[Bug 597307] Review Request: fastx_toolkit - Tools to process short-reads FASTA/FASTQ files

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https://bugzilla.redhat.com/show_bug.cgi?id=597307

--- Comment #6 from Jussi Lehtola <jussi.lehtola@xxxxxx> 2010-08-24 12:58:07 EDT ---
rpmlint output:
fastx_toolkit.src: W: spelling-error %description -l en_US preprocessing ->
reprocessing, p reprocessing, preprocessed
fastx_toolkit.src: W: spelling-error %description -l en_US preprocess ->
reprocess, p reprocess, processors
fastx_toolkit.src:8: W: mixed-use-of-spaces-and-tabs (spaces: line 1, tab: line
8)
fastx_toolkit.x86_64: W: spelling-error %description -l en_US preprocessing ->
reprocessing, p reprocessing, preprocessed
fastx_toolkit.x86_64: W: spelling-error %description -l en_US preprocess ->
reprocess, p reprocess, processors
fastx_toolkit.x86_64: W: no-manual-page-for-binary fasta_clipping_histogram.pl
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastq_quality_trimmer
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_quality_stats
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastq_quality_filter
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_trimmer
fastx_toolkit.x86_64: W: no-manual-page-for-binary
fastq_quality_boxplot_graph.sh
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_barcode_splitter.pl
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastq_quality_converter
fastx_toolkit.x86_64: W: no-manual-page-for-binary
fastx_nucleotide_distribution_line_graph.sh
fastx_toolkit.x86_64: W: no-manual-page-for-binary fasta_formatter
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_collapser
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_renamer
fastx_toolkit.x86_64: W: no-manual-page-for-binary fasta_nucleotide_changer
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_reverse_complement
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastq_to_fasta
fastx_toolkit.x86_64: W: no-manual-page-for-binary
fastx_nucleotide_distribution_graph.sh
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastq_masker
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_artifacts_filter
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_uncollapser
fastx_toolkit.x86_64: W: no-manual-page-for-binary fastx_clipper
fastx_toolkit-debuginfo.x86_64: W: spelling-error Summary(en_US) fastx -> fast,
fasts, fast x
fastx_toolkit-debuginfo.x86_64: W: spelling-error %description -l en_US fastx
-> fast, fasts, fast x
fastx_toolkit-devel.x86_64: W: spelling-error Summary(en_US) fastx -> fast,
fasts, fast x
fastx_toolkit-devel.x86_64: W: spelling-error %description -l en_US fastx ->
fast, fasts, fast x
fastx_toolkit-devel.x86_64: W: spurious-executable-perm
/usr/share/doc/fastx_toolkit-devel-0.0.13/galaxy/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh
4 packages and 0 specfiles checked; 0 errors, 30 warnings.

- Check your tabs vs spaces.

- Placing the galaxy stuff somewhere else than %doc gets rid of the exec perm
warning. When packaging the galaxy stuff, be sure not to include any Makefiles
or the like.

- Please use
 http://hannonlab.cshl.edu/fastx_toolkit/
as the URL. It's nicer not to have macros in the URL, so one can cut'n'paste
from the spec.

- Don't ship the m4 files, as instructed by Michael.

**

MUST: The package does not yet exist in Fedora. The Review Request is not a
duplicate. OK
MUST: The spec file for the package is legible and macros are used
consistently. OK
MUST: The package must be named according to the Package Naming Guidelines. OK
MUST: The spec file name must match the base package %{name}. OK
MUST: The package must be licensed with a Fedora approved license and meet the 
Licensing Guidelines. OK

MUST: The License field in the package spec file must match the actual license.
NEEDSWORK
- License is AGPLv3+, not AGPLv3.

MUST: The sources used to build the package must match the upstream source, as
provided in the spec URL. OK
6d233ff4ae3d52c457d447179f073a56  fastx_toolkit-0.0.13.tar.bz2
6d233ff4ae3d52c457d447179f073a56  ../SOURCES/fastx_toolkit-0.0.13.tar.bz2

MUST: The package MUST successfully compile and build into binary rpms. OK
MUST: The spec file MUST handle locales properly. N/A

MUST: Optflags are used and time stamps preserved. NEEDSWORK
- As already pointed out by Michael, the build process overrides the Fedora
optimization flags.
- Use
 make %{?_smp_mflags} CFLAGS="$RPM_OPT_FLAGS" CXXFLAGS="$RPM_OPT_FLAGS"
to correct this.
- Also, please use
 make install INSTALL="install -p"
to keep the time stamps in %install.

MUST: Packages containing shared library files must call ldconfig. N/A
MUST: A package must own all directories that it creates or require the package
that owns the directory. OK

MUST: Files only listed once in %files listings. OK
- Maybe again make things a bit more verbose with
 %{_bindir}/fast*
?

MUST: Debuginfo package is complete. OK
MUST: Permissions on files must be set properly. OK
MUST: Large documentation files must go in a -doc subpackage. N/A
MUST: All relevant items are included in %doc. Items in %doc do not affect
runtime of application. OK
MUST: Header files must be in a -devel package. N/A
MUST: Static libraries must be in a -static package. N/A
MUST: If a package contains library files with a suffix then library files
ending in .so 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. N/A
MUST: Packages does not contain any .la libtool archives. N/A
MUST: Desktop files are installed properly. N/A
MUST: No file conflicts with other packages and no general names. OK
SHOULD: %{?dist} tag is used in release. OK
SHOULD: If the package does not include license text(s) as separate files from
upstream, the packager should query upstream to include it. OK
SHOULD: The package builds in mock. OK
EPEL: Clean section exists. OK
EPEL: Buildroot cleaned before install. OK
EPEL: Packages containing pkgconfig(.pc) files must 'Requires: pkgconfig'. N/A

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