[Bug 491490] Review Request: ghmm - A library with data structures and algorithms for Hidden Markov Models

Sun May 31 14:41:59 UTC 2009

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https://bugzilla.redhat.com/show_bug.cgi?id=491490

D Haley <mycae at yahoo.com> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |mycae at yahoo.com

--- Comment #1 from D Haley <mycae at 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 at 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

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