenzi ke...@scrye.com changed: What|Removed |Added Flags|fedora-cvs? |fedora-cvs+ -- 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@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730 --- Comment #15 from Kevin Fenzi ke...@scrye.com --- There's no scm request here... Please see: http://fedoraproject.org/wiki/Package_SCM_admin_requests -- 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@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730 Kevin Fenzi ke...@scrye.com changed: What|Removed |Added Flags|fedora-cvs? | -- 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@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730 Antonio Trande anto.tra...@gmail.com changed: What|Removed |Added Flags||fedora-cvs? --- Comment #16 from Antonio Trande anto.tra...@gmail.com --- Sorry. New Package SCM Request === Package Name: seqan Short Description: Open-source software C++ library for LC/MS data management and analyses Upstream URL: http://open-ms.sourceforge.net/ Owners: sagitter Branches: f20 -- 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@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730 --- Comment #17 from Antonio Trande anto.tra...@gmail.com --- Sorry again. This is correct. New Package SCM Request === Package Name: seqan Short Description: Open-source software C++ library for LC/MS data management and analyses Upstream URL: http://www.seqan.de/ Owners: sagitter Branches: f20 -- 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@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730 Antonio Trande anto.tra...@gmail.com changed: What|Removed |Added Flags||fedora-cvs? --- Comment #14 from Antonio Trande anto.tra...@gmail.com --- Thanks! -- 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@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730 --- Comment #12 from Antonio Trande anto.tra...@gmail.com --- (In reply to Sandro Mani from comment #11) Looks like the builder is running out of memory, you can try removing the -pipe flag from OPTFLAGS. On koji is working; tried only in rawhide. Spec URL: http://sagitter.fedorapeople.org/SeqAn/seqan.spec SRPM URL: http://sagitter.fedorapeople.org/SeqAn/seqan-1.4.1-2.fc20.src.rpm -- 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@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730
Sandro Mani manisan...@gmail.com changed:
What|Removed |Added
Flags|fedora-review? |fedora-review+
--- Comment #13 from Sandro Mani manisan...@gmail.com ---
Please also mark %{_docdir}/seqan/ as %doc before importing. Rest is good.
Package approved!
Concerning alglib, I'd say if Alexey doesn't do his review by mid-week then I'd
appreciate if you could proceed with yours.
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[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730 Antonio Trande anto.tra...@gmail.com changed: What|Removed |Added Summary|Review Request: seqan-devel |Review Request: seqan - |- Open source C++ library |Open source C++ library of |of efficient algorithms and |efficient algorithms and |data structures |data structures -- 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@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730 --- Comment #6 from Antonio Trande anto.tra...@gmail.com --- Package renamed as seqan. It now compiles and builds an application package and a devel one. Spec URL: http://sagitter.fedorapeople.org/SeqAn/seqan.spec SRPM URL: http://sagitter.fedorapeople.org/SeqAn/seqan-1.4.1-1.fc20.src.rpm Note Compiler seems not able to complete all operations by using -O2 optimization flag as requested by packaging guidelines. My PC memory seems not sufficient to finish SeqAn apps compilation here so I must to base my tests only on Koji or Copr builds. Any help about this problem is welcome. Koji build in rawhide: http://koji.fedoraproject.org/koji/taskinfo?taskID=7045251 -- 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@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730 Sandro Mani manisan...@gmail.com changed: What|Removed |Added Status|NEW |ASSIGNED CC||manisan...@gmail.com Assignee|nob...@fedoraproject.org|manisan...@gmail.com Flags||fedora-review? -- 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@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730
--- Comment #7 from Sandro Mani manisan...@gmail.com ---
Full review below. Main points:
- [!]: Provides: bundled(gnulib) in place as required, see
http://fedoraproject.org/wiki/Packaging:No_Bundled_Libraries#Packages_granted_exceptions
- I guess the documentation of the various executables should go inside
/usr/share/doc/seqan, not directly in /usr/share/doc
- The spec contains a few lines with blank spaces at the end of a line
- rpmlint:
seqan.x86_64: W: wrong-file-end-of-line-encoding /usr/share/doc/stellar/README
seqan.x86_64: W: wrong-file-end-of-line-encoding
/usr/share/doc/breakpoint_calculator/example/alignment.maf
- many rpmlint spurious-executable-perm warnings, I guess the your fix in
%build did not work, I'd suggest replacing it with
find %{buildroot}%{_includedir}/seqan -type f -exec chmod 644 {} \;
- You could replace
pushd build/Release
make install DESTDIR=%{buildroot}
popd
by
%make_install -C build/Release
I had no issues compiling with -O2, that is omitting
-DCMAKE_CXX_FLAGS=$SEQAN_OPT_FLAGS \
-DCMAKE_C_FLAGS=$SEQAN_OPT_FLAGS \
and the whole block setting SEQAN_OPT_FLAGS
Package Review
==
Legend:
[x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated
[ ] = Manual review needed
= MUST items =
C/C++:
[!]: Provides: bundled(gnulib) in place as required.
Note: Sources not installed
[x]: Package does not contain kernel modules.
[x]: Package contains no static executables.
[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: There is no build directory. Running licensecheck on vanilla
upstream sources. No licenses found. Please check the source files for
licenses manually.
[x]: License file installed when any subpackage combination is installed.
[x]: %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.
[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.
[-]: 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 655360 bytes in 102 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 %doc.
[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 $RPM_BUILD_ROOT) at the
beginning of %install.
[x]: Macros in Summary, %description expandable at SRPM build time.
[x]: Package does not contain duplicates in %files.
[x]: Permissions on files are set properly.
[x]: Package use %makeinstall only when make install' ' DESTDIR=... doesn't
work.
[x]: Package is named using only allowed ASCII characters.
[x]: Package do not use a name that already exist
[x]: Package is not relocatable.
[x]: Sources used to build the package match the upstream source, as provided
in the spec URL.
[x]: Spec file name must match the spec package %{name}, in the format
%{name}.spec.
[x]: File names are valid UTF-8.
[x]: Packages must not store files
[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730 --- Comment #8 from Antonio Trande anto.tra...@gmail.com --- (In reply to Sandro Mani from comment #7) I had no issues compiling with -O2, that is omitting -DCMAKE_CXX_FLAGS=$SEQAN_OPT_FLAGS \ -DCMAKE_C_FLAGS=$SEQAN_OPT_FLAGS \ and the whole block setting SEQAN_OPT_FLAGS Have you even tried with koji in f20? None compiler error? -- 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@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730 --- Comment #9 from Sandro Mani manisan...@gmail.com --- Ah uhm no I did a local mock build. What error did you get with koji? -- 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@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730
--- Comment #10 from Antonio Trande anto.tra...@gmail.com ---
Have you even tried with koji in f20?
Ops! You can't do that in f20 because coir-or-lemon is not available yet.
Sorry.
However, most times it was like that:
...
{standard input}: Assembler messages:
{standard input}:604289: Warning: end of file not at end of a line; newline
inserted
{standard input}: Error: open CFI at the end of file; missing .cfi_endproc
directive
c++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See http://bugzilla.redhat.com/bugzilla for instructions.
core/apps/pair_align/CMakeFiles/pair_align.dir/build.make:57: recipe for target
'core/apps/pair_align/CMakeFiles/pair_align.dir/pair_align.cpp.o' failed
make[2]: Leaving directory '/builddir/build/BUILD/seqan-1.4.1/build/Release'
make[2]: *** [core/apps/pair_align/CMakeFiles/pair_align.dir/pair_align.cpp.o]
Error 4
CMakeFiles/Makefile2:621: recipe for target
'core/apps/pair_align/CMakeFiles/pair_align.dir/all' failed
make[1]: *** [core/apps/pair_align/CMakeFiles/pair_align.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs
Linking CXX executable ../../../bin/stellar
Log:
http://copr-be.cloud.fedoraproject.org/results/sagitter/OpenMS/fedora-rawhide-x86_64/seqan-1.4.1-1.fc20/build.log
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[Bug 1105730] Review Request: seqan - Open source C++ library of efficient algorithms and data structures
https://bugzilla.redhat.com/show_bug.cgi?id=1105730 --- Comment #11 from Sandro Mani manisan...@gmail.com --- Looks like the builder is running out of memory, you can try removing the -pipe flag from OPTFLAGS. -- 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@lists.fedoraproject.org https://admin.fedoraproject.org/mailman/listinfo/package-review
