Fedora Account System
Red Hat Associate
Red Hat Customer
Spec URL: https://sagitter.fedorapeople.org/libSEDML/libSEDML.spec SRPM URL: https://sagitter.fedorapeople.org/libSEDML/libSEDML-0.3.0-1.20141230gitb455cd.fc21.src.rpm Description: C# library that fully supports SED-ML for SBML as well as CellML models for creation of the description just as for the execution of Simulation Experiments. This project makes use of libSBML XML layer as well as code generation as starting point to produce a library for reading and writing of SED-ML models. Fedora Account System Username: sagitter
Spec URL: https://sagitter.fedorapeople.org/libSEDML/libSEDML.spec SRPM URL: https://sagitter.fedorapeople.org/libSEDML/libSEDML-0.3.0-2.20141230gitb455cd.fc21.src.rpm Excluded the packaging of the static file.
Spec URL: https://sagitter.fedorapeople.org/libSEDML/libsedml.spec SRPM URL: https://sagitter.fedorapeople.org/libSEDML/libsedml-0.3.0-3.20141230gitb455cd.fc21.src.rpm
Spec URL: https://sagitter.fedorapeople.org/libSEDML/libsedml.spec SRPM URL: https://sagitter.fedorapeople.org/libSEDML/libsedml-0.3.0-4.20141230gitb455cd.fc21.src.rpm - Set installation directory of the java library
I'll review this once we get libsbml in proper shape again.
(In reply to Zbigniew Jędrzejewski-Szmek from comment #4) > I'll review this once we get libsbml in proper shape again. Thank you. libsbml-5.11.4 has been released recently but there are still problems in Fedora >22. I hope to fix them as soon as possible.
I'm going to update this package to the latest commit.
Will you be preparing an update, or should I review this version? Looking at the spec file, at least the %descriptions are wrong: they are all the same.
(In reply to Zbigniew Jędrzejewski-Szmek from comment #7) > Will you be preparing an update, or should I review this version? I'm preparing an update. > > Looking at the spec file, at least the %descriptions are wrong: they are all > the same. Indeed.
Please, wait that latest libsbml build finishes on rawhide. Spec URL: https://sagitter.fedorapeople.org/libSEDML/libsedml.spec SRPM URL: https://sagitter.fedorapeople.org/libSEDML/libsedml-0.3.0-5.20150422git235bb5.fc22.src.rpm
- Set CSHARP compiler on F23 Spec URL: https://sagitter.fedorapeople.org/libSEDML/libsedml.spec SRPM URL: https://sagitter.fedorapeople.org/libSEDML/libsedml-0.3.0-6.20150422git235bb5.fc22.src.rpm
%description: please expand SED-ML abbreviation and/or add a few words explaining what this package does in a way that is understandable for a lay person. %package devel %description: it's enough to say This package contains headers for %{name}. Shouldn't python-SEDML be python-libsedml? This would match python-sbml. https://fedoraproject.org/wiki/Packaging:NamingGuidelines#Addon_Packages_.28python_modules.29 says: "When in doubt, use the name of the module that you type to import it in a script." Also java-libsedml instead of java-SEDML? I think using capitalized SEDML only makes sense if the actual module name contains that. For ruby, perl, R that is true, for other bindings not. What about python3 subpackage? - Packages have proper BuildRequires/Requires on jpackage-utils Binary package needs that according to https://fedoraproject.org/wiki/Packaging:Java#BuildRequires_and_Requires. According to https://fedoraproject.org/wiki/Packaging:Mono, gacutil should be called in %build. I'd use the same license and doc dirs for all subpackages: %global _docdir_fmt %{name}. Shouldn't libsedml-sharp require mono-core? Use %make_install macro to replace make DESTDIR=$RPM_BUILD_ROOT install ?
(In reply to Zbigniew Jędrzejewski-Szmek from comment #11) > %description: please expand SED-ML abbreviation and/or add a few words > explaining what this package does in a way that is understandable for a lay > person. > > %package devel %description: it's enough to say > This package contains headers for %{name}. > > Shouldn't python-SEDML be python-libsedml? This would match python-sbml. > https://fedoraproject.org/wiki/Packaging:NamingGuidelines#Addon_Packages_. > 28python_modules.29 says: "When in doubt, use the name of the module that > you type to import it in a script." > > Also java-libsedml instead of java-SEDML? I think using capitalized SEDML > only makes sense if the actual module name contains that. For ruby, perl, R > that is true, for other bindings not. Okay. > > What about python3 subpackage? I don't know if Python3 is supported. I will ask to upstream. > > - Packages have proper BuildRequires/Requires on jpackage-utils > Binary package needs that according to > https://fedoraproject.org/wiki/Packaging:Java#BuildRequires_and_Requires. Okay. > > According to https://fedoraproject.org/wiki/Packaging:Mono, gacutil should > be called in %build. You meant in %install. gacutil command fails: + mkdir -p /home/sagitter/rpmbuild/BUILDROOT/libsedml-0.3.0-7.20150422git235bb5.fc22.x86_64/usr/lib/mono/gac + gacutil -i build/bindings/csharp/libsedmlcsP.dll -f -package libsedml-sharp -root /home/sagitter/rpmbuild/BUILDROOT/libsedml-0.3.0-7.20150422git235bb5.fc22.x86_64/usr/lib Failure adding assembly build/bindings/csharp/libsedmlcsP.dll to the cache: Attempt to install an assembly without a strong name If i remember fine, this error appeared also in libsbml ('gacutil' call is missing in libsbml, i see). Do you know how to fix it? > > I'd use the same license and doc dirs for all subpackages: %global > _docdir_fmt %{name}. > > Shouldn't libsedml-sharp require mono-core? Okay. > > Use %make_install macro to replace make DESTDIR=$RPM_BUILD_ROOT install ? They are equivalent.
(In reply to Antonio Trande from comment #12) > > What about python3 subpackage? > I don't know if Python3 is supported. > I will ask to upstream. SWIG supports both, so the code at least supports it. Would be a shame not to have it. > > According to https://fedoraproject.org/wiki/Packaging:Mono, gacutil should > > be called in %build. > > You meant in %install. > gacutil command fails: > > + mkdir -p > /home/sagitter/rpmbuild/BUILDROOT/libsedml-0.3.0-7.20150422git235bb5.fc22. > x86_64/usr/lib/mono/gac > + gacutil -i build/bindings/csharp/libsedmlcsP.dll -f -package > libsedml-sharp -root > /home/sagitter/rpmbuild/BUILDROOT/libsedml-0.3.0-7.20150422git235bb5.fc22. > x86_64/usr/lib > Failure adding assembly build/bindings/csharp/libsedmlcsP.dll to the cache: > Attempt to install an assembly without a strong name > > If i remember fine, this error appeared also in libsbml ('gacutil' call is > missing in libsbml, i see). Do you know how to fix it? I copied the mono subpackage from your spec. I know less than you ;) OK, let's keep it as is. > > Use %make_install macro to replace make DESTDIR=$RPM_BUILD_ROOT install ? > They are equivalent. I know, %make_install is just shorter.
(In reply to Zbigniew Jędrzejewski-Szmek from comment #13) > (In reply to Antonio Trande from comment #12) > > > What about python3 subpackage? > > I don't know if Python3 is supported. > > I will ask to upstream. > SWIG supports both, so the code at least supports it. Would be a shame not > to have it. I will. > > > > According to https://fedoraproject.org/wiki/Packaging:Mono, gacutil should > > > be called in %build. > > > > You meant in %install. > > gacutil command fails: > > > > + mkdir -p > > /home/sagitter/rpmbuild/BUILDROOT/libsedml-0.3.0-7.20150422git235bb5.fc22. > > x86_64/usr/lib/mono/gac > > + gacutil -i build/bindings/csharp/libsedmlcsP.dll -f -package > > libsedml-sharp -root > > /home/sagitter/rpmbuild/BUILDROOT/libsedml-0.3.0-7.20150422git235bb5.fc22. > > x86_64/usr/lib > > Failure adding assembly build/bindings/csharp/libsedmlcsP.dll to the cache: > > Attempt to install an assembly without a strong name > > > > If i remember fine, this error appeared also in libsbml ('gacutil' call is > > missing in libsbml, i see). Do you know how to fix it? > I copied the mono subpackage from your spec. I know less than you ;) > OK, let's keep it as is. https://github.com/fbergmann/libSEDML/issues/10#issuecomment-109584374
- Description improved - Sub-packages main name changed to libsedml for Python, Java - Packaged Python3 bindings Spec URL: https://sagitter.fedorapeople.org/libSEDML/libsedml.spec SRPM URL: https://sagitter.fedorapeople.org/libSEDML/libsedml-0.3.0-7.20150422git235bb5.fc22.src.rpm
====== Questions/issues ====== python2-libsedml name is a violation of guidelines, imho. It should be python-libsedml. Why does java-libsedml require libsedml-devel? Shouldn't it be libsedml? > I'd use the same license and doc dirs for all subpackages: %global > _docdir_fmt %{name}. In particular, since every sub package has the same set of files, if a user installed all subpackages, and they wanted to look at the documentation, they would simply waste time before they realized that all the READMEs are identical. fedora-review output: ===== MUST items ===== C/C++: [-]: Provides: bundled(gnulib) in place as required. I don't see gnulib being used anywhere. [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. BSD two-clause. [x]: License field in the package spec file matches the actual license. [x]: License file installed when any subpackage combination is installed. [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. [-]: Large documentation must go in a -doc subpackage. Large could be size (~1MB) or number of files. Note: Documentation size is 71680 bytes in 14 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 %license. [x]: Package requires other packages for directories it uses. [x]: Package must own all directories that it creates. [x]: Package does not own files or directories owned by other packages. [x]: All build dependencies are listed in BuildRequires, except for any that are listed in the exceptions section of Packaging Guidelines. [x]: Package uses either %{buildroot} or $RPM_BUILD_ROOT [x]: Package does not run rm -rf %{buildroot} (or $RPM_BUILD_ROOT) at the beginning of %install. [x]: Macros in Summary, %description expandable at SRPM build time. [x]: Dist tag is present. [x]: Package does not contain duplicates in %files. [x]: Permissions on files are set properly. [x]: Package use %makeinstall only when make install DESTDIR=... doesn't work. [x]: Package is named using only allowed ASCII characters. [x]: Package does not use a name that already exists. [x]: Package is not relocatable. [x]: Sources used to build the package match the upstream source, as provided in the spec URL. [x]: Spec file name must match the spec package %{name}, in the format %{name}.spec. [x]: File names are valid UTF-8. [x]: Packages must not store files under /srv, /opt or /usr/local Java: [x]: Bundled jar/class files should be removed before build Maven: [-]: If package contains pom.xml files install it (including metadata) 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: [-]: Binary eggs must be removed in %prep [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 (apart from the naming issue) [x]: Package contains BR: python2-devel or python3-devel Rpmlint ------- Checking: libsedml-0.3.0-7.20150422git235bb5.fc23.x86_64.rpm libsedml-devel-0.3.0-7.20150422git235bb5.fc23.x86_64.rpm python2-libsedml-0.3.0-7.20150422git235bb5.fc23.x86_64.rpm python3-libsedml-0.3.0-7.20150422git235bb5.fc23.x86_64.rpm java-libsedml-0.3.0-7.20150422git235bb5.fc23.x86_64.rpm perl-SEDML-0.3.0-7.20150422git235bb5.fc23.x86_64.rpm ruby-SEDML-0.3.0-7.20150422git235bb5.fc23.x86_64.rpm R-SEDML-0.3.0-7.20150422git235bb5.fc23.x86_64.rpm libsedml-sharp-0.3.0-7.20150422git235bb5.fc23.x86_64.rpm libsedml-0.3.0-7.20150422git235bb5.fc23.src.rpm libsedml.x86_64: W: spelling-error %description -l en_US libSBML -> Librium libsedml-devel.x86_64: W: only-non-binary-in-usr-lib libsedml-devel.x86_64: W: no-documentation java-libsedml.x86_64: W: no-documentation ruby-SEDML.x86_64: W: spelling-error %description -l en_US libSEDML -> licensed R-SEDML.x86_64: E: zero-length /usr/lib64/R/library/libSEDML/help/libSEDML.rdb R-SEDML.x86_64: E: zero-length /usr/lib64/R/library/libSEDML/help/AnIndex libsedml-sharp.x86_64: W: spelling-error %description -l en_US csharp -> sharp, c sharp, cs harp libsedml.src: W: spelling-error %description -l en_US libSBML -> Librium 10 packages and 0 specfiles checked; 2 errors, 7 warnings. Unversioned so-files -------------------- python2-libsedml: /usr/lib64/python2.7/site-packages/libsedml/_libsedml.so python3-libsedml: /usr/lib64/python3.4/site-packages/libsedml/_libsedml.so java-libsedml: /usr/lib64/libsedml/libsedmlj.so perl-SEDML: /usr/lib64/perl5/vendor_perl/auto/libSEDML/LibSEDML.so ruby-SEDML: /usr/lib64/ruby/vendor_ruby/libSEDML.so R-SEDML: /usr/lib64/R/library/libSEDML/libs/libSEDML.so libsedml-sharp: /usr/lib/mono/libsedmlcsP/libsedmlcs.so Looks OK.
(In reply to Zbigniew Jędrzejewski-Szmek from comment #16) > ====== Questions/issues ====== > > python2-libsedml name is a violation of guidelines, imho. It should be > python-libsedml. You're right. > > Why does java-libsedml require libsedml-devel? Shouldn't it be libsedml? Neither of the two. I thought that Java library was linked to a library in /usr/lib?; actually java provides an own 'libsbmlj.so' installed in /usr/lib?. See http://sbml.org/Software/libSBML/docs/cpp-api/libsbml-installation.html#locations > > > I'd use the same license and doc dirs for all subpackages: %global > > _docdir_fmt %{name}. > In particular, since every sub package has the same set of files, if a user > installed all subpackages, and they wanted to look at the documentation, > they would simply waste time before they realized that all the READMEs are > identical. > Done. Spec URL: https://sagitter.fedorapeople.org/libSEDML/libsedml.spec SRPM URL: https://sagitter.fedorapeople.org/libSEDML/libsedml-0.3.0-8.20150422git235bb5.fc22.src.rpm
(In reply to Antonio Trande from comment #17) > > > > Why does java-libsedml require libsedml-devel? Shouldn't it be libsedml? > > Neither of the two. I thought that Java library was linked to a library in > /usr/lib?; actually java provides an own 'libsbmlj.so' installed in > /usr/lib?. See > http://sbml.org/Software/libSBML/docs/cpp-api/libsbml-installation. > html#locations > Sorry, that link is to libsbml.
Looks good. Package is APPROVED.
Thank you very much. New Package SCM Request ======================= Package Name: libsedml Short Description: Library that fully supports SED-ML for SBML Upstream URL: https://github.com/fbergmann/libSEDML Owners: sagitter Branches: f22
Git done (by process-git-requests).
libsedml-0.3.0-8.20150422git235bb5.fc22 has been submitted as an update for Fedora 22. https://admin.fedoraproject.org/updates/libsedml-0.3.0-8.20150422git235bb5.fc22
libsedml-0.3.0-8.20150422git235bb5.fc22 has been pushed to the Fedora 22 testing repository.
libsedml-0.3.0-10.20150422git235bb5.fc22 has been submitted as an update for Fedora 22. https://admin.fedoraproject.org/updates/libsedml-0.3.0-10.20150422git235bb5.fc22
libsedml-0.3.0-12.20150422git235bb5.fc22 has been submitted as an update for Fedora 22. https://admin.fedoraproject.org/updates/libsedml-0.3.0-12.20150422git235bb5.fc22
libsedml-0.3.0-12.20150422git235bb5.fc22 has been pushed to the Fedora 22 stable repository. If problems still persist, please make note of it in this bug report.