Spec URL: http://sagitter.fedorapeople.org/SeqAn/seqan-devel.spec SRPM URL: http://sagitter.fedorapeople.org/SeqAn/seqan-devel-1.4.1-1.fc20.src.rpm Description: SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. Our library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance. Fedora Account System Username: sagitter Note: this package just contains header files and development documentation; these libraries will be needed for a next package that i wish to review. It also contains code for building other various applications, not necessary for my purpose.
*** Bug 717473 has been marked as a duplicate of this bug. ***
Ths package should be named as seqan although it's a header-only package. https://fedoraproject.org/wiki/Packaging:Guidelines#Packaging_Header_Only_Libraries
Calling it seqan would presumably cause trouble if anyone wants the tools rather than just the headers. The packaging I unfortunately did simultaneously, (see #717473) includes both, like the Debian package. I assume it's clear that tophat won't currently build with this version.
(In reply to Dave Love from comment #3) > Calling it seqan would presumably cause trouble if anyone wants the tools > rather > than just the headers. The packaging I unfortunately did simultaneously, > (see #717473) > includes both, like the Debian package. > > I assume it's clear that tophat won't currently build with this version. Hi Dave. If you need a complete packaging of SeqAn (headers + tools), I'm willing to leave to you this package; later, I'll review it.
I (my users) don't need the tools as far as I know. I assumed the whole thing should be built, but I don't know how that fits with any policy or anyone else's possible needs. I only did seqan for tophat, so I don't really care, and am happy if tophat appears somehow. I don't currently have sponsorship, so it wouldn't make sense for me to take it over, and I'm not clever enough to hack C++ in a reasonable time to get tophat built against this version :-/.
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
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 under /srv, /opt or /usr/local ===== SHOULD items ===== Generic: [x]: Uses parallel make %{?_smp_mflags} macro. [-]: 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]: Fully versioned dependency in subpackages if applicable. Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in seqan-devel -> unneeded I suppose since no libraries are shipped [?]: 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. [-]: %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]: Dist tag is present (not strictly required in GL). [x]: No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin. [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: No rpmlint messages. [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: seqan-1.4.1-1.fc21.x86_64.rpm seqan-devel-1.4.1-1.fc21.x86_64.rpm seqan-1.4.1-1.fc21.src.rpm seqan.x86_64: W: spelling-error %description -l en_US extensibility -> sensibility, extensible 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 seqan.x86_64: W: no-manual-page-for-binary sak seqan.x86_64: W: no-manual-page-for-binary masai_output_se seqan.x86_64: W: no-manual-page-for-binary tree_recon seqan.x86_64: W: no-manual-page-for-binary alf seqan.x86_64: W: no-manual-page-for-binary sgip seqan.x86_64: W: no-manual-page-for-binary snp_store seqan.x86_64: W: no-manual-page-for-binary pair_align seqan.x86_64: W: no-manual-page-for-binary rabema_evaluate seqan.x86_64: W: no-manual-page-for-binary breakpoint_calculator seqan.x86_64: W: no-manual-page-for-binary splazers seqan.x86_64: W: no-manual-page-for-binary mason seqan.x86_64: W: no-manual-page-for-binary dfi seqan.x86_64: W: no-manual-page-for-binary micro_razers seqan.x86_64: W: no-manual-page-for-binary rabema_prepare_sam seqan.x86_64: W: no-manual-page-for-binary razers seqan.x86_64: W: no-manual-page-for-binary searchjoin seqan.x86_64: W: no-manual-page-for-binary razers2 seqan.x86_64: W: no-manual-page-for-binary razers3 seqan.x86_64: W: no-manual-page-for-binary seqan_tcoffee seqan.x86_64: W: no-manual-page-for-binary rabema_build_gold_standard seqan.x86_64: W: no-manual-page-for-binary masai_output_pe seqan.x86_64: W: no-manual-page-for-binary stellar seqan.x86_64: W: no-manual-page-for-binary gustaf seqan.x86_64: W: no-manual-page-for-binary insegt seqan.x86_64: W: no-manual-page-for-binary rep_sep seqan.x86_64: W: no-manual-page-for-binary masai_mapper seqan.x86_64: W: no-manual-page-for-binary param_chooser seqan.x86_64: W: no-manual-page-for-binary masai_indexer seqan.x86_64: W: no-manual-page-for-binary seqcons seqan.x86_64: W: no-manual-page-for-binary variant_comp seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/file/file_stream.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/index/index_fm_prefix_sum_table.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/index/index_fm_compressed_sa.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/index/index_fm_sparse_string.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/math/math_rational.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/index_extras.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/index/index_fm_rank_support_bit_string.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/random/ext_MersenneTwister.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/index/index_fm_rank_dictionary_wt.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/store/store_io_ucsc.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/index/index_fm_right_array_binary_tree.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/parallel/parallel_atomic_primitives.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/index/find_pigeonhole.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/platform.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/bam_io/cigar.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/index/index_fm_rank_support_bit_string_iterator.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/index/index_fm_right_array_binary_tree_iterator.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/parallel.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/store/store_io_gff.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/parallel/parallel_splitting.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/math/math_operators.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/index/shape_threshold.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/parallel/parallel_atomic_misc.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/index/index_fm_compressed_sa_iterator.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/parallel/parallel_macros.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/misc/misc_name_store_cache.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/index/index_fm_lf_table.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/math/math_common_factor.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/math.h seqan-devel.x86_64: W: spurious-executable-perm /usr/include/seqan/index/pizzachili_api.h seqan.src: W: spelling-error %description -l en_US extensibility -> sensibility, extensible 3 packages and 0 specfiles checked; 0 errors, 64 warnings. Rpmlint (installed packages) ---------------------------- # rpmlint seqan seqan-devel (none): E: no installed packages by name seqan (none): E: no installed packages by name seqan-devel 0 packages and 0 specfiles checked; 0 errors, 0 warnings. # echo 'rpmlint-done:' Requires -------- seqan (rpmlib, GLIBC filtered): libbz2.so.1()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.4)(64bit) libgcc_s.so.1(GCC_4.0.0)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libgomp.so.1(OMP_3.0)(64bit) libm.so.6()(64bit) libpthread.so.0()(64bit) librt.so.1()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.2.3)(64bit) libz.so.1(ZLIB_1.2.3.3)(64bit) rtld(GNU_HASH) seqan-devel (rpmlib, GLIBC filtered): Provides -------- seqan: seqan seqan(x86-64) seqan-devel: seqan-devel seqan-devel(x86-64) Source checksums ---------------- http://packages.seqan.de/seqan-src/seqan-src-1.4.1.tar.gz : CHECKSUM(SHA256) this package : 47c4cf698d9879000b7de514a5cb425c18c26c8b8a81e469da23b757f7680a8e CHECKSUM(SHA256) upstream package : 47c4cf698d9879000b7de514a5cb425c18c26c8b8a81e469da23b757f7680a8e Generated by fedora-review 0.5.1 (bb9bf27) last change: 2013-12-13 Command line :/usr/bin/fedora-review -o-v --enable-plugin=tmpfs -b 1105730 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, EPEL5, BATCH, DISTTAG
(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?
Ah uhm no I did a local mock build. What error did you get with koji?
>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
Looks like the builder is running out of memory, you can try removing the -pipe flag from OPTFLAGS.
(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
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.
Thanks!
There's no scm request here... Please see: http://fedoraproject.org/wiki/Package_SCM_admin_requests
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
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
Git done (by process-git-requests).
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
seqan-1.4.1-2.fc20 has been pushed to the Fedora 20 testing repository.
seqan-1.4.1-2.fc20 has been pushed to the Fedora 20 stable repository.