Re: RFS: prinseq-lite: added dependencies to fix autopkgtest failures
Hi Andreas, On 2020-05-19 09:55, Andreas Tille wrote: > On Tue, May 19, 2020 at 06:45:41AM +0300, mer...@debian.org wrote: >> Embedded copies of netlib seem abundant in Debian [1]. I suggest looking >> into debian/copyright of these packages. It is curious, however, that >> netlib is not packaged as a stand-alone package, but embedded everywhere >> instead. > I think libblas-dev is your friend - may be discussing on Debian Science. This is interesting. It is worth checking whether Math::Cephes could be linked against BLAS. If so, embedded netlib sources could be excluded. Best, Andrius
Statistics::PCA and friends
Good day everyone, Last month I packaged a program, prinseq-lite, for the Debian Med team, which provides a graphing command which has two flavors: - one with full options: prinseq-graphs.pl; - one with missing graphs in output: prinseq-graphs-noPCA.pl. I only enabled the limited flavor missing PCA diagrams because it requires the Statistics::PCA module, which is currently missing from Debian. However, for the sake of completeness, it would be nice to have the full capability available natively into Debian. I had a look at the Debian Perl policy[1], and gave a try to the command dh-make-perl, following the nice recommendations of the Debian Med Team fellows, and have a few skeletons of packages, which still need a bit of work but are taking shape: - libstatistics-pca-perl - libmath-matrixreal-perl - libmath-cephes-perl, although this one made me trigger a discussion regarding copyright statements, and library convenience copies on Debian Med list[2,3]) I'm at a point where I understand it would be nice that a few more eyeballs should able to have a look at my hacks. :) May I make use of the perl-team modules namespace to host the repositories for these modules ? If necessary, my Salsa account is emollier. Kind Regards, -- Étienne Mollier Fingerprint: 5ab1 4edf 63bb ccff 8b54 2fa9 59da 56fe fff3 882d Help find cures against the Covid-19 ! Give CPU cycles: * Rosetta@home: https://boinc.bakerlab.org/rosetta/ * Folding@home: https://foldingathome.org/ [1] https://www.debian.org/doc/packaging-manuals/perl-policy/ [2] https://lists.debian.org/debian-med/2020/05/msg00153.html [3] https://lists.debian.org/debian-med/2020/05/msg00156.html signature.asc Description: PGP signature
Re: RFS: prinseq-lite: added dependencies to fix autopkgtest failures
Hi Andreas, Hi Andrius, mer...@debian.org, on 2020-05-19 12:02:15 +0300: > On 2020-05-19 09:55, Andreas Tille wrote: > > On Tue, May 19, 2020 at 06:45:41AM +0300, mer...@debian.org wrote: > > > Embedded copies of netlib seem abundant in Debian [1]. I suggest looking > > > into debian/copyright of these packages. It is curious, however, that > > > netlib is not packaged as a stand-alone package, but embedded everywhere > > > instead. > > I think libblas-dev is your friend - may be discussing on Debian Science. > This is interesting. It is worth checking whether Math::Cephes could be > linked against BLAS. If so, embedded netlib sources could be excluded. For what it's worth, looking at the C code embeded into the Perl modules, this seems to be the result of a swig wrapping. I'm a bit unsure how the relinking is supposed to occur in that kind of cases (maybe it's not too hard, I just haven't dived into this sort of thing yet). But yes, I understand that avoiding convenience copies in the source code is definitely wanted by the Debian Policy. Kind Regards, -- Étienne Mollier Fingerprint: 5ab1 4edf 63bb ccff 8b54 2fa9 59da 56fe fff3 882d Help find cures against the Covid-19 ! Give CPU cycles: * Rosetta@home: https://boinc.bakerlab.org/rosetta/ * Folding@home: https://foldingathome.org/ signature.asc Description: PGP signature
Re: RFS: prinseq-lite: added dependencies to fix autopkgtest failures
Hi Étienne, On 2020-05-19 23:01, Étienne Mollier wrote: > For what it's worth, looking at the C code embeded into the Perl > modules, this seems to be the result of a swig wrapping. I'm a > bit unsure how the relinking is supposed to occur in that kind > of cases (maybe it's not too hard, I just haven't dived into > this sort of thing yet). But yes, I understand that avoiding > convenience copies in the source code is definitely wanted by > the Debian Policy. Swig wrappers could (and, in my understanding of Debian policies of rebuilding things from source, should) be regenerated from Cephes.i file. Best, Andrius signature.asc Description: OpenPGP digital signature
