Spec URL: http://in.waw.pl/~zbyszek/fedora/bionetgen.spec SRPM URL: http://in.waw.pl/~zbyszek/fedora/bionetgen-2.2.5-1.fc22.src.rpm Description: BioNetGen is software for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks. The BioNetGen language has recently been extended to include explicit representation of compartments. A review of methods for rule-based modeling is available in Science Signaling (Sci. STKE, 18 July 2006, Issue 344, p. re6). BioNetGen is presently a mixture of Perl and C++. Network generation is currently implemented in Perl, the network simulator is C++, and a new language parser is being developed with ANTLR. Fedora Account System Username: zbyszek Some notes: the package makes all perl modules top-level, so they are not really suitable for use from outside. A huge __provides_exclude/__requires_exclude is necessary to work around this. I'll try to work with upstream to fix that.
Copr build: https://copr-fe.cloud.fedoraproject.org/coprs/zbyszek/neurord/build/61114/
As mentioned in the mailing list, I can review all these three packages. We have break coming up (from Thursday) and I can review it that day. I am assigning the bugs to myself. If someone wants to go review the packages before I get to it, please go ahead.
Hi, here is the detailed review. Package Review ============== Legend: [x] = Pass, [!] = Fail, [-] = Not applicable, [?] = Not evaluated [ ] = Manual review needed Issues: ======= - 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. Note: Cannot find LICENSE.txt in rpm(s) See: http://fedoraproject.org/wiki/Packaging/LicensingGuidelines#License_Text ---> Bogus warning. License is installed using %license macro and hence no shown under %doc. ===== MUST items ===== C/C++: [x]: Package does not contain kernel modules. [x]: Package contains no static executables. [x]: Package does not contain any libtool archives (.la) [x]: Rpath absent or only used for internal libs. Generic: [x]: Package is licensed with an open-source compatible license and meets other legal requirements as defined in the legal section of Packaging Guidelines. [x]: License field in the package spec file matches the actual license. Note: Checking patched sources after %prep for licenses. Licenses found: "MIT/X11 (BSD like)", "BSD (2 clause)", "GPL (v2 or later)", "GPL (v3 or later)", "Unknown or generated". 349 files have unknown license. Detailed output of licensecheck in /home/mukundan/ownCloud/pkg_reviews/1167467-bionetgen/licensecheck.txt ---> This looks fine. [x]: License file installed when any subpackage combination is installed. [x]: Package must own all directories that it creates. Note: Directories without known owners: /usr/share/licenses ---> Bogus warning. Directory provided by filesystem package in rawhide. [x]: %build honors applicable compiler flags or justifies otherwise. [x]: Package contains no bundled libraries without FPC exception. ---> depends on sundials, bundled items removed in prep. [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 [-]: 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 30720 bytes in 3 files. [x]: Package complies to the Packaging Guidelines [x]: Package successfully compiles and builds into binary rpms on at least one supported primary architecture. [x]: Package installs properly. [x]: Rpmlint is run on all rpms the build produces. Note: There are rpmlint messages (see attachment). [x]: Package requires other packages for directories it uses. [x]: Package 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 Perl: [x]: Package contains the mandatory BuildRequires and Requires:. ===== SHOULD items ===== Generic: [x]: 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 bionetgen- perl [x]: Package functions as described. [x]: Latest version is packaged. [x]: Package does not include license text files separate from upstream. [x]: Description and summary sections in the package spec file contains translations for supported Non-English languages, if available. [x]: Package should compile and build into binary rpms on all supported architectures. [x]: %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]: Uses parallel make %{?_smp_mflags} macro. [x]: SourceX is a working URL. [x]: Spec use %global instead of %define unless justified. ===== EXTRA items ===== Generic: [!]: Package should not use obsolete m4 macros Note: Some obsoleted macros found, see the attachment. See: https://fedorahosted.org/FedoraReview/wiki/AutoTools ---> Changing this to [x]. As far as I can tell from the configure.ac file and auto{conf/make} docs, all else seems fine. Spec file correctly changes some of the obsolete macros. From the spec, sed -i 's/AC_PROG_LIBTOOL/AM_PROG_AR\nLT_INIT/' configure.ac sed -i 's/cvode-2\.6\.0//; s/muparser_v2_2_3//' configure.ac Makefile.am The error mentioned here, AutoTools: Obsoleted m4s found ------------------------------ AC_PROG_LIBTOOL found in: BioNetGen-2.2.5-stable/Network3/cvode-2.6.0/configure.ac:91 is bogus since the entire directory is removed in %prep (bundled stuff). [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: bionetgen-2.2.5-1.fc22.x86_64.rpm bionetgen-perl-2.2.5-1.fc22.noarch.rpm bionetgen-2.2.5-1.fc22.src.rpm bionetgen.x86_64: W: spelling-error %description -l en_US transduction -> transaction, introductions, transducer bionetgen.x86_64: W: no-manual-page-for-binary run_network bionetgen-perl.noarch: W: no-documentation bionetgen.src: W: spelling-error %description -l en_US transduction -> transaction, introductions, transducer bionetgen.src: W: invalid-url Source0: https://bionetgen.googlecode.com/files/BioNetGen-2.2.5-stable.zip HTTP Error 404: Not Found ---> Bogus. Perhaps, the network was down temporarily. 3 packages and 0 specfiles checked; 0 errors, 5 warnings. Rpmlint (installed packages) ---------------------------- ]0;<mock-chroot><mock-chroot>[root@imladris /]# rpmlint bionetgen-perl bionetgen bionetgen-perl.noarch: W: no-documentation bionetgen.x86_64: W: spelling-error %description -l en_US transduction -> transaction, introductions, transducer bionetgen.x86_64: W: no-manual-page-for-binary run_network 2 packages and 0 specfiles checked; 0 errors, 3 warnings. ]0;<mock-chroot><mock-chroot>[root@imladris /]# echo 'rpmlint-done:' Requires -------- bionetgen-perl (rpmlib, GLIBC filtered): /usr/bin/perl bionetgen perl(Carp) perl(Class::Struct) perl(Config) perl(Cwd) perl(Data::Dumper) perl(Exporter) perl(File::Basename) perl(File::Path) perl(File::Spec) perl(FindBin) perl(Getopt::Long) perl(IO::Handle) perl(IO::Select) perl(IPC::Open3) perl(List::Util) perl(Math::Trig) perl(POSIX) perl(Scalar::Util) perl(Symbol) perl(constant) perl(lib) perl(strict) perl(vars) perl(warnings) bionetgen (rpmlib, GLIBC filtered): bionetgen-perl libc.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libmuparser.so.2()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libsundials_cvode.so.1()(64bit) libsundials_nvecserial.so.0()(64bit) perl(:MODULE_COMPAT_5.20.1) rtld(GNU_HASH) Provides -------- bionetgen-perl: bionetgen-perl bionetgen: bionetgen bionetgen(x86-64) Source checksums ---------------- https://bionetgen.googlecode.com/files/BioNetGen-2.2.5-stable.zip : CHECKSUM(SHA256) this package : 4186ae1b8990e192775ead0bb7ae40170802d859bb9396047deb8cedaa02ad03 CHECKSUM(SHA256) upstream package : 4186ae1b8990e192775ead0bb7ae40170802d859bb9396047deb8cedaa02ad03 Generated by fedora-review 0.5.2 (63c24cb) last change: 2014-07-14 Command line :/usr/bin/fedora-review -m fedora-rawhide-x86_64 -b 1167467 Buildroot used: fedora-rawhide-x86_64 Active plugins: Generic, Shell-api, C/C++, Perl Disabled plugins: Java, Python, fonts, SugarActivity, Ocaml, Haskell, R, PHP, Ruby Disabled flags: EXARCH, EPEL5, BATCH, DISTTAG
I have nothing to complain about. Package APPROVED.
Damn, too hasty. The scratch build failed on ARM. :( http://koji.fedoraproject.org/koji/taskinfo?taskID=8266197 Getting requirements for bionetgen-2.2.5-1.fc22.src --> autoconf-2.69-16.fc22.noarch --> automake-1.14.1-6.fc22.noarch --> libtool-2.4.2-31.fc22.armv7hl --> muParser-devel-2.2.3-5.fc22.armv7hl --> openmpi-devel-1.8.3-3.fc22.armv7hl --> sundials-devel-2.5.0-6.fc22.armv7hl Error: No Package found for compat-gcc-34-g77
So, this would be - [!]: Package should compile and build into binary rpms on all supported architectures.
(In reply to Mukundan Ragavan from comment #6) > So, this would be - > > [!]: Package should compile and build into binary rpms on all supported > architectures. Ah, I forgot (again) that copr does only x86 builds. But fortunately the dependency on f77 was not actually needed. I think I added it because of the embedded libraries and then forgot to remove it. Spec URL: http://in.waw.pl/~zbyszek/fedora/bionetgen.spec SRPM URL: http://in.waw.pl/~zbyszek/fedora/bionetgen-2.2.5-2.fc22.src.rpm Koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=8267165
That fixes it! Package APPROVED. No more snafus from my part. :)
Thank you for the quick review! New Package SCM Request ======================= Package Name: bionetgen Short Description: Software for rule-based modeling of biochemical systems Upstream URL: http://bionetgen.org/index.php/Main_Page Owners: zbyszek Branches: f19 f20 f21 epel7 InitialCC:
Git done (by process-git-requests).
Updates have been submitted. Thanks once again for the quick review!