Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.
Summary: Review Request: ghmm - A library with data structures and algorithms for Hidden Markov Models
https://bugzilla.redhat.com/show_bug.cgi?id=491490
Summary: Review Request: ghmm - A library with data structures and algorithms for Hidden Markov Models Product: Fedora Version: rawhide Platform: All OS/Version: Linux Status: NEW Severity: medium Priority: medium Component: Package Review AssignedTo: nobody@fedoraproject.org ReportedBy: konrad@tylerc.org QAContact: extras-qa@fedoraproject.org CC: notting@redhat.com, fedora-package-review@redhat.com Estimated Hours: 0.0 Classification: Fedora
Spec URL: http://konradm.fedorapeople.org/fedora/SPECS/ghmm.spec SRPM URL: http://konradm.fedorapeople.org/fedora/SRPMS/ghmm-0.7-1.svn2251.fc10.src.rpm Description: The General Hidden Markov Model library (GHMM) is a freely available LGPL-ed C library implementing efficient data structures and algorithms for basic and extended HMMs.
It is developed by the Algorithmics group at the Max Planck Institute for Molecular Genetics.
Features: * Discrete and continuous emissions * Mixtures of PDFs for continuous emissions * Non-homogenous Markov chains * Pair HMMs (contributed by Genoscope) * Clustering and mixture modelling for HMMs * Graphical Editor HMMEd * Python bindings * XML-based file format
Note: This is a SAGE package (https://fedoraproject.org/wiki/SIGs/SciTech/SAGE).
Rpmlint output: ghmm.spec:72: W: rpm-buildroot-usage %prep -e 's|$(PYTHON) setup.py install.*$|$(PYTHON) setup.py install -O1 --skip-build --root ${RPM_BUILD_ROOT}|' \ ghmm.src:72: W: rpm-buildroot-usage %prep -e 's|$(PYTHON) setup.py install.*$|$(PYTHON) setup.py install -O1 --skip-build --root ${RPM_BUILD_ROOT}|' \
These are used so that when python libs are built/installed during the make process, they use the correct flags. RPM_BUILD_ROOT is not defined here, it's just reference when the makefile is run in %build/%install.
ghmm.x86_64: W: shared-lib-calls-exit /usr/lib64/libghmm.so.1.0.0 exit@GLIBC_2.2.5
Poor programming practice, not a packaging problem.
ghmm-devel.x86_64: W: no-documentation ghmm-static.x86_64: W: no-documentation
Ignorable.
This builds in koji: http://koji.fedoraproject.org/koji/taskinfo?taskID=1252576
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=491490
D Haley mycae@yahoo.com changed:
What |Removed |Added ---------------------------------------------------------------------------- CC| |mycae@yahoo.com
--- Comment #1 from D Haley mycae@yahoo.com 2009-05-31 10:41:56 EDT --- Its me again. Here are my comments for this package.
General comments:
* For ease of update, I recommend defining a svnrev macro, then using that where appropriate. * DTD is named in an unusual manner, with version number after .dtd --should this be renamed? *-config script needs correcting to produce appropriate output when called with multiple flags. This is the same problem as for bug 475065 (why is this identical to the other one?)
*"# Commented out because it seems broken" - is the check failing, or just not running?
Review comments:
# MUST: rpmlint must be run on every package. The output should be posted in the review. $ rpmlint -v ghmm.spec ../SRPMS/ghmm-0.7-1.svn2251.fc10.src.rpm ../RPMS/i386/ghmm-0.7-1.svn2251.fc10.i386.rpm ../RPMS/i386/ghmm-static-0.7-1.svn2251.fc10.i386.rpm ../RPMS/i386/ghmm-devel-0.7-1.svn2251.fc10.i386.rpm ../RPMS/i386/ghmm-debuginfo-0.7-1.svn2251.fc10.i386.rpm ghmm.spec:71: W: rpm-buildroot-usage %prep -e 's|$(PYTHON) setup.py install.*$|$(PYTHON) setup.py install -O1 --skip-build --root ${RPM_BUILD_ROOT}|' \ ghmm.src: I: checking ghmm.src:71: W: rpm-buildroot-usage %prep -e 's|$(PYTHON) setup.py install.*$|$(PYTHON) setup.py install -O1 --skip-build --root ${RPM_BUILD_ROOT}|' \ ghmm.i386: I: checking ghmm.i386: W: shared-lib-calls-exit /usr/lib/libghmm.so.1.0.0 exit@GLIBC_2.0 ghmm-static.i386: I: checking ghmm-static.i386: W: no-documentation ghmm-devel.i386: I: checking ghmm-devel.i386: W: no-documentation ghmm-debuginfo.i386: I: checking 5 packages and 1 specfiles checked; 0 errors, 5 warnings.
Please notify upstream about the exit() call, and ask for a fix; notification of upstream is required, upstream response is not, although reply should be given here if upstream responds.
# 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 . FAIL : Running my quick and dirty grep (x`grep "any later"` != x"") over the files indicates that the following files don't have an LGPLv2+ boilerplate: Bad: ./ghmmwrapper/ghmmwrapper_wrap.c Bad: ./tests/two_states_three_symbols.c Bad: ./tests/read_fa.c Bad: ./tests/read_smodel.c Bad: ./tests/label_higher_order_test.c Bad: ./tests/randvar_test.c Bad: ./tests/generate_PHI.c Bad: ./tests/shmm_viterbi_test.c Bad: ./tests/chmm_test.c Bad: ./tests/libxml-test.c Bad: ./tests/ghmmunittests.c Bad: ./tests/sequences_old_format.c Bad: ./tests/chmm.c Bad: ./tests/root_finder_test.c Bad: ./tests/test_gsl_ran_gaussian_tail.c Bad: ./tests/sequences_test.c Bad: ./tests/coin_toss_test.c Bad: ./tools/smo2xml.c Bad: ./tools/probdist.c Bad: ./tools/scluster.c Bad: ./tools/smix_hmm.c Bad: ./tools/cluster.c Bad: ./ghmm/mt19937ar.c Bad: ./ghmm/psequence.h Bad: ./ghmm/obsolete.h Bad: ./win_config.h Bad: ./config.h
./ghmm/mt19937ar.c appears to have BSD style licence, and others no licence at all.
* Also the copyright file says parts are from the Sun BSD style licence, but no clear relation as to which source files this applies to is given.
* The COPYING links to the GPL, which is included but their website says LGPL. This needs to be clarified by upstream.
* Requiring the GNU Scientific Library will make the package GPLv3(+?), not LGPL.
* Finally the COPYING file must be bundled into %doc as this is the user "recieving" a copy of the LGPL/GPL (additional to COPYRIGHT.txt).
This will all need to be fixed. At the very least you need to change the licence field, as the licences are mixed. You should notify upstream about this so they can relicence, and/or fix the missing licences.
# MUST: The License field in the package spec file must match the actual license. FAIL: see above # 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. FAIL: see above # 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 pacKoji OKkage, please see the Source URL Guidelines for how to deal with this. FAIL: $ svn export -r2251 https://ghmm.svn.sourceforge.net/svnroot/ghmm/trunk/ghmm ghmm $ tar -cjf ghmm.tar.bz2 ghmm/ $ md5sum ghmm.tar.bz2 5a410a91489785811535622a89bd25ab ghmm.tar.bz2 $ md5sum ../ghmm.tar.bz2 00c08b65e71b51e63b2922ea9ce4883b ../ghmm.tar.bz2 Could not reproduce MD5 included in SRPM. Please check and advise of correct MD5.
Also, please provide exact SVN (including rev number) command for a current checkout, so md5 can match if someone executes the suggested command.
# MUST: The package MUST successfully compile and build into binary rpms on at least one primary architecture. Koji OK. # 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. 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. FAIL: please fix # 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, but I strongly recommend defining an svn version number macro # MUST: The package must contain code, or permissable content. OK, pending licence clarification. # 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). OK # 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. OK # MUST: Static libraries must be in a -static package. OK # 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. OK # MUST: In the vast majority of cases, devel packages must require the base package using a fully versioned dependency: Requires: %{name} = %{version}-%{release} OK # MUST: Packages must NOT contain any .la libtool archives, these must be removed in the spec if they are built. OK # 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
* SHOULD: If the source package does not include license text(s) as a separate file from upstream, the packager SHOULD query upstream to include it. FAIL: See earlier licence problems * SHOULD: The description and summary sections in the package spec file should contain translations for supported Non-English languages, if available. N/A * SHOULD: The reviewer should test that the package builds in mock. Koji OK * SHOULD: The package should compile and build into binary rpms on all supported architectures. FAIL: Please run scratch tasks for each fedora version (i.e. also do F-9 F-10) * SHOULD: The reviewer should test that the package functions as described. A package should not segfault instead of running, for example. FAIL: Not checked by reviewer (me), will check on next SRPM. * SHOULD: If scriptlets are used, those scriptlets must be sane. This is vague, and left up to the reviewers judgement to determine sanity. OK * SHOULD: Usually, subpackages other than devel should require the base package using a fully versioned dependency. OK * SHOULD: The placement of pkgconfig(.pc) files depends on their usecase, and this is usually for development purposes, so should be placed in a -devel pkg. A reasonable exception is that the main pkg itself is a devel tool not installed in a user runtime, e.g. gcc or gdb. N/A * SHOULD: If the package has file dependencies outside of /etc, /bin, /sbin, /usr/bin, or /usr/sbin consider requiring the package which provides the file instead of the ile itself. N/A
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=491490
--- Comment #2 from D Haley mycae@yahoo.com 2009-05-31 10:45:10 EDT --- Also, can you set the depends upon and blocks fields for this bug?
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=491490
Jason Tibbitts tibbs@math.uh.edu changed:
What |Removed |Added ---------------------------------------------------------------------------- Flag| |needinfo?(konrad@tylerc.org | |)
--- Comment #3 from Jason Tibbitts tibbs@math.uh.edu 2009-07-01 19:45:21 EDT --- It's been a month since that nice review work by D Haley without response. Did you wish to continue with this package? I'll go ahead and close it out soon if there's no further progress.
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=491490
Conrad Meyer konrad@tylerc.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Flag|needinfo?(konrad@tylerc.org | |) |
--- Comment #4 from Conrad Meyer konrad@tylerc.org 2009-07-05 16:12:04 EDT --- Ah, sorry, I didn't notice that I wasn't receiving email from this account for the past month or so. I plan to follow up on the review, I'm just catching up to all the mail I've missed. Sorry.
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=491490
--- Comment #5 from Jason Tibbitts tibbs@math.uh.edu 2009-08-20 18:14:11 EDT --- Any chance of being caught up soon? Should this ticket stay open?
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=491490
Conrad Meyer konrad@tylerc.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |CLOSED Resolution| |WONTFIX
--- Comment #6 from Conrad Meyer konrad@tylerc.org 2009-08-20 19:48:20 EDT --- I haven't had time, sorry. This should probably be closed.
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=491490
D Haley mycae@yahoo.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Keywords| |Reopened Status|CLOSED |ASSIGNED Resolution|WONTFIX |
--- Comment #7 from D Haley mycae@yahoo.com 2009-08-22 22:31:34 EDT --- I have notified upstream of the licencing and rpmlint issues, and am happy to complete this package (provided someone else reviews of course :) ).
I have also found that their unit tests fail on my machine, and have notified upstream:
#Upstream has been notified of exit() calls. #https://sourceforge.net/tracker/?func=detail&aid=2842844&group_id=67... #Upstream has been notified of licencing issues #https://sourceforge.net/tracker/?func=detail&aid=2842854&group_id=67... #Upstream has been notfied of unit test problems #https://sourceforge.net/tracker/?func=detail&aid=2842847&group_id=67...
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=491490
--- Comment #8 from D Haley mycae@yahoo.com 2009-10-09 23:53:10 EDT --- SPEC URL: http://dhd.selfip.com/427e/ghmm.spec SRPM URL: http://dhd.selfip.com/427e/ghmm-0.7-2.svn2286.fc10.src.rpm
Koji Builds: F10:http://koji.fedoraproject.org/koji/taskinfo?taskID=1739149 F11:http://koji.fedoraproject.org/koji/taskinfo?taskID=1739154 F12:http://koji.fedoraproject.org/koji/taskinfo?taskID=1739159
Rpmlint output: rpmlint `cat tmp | awk '{print $2}'` ghmm.src:94: W: rpm-buildroot-usage %prep -e 's|$(PYTHON) setup.py install.*$|$(PYTHON) setup.py install -O1 --skip-build --root ${RPM_BUILD_ROOT}|' \ ghmm.i386: W: shared-lib-calls-exit /usr/lib/libghmm.so.1.0.0 exit@GLIBC_2.0 ghmm-static.i386: W: no-documentation ghmm-devel.i386: W: no-documentation 5 packages and 0 specfiles checked; 0 errors, 4 warnings.
$ cat tmp Wrote: /home/makerpm/rpmbuild/SRPMS/ghmm-0.7-2.svn2286.fc10.src.rpm Wrote: /home/makerpm/rpmbuild/RPMS/i386/ghmm-0.7-2.svn2286.fc10.i386.rpm Wrote: /home/makerpm/rpmbuild/RPMS/i386/ghmm-static-0.7-2.svn2286.fc10.i386.rpm Wrote: /home/makerpm/rpmbuild/RPMS/i386/ghmm-devel-0.7-2.svn2286.fc10.i386.rpm Wrote: /home/makerpm/rpmbuild/RPMS/i386/ghmm-debuginfo-0.7-2.svn2286.fc10.i386.rpm
Just a note : I had some problems with the MD5 checking owing to SVN modifying then files date fields to match my local timezone. the instructions in the SPEC file seemed to work. You can do a full diff to see the changes if need be.
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=491490
Thomas Spura spurath@students.uni-mainz.de changed:
What |Removed |Added ---------------------------------------------------------------------------- CC| |spurath@students.uni-mainz. | |de
--- Comment #9 from Thomas Spura spurath@students.uni-mainz.de 2009-10-18 20:34:17 EDT --- Hmm, rpmbuild -ba faild:
Installed, but unpacked: /usr/lib/python2.6/site-packages/HMMEd-0.8-py2.6.egg-info /usr/lib/python2.6/site-packages/HMMEditingContext.py /usr/lib/python2.6/site-packages/HMMEditingContext.pyc /usr/lib/python2.6/site-packages/HMMEditingContext.pyo /usr/lib/python2.6/site-packages/HMMEditor.py /usr/lib/python2.6/site-packages/HMMEditor.pyc /usr/lib/python2.6/site-packages/HMMEditor.pyo /usr/lib/python2.6/site-packages/ObjectHMM.py /usr/lib/python2.6/site-packages/ObjectHMM.pyc /usr/lib/python2.6/site-packages/ObjectHMM.pyo
on 64bit python_sitearch is /usr/lib64/python2.6/site-packages.
Don't know why koji could build and rpmbuild don't...
Why do you sed in %setup? for CFLAGS
You can export CFLAGS in the %configure line with CFLAGS="${RPM_OPT_FLAGS}" %configure --enable-gsl --enable-experimental --enable-unsupported
--enable-atlas and --disable-static would be good.
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=491490
--- Comment #10 from Thomas Spura spurath@students.uni-mainz.de 2009-10-18 20:35:29 EDT --- And from https://bugzilla.redhat.com/show_bug.cgi?id=491545#c8 you should use your own review request and dublicate this… (whyever ;))
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=491490
D Haley mycae@yahoo.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |CLOSED Resolution| |NOTABUG
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=491490
--- Comment #11 from D Haley mycae@yahoo.com 2009-10-23 10:07:46 EDT --- New report is at Bug 530568
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=491490
Thomas Spura tomspur@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Resolution|NOTABUG |DUPLICATE
--- Comment #12 from Thomas Spura tomspur@fedoraproject.org 2009-10-23 12:22:15 EDT ---
*** This bug has been marked as a duplicate of 530568 ***
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=491490
--- Comment #13 from Fedora Update System updates@fedoraproject.org 2009-10-29 06:33:33 EDT --- ghmm-0.7-4.svn2286.fc11 has been submitted as an update for Fedora 11. http://admin.fedoraproject.org/updates/ghmm-0.7-4.svn2286.fc11
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=491490
--- Comment #14 from Fedora Update System updates@fedoraproject.org 2009-10-29 06:33:39 EDT --- ghmm-0.7-4.svn2286.el5 has been submitted as an update for Fedora EPEL 5. http://admin.fedoraproject.org/updates/ghmm-0.7-4.svn2286.el5
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=491490
--- Comment #15 from Fedora Update System updates@fedoraproject.org 2009-11-20 18:27:39 EDT --- ghmm-0.7-4.svn2286.el5 has been pushed to the Fedora EPEL 5 stable repository. If problems still persist, please make note of it in this bug report.
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=491490
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Fixed In Version| |0.7-4.svn2286.el5 Resolution|DUPLICATE |ERRATA
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=491490
--- Comment #16 from Fedora Update System updates@fedoraproject.org 2009-11-30 23:46:22 EDT --- ghmm-0.7-4.svn2286.fc11 has been pushed to the Fedora 11 stable repository. If problems still persist, please make note of it in this bug report.
Please do not reply directly to this email. All additional comments should be made in the comments box of this bug.
https://bugzilla.redhat.com/show_bug.cgi?id=491490
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Fixed In Version|0.7-4.svn2286.el5 |0.7-4.svn2286.fc11
package-review@lists.fedoraproject.org