Spec URL: http://verdurin.org.uk/~verdurin/fedora/reviews/bfast/bfast.spec SRPM URL: http://verdurin.org.uk/~verdurin/fedora/reviews/bfast/bfast-0.6.4d-3.fc12.src.rpm Description: BFAST facilitates the fast and accurate mapping of short reads to reference sequences, where mapping billions of short reads with variants is of utmost importance.
Hi, I will review your package. At first sight, the .spec looks quite good. Anyway there are some compilation issues in 32-bit architecture only: http://koji.fedoraproject.org/koji/taskinfo?taskID=2261932 As you can see in the logs, the configure script fails to detect basic glibc functions and headers (string.h, limits.h, etc), so the compilation cannot be run correctly. It comes from the fact that the 64-bit flag -m64 is always enabled, whatever the architecture, when dependencies are detected in configure; as given in configure.ac: extended_CFLAGS="-m64 -D_FILE_OFFSET_BITS=64"; [...] CFLAGS="${default_CFLAGS} ${extended_CFLAGS}"; A (quick) solution could be to remove -m64 from extended_CFLAGS in configure, like this in your .spec: %prep %setup -q %patch0 -p1 sed -i '/^extended_CFLAGS=/ s/-m64//' configure Since RPM_OPT_FLAGS obviously already contains -m64, this change doesn't affect 64-bit builds. But you must report this issue to the bfast developers. By the way, submit also your patch about pthread, the missing pthread flags are a serious problem when building the program on Linux.
Thanks for taking a look. I'll make a new version with a fix for the 32-bit problem in a day or so. Yes, I will report that and the need for the pthread patch.
There's a new release with the suggested fix at: http://verdurin.org.uk/~verdurin/fedora/reviews/bfast/bfast.spec and http://verdurin.org.uk/~verdurin/fedora/reviews/bfast/bfast-0.6.4d-4.fc13.src.rpm I've contacted upstream about this problem and the pthread patch. It builds for the i686 arch now: http://koji.fedoraproject.org/koji/taskinfo?taskID=2266299
Great :) The package looks technically good now :) Just two little things now: - it seems that a header (bfast/kseq.h) is licensed under the MIT license. Maybe the License tag should reflect this: License: GPLv2 and MIT - Maybe the project URL should point to http://bfast.sourceforge.net/. This URL redirects to the mediawiki link you used. It's just a nonmandatory suggestion, for convenience, in case the project decides to leave mediawiki ^^. Once the license corrected, I will approve this package :)
Okay, I've amended the license tag, fixed the URL (I agree that address is less ugly and is indeed the one the authors request people us in citations) and added a lengthier description: http://verdurin.org.uk/~verdurin/fedora/reviews/bfast/bfast.spec http://verdurin.org.uk/~verdurin/fedora/reviews/bfast/bfast-0.6.4d-5.fc13.src.rpm
That looks fine :) Here is the review: https://bugzilla.redhat.com/show_bug.cgi?id=606288 Hi, Here is a review of bfast: * MUST: rpmlint must be run on every package. The output should be posted in the review. No serious issues on the binary and debug packages (only warnings about man pages not provided upstream and false-positive mispellings) * MUST: The package must be named according to the Package Naming Guidelines . OK * MUST: The spec file name must match the base package %{name}, in the format %{name}.spec unless your package has an exemption. OK * MUST: The package must meet the Packaging Guidelines OK * MUST: The package must be licensed with a Fedora approved license and meet the Licensing Guidelines OK (GPLv2 and MIT) * MUST: The License field in the package spec file must match the actual license. OK * MUST: 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 must be included in %doc. OK * MUST: The spec file must be written in American English. OK * MUST: The spec file for the package MUST be legible. OK * MUST: The sources used to build the package must match the upstream source, as provided in the spec URL. Reviewers should use md5sum for this task. If no upstream URL can be specified for this package, please see the Source URL Guidelines for how to deal with this. OK (RPM source archive has the same MD5 sum than the one downloaded: a1443f8b0c5d1169f1b88730bdd29d95) * MUST: The package MUST successfully compile and build into binary rpms on at least one primary architecture. OK (tested on koji, OK on F13 and rawhide : http://koji.fedoraproject.org/koji/taskinfo?taskID=2268883) * MUST: If the package does not successfully compile, build or work on an architecture, then those architectures should be listed in the spec in ExcludeArch. Each architecture listed in ExcludeArch MUST have a bug filed in bugzilla, describing the reason that the package does not compile/build/work on that architecture. The bug number MUST be placed in a comment, next to the corresponding ExcludeArch line. N/A * MUST: All build dependencies must be listed in BuildRequires, except for any that are listed in the exceptions section of the Packaging Guidelines; inclusion of those as BuildRequires is optional. Apply common sense. OK * MUST: The spec file MUST handle locales properly. This is done by using the %find_lang macro. Using %{_datadir}/locale/* is strictly forbidden. N/A * MUST: Every binary RPM package (or subpackage) which stores shared library files (not just symlinks) in any of the dynamic linker's default paths, must call ldconfig in %post and %postun. N/A * MUST: Packages must NOT bundle copies of system libraries. OK * MUST: If the package is designed to be relocatable, the packager must state this fact in the request for review, along with the rationalization for relocation of that specific package. Without this, use of Prefix: /usr is considered a blocker. N/A * MUST: A package must own all directories that it creates. If it does not create a directory that it uses, then it should require a package which does create that directory. OK * MUST: A Fedora package must not list a file more than once in the spec file's %files listings. OK * MUST: Permissions on files must be set properly. Executables should be set with executable permissions, for example. Every %files section must include a %defattr(...) line. OK * MUST: Each package must have a %clean section, which contains rm -rf %{buildroot} (or $RPM_BUILD_ROOT). OK * MUST: Each package must consistently use macros. OK * MUST: The package must contain code, or permissable content. OK * MUST: Large documentation files must go in a -doc subpackage. (The definition of large is left up to the packager's best judgement, but is not restricted to size. Large can refer to either size or quantity). N/A * MUST: If a package includes something as %doc, it must not affect the runtime of the application. To summarize: If it is in %doc, the program must run properly if it is not present. OK * MUST: Header files must be in a -devel package. N/A * MUST: Static libraries must be in a -static package. N/A * MUST: Packages containing pkgconfig(.pc) files must 'Requires: pkgconfig' (for directory ownership and usability). N/A * MUST: If a package contains library files with a suffix (e.g. libfoo.so.1.1), then library files that end in .so (without suffix) must go in a -devel package. N/A * MUST: In the vast majority of cases, devel packages must require the base package using a fully versioned dependency: Requires: %{name} = %{version}-%{release} N/A * MUST: Packages must NOT contain any .la libtool archives, these must be removed in the spec if they are built. N/A * MUST: Packages containing GUI applications must include a %{name}.desktop file, and that file must be properly installed with desktop-file-install in the %install section. If you feel that your packaged GUI application does not need a .desktop file, you must put a comment in the spec file with your explanation. N/A * MUST: Packages must not own files or directories already owned by other packages. The rule of thumb here is that the first package to be installed should own the files or directories that other packages may rely upon. This means, for example, that no package in Fedora should ever share ownership with any of the files or directories owned by the filesystem or man package. If you feel that you have a good reason to own a file or directory that another package owns, then please present that at package review time. OK * MUST: At the beginning of %install, each package MUST run rm -rf %{buildroot} (or $RPM_BUILD_ROOT). OK * MUST: All filenames in rpm packages must be valid UTF-8. OK This package is APPROVED!
New Package CVS Request ======================= Package Name: bfast Short Description: Blat-like Fast Accurate Search Tool Owners: verdurin Branches: F-12 F-13 EL-5 EL-6 InitialCC:
CVS done (by process-cvs-requests.py).
bfast-0.6.4d-5.fc12 has been submitted as an update for Fedora 12. http://admin.fedoraproject.org/updates/bfast-0.6.4d-5.fc12
bfast-0.6.4d-5.fc13 has been submitted as an update for Fedora 13. http://admin.fedoraproject.org/updates/bfast-0.6.4d-5.fc13
bfast-0.6.4d-5.fc13 has been pushed to the Fedora 13 testing repository. If problems still persist, please make note of it in this bug report. If you want to test the update, you can install it with su -c 'yum --enablerepo=updates-testing update bfast'. You can provide feedback for this update here: http://admin.fedoraproject.org/updates/bfast-0.6.4d-5.fc13
bfast-0.6.4d-5.fc12 has been pushed to the Fedora 12 testing repository. If problems still persist, please make note of it in this bug report. If you want to test the update, you can install it with su -c 'yum --enablerepo=updates-testing update bfast'. You can provide feedback for this update here: http://admin.fedoraproject.org/updates/bfast-0.6.4d-5.fc12
bfast-0.6.4d-5.fc12 has been pushed to the Fedora 12 stable repository. If problems still persist, please make note of it in this bug report.
bfast-0.6.4d-5.fc13 has been pushed to the Fedora 13 stable repository. If problems still persist, please make note of it in this bug report.