[Debian-med-packaging] perl path issue with MEME package?

[Andreas Tille]

Hi Faheem,

On Wed, Jan 16, 2013 at 04:27:08PM +0530, Faheem Mitha wrote:
> 
> >I built it from the current version of the Debian packaging in
> >svn. Can you tell me where you removed
> >/usr/share/man/man1/readseq.1.gz from the meme package? I don't
> >see any mention of it in the Debian packaging.
> 
> I just confirmed the Debian packaging is current, and rebuilt the
> package, and the following file is in the Debian package. I assume
> it is not supposed to be.
> 
> rw-r--r-- root/root        20 2013-01-16 16:13 ./usr/share/man/man1/readseq.1.gz

I need to check this.  I just realised in the build log some errors:

 
mkdir -p debian/tmp-manpages
/usr/bin/pod2man debian/tmp/usr/bin/alphtype > debian/tmp-manpages/alphtype.1;  /usr/bin/pod2man debian/tmp/usr/bin/ama > debian/tmp-manpages/ama.1;  /usr/bin/pod2man debian/tmp/usr/bin/ama-qvalues > debian/tmp-manpages/ama-qvalues.1;  /usr/bin/pod2man debian/tmp/usr/bin/ame > debian/tmp-manpages/ame.1;  /usr/bin/pod2man debian/tmp/usr/bin/beadstring > debian/tmp-manpages/beadstring.1;  /usr/bin/pod2man debian/tmp/usr/bin/beeml2meme > debian/tmp-manpages/beeml2meme.1;  /usr/bin/pod2man debian/tmp/usr/bin/cat_max > debian/tmp-manpages/cat_max.1;  /usr/bin/pod2man debian/tmp/usr/bin/centrimo > debian/tmp-manpages/centrimo.1;  /usr/bin/pod2man debian/tmp/usr/bin/ceqlogo > debian/tmp-manpages/ceqlogo.1;  /usr/bin/pod2man debian/tmp/usr/bin/changetoweb > debian/tmp-manpages/changetoweb.1;  /usr/bin/pod2man debian/tmp/usr/bin/chen2meme > debian/tmp-manpages/chen2meme.1;  /usr/bin/pod2man debian/tmp/usr/bin/clustalw-io > debian/tmp-manpages/clustalw-io.1;  /usr/bin/pod2man debian/tmp/usr/bin/clustalw2fasta > debian/tmp-manpages/clustalw2fasta.1;  /usr/bin/pod2man debian/tmp/usr/bin/clustalw2phylip > debian/tmp-manpages/clustalw2phylip.1;  /usr/bin/pod2man debian/tmp/usr/bin/compare_dates > debian/tmp-manpages/compare_dates.1;  /usr/bin/pod2man debian/tmp/usr/bin/compute-prior-dist > debian/tmp-manpages/compute-prior-dist.1;  /usr/bin/pod2man debian/tmp/usr/bin/compute-uniform-priors > debian/tmp-manpages/compute-uniform-priors.1;  /usr/bin/pod2man debian/tmp/usr/bin/download > debian/tmp-manpages/download.1;  /usr/bin/pod2man debian/tmp/usr/bin/draw-mhmm > debian/tmp-manpages/draw-mhmm.1;  /usr/bin/pod2man debian/tmp/usr/bin/dreme > debian/tmp-manpages/dreme.1;  /usr/bin/pod2man debian/tmp/usr/bin/dust > debian/tmp-manpages/dust.1;  /usr/bin/pod2man debian/tmp/usr/bin/fasta-center > debian/tmp-manpages/fasta-center.1;  /usr/bin/pod2man debian/tmp/usr/bin/fasta-dinucleotide-shuffle > debian/tmp-manpages/fasta-dinucleotide-shuffle.1;  /usr/bin/pod2man debian/tmp/usr/bin/fasta-dinucleotide-shuffle.py > debian/tmp-manpages/fasta-dinucleotide-shuffle.py.1;  /usr/bin/pod2man debian/tmp/usr/bin/fasta-fetch > debian/tmp-manpages/fasta-fetch.1;  /usr/bin/pod2man debian/tmp/usr/bin/fasta-get-markov > debian/tmp-manpages/fasta-get-markov.1;  /usr/bin/pod2man debian/tmp/usr/bin/fasta-hamming-enrich > debian/tmp-manpages/fasta-hamming-enrich.1;  /usr/bin/pod2man debian/tmp/usr/bin/fasta-hamming-enrich.py > debian/tmp-manpages/fasta-hamming-enrich.py.1;  /usr/bin/pod2man debian/tmp/usr/bin/fasta-io > debian/tmp-manpages/fasta-io.1;  /usr/bin/pod2man debian/tmp/usr/bin/fasta-make-index > debian/tmp-manpages/fasta-make-index.1;  /usr/bin/pod2man debian/tmp/usr/bin/fasta-shuffle-letters > debian/tmp-manpages/fasta-shuffle-letters.1;  /usr/bin/pod2man debian/tmp/usr/bin/fasta-subsample > debian/tmp-manpages/fasta-subsample.1;  /usr/bin/pod2man debian/tmp/usr/bin/fasta-unique-names > debian/tmp-manpages/fasta-unique-names.1;  /usr/bin/pod2man debian/tmp/usr/bin/fimo > debian/tmp-manpages/fimo.1;  /usr/bin/pod2man debian/tmp/usr/bin/fitevd > debian/tmp-manpages/fitevd.1;  /usr/bin/pod2man debian/tmp/usr/bin/gendb > debian/tmp-manpages/gendb.1;  /usr/bin/pod2man debian/tmp/usr/bin/get_db_csv > debian/tmp-manpages/get_db_csv.1;  /usr/bin/pod2man debian/tmp/usr/bin/getsize > debian/tmp-manpages/getsize.1;  /usr/bin/pod2man debian/tmp/usr/bin/gomo > debian/tmp-manpages/gomo.1;  /usr/bin/pod2man debian/tmp/usr/bin/gomo_highlight > debian/tmp-manpages/gomo_highlight.1;  /usr/bin/pod2man debian/tmp/usr/bin/hart2meme-bkg > debian/tmp-manpages/hart2meme-bkg.1;  /usr/bin/pod2man debian/tmp/usr/bin/hartemink2psp > debian/tmp-manpages/hartemink2psp.1;  /usr/bin/pod2man debian/tmp/usr/bin/hypergeometric.py > debian/tmp-manpages/hypergeometric.py.1;  /usr/bin/pod2man debian/tmp/usr/bin/iupac2meme > debian/tmp-manpages/iupac2meme.1;  /usr/bin/pod2man debian/tmp/usr/bin/jaspar2meme > debian/tmp-manpages/jaspar2meme.1;  /usr/bin/pod2man debian/tmp/usr/bin/llr > debian/tmp-manpages/llr.1;  /usr/bin/pod2man debian/tmp/usr/bin/log-hmm > debian/tmp-manpages/log-hmm.1;  /usr/bin/pod2man debian/tmp/usr/bin/mast > debian/tmp-manpages/mast.1;  /usr/bin/pod2man debian/tmp/usr/bin/mast2txt > debian/tmp-manpages/mast2txt.1;  /usr/bin/pod2man debian/tmp/usr/bin/mcast > debian/tmp-manpages/mcast.1;  /usr/bin/pod2man debian/tmp/usr/bin/meme > debian/tmp-manpages/meme.1;  /usr/bin/pod2man debian/tmp/usr/bin/meme-chip > debian/tmp-manpages/meme-chip.1;  /usr/bin/pod2man debian/tmp/usr/bin/meme-get-motif > debian/tmp-manpages/meme-get-motif.1;  /usr/bin/pod2man debian/tmp/usr/bin/meme-xml-html > debian/tmp-manpages/meme-xml-html.1;  /usr/bin/pod2man debian/tmp/usr/bin/meme.bin > debian/tmp-manpages/meme.bin.1;  /usr/bin/pod2man debian/tmp/usr/bin/meme2images > debian/tmp-manpages/meme2images.1;  /usr/bin/pod2man debian/tmp/usr/bin/meme2meme > debian/tmp-manpages/meme2meme.1;  /usr/bin/pod2man debian/tmp/usr/bin/meme_p > debian/tmp-manpages/meme_p.1;  /usr/bin/pod2man debian/tmp/usr/bin/metameme > debian/tmp-manpages/metameme.1;  /usr/bin/pod2man debian/tmp/usr/bin/mhmm > debian/tmp-manpages/mhmm.1;  /usr/bin/pod2man debian/tmp/usr/bin/mhmm-io > debian/tmp-manpages/mhmm-io.1;  /usr/bin/pod2man debian/tmp/usr/bin/mhmm2html > debian/tmp-manpages/mhmm2html.1; Can't open debian/tmp/usr/bin/log-hmm: No such file or directory at /usr/bin/pod2man line 60
Can't open debian/tmp/usr/bin/meme_p: No such file or directory at /usr/bin/pod2man line 60


So this approach is obviosely unreliable and leads to unpredictable
results.  Need more time to check this.

Kind regards

         Andreas.

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