Spec URL: http://in.waw.pl/~zbyszek/libsbml.spec SRPM URL: http://in.waw.pl/~zbyszek/libsbml-5.11.0-1.fc22.src.rpm Fedora Account System Username: zbyszek Description: LibSBML is an open-source programming library designed to read, write, manipulate, translate, and validate SBML files and data streams. It is not an application itself (though it does come with example programs), but rather a library you can embed in other applications. LibSBML %{version} understands SBML Level 3 Version 1 and older, as well as the draft SBML Level 2 Layout proposal by Gauges, Rost, Sahle and Wegner. It's written in ISO C and C++ but can also be used from C#, Java, MATLAB, Octave, Perl, Python, and Ruby. koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=8348888
Tests fail on i686... I'll try to get this fixed, and disable the tests otherwise.
Hi Zbigniew, The files don't seem to be accessible at the moment. re: tests -- ouch, double-free errors. Any idea if that's a problem with the test suite itself or LibSBML as a whole? If the former, fixing / disabling the test suite only on i686 with an %ifarch might be sufficient. If the latter... perhaps use an ExcludeArch to not build on i686 for now?
Yikes, wrong URLs. But I want to make an update anyway, so let me do this first. I reported build issues upstream [1, 2], and was advised to try cmake instead. But cmake install things in different places, does not install egg-info, and is in general more problematic than automake. I'll stay with automake for now. [1] https://sourceforge.net/p/sbml/libsbml/388/ [2] https://sourceforge.net/p/sbml/libsbml/389/ LibSBML is generally usable, I'll later submit a program which uses it for review, and it seems to work. This crash might be a test suite issue. I disabled the tests for now, and will wait for the upstream response. They have been very responsive, so hopefully this will get resolved quickly. Spec URL: http://in.waw.pl/~zbyszek/fedora/libsbml.spec SRPM URL: http://in.waw.pl/~zbyszek/fedora/libsbml-5.11.0-1.fc22.src.rpm koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=8358017
Koji builds (w/o tests) took approx 3h. And it failed because of an error in the dependecy. Spec URL: http://in.waw.pl/~zbyszek/fedora/libsbml.spec SRPM URL: http://in.waw.pl/~zbyszek/fedora/libsbml-5.11.0-2.fc22.src.rpm koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=8361292
OK, I'm pretty happy with this version. Sorry for the all the updates. This one uses cmake, all tests pass, and documentation is built properly, and there's a python3 subpackage. Spec URL: http://in.waw.pl/~zbyszek/fedora/libsbml.spec SRPM URL: http://in.waw.pl/~zbyszek/fedora/libsbml-5.11.0-3.fc22.src.rpm koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=8379118
OK, arm was busted. After talking with upstream, I added ExludeArch: arm. Spec URL: http://in.waw.pl/~zbyszek/fedora/libsbml.spec SRPM URL: http://in.waw.pl/~zbyszek/fedora/libsbml-5.11.0-4.fc22.src.rpm koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=8416890
Created attachment 976718 [details] License check License check results. The non-LGPL files need to be examined more carefully, esp since some of them are under the stronger GPL license
Ah, scratch that, on closer examination the only GPLed files are auto-generated by Bison (and there is an exception allowing relicensing as long as the product is not a parser generator), and the rest are only used at build time and described in LICENSE.txt (which you should include, I think, in addition to COPYING.txt) I'm working through the rest of the review, but while doing that, I'm a bit concerned that libSBML bundles MiniZip. Might need an FPC exception for that... we should try and look for precedents first?
@Zbigniew Jędrzejewski-Szmek, i have seen this review request just now. I opened another one for libsbml some days ago (https://bugzilla.redhat.com/show_bug.cgi?id=1177625). Can you implement render's support in your package (http://sourceforge.net/projects/sbml/files/libsbml/5.11.0/experimental/source/render-5.11.0-beta-1.zip/download)? I need it because required by COPASI software that i'm packaging for Fedora.
(In reply to Michel Alexandre Salim from comment #8) > I'm a bit concerned that libSBML bundles MiniZip. minizip is packaged for Fedora, so it is "only" a question of linking to the shared library. Doesn't seem to complicated in this case. (In reply to Antonio Trande from coyomment #9) > i have seen this review request just now. I opened another one for libsbml > some days ago (https://bugzilla.redhat.com/show_bug.cgi?id=1177625). Co-maintainers welcome! > Can you implement render's support in your package > (http://sourceforge.net/projects/sbml/files/libsbml/5.11.0/experimental/ > source/render-5.11.0-beta-1.zip/download)? > I need it because required by COPASI software that i'm packaging for Fedora. Sure. I see that you packaged all the bindings... I wanted to leave that for the future, until somebody requests it, but since you need it, let's add it now.
(In reply to Zbigniew Jędrzejewski-Szmek from comment #10) > (In reply to Antonio Trande from coyomment #9) > > i have seen this review request just now. I opened another one for libsbml > > some days ago (https://bugzilla.redhat.com/show_bug.cgi?id=1177625). > Co-maintainers welcome! Okay. I'm willing. > > > Can you implement render's support in your package > > (http://sourceforge.net/projects/sbml/files/libsbml/5.11.0/experimental/ > > source/render-5.11.0-beta-1.zip/download)? > > I need it because required by COPASI software that i'm packaging for Fedora. > Sure. I see that you packaged all the bindings... I wanted to leave that for > the future, until somebody requests it, but since you need it, let's add it > now. Okay. Thank you.
*** Bug 1177625 has been marked as a duplicate of this bug. ***
Spec URL: http://in.waw.pl/~zbyszek/fedora/libsbml.spec SRPM URL: http://in.waw.pl/~zbyszek/fedora/libsbml-5.11.0-5.fc22.src.rpm koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=8541928 version -5: unbundle minizip, add render extension.
(In reply to Zbigniew Jędrzejewski-Szmek from comment #13) > Spec URL: http://in.waw.pl/~zbyszek/fedora/libsbml.spec > SRPM URL: http://in.waw.pl/~zbyszek/fedora/libsbml-5.11.0-5.fc22.src.rpm > koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=8541928 > > version -5: unbundle minizip, add render extension. There is code for Octave, C#, Java, Ruby bindings with related tests which can be included in this SPEC file. Some patches have been added by upstream maintainer for RPM packaging in Fedora (http://sourceforge.net/p/sbml/libsbml/milestone/libSBML-5.11.0/). Why ignore them?
(In reply to Antonio Trande from comment #14) > Why ignore them? Jest plain laziness^W^W minimization of work. Package description has the following text: "LibSBML is compiled with Python and PERL bindings for Fedora. If you need additional bindings, feel free to create a bug report." I suspect that for those esoteric binding the use will be close to nil. But if you think that there are users who will use C# and other bindings, we can add them.
(In reply to Zbigniew Jędrzejewski-Szmek from comment #15) > (In reply to Antonio Trande from comment #14) > > Why ignore them? > Jest plain laziness^W^W minimization of work. > > Package description has the following text: "LibSBML is compiled with Python > and PERL bindings for Fedora. If you need additional bindings, feel free to > create a bug report." I suspect that for those esoteric binding the use will > be close to nil. But if you think that there are users who will use C# and > other bindings, we can add them. Well, libsbml/libsedml/linsbw/copasi maintainers helped me a lot in these days for all bindings. I think they are still interested but i don't know if these libraries are really useful to somebody.
OK, let's not waste this work. Spec URL: http://in.waw.pl/~zbyszek/fedora/libsbml.spec SRPM URL: http://in.waw.pl/~zbyszek/fedora/libsbml-5.11.0-5.fc22.src.rpm koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=8579886 version -6: add mono, java, r, ruby, octave subpackages. Make individual subpackages conditional (rpmbuild --without docs --without check ...). There's a slight problem with the java bindings: documentation is not installed, the examples are not installed, and the examples all use System.loadLibrary. To work under Linux, they should be converted to System.load [1]. I think it would be best to do this as an upstream patch, so I left it for later. Something like [2], but less ugly. [1] http://fedoraproject.org/wiki/Packaging:Java#Packaging_JAR_files_that_use_JNI [2] http://fedoraproject.org/wiki/JavaSystemLoadExample
Correct srpm URL: Spec URL: http://in.waw.pl/~zbyszek/fedora/libsbml.spec SRPM URL: http://in.waw.pl/~zbyszek/fedora/libsbml-5.11.0-6.fc22.src.rpm koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=8579886
@Michel If you haven't time for this review, leave it to me.
Ping?
Hi guys. Apologies, been busy setting up at a new job. I have some time now, but if Antonio wants to take over that's fine too. Why don't we both do the review and that way ensure it's a thorough one?
Fine with me ;)
Hi both, There are some file ownership issues (see below), and when I build on my local mock instance, somehow the Ruby subpackage includes all the documentation files that are also in -docs: $ ls -lhrS *.rpm | tail -n3 17:46 michel@fedora21 -rw-rw-r--. 1 michel mock 26M Peb 3 14:12 libsbml-docs-5.11.0-6.fc21.noarch.rpm -rw-rw-r--. 1 michel mock 28M Peb 3 14:11 ruby-SBML-5.11.0-6.fc21.x86_64.rpm -rw-rw-r--. 1 michel mock 76M Peb 3 14:13 libsbml-debuginfo-5.11.0-6.fc21.x86_64.rpm Package Review ============== Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated [ ] = Manual review needed Issues: ======= - Packages have proper BuildRequires/Requires on jpackage-utils - Javadocs are placed in %{_javadocdir}/%{name} (no -%{version} symlink) Note: No javadoc subpackage present See: https://fedoraproject.org/wiki/Packaging:Java#Javadoc_installation - Javadoc documentation files are generated and included in -javadoc subpackage Note: No javadoc subpackage present See: https://fedoraproject.org/wiki/Packaging:Java#Javadoc_installation - Large documentation must go in a -doc subpackage. Large could be size (~1MB) or number of files. Note: Documentation size is 574330880 bytes in 12918 files. See: http://fedoraproject.org/wiki/Packaging/Guidelines#PackageDocumentation ===== MUST items ===== C/C++: [x]: Package does not contain kernel modules. [x]: Package contains no static executables. [x]: Development (unversioned) .so files in -devel subpackage, if present. Note: Unversioned so-files in private %_libdir subdirectory (see attachment). Verify they are not in ld path. [x]: Header files in -devel subpackage, if present. [x]: ldconfig called in %post and %postun if required. [x]: Package does not contain any libtool archives (.la) [x]: Rpath absent or only used for internal libs. Generic: [x]: Package successfully compiles and builds into binary rpms on at least one supported primary architecture. Note: Using prebuilt packages [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: "LGPL", "GPL (v3 or later)", "Unknown or generated", "MIT/X11 (BSD like)", "*No copyright* LGPL (with incorrect FSF address)", "BSD (3 clause)", "LGPL (with incorrect FSF address)". 1118 files have unknown license. Detailed output of licensecheck in /home/michel/reviews/1173159 -libsbml-manual/review-libsbml/licensecheck.txt [x]: License file installed when any subpackage combination is installed. Note: License text declares in subpackages except for -devel, but they point to same file anyway so only one copy is on disk [x]: Package requires other packages for directories it uses. Note: Directories without known owners: /usr/lib/mono, /usr/lib64/libsbml - libsbml-sharp needs to Requires: mono-core [!]: Package must own all directories that it creates. Note: No known owner of /usr/lib64/libsbml - java-libsbml needs to own %{_libdir}/libsbml [x]: %build honors applicable compiler flags or justifies otherwise. [x]: All build dependencies are listed in BuildRequires, except for any that are listed in the exceptions section of Packaging Guidelines. Note: Using prebuilt rpms. [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. [x]: Development files must be in a -devel package [x]: Package uses nothing in %doc for runtime. [!]: Package consistently uses macros (instead of hard-coded directory names). Use %{_monodir} instead of %{_prefix}/lib/mono [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. see libsbml-sharp note above [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. [?]: Package is not known to require an ExcludeArch tag. note - it does but is marked as such -- this is fine [x]: Package complies to the Packaging Guidelines [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 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]: 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 Java: [x]: Bundled jar/class files should be removed before build Maven: [-]: If package contains pom.xml files install it (including depmaps) even when building with ant [x]: Old add_to_maven_depmap macro is not being used Perl: [x]: Package contains the mandatory BuildRequires and Requires:. Python: [x]: 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. [x]: Package meets the Packaging Guidelines::Python [x]: Package contains BR: python2-devel or python3-devel [-]: Binary eggs must be removed in %prep ===== SHOULD items ===== Generic: [x]: Reviewer should test that the package builds in mock. [-]: 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 libsbml- docs [?]: Package functions as described. [x]: Latest version is packaged. [x]: Package does not include license text files separate from upstream. [x]: Patches link to upstream bugs/comments/lists or are otherwise justified. [-]: Scriptlets must be sane, if 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. [?]: Packages should try to preserve timestamps of original installed files. Not sure if configure_file does this but it's not that important as we don't have shared files in multilib installs [x]: Packager, Vendor, PreReq, Copyright tags should not be in spec file [x]: Sources can be downloaded from URI in Source: tag [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]: The placement of pkgconfig(.pc) files are correct. [x]: SourceX is a working URL. [x]: Spec use %global instead of %define unless justified. Java: [-]: Packages are noarch unless they use JNI Note: libsbml subpackage is not noarch. Please verify manually Package does use JNI (to communicate with libsbml) so this is fine [x]: Package uses upstream build method (ant/maven/etc.) ===== 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 290048000 bytes in /usr/share ruby- SBML-5.11.0-6.fc21.x86_64.rpm:289546240 See: http://fedoraproject.org/wiki/Packaging:ReviewGuidelines#Package_Review_Guidelines [x]: Rpmlint is run on all installed packages. Note: There are rpmlint messages (see attachment). [x]: Spec file according to URL is the same as in SRPM. Rpmlint ------- Checking: libsbml-5.11.0-6.fc21.x86_64.rpm libsbml-devel-5.11.0-6.fc21.x86_64.rpm python-libsbml-5.11.0-6.fc21.x86_64.rpm python3-libsbml-5.11.0-6.fc21.x86_64.rpm perl-LibSBML-5.11.0-6.fc21.x86_64.rpm ruby-SBML-5.11.0-6.fc21.x86_64.rpm java-libsbml-5.11.0-6.fc21.x86_64.rpm octave-SBML-5.11.0-6.fc21.x86_64.rpm R-libSBML-5.11.0-6.fc21.x86_64.rpm libsbml-sharp-5.11.0-6.fc21.x86_64.rpm libsbml-docs-5.11.0-6.fc21.noarch.rpm libsbml-5.11.0-6.fc21.src.rpm libsbml-devel.x86_64: W: only-non-binary-in-usr-lib libsbml-devel.x86_64: W: no-documentation libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/ListOfCurveElements.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/ColorDefinition.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/GraphicalPrimitive1D.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/RelAbsVector.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/Polygon.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/Transformation.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/Style.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/Text.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/GlobalStyle.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/RenderGroup.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/Ellipse.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/GraphicalPrimitive2D.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/GradientBase.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/RadialGradient.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/GradientStop.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/RenderPoint.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/RenderInformationBase.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/RenderCurve.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/Rectangle.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/RenderCubicBezier.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/LineEnding.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/Image.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/LocalStyle.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/LinearGradient.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/GlobalRenderInformation.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/LocalRenderInformation.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/Transformation2D.h python-libsbml.x86_64: W: no-documentation python3-libsbml.x86_64: W: no-documentation perl-LibSBML.x86_64: W: no-documentation ruby-SBML.x86_64: W: spelling-error Summary(en_US) libSBML -> Librium ruby-SBML.x86_64: W: spelling-error %description -l en_US libSBML -> Librium ruby-SBML.x86_64: W: dangling-relative-symlink /usr/share/doc/libsbml/README-ruby.txt src/bindings/ruby/README.txt java-libsbml.x86_64: W: no-documentation octave-SBML.x86_64: W: spelling-error Summary(en_US) libSBML -> Librium octave-SBML.x86_64: W: spelling-error %description -l en_US libSBML -> Librium octave-SBML.x86_64: W: no-documentation R-libSBML.x86_64: W: no-documentation R-libSBML.x86_64: E: zero-length /usr/lib64/R/library/libSBML/help/libSBML.rdb R-libSBML.x86_64: E: zero-length /usr/lib64/R/library/libSBML/help/AnIndex libsbml-sharp.x86_64: W: no-documentation libsbml.src:175: W: unversioned-explicit-provides bundled(jquery) libsbml.src:344: W: macro-in-comment %{name} libsbml.src:350: W: macro-in-comment %{name} libsbml.src:391: E: hardcoded-library-path in %{_prefix}/lib/mono/libsbmlcsP/ 12 packages and 0 specfiles checked; 30 errors, 17 warnings. Rpmlint (installed packages) ---------------------------- Cannot parse rpmlint output: Requires -------- python3-libsbml (rpmlib, GLIBC filtered): libbz2.so.1()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libminizip.so.1()(64bit) libpython3.4m.so.1.0()(64bit) libsbml(x86-64) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.1)(64bit) libz.so.1()(64bit) python(abi) rtld(GNU_HASH) perl-LibSBML (rpmlib, GLIBC filtered): libbz2.so.1()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libminizip.so.1()(64bit) libperl.so.5.18()(64bit) libsbml(x86-64) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.1)(64bit) libz.so.1()(64bit) perl(:MODULE_COMPAT_5.18.4) perl(DynaLoader) perl(Exporter) perl(base) perl(vars) rtld(GNU_HASH) libsbml-sharp (rpmlib, GLIBC filtered): libbz2.so.1()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libminizip.so.1()(64bit) libsbml(x86-64) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.1)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) libsbml (rpmlib, GLIBC filtered): /sbin/ldconfig libbz2.so.1()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libminizip.so.1()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.1)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) ruby-SBML (rpmlib, GLIBC filtered): libbz2.so.1()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libminizip.so.1()(64bit) libruby.so.2.1()(64bit) libsbml(x86-64) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.1)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) ruby(release) octave-SBML (rpmlib, GLIBC filtered): libbz2.so.1()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) libm.so.6()(64bit) libminizip.so.1()(64bit) liboctave.so.2()(64bit) liboctinterp.so.2()(64bit) libsbml(x86-64) libsbml.so.5()(64bit) libstdc++.so.6()(64bit) libxml2.so.2()(64bit) libz.so.1()(64bit) octave octave(api) rtld(GNU_HASH) python-libsbml (rpmlib, GLIBC filtered): libbz2.so.1()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libminizip.so.1()(64bit) libpython2.7.so.1.0()(64bit) libsbml(x86-64) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.1)(64bit) libz.so.1()(64bit) python(abi) rtld(GNU_HASH) java-libsbml (rpmlib, GLIBC filtered): java-headless jpackage-utils libbz2.so.1()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libminizip.so.1()(64bit) libsbml(x86-64) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.1)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) R-libSBML (rpmlib, GLIBC filtered): R-core libR.so()(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libminizip.so.1()(64bit) libsbml(x86-64) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.1)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) libsbml-docs (rpmlib, GLIBC filtered): libsbml libsbml-devel (rpmlib, GLIBC filtered): /usr/bin/pkg-config libsbml(x86-64) libsbml.so.5()(64bit) pkgconfig(libxml-2.0) Provides -------- python3-libsbml: python3-libsbml python3-libsbml(x86-64) perl-LibSBML: perl(LibSBML) perl(LibSBML::ASTBase) perl(LibSBML::ASTBasePlugin) perl(LibSBML::ASTNode) perl(LibSBML::ASTNodeList) perl(LibSBML::AlgebraicRule) perl(LibSBML::AssignmentRule) perl(LibSBML::Association) perl(LibSBML::BoundingBox) perl(LibSBML::CVTerm) perl(LibSBML::CVTermList) perl(LibSBML::CobraToFbcConverter) perl(LibSBML::ColorDefinition) perl(LibSBML::CompBase) perl(LibSBML::CompExtension) perl(LibSBML::CompFlatteningConverter) perl(LibSBML::CompModelPlugin) perl(LibSBML::CompPkgNamespaces) perl(LibSBML::CompSBMLDocumentPlugin) perl(LibSBML::CompSBasePlugin) perl(LibSBML::Compartment) perl(LibSBML::CompartmentGlyph) perl(LibSBML::CompartmentType) perl(LibSBML::Constraint) perl(LibSBML::ConversionOption) perl(LibSBML::ConversionProperties) perl(LibSBML::CubicBezier) perl(LibSBML::Curve) perl(LibSBML::Date) perl(LibSBML::DateList) perl(LibSBML::DefaultTerm) perl(LibSBML::Delay) perl(LibSBML::Deletion) perl(LibSBML::Dimensions) perl(LibSBML::ElementFilter) perl(LibSBML::Ellipse) perl(LibSBML::Event) perl(LibSBML::EventAssignment) perl(LibSBML::ExternalModelDefinition) perl(LibSBML::FbcExtension) perl(LibSBML::FbcModelPlugin) perl(LibSBML::FbcPkgNamespaces) perl(LibSBML::FbcSpeciesPlugin) perl(LibSBML::FbcToCobraConverter) perl(LibSBML::FluxBound) perl(LibSBML::FluxObjective) perl(LibSBML::FunctionDefinition) perl(LibSBML::FunctionTerm) perl(LibSBML::GeneAssociation) perl(LibSBML::GeneralGlyph) perl(LibSBML::GlobalRenderInformation) perl(LibSBML::GlobalStyle) perl(LibSBML::GradientBase) perl(LibSBML::GradientStop) perl(LibSBML::GraphicalObject) perl(LibSBML::GraphicalPrimitive1D) perl(LibSBML::GraphicalPrimitive2D) perl(LibSBML::ISBMLExtensionNamespaces) perl(LibSBML::IdList) perl(LibSBML::IdentifierTransformer) perl(LibSBML::Image) perl(LibSBML::InitialAssignment) perl(LibSBML::Input) perl(LibSBML::KineticLaw) perl(LibSBML::L3ParserSettings) perl(LibSBML::Layout) perl(LibSBML::LayoutExtension) perl(LibSBML::LayoutModelPlugin) perl(LibSBML::LayoutPkgNamespaces) perl(LibSBML::LayoutSpeciesReferencePlugin) perl(LibSBML::LineEnding) perl(LibSBML::LineSegment) perl(LibSBML::LinearGradient) perl(LibSBML::ListOf) perl(LibSBML::ListOfColorDefinitions) perl(LibSBML::ListOfCompartmentGlyphs) perl(LibSBML::ListOfCompartmentTypes) perl(LibSBML::ListOfCompartments) perl(LibSBML::ListOfConstraints) perl(LibSBML::ListOfCurveElements) perl(LibSBML::ListOfDeletions) perl(LibSBML::ListOfDrawables) perl(LibSBML::ListOfEventAssignments) perl(LibSBML::ListOfEvents) perl(LibSBML::ListOfExternalModelDefinitions) perl(LibSBML::ListOfFluxBounds) perl(LibSBML::ListOfFluxObjectives) perl(LibSBML::ListOfFunctionDefinitions) perl(LibSBML::ListOfFunctionTerms) perl(LibSBML::ListOfGeneAssociations) perl(LibSBML::ListOfGlobalRenderInformation) perl(LibSBML::ListOfGlobalStyles) perl(LibSBML::ListOfGradientDefinitions) perl(LibSBML::ListOfGradientStops) perl(LibSBML::ListOfGraphicalObjects) perl(LibSBML::ListOfInitialAssignments) perl(LibSBML::ListOfInputs) perl(LibSBML::ListOfLayouts) perl(LibSBML::ListOfLineEndings) perl(LibSBML::ListOfLineSegments) perl(LibSBML::ListOfLocalParameters) perl(LibSBML::ListOfLocalRenderInformation) perl(LibSBML::ListOfLocalStyles) perl(LibSBML::ListOfModelDefinitions) perl(LibSBML::ListOfObjectives) perl(LibSBML::ListOfOutputs) perl(LibSBML::ListOfParameters) perl(LibSBML::ListOfPorts) perl(LibSBML::ListOfQualitativeSpecies) perl(LibSBML::ListOfReactionGlyphs) perl(LibSBML::ListOfReactions) perl(LibSBML::ListOfReferenceGlyphs) perl(LibSBML::ListOfReplacedElements) perl(LibSBML::ListOfRules) perl(LibSBML::ListOfSpecies) perl(LibSBML::ListOfSpeciesGlyphs) perl(LibSBML::ListOfSpeciesReferenceGlyphs) perl(LibSBML::ListOfSpeciesReferences) perl(LibSBML::ListOfSpeciesTypes) perl(LibSBML::ListOfSubmodels) perl(LibSBML::ListOfTextGlyphs) perl(LibSBML::ListOfTransitions) perl(LibSBML::ListOfUnitDefinitions) perl(LibSBML::ListOfUnits) perl(LibSBML::LocalParameter) perl(LibSBML::LocalRenderInformation) perl(LibSBML::LocalStyle) perl(LibSBML::Model) perl(LibSBML::ModelCreator) perl(LibSBML::ModelCreatorList) perl(LibSBML::ModelDefinition) perl(LibSBML::ModelHistory) perl(LibSBML::ModifierSpeciesReference) perl(LibSBML::OFStream) perl(LibSBML::OStream) perl(LibSBML::OStringStream) perl(LibSBML::Objective) perl(LibSBML::Output) perl(LibSBML::Parameter) perl(LibSBML::Point) perl(LibSBML::Polygon) perl(LibSBML::Port) perl(LibSBML::Priority) perl(LibSBML::QualExtension) perl(LibSBML::QualModelPlugin) perl(LibSBML::QualPkgNamespaces) perl(LibSBML::QualitativeSpecies) perl(LibSBML::RDFAnnotationParser) perl(LibSBML::RadialGradient) perl(LibSBML::RateRule) perl(LibSBML::Reaction) perl(LibSBML::ReactionGlyph) perl(LibSBML::Rectangle) perl(LibSBML::ReferenceGlyph) perl(LibSBML::RelAbsVector) perl(LibSBML::RenderCubicBezier) perl(LibSBML::RenderCurve) perl(LibSBML::RenderExtension) perl(LibSBML::RenderGraphicalObjectPlugin) perl(LibSBML::RenderGroup) perl(LibSBML::RenderInformationBase) perl(LibSBML::RenderLayoutPlugin) perl(LibSBML::RenderListOfLayoutsPlugin) perl(LibSBML::RenderPkgNamespaces) perl(LibSBML::RenderPoint) perl(LibSBML::ReplacedBy) perl(LibSBML::ReplacedElement) perl(LibSBML::Replacing) perl(LibSBML::Rule) perl(LibSBML::SBMLConstructorException) perl(LibSBML::SBMLConverter) perl(LibSBML::SBMLConverterRegistry) perl(LibSBML::SBMLDocument) perl(LibSBML::SBMLDocumentPlugin) perl(LibSBML::SBMLError) perl(LibSBML::SBMLErrorLog) perl(LibSBML::SBMLExtension) perl(LibSBML::SBMLExtensionException) perl(LibSBML::SBMLExtensionRegistry) perl(LibSBML::SBMLExternalValidator) perl(LibSBML::SBMLFileResolver) perl(LibSBML::SBMLFunctionDefinitionConverter) perl(LibSBML::SBMLIdConverter) perl(LibSBML::SBMLInferUnitsConverter) perl(LibSBML::SBMLInitialAssignmentConverter) perl(LibSBML::SBMLLevelVersionConverter) perl(LibSBML::SBMLLocalParameterConverter) perl(LibSBML::SBMLNamespaces) perl(LibSBML::SBMLNamespacesList) perl(LibSBML::SBMLReactionConverter) perl(LibSBML::SBMLReader) perl(LibSBML::SBMLResolver) perl(LibSBML::SBMLResolverRegistry) perl(LibSBML::SBMLRuleConverter) perl(LibSBML::SBMLStripPackageConverter) perl(LibSBML::SBMLTransforms) perl(LibSBML::SBMLUnitsConverter) perl(LibSBML::SBMLUri) perl(LibSBML::SBMLValidator) perl(LibSBML::SBMLWriter) perl(LibSBML::SBO) perl(LibSBML::SBase) perl(LibSBML::SBaseExtensionPoint) perl(LibSBML::SBaseList) perl(LibSBML::SBasePlugin) perl(LibSBML::SBaseRef) perl(LibSBML::SimpleSpeciesReference) perl(LibSBML::Species) perl(LibSBML::SpeciesGlyph) perl(LibSBML::SpeciesReference) perl(LibSBML::SpeciesReferenceGlyph) perl(LibSBML::SpeciesType) perl(LibSBML::StoichiometryMath) perl(LibSBML::StringSet) perl(LibSBML::Style) perl(LibSBML::Submodel) perl(LibSBML::SyntaxChecker) perl(LibSBML::Text) perl(LibSBML::TextGlyph) perl(LibSBML::Transformation) perl(LibSBML::Transformation2D) perl(LibSBML::Transition) perl(LibSBML::Trigger) perl(LibSBML::Unit) perl(LibSBML::UnitDefinition) perl(LibSBML::XMLAttributes) perl(LibSBML::XMLConstructorException) perl(LibSBML::XMLError) perl(LibSBML::XMLErrorLog) perl(LibSBML::XMLInputStream) perl(LibSBML::XMLNamespaces) perl(LibSBML::XMLNode) perl(LibSBML::XMLOutputStream) perl(LibSBML::XMLOwningOutputFileStream) perl(LibSBML::XMLOwningOutputStringStream) perl(LibSBML::XMLToken) perl(LibSBML::XMLTriple) perl(LibSBML::double_array) perl(LibSBML::int_array) perl(LibSBMLc) perl-LibSBML perl-LibSBML(x86-64) libsbml-sharp: libsbml-sharp libsbml-sharp(x86-64) libsbmlcs.so()(64bit) libsbml: libsbml libsbml(x86-64) libsbml.so.5()(64bit) ruby-SBML: libSBML.so()(64bit) ruby(SBML) ruby-SBML ruby-SBML(x86-64) octave-SBML: octave-SBML octave-SBML(x86-64) python-libsbml: python-libsbml python-libsbml(x86-64) java-libsbml: java-libsbml java-libsbml(x86-64) libsbmlj.so()(64bit) R-libSBML: R-libSBML R-libSBML(x86-64) libSBML.so()(64bit) libsbml-docs: bundled(jquery) libsbml-docs libsbml-devel: libsbml-devel libsbml-devel(x86-64) pkgconfig(libsbml) Unversioned so-files -------------------- python-libsbml: /usr/lib64/python2.7/site-packages/libsbml/_libsbml.so python3-libsbml: /usr/lib64/python3.4/site-packages/libsbml/_libsbml.so perl-LibSBML: /usr/lib64/perl5/vendor_perl/auto/libSBML/LibSBML.so ruby-SBML: /usr/lib64/ruby/vendor_ruby/libSBML.so java-libsbml: /usr/lib64/libsbml/libsbmlj.so R-libSBML: /usr/lib64/R/library/libSBML/libs/libSBML.so libsbml-sharp: /usr/lib/mono/libsbmlcsP/libsbmlcs.so Source checksums ---------------- http://sourceforge.net/projects/sbml/files/libsbml/5.11.0/stable/libSBML-5.11.0-core-plus-packages-src.tar.gz : CHECKSUM(SHA256) this package : b21931ca7461494915c617b30d4a9f2cafe831d6ce74989b3e5874e6e3c3f72b CHECKSUM(SHA256) upstream package : b21931ca7461494915c617b30d4a9f2cafe831d6ce74989b3e5874e6e3c3f72b http://sourceforge.net/projects/sbml/files/libsbml/5.11.0/experimental/source/render-5.11.0-beta-1.zip : CHECKSUM(SHA256) this package : 5ed5cec563260201b958d790543f5dac8a516a088c4ced52f85cf5fc9e495e69 CHECKSUM(SHA256) upstream package : 5ed5cec563260201b958d790543f5dac8a516a088c4ced52f85cf5fc9e495e69 Generated by fedora-review 0.5.2 (63c24cb) last change: 2014-07-14 Command line :/usr/bin/fedora-review -n libsbml -p Buildroot used: fedora-21-x86_64 Active plugins: Java, C/C++, Python, Shell-api, Perl, Generic Disabled plugins: fonts, SugarActivity, Ocaml, Haskell, R, PHP, Ruby Disabled flags: EXARCH, EPEL5, BATCH, DISTTAG
(In reply to Michel Alexandre Salim from comment #23) > Issues: > ======= > - Packages have proper BuildRequires/Requires on jpackage-utils I think they have. There's BR:java-devel, and R:java-headless,jpackage-utils, which seems to agree with https://fedoraproject.org/wiki/Packaging:Java#BuildRequires_and_Requires. > - Javadocs are placed in %{_javadocdir}/%{name} (no -%{version} symlink) > Note: No javadoc subpackage present > See: https://fedoraproject.org/wiki/Packaging:Java#Javadoc_installation It's optional. I'd like to skip it for now, since the package is complicated enough anyway. > - Javadoc documentation files are generated and included in -javadoc > subpackage > Note: No javadoc subpackage present > See: https://fedoraproject.org/wiki/Packaging:Java#Javadoc_installation > - Large documentation must go in a -doc subpackage. Large could be size > (~1MB) > or number of files. > Note: Documentation size is 574330880 bytes in 12918 files. > See: > http://fedoraproject.org/wiki/Packaging/Guidelines#PackageDocumentation Freaking %doc macro. Fixed. > - libsbml-sharp needs to Requires: mono-core Done. > [!]: Package must own all directories that it creates. > Note: No known owner of /usr/lib64/libsbml > - java-libsbml needs to own %{_libdir}/libsbml Done. > Use %{_monodir} instead of %{_prefix}/lib/mono Done. > [!]: Requires correct, justified where necessary. > see libsbml-sharp note above Ack. > [?]: Package is not known to require an ExcludeArch tag. > note - it does but is marked as such -- this is fine Upstream has acknowledged the issue, but the fix might not be easy. > [!]: Large data in /usr/share should live in a noarch subpackage if package > is > arched. > Note: Arch-ed rpms have a total of 290048000 bytes in /usr/share ruby- > SBML-5.11.0-6.fc21.x86_64.rpm:289546240 Should be fixed now. > libsbml-devel.x86_64: E: incorrect-fsf-address > /usr/include/sbml/packages/render/sbml/ListOfCurveElements.h I'll ping upstram. > ruby-SBML.x86_64: W: dangling-relative-symlink > /usr/share/doc/libsbml/README-ruby.txt src/bindings/ruby/README.txt Yikes, fixed. > libsbml.src:344: W: macro-in-comment %{name} > libsbml.src:350: W: macro-in-comment %{name} Fixed. > libsbml.src:391: E: hardcoded-library-path in %{_prefix}/lib/mono/libsbmlcsP/ > 12 packages and 0 specfiles checked; 30 errors, 17 warnings. I think it's fine. Spec URL: http://in.waw.pl/~zbyszek/fedora/libsbml.spec SRPM URL: http://in.waw.pl/~zbyszek/fedora/libsbml-5.11.0-8.fc22.src.rpm koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=8810346 (build, but I hope it'll be fine)
Another version, with a fix from https://sourceforge.net/p/sbml/libsbml/393/. It builds on amd64, i386, arm, s390, s390x. There's some glitch in doc generation on s390/s390x. Spec URL: http://in.waw.pl/~zbyszek/fedora/libsbml.spec SRPM URL: http://in.waw.pl/~zbyszek/fedora/libsbml-5.11.0-9.fc22.src.rpm koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=8837245
Weird, fails to build locally on my F21 machine: Creating: libsbml.jar CMake Error at /builddir/build/BUILD/libSBML-5.11.0-Source/src/bindings/java/compile-native-files.cmake:66 (message): Could not compile java wrappers: warning: [options] bootstrap class path not set in conjunction with -source 1.5 warning: [options] source value 1.5 is obsolete and will be removed in a future release warning: [options] target value 1.5 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. java-files/org/sbml/libsbml/ListOfSpeciesReferenceGlyphs.java:86: error: cannot find symbol public SpeciesReferenceGlyph get(long n) { ^ symbol: class SpeciesReferenceGlyph location: class ListOfSpeciesReferenceGlyphs java-files/org/sbml/libsbml/ListOfSpeciesReferenceGlyphs.java:91: error: cannot find symbol public SpeciesReferenceGlyph get(String sid) { ^ symbol: class SpeciesReferenceGlyph location: class ListOfSpeciesReferenceGlyphs java-files/org/sbml/libsbml/ListOfSpeciesReferenceGlyphs.java:96: error: cannot find symbol public SpeciesReferenceGlyph remove(long n) { ^ symbol: class SpeciesReferenceGlyph location: class ListOfSpeciesReferenceGlyphs [SNIP - many more errors] java-files/org/sbml/libsbml/LayoutExtension.java:155: error: cannot find symbol return new SpeciesReferenceGlyph(cPtr, owner); ^ symbol: class SpeciesReferenceGlyph location: class LayoutExtension 50 errors 4 warnings src/bindings/java/CMakeFiles/binding_java_jar.dir/build.make:56: recipe for target 'src/bindings/java/libsbmlj.jar' failed make[2]: Leaving directory '/builddir/build/BUILD/libSBML-5.11.0-Source/build' CMakeFiles/Makefile2:2455: recipe for target 'src/bindings/java/CMakeFiles/binding_java_jar.dir/all' failed make[2]: *** [src/bindings/java/libsbmlj.jar] Error 1 make[1]: *** [src/bindings/java/CMakeFiles/binding_java_jar.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs....
Spec URL: http://in.waw.pl/~zbyszek/fedora/libsbml.spec SRPM URL: http://in.waw.pl/~zbyszek/fedora/libsbml-5.11.0-10.fc22.src.rpm It seems that the java build is broken. Antonio had a comment about that in his spec, which I removed because the parallel build seemed to work. I made it serial again for now.
All the remaining issues addressed -- this package is ACCEPTED Package Review ============== Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated [ ] = Manual review needed Issues: ======= - Javadocs are placed in %{_javadocdir}/%{name} (no -%{version} symlink) Note: No javadoc subpackage present See: https://fedoraproject.org/wiki/Packaging:Java#Javadoc_installation - Javadoc documentation files are generated and included in -javadoc subpackage Note: No javadoc subpackage present See: https://fedoraproject.org/wiki/Packaging:Java#Javadoc_installation ===== MUST items ===== C/C++: [x]: Package does not contain kernel modules. [x]: Package contains no static executables. [x]: Development (unversioned) .so files in -devel subpackage, if present. Note: Unversioned so-files in private %_libdir subdirectory (see attachment). Verify they are not in ld path. [x]: Header files in -devel subpackage, if present. [x]: ldconfig called in %post and %postun if required. [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: "LGPL", "GPL (v3 or later)", "Unknown or generated", "MIT/X11 (BSD like)", "*No copyright* LGPL (with incorrect FSF address)", "BSD (3 clause)", "LGPL (with incorrect FSF address)". 1118 files have unknown license. Detailed output of licensecheck in /home/michel/sources/fedora/reviews/1173159-libsbml/licensecheck.txt [x]: License file installed when any subpackage combination is installed. [x]: Package requires other packages for directories it uses. [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. [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. [x]: Large documentation must go in a -doc subpackage. Large could be size (~1MB) or number of files. Note: Documentation size is 276480 bytes in 6 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 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 Java: [x]: Bundled jar/class files should be removed before build Maven: [-]: If package contains pom.xml files install it (including depmaps) even when building with ant [x]: Old add_to_maven_depmap macro is not being used Perl: [x]: Package contains the mandatory BuildRequires and Requires:. Python: [x]: 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. [x]: Package meets the Packaging Guidelines::Python [x]: Package contains BR: python2-devel or python3-devel [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). [x]: Fully versioned dependency in subpackages if applicable. Note: No Requires: %{name}%{?_isa} = %{version}-%{release} in libsbml-doc [?]: Package functions as described. [x]: Latest version is packaged. [x]: Package does not include license text files separate from upstream. [x]: Patches link to upstream bugs/comments/lists or are otherwise justified. [-]: Scriptlets must be sane, if 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. [?]: 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]: The placement of pkgconfig(.pc) files are correct. [x]: SourceX is a working URL. [x]: Spec use %global instead of %define unless justified. Java: [-]: Packages are noarch unless they use JNI JNI is used [x]: Package uses upstream build method (ant/maven/etc.) ===== 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: libsbml-5.11.0-10.fc21.x86_64.rpm libsbml-devel-5.11.0-10.fc21.x86_64.rpm python-libsbml-5.11.0-10.fc21.x86_64.rpm python3-libsbml-5.11.0-10.fc21.x86_64.rpm perl-LibSBML-5.11.0-10.fc21.x86_64.rpm ruby-SBML-5.11.0-10.fc21.x86_64.rpm java-libsbml-5.11.0-10.fc21.x86_64.rpm octave-SBML-5.11.0-10.fc21.x86_64.rpm R-libSBML-5.11.0-10.fc21.x86_64.rpm libsbml-sharp-5.11.0-10.fc21.x86_64.rpm libsbml-doc-5.11.0-10.fc21.noarch.rpm libsbml-5.11.0-10.fc21.src.rpm libsbml-devel.x86_64: W: only-non-binary-in-usr-lib libsbml-devel.x86_64: W: no-documentation libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/ListOfCurveElements.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/ColorDefinition.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/GraphicalPrimitive1D.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/RelAbsVector.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/Polygon.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/Transformation.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/Style.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/Text.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/GlobalStyle.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/RenderGroup.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/Ellipse.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/GraphicalPrimitive2D.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/GradientBase.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/RadialGradient.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/GradientStop.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/RenderPoint.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/RenderInformationBase.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/RenderCurve.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/Rectangle.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/RenderCubicBezier.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/LineEnding.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/Image.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/LocalStyle.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/LinearGradient.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/GlobalRenderInformation.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/LocalRenderInformation.h libsbml-devel.x86_64: E: incorrect-fsf-address /usr/include/sbml/packages/render/sbml/Transformation2D.h python-libsbml.x86_64: W: no-documentation python3-libsbml.x86_64: W: no-documentation perl-LibSBML.x86_64: W: no-documentation ruby-SBML.x86_64: W: spelling-error Summary(en_US) libSBML -> Librium ruby-SBML.x86_64: W: spelling-error %description -l en_US libSBML -> Librium java-libsbml.x86_64: W: no-documentation octave-SBML.x86_64: W: spelling-error Summary(en_US) libSBML -> Librium octave-SBML.x86_64: W: spelling-error %description -l en_US libSBML -> Librium octave-SBML.x86_64: W: no-documentation R-libSBML.x86_64: W: no-documentation R-libSBML.x86_64: E: zero-length /usr/lib64/R/library/libSBML/help/libSBML.rdb R-libSBML.x86_64: E: zero-length /usr/lib64/R/library/libSBML/help/AnIndex libsbml-sharp.x86_64: W: no-documentation libsbml.src:181: W: unversioned-explicit-provides bundled(jquery) 12 packages and 0 specfiles checked; 29 errors, 14 warnings. Rpmlint (installed packages) ---------------------------- Cannot parse rpmlint output: Requires -------- python3-libsbml (rpmlib, GLIBC filtered): libbz2.so.1()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libminizip.so.1()(64bit) libpython3.4m.so.1.0()(64bit) libsbml(x86-64) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.1)(64bit) libz.so.1()(64bit) python(abi) rtld(GNU_HASH) perl-LibSBML (rpmlib, GLIBC filtered): libbz2.so.1()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libminizip.so.1()(64bit) libperl.so.5.18()(64bit) libsbml(x86-64) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.1)(64bit) libz.so.1()(64bit) perl(:MODULE_COMPAT_5.18.4) perl(DynaLoader) perl(Exporter) perl(base) perl(vars) rtld(GNU_HASH) libsbml-sharp (rpmlib, GLIBC filtered): libbz2.so.1()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libminizip.so.1()(64bit) libsbml(x86-64) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.1)(64bit) libz.so.1()(64bit) mono-core rtld(GNU_HASH) libsbml (rpmlib, GLIBC filtered): /sbin/ldconfig libbz2.so.1()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libminizip.so.1()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.1)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) libsbml-doc (rpmlib, GLIBC filtered): libsbml ruby-SBML (rpmlib, GLIBC filtered): libbz2.so.1()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libminizip.so.1()(64bit) libruby.so.2.1()(64bit) libsbml(x86-64) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.1)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) ruby(release) octave-SBML (rpmlib, GLIBC filtered): libbz2.so.1()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) libm.so.6()(64bit) libminizip.so.1()(64bit) liboctave.so.2()(64bit) liboctinterp.so.2()(64bit) libsbml(x86-64) libsbml.so.5()(64bit) libstdc++.so.6()(64bit) libxml2.so.2()(64bit) libz.so.1()(64bit) octave octave(api) rtld(GNU_HASH) python-libsbml (rpmlib, GLIBC filtered): libbz2.so.1()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libminizip.so.1()(64bit) libpython2.7.so.1.0()(64bit) libsbml(x86-64) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.1)(64bit) libz.so.1()(64bit) python(abi) rtld(GNU_HASH) java-libsbml (rpmlib, GLIBC filtered): java-headless jpackage-utils libbz2.so.1()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libminizip.so.1()(64bit) libsbml(x86-64) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.1)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) R-libSBML (rpmlib, GLIBC filtered): R-core libR.so()(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libminizip.so.1()(64bit) libsbml(x86-64) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.1)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) libsbml-devel (rpmlib, GLIBC filtered): /usr/bin/pkg-config libsbml(x86-64) libsbml.so.5()(64bit) pkgconfig(libxml-2.0) Provides -------- python3-libsbml: python3-libsbml python3-libsbml(x86-64) perl-LibSBML: perl(LibSBML) perl(LibSBML::ASTBase) perl(LibSBML::ASTBasePlugin) perl(LibSBML::ASTNode) perl(LibSBML::ASTNodeList) perl(LibSBML::AlgebraicRule) perl(LibSBML::AssignmentRule) perl(LibSBML::Association) perl(LibSBML::BoundingBox) perl(LibSBML::CVTerm) perl(LibSBML::CVTermList) perl(LibSBML::CobraToFbcConverter) perl(LibSBML::ColorDefinition) perl(LibSBML::CompBase) perl(LibSBML::CompExtension) perl(LibSBML::CompFlatteningConverter) perl(LibSBML::CompModelPlugin) perl(LibSBML::CompPkgNamespaces) perl(LibSBML::CompSBMLDocumentPlugin) perl(LibSBML::CompSBasePlugin) perl(LibSBML::Compartment) perl(LibSBML::CompartmentGlyph) perl(LibSBML::CompartmentType) perl(LibSBML::Constraint) perl(LibSBML::ConversionOption) perl(LibSBML::ConversionProperties) perl(LibSBML::CubicBezier) perl(LibSBML::Curve) perl(LibSBML::Date) perl(LibSBML::DateList) perl(LibSBML::DefaultTerm) perl(LibSBML::Delay) perl(LibSBML::Deletion) perl(LibSBML::Dimensions) perl(LibSBML::ElementFilter) perl(LibSBML::Ellipse) perl(LibSBML::Event) perl(LibSBML::EventAssignment) perl(LibSBML::ExternalModelDefinition) perl(LibSBML::FbcExtension) perl(LibSBML::FbcModelPlugin) perl(LibSBML::FbcPkgNamespaces) perl(LibSBML::FbcSpeciesPlugin) perl(LibSBML::FbcToCobraConverter) perl(LibSBML::FluxBound) perl(LibSBML::FluxObjective) perl(LibSBML::FunctionDefinition) perl(LibSBML::FunctionTerm) perl(LibSBML::GeneAssociation) perl(LibSBML::GeneralGlyph) perl(LibSBML::GlobalRenderInformation) perl(LibSBML::GlobalStyle) perl(LibSBML::GradientBase) perl(LibSBML::GradientStop) perl(LibSBML::GraphicalObject) perl(LibSBML::GraphicalPrimitive1D) perl(LibSBML::GraphicalPrimitive2D) perl(LibSBML::ISBMLExtensionNamespaces) perl(LibSBML::IdList) perl(LibSBML::IdentifierTransformer) perl(LibSBML::Image) perl(LibSBML::InitialAssignment) perl(LibSBML::Input) perl(LibSBML::KineticLaw) perl(LibSBML::L3ParserSettings) perl(LibSBML::Layout) perl(LibSBML::LayoutExtension) perl(LibSBML::LayoutModelPlugin) perl(LibSBML::LayoutPkgNamespaces) perl(LibSBML::LayoutSpeciesReferencePlugin) perl(LibSBML::LineEnding) perl(LibSBML::LineSegment) perl(LibSBML::LinearGradient) perl(LibSBML::ListOf) perl(LibSBML::ListOfColorDefinitions) perl(LibSBML::ListOfCompartmentGlyphs) perl(LibSBML::ListOfCompartmentTypes) perl(LibSBML::ListOfCompartments) perl(LibSBML::ListOfConstraints) perl(LibSBML::ListOfCurveElements) perl(LibSBML::ListOfDeletions) perl(LibSBML::ListOfDrawables) perl(LibSBML::ListOfEventAssignments) perl(LibSBML::ListOfEvents) perl(LibSBML::ListOfExternalModelDefinitions) perl(LibSBML::ListOfFluxBounds) perl(LibSBML::ListOfFluxObjectives) perl(LibSBML::ListOfFunctionDefinitions) perl(LibSBML::ListOfFunctionTerms) perl(LibSBML::ListOfGeneAssociations) perl(LibSBML::ListOfGlobalRenderInformation) perl(LibSBML::ListOfGlobalStyles) perl(LibSBML::ListOfGradientDefinitions) perl(LibSBML::ListOfGradientStops) perl(LibSBML::ListOfGraphicalObjects) perl(LibSBML::ListOfInitialAssignments) perl(LibSBML::ListOfInputs) perl(LibSBML::ListOfLayouts) perl(LibSBML::ListOfLineEndings) perl(LibSBML::ListOfLineSegments) perl(LibSBML::ListOfLocalParameters) perl(LibSBML::ListOfLocalRenderInformation) perl(LibSBML::ListOfLocalStyles) perl(LibSBML::ListOfModelDefinitions) perl(LibSBML::ListOfObjectives) perl(LibSBML::ListOfOutputs) perl(LibSBML::ListOfParameters) perl(LibSBML::ListOfPorts) perl(LibSBML::ListOfQualitativeSpecies) perl(LibSBML::ListOfReactionGlyphs) perl(LibSBML::ListOfReactions) perl(LibSBML::ListOfReferenceGlyphs) perl(LibSBML::ListOfReplacedElements) perl(LibSBML::ListOfRules) perl(LibSBML::ListOfSpecies) perl(LibSBML::ListOfSpeciesGlyphs) perl(LibSBML::ListOfSpeciesReferenceGlyphs) perl(LibSBML::ListOfSpeciesReferences) perl(LibSBML::ListOfSpeciesTypes) perl(LibSBML::ListOfSubmodels) perl(LibSBML::ListOfTextGlyphs) perl(LibSBML::ListOfTransitions) perl(LibSBML::ListOfUnitDefinitions) perl(LibSBML::ListOfUnits) perl(LibSBML::LocalParameter) perl(LibSBML::LocalRenderInformation) perl(LibSBML::LocalStyle) perl(LibSBML::Model) perl(LibSBML::ModelCreator) perl(LibSBML::ModelCreatorList) perl(LibSBML::ModelDefinition) perl(LibSBML::ModelHistory) perl(LibSBML::ModifierSpeciesReference) perl(LibSBML::OFStream) perl(LibSBML::OStream) perl(LibSBML::OStringStream) perl(LibSBML::Objective) perl(LibSBML::Output) perl(LibSBML::Parameter) perl(LibSBML::Point) perl(LibSBML::Polygon) perl(LibSBML::Port) perl(LibSBML::Priority) perl(LibSBML::QualExtension) perl(LibSBML::QualModelPlugin) perl(LibSBML::QualPkgNamespaces) perl(LibSBML::QualitativeSpecies) perl(LibSBML::RDFAnnotationParser) perl(LibSBML::RadialGradient) perl(LibSBML::RateRule) perl(LibSBML::Reaction) perl(LibSBML::ReactionGlyph) perl(LibSBML::Rectangle) perl(LibSBML::ReferenceGlyph) perl(LibSBML::RelAbsVector) perl(LibSBML::RenderCubicBezier) perl(LibSBML::RenderCurve) perl(LibSBML::RenderExtension) perl(LibSBML::RenderGraphicalObjectPlugin) perl(LibSBML::RenderGroup) perl(LibSBML::RenderInformationBase) perl(LibSBML::RenderLayoutPlugin) perl(LibSBML::RenderListOfLayoutsPlugin) perl(LibSBML::RenderPkgNamespaces) perl(LibSBML::RenderPoint) perl(LibSBML::ReplacedBy) perl(LibSBML::ReplacedElement) perl(LibSBML::Replacing) perl(LibSBML::Rule) perl(LibSBML::SBMLConstructorException) perl(LibSBML::SBMLConverter) perl(LibSBML::SBMLConverterRegistry) perl(LibSBML::SBMLDocument) perl(LibSBML::SBMLDocumentPlugin) perl(LibSBML::SBMLError) perl(LibSBML::SBMLErrorLog) perl(LibSBML::SBMLExtension) perl(LibSBML::SBMLExtensionException) perl(LibSBML::SBMLExtensionRegistry) perl(LibSBML::SBMLExternalValidator) perl(LibSBML::SBMLFileResolver) perl(LibSBML::SBMLFunctionDefinitionConverter) perl(LibSBML::SBMLIdConverter) perl(LibSBML::SBMLInferUnitsConverter) perl(LibSBML::SBMLInitialAssignmentConverter) perl(LibSBML::SBMLLevelVersionConverter) perl(LibSBML::SBMLLocalParameterConverter) perl(LibSBML::SBMLNamespaces) perl(LibSBML::SBMLNamespacesList) perl(LibSBML::SBMLReactionConverter) perl(LibSBML::SBMLReader) perl(LibSBML::SBMLResolver) perl(LibSBML::SBMLResolverRegistry) perl(LibSBML::SBMLRuleConverter) perl(LibSBML::SBMLStripPackageConverter) perl(LibSBML::SBMLTransforms) perl(LibSBML::SBMLUnitsConverter) perl(LibSBML::SBMLUri) perl(LibSBML::SBMLValidator) perl(LibSBML::SBMLWriter) perl(LibSBML::SBO) perl(LibSBML::SBase) perl(LibSBML::SBaseExtensionPoint) perl(LibSBML::SBaseList) perl(LibSBML::SBasePlugin) perl(LibSBML::SBaseRef) perl(LibSBML::SimpleSpeciesReference) perl(LibSBML::Species) perl(LibSBML::SpeciesGlyph) perl(LibSBML::SpeciesReference) perl(LibSBML::SpeciesReferenceGlyph) perl(LibSBML::SpeciesType) perl(LibSBML::StoichiometryMath) perl(LibSBML::StringSet) perl(LibSBML::Style) perl(LibSBML::Submodel) perl(LibSBML::SyntaxChecker) perl(LibSBML::Text) perl(LibSBML::TextGlyph) perl(LibSBML::Transformation) perl(LibSBML::Transformation2D) perl(LibSBML::Transition) perl(LibSBML::Trigger) perl(LibSBML::Unit) perl(LibSBML::UnitDefinition) perl(LibSBML::XMLAttributes) perl(LibSBML::XMLConstructorException) perl(LibSBML::XMLError) perl(LibSBML::XMLErrorLog) perl(LibSBML::XMLInputStream) perl(LibSBML::XMLNamespaces) perl(LibSBML::XMLNode) perl(LibSBML::XMLOutputStream) perl(LibSBML::XMLOwningOutputFileStream) perl(LibSBML::XMLOwningOutputStringStream) perl(LibSBML::XMLToken) perl(LibSBML::XMLTriple) perl(LibSBML::double_array) perl(LibSBML::int_array) perl(LibSBMLc) perl-LibSBML perl-LibSBML(x86-64) libsbml-sharp: libsbml-sharp libsbml-sharp(x86-64) libsbmlcs.so()(64bit) libsbml: libsbml libsbml(x86-64) libsbml.so.5()(64bit) libsbml-doc: bundled(jquery) libsbml-doc ruby-SBML: libSBML.so()(64bit) ruby(SBML) ruby-SBML ruby-SBML(x86-64) octave-SBML: octave-SBML octave-SBML(x86-64) python-libsbml: python-libsbml python-libsbml(x86-64) java-libsbml: java-libsbml java-libsbml(x86-64) libsbmlj.so()(64bit) R-libSBML: R-libSBML R-libSBML(x86-64) libSBML.so()(64bit) libsbml-devel: libsbml-devel libsbml-devel(x86-64) pkgconfig(libsbml) Unversioned so-files -------------------- python-libsbml: /usr/lib64/python2.7/site-packages/libsbml/_libsbml.so python3-libsbml: /usr/lib64/python3.4/site-packages/libsbml/_libsbml.so perl-LibSBML: /usr/lib64/perl5/vendor_perl/auto/libSBML/LibSBML.so ruby-SBML: /usr/lib64/ruby/vendor_ruby/libSBML.so java-libsbml: /usr/lib64/libsbml/libsbmlj.so R-libSBML: /usr/lib64/R/library/libSBML/libs/libSBML.so libsbml-sharp: /usr/lib/mono/libsbmlcsP/libsbmlcs.so Source checksums ---------------- http://sourceforge.net/projects/sbml/files/libsbml/5.11.0/stable/libSBML-5.11.0-core-plus-packages-src.tar.gz : CHECKSUM(SHA256) this package : b21931ca7461494915c617b30d4a9f2cafe831d6ce74989b3e5874e6e3c3f72b CHECKSUM(SHA256) upstream package : b21931ca7461494915c617b30d4a9f2cafe831d6ce74989b3e5874e6e3c3f72b http://sourceforge.net/projects/sbml/files/libsbml/5.11.0/experimental/source/render-5.11.0-beta-1.zip : CHECKSUM(SHA256) this package : 5ed5cec563260201b958d790543f5dac8a516a088c4ced52f85cf5fc9e495e69 CHECKSUM(SHA256) upstream package : 5ed5cec563260201b958d790543f5dac8a516a088c4ced52f85cf5fc9e495e69 Generated by fedora-review 0.5.2 (63c24cb) last change: 2014-07-14 Command line :/usr/bin/fedora-review -b 1173159 Buildroot used: fedora-21-x86_64 Active plugins: Java, C/C++, Python, Shell-api, Perl, Generic Disabled plugins: fonts, SugarActivity, Ocaml, Haskell, R, PHP, Ruby Disabled flags: EXARCH, EPEL5, BATCH, DISTTAG
Thank you for the review! New Package SCM Request ======================= Package Name: libsbml Short Description: Systems Biology Markup Language Library Upstream URL: http://schmidt.nuigalway.ie/tomlib/ Owners: zbyszek sagitter Branches: f21 f20 InitialCC:
New Package SCM Request ======================= Package Name: libsbml Short Description: Systems Biology Markup Language Library Upstream URL: http://sbml.org/Software/libSBML Owners: zbyszek sagitter Branches: f21 f20 InitialCC:
Git done (by process-git-requests).
libsbml-5.11.0-11.fc21 has been submitted as an update for Fedora 21. https://admin.fedoraproject.org/updates/libsbml-5.11.0-11.fc21
(In reply to Fedora Update System from comment #32) > libsbml-5.11.0-11.fc21 has been submitted as an update for Fedora 21. > https://admin.fedoraproject.org/updates/libsbml-5.11.0-11.fc21 libsbml is not built in rawhide.
I know ;) If segfaults in tests fairly reliably. I was hoping that this might be caused by some gcc issues and resolve itself on its own. If you could take a look, it'd be great.
libsbml-5.11.0-11.fc21 has been pushed to the Fedora 21 testing repository.
libsbml-5.11.0-11.fc21 has been pushed to the Fedora 21 stable repository.