[Bug 697836] Review Request: mmseq - Haplotype and isoform specific expression estimation for RNA-seq

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https://bugzilla.redhat.com/show_bug.cgi?id=697836

--- Comment #4 from Volker FrÃhlich <volker27@xxxxxx> 2011-05-14 05:55:08 EDT ---
The naming guidelines are not met for this pre-release version. Please see the
review below for details and correct it.

Concerning the current FSF address, please see
https://bugzilla.redhat.com/show_bug.cgi?id=690919#c5
It is not considered as a blocker, so it is up to you.

Please correct the VERSION file prior building, as it contains the wrong
version number. I'd also exclude it from the file section, as it serves no use
as far as I can see. 

I'd prefer having a new line for every BuildRequires, as it is clearer. You can
also be more specific on the script file names in the files section.

If you don't plan to introduce the package into EPEL, you can drop the clean
section, the rm -rf %{buildroot} and the BuildRoot definition. It seems like,
there are no samtools in EPEL yet.

Remove the extra white-space in front of the word "Example".

I'm not sure if zlib is used at all. It's in the flags, but I can't see how
they'd use it. This might not be important.

--------------------------------------------------------
Review:

[+] Good
[-] Needs work
[0] Does not apply

MUST:
=====

[+] rpmlint:

[makerpm@fedora14 mmseq_0.9.10b]$ rpmlint
/var/lib/mock/fedora-rawhide-x86_64/result/mmseq-*
mmseq.src: W: spelling-error Summary(en_US) Haplotype -> Haplology, Holotype,
Haplography
mmseq.src: W: spelling-error Summary(en_US) isoform -> iodoform, isomorph,
proforma
mmseq.src: W: spelling-error %description -l en_US haplotype -> haplology,
holotype, haplography
mmseq.src: W: spelling-error %description -l en_US isoform -> iodoform,
isomorph, proforma
mmseq.src: W: spelling-error %description -l en_US multi -> mulch, mufti
mmseq.x86_64: W: spelling-error Summary(en_US) Haplotype -> Haplology,
Holotype, Haplography
mmseq.x86_64: W: spelling-error Summary(en_US) isoform -> iodoform, isomorph,
proforma
mmseq.x86_64: W: spelling-error %description -l en_US haplotype -> haplology,
holotype, haplography
mmseq.x86_64: W: spelling-error %description -l en_US isoform -> iodoform,
isomorph, proforma
mmseq.x86_64: W: spelling-error %description -l en_US multi -> mulch, mufti
mmseq.x86_64: E: incorrect-fsf-address /usr/bin/testregexp.rb
mmseq.x86_64: E: incorrect-fsf-address /usr/bin/sam2hits.rb
mmseq.x86_64: E: incorrect-fsf-address /usr/bin/filterGTF.rb
mmseq.x86_64: E: incorrect-fsf-address /usr/bin/fastagrep.sh
mmseq.x86_64: E: incorrect-fsf-address /usr/bin/haploref.rb
mmseq.x86_64: W: no-manual-page-for-binary haploref.rb
mmseq.x86_64: W: no-manual-page-for-binary ensembl_gtf_to_gff.pl
mmseq.x86_64: W: no-manual-page-for-binary mmseq
mmseq.x86_64: W: no-manual-page-for-binary get_isize.rb
mmseq.x86_64: W: no-manual-page-for-binary bam2hits
mmseq.x86_64: W: no-manual-page-for-binary fastagrep.sh
mmseq.x86_64: W: no-manual-page-for-binary filterGTF.rb
mmseq.x86_64: W: no-manual-page-for-binary sam2hits.rb
mmseq.x86_64: W: no-manual-page-for-binary testregexp.rb
mmseq.x86_64: W: no-manual-page-for-binary pileup.sh
mmseq-debuginfo.x86_64: E: incorrect-fsf-address
/usr/src/debug/mmseq_0.9.10b/mmseq.cpp
mmseq-debuginfo.x86_64: E: incorrect-fsf-address
/usr/src/debug/mmseq_0.9.10b/sokal.cc
3 packages and 0 specfiles checked; 7 errors, 20 warnings.

[-] Naming according to the Package Naming Guidelines: Please see
http://fedoraproject.org/wiki/PackageNamingGuidelines#NonNumericRelease
[+] Spec file matches base package name
[+] Packaging guidelines met
[+] License approved for Fedora
[+] License field in spec matches code
[+] License file included, if source package includes it
[+] Spec in American English
[+] Spec is legible
[+] Sources match upstream md5sum: 1f1c5b338eec23994fd84edb7e00b17a
[+] Compiles and builds into binary RPMs on at least one primary architecture:
http://koji.fedoraproject.org/koji/taskinfo?taskID=3071848

[0] ExcludeArch is specified and commented
[0] Locales are handled correctly
[+] All build dependencies listed
[0] Calls ldconfig for its shared libraries
[+] No bundled system libraries
[0] Stated as relocatable package
[+] Owns all its directories or requires package that does
[+] No file listing duplicates
[+] File permissions correct
[+] Consistent use of macros
[+] Code or permissible content
[0] Large documentation in -doc subpackage
[+] No runtime dependency of files listed as %doc
[0] Header files in -devel subpackage
[0] Static files in -static subpackage
[0] Library files without suffix in -devel subpackage
[0] Devel-package requires base package
[0] No .la libtool archives
[0] GUI application includes properly installed %{name}.desktop file
[+] No files or directories owned, that other packages own
[+] Filenames in packages are UTF-8

SHOULD:
=======

[0] Query upstream if no license text is included
[+] Package builds in mock: Tried fedora-rawhide-x86_64, fedora-rawhide-i386
[?] Package works as described -- Haven't tried
[0] Scriptlets are sane, if used
[0] Subpackages other than -devel should require base package (versioned)
[0] pkgconfig files in -devel subpackage
[0] Dependencies outside of /etc, /bin, /sbin, /usr/bin, or /usr/sbin consider
requiring the package which provides the file instead of the file itself
[-] Contain man pages, where they make sense -- Please try to query upstream on
this.

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