Re: RFS : libdistlib-java
Hi Andreas, Le 25/05/2020 à 23:12, Andreas Tille a écrit : > Hi Pierre, > > On Mon, May 25, 2020 at 10:47:58PM +0200, Pierre Gruet wrote: >> I have packaged libdistlib-java, which is a Java implementation of >> several cdf, pdf, quantile and simulation functions from R, originally >> written in C. >> > [...] >> >> Would it be possible to have a review? It would be precious, as this is >> my first initial packaging! > > Looks pretty good. The only nitpicking comment would be that > in d/changelog you are repeating the version number inside the > text section. I left it as is but its a bit redundant. > Thanks for the review, the upload and this comment! I shall avoid such redundancy next time. > [...] > > Its uploaded now. Thanks a lot again > > Andreas. > > Have a nice afternoon, Best regards, Pierre
Bug#961619: ITP: libmath-cephes-perl -- perl interface to the math cephes library
Package: wnpp Owner: Etienne Mollier Severity: wishlist X-Debbugs-CC: debian-de...@lists.debian.org, debian-p...@lists.debian.org, debian-med@lists.debian.org * Package name: libmath-cephes-perl Version : 0.5305 Upstream Author : Shlomi Fish * URL : https://metacpan.org/release/Math-Cephes * License : Artistic or GPL-1+ Programming Lang: Perl Description : perl interface to the math cephes library Math::Cephes provides an interface to over 150 mathematical functions of the cephes math library of Stephen Moshier, including trigonometric, hyperbolic, exponential, logarithmic, Bessel, Gamma, Beta, elliptic integrals, hypergeometric, distribution functions, etc. Some common constants, such as PI and SQRT2, are also available. As well, there is support for arithmetic operations for fractions (adding, subtracting, dividing, multiplying) and also for various functions of complex numbers. The package will be maintained under the umbrella of the Debian Perl Group. -- Generated with the help of dpt-gen-itp(1) from pkg-perl-tools. This package is one of the dependencies of Statistics::PCA, which in turn is necessary to enable PCA graphs in the package prinseq-lite. The source code of the package for Math::Cephes is available on Salsa: https://salsa.debian.org/perl-team/modules/packages/libmath-cephes-perl 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/
Re: RFS: prinseq-lite: added dependencies to fix autopkgtest failures
Hi Andrius, mer...@debian.org, on 2020-05-20 06:24:47 +0300: > 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. It makes sense. In that particular case though, after a bit of reading and quite some testing, the resulting Cephes.pm regenerated by swig fails the build time testing. I don't exclude this is caused by a mishandling of mine with swig. Here is the kind of command I was considering in d/rules: swig -perl5 -module Math::Cephes -I$(CURDIR)libmd/ \ -o $(CURDIR)/lib/Math/Cephes.pm Cephes.i But I'm afraid to suspect manual modifications in Cephes.pm. Maybe I'll leave these files as such for the moment. Anyway, thanks for the pointer! I believe I learned something useful with swig. 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: undefined vdb_mbed functions in ncbi-vdb2 library - ran out of ideas
"Aaron M. Ucko" writes: > I didn't find as much time as I hoped, but I just pushed changes to > correct sra-sdk's accidental cutover to ncbi-vdb, and will follow up > with my tweaks to both packages when I get a chance. I think I finally have everything in order and on track to migrate, so please don't upload either ncbi-vdb or sra-sdk for non-urgent matters until that happens. (In particular, please hold off for now on updating sra-sdk to the new 2.10.7 point release that showed up along the way.) Thanks! -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu
Re: Statistics::PCA and friends
Hi Gregor, gregor herrmann, on 2020-05-23 14:20:12 +0200: > Thanks for your changes; I just pulled, made one tiny change and > uploaded the package to NEW. and thank you for your upload. :) I believe the package for the Math::Cephes should be in good shape as well, if you, or someone else of the Perl team, wish to review it. For information, there are a few things which might be worth being aware of, at least: * the Cephes library has copyrighted material which I'm half comfortable with, although it is freely redistribuable, and it has already been used in other Debian packages in the past, it concerns the work of Stephen L. Moshier; * I'm under the impression the module should be rebuilt from the swig file Cephes.i, but since the build time testing is failing if I do so, I left lib/Math/Cephes.pm untouched for the time being. I don't know how much of a concern these points are, but for information... 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: gbp related issues with importing new upstream release for raxml-ng
Hi Shayan, On Tue, 26 May 2020, 19:42 Shayan Doust, wrote: > dpkg-source: info: you can integrate the local changes with dpkg-source > --commit > dpkg-source: error: aborting due to unexpected upstream changes, see > /tmp/raxml-ng_0.2.0-1.diff.8CFoS7 > dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status > 2 > A quick guess: maybe topost entry of d/changelog has an version number? If so, updating it should fix this. Hope this helps, Andrius >
Re: gbp related issues with importing new upstream release for raxml-ng
On Tue, 26 May 2020, 21:25 Andrius Merkys, wrote: > A quick guess: maybe topost entry of d/changelog has an version number? If > so, updating it should fix this. > I meant: an old version number. Andrius >
Re: gbp related issues with importing new upstream release for raxml-ng
On Tue, 26 May 2020, 22:03 Shayan Doust, wrote: > That fixed it - thanks. That didn't come into mind because I was under > the impression that the version in the changelog didn't make such major > difference but the git tag itself. > I remember this took quite some time for me to figure it out myself too :) Best, Andrius >
Re: gbp related issues with importing new upstream release for raxml-ng
On Tue, May 26, 2020 at 10:14:11PM +0300, Andrius Merkys wrote: > > I remember this took quite some time for me to figure it out myself too :) gbp checks out the tarball from pristine-tar that matches the version number in d/changelog. If this does not fit the content of the files inside master branch you get the said error. Kind regards Andreas. -- http://fam-tille.de
Re: Bug#961619: ITP: libmath-cephes-perl -- perl interface to the math cephes library
Hi Étienne, On Tue, May 26, 2020 at 07:10:49PM +0200, Étienne Mollier wrote: > ... > The package will be maintained under the umbrella of the Debian Perl Group. Thanks for packaging this. I guess sponsoring is no issue in Debian Perl Group - please let us know if this assumption is wrong. Kind regards Andreas. -- http://fam-tille.de
Re: gbp related issues with importing new upstream release for raxml-ng
On Tue, May 26, 2020 at 09:38:38PM +0200, Andreas Tille wrote: > On Tue, May 26, 2020 at 10:14:11PM +0300, Andrius Merkys wrote: > > > > I remember this took quite some time for me to figure it out myself too :) > > gbp checks out the tarball from pristine-tar that matches the version > number in d/changelog. If this does not fit the content of the files > inside master branch you get the said error. BTW, if you would have done apt-get install routine-update routine-update you would not have run into this since the version number in d/changelog is bumped automatically. ;-) So far for the advertising Andreas. -- http://fam-tille.de
Re: undefined vdb_mbed functions in ncbi-vdb2 library - ran out of ideas
Hi Aaron, On Tue, May 26, 2020 at 01:41:41PM -0400, Aaron M. Ucko wrote: > I think I finally have everything in order and on track to migrate, so > please don't upload either ncbi-vdb or sra-sdk for non-urgent matters > until that happens. (In particular, please hold off for now on updating > sra-sdk to the new 2.10.7 point release that showed up along the way.) Thanks a lot for this. As far as it concerns me I'm super happy that some obviously competent maintainer picked up this set of packages and will not touch it without any big need. Kind regards Andreas. -- http://fam-tille.de
Re: RFS: prinseq-lite: added dependencies to fix autopkgtest failures
Hi Étienne, On Tue, May 26, 2020 at 07:41:48PM +0200, Étienne Mollier wrote: > > Swig wrappers could (and, in my understanding of Debian policies of > > rebuilding things from source, should) be regenerated from Cephes.i file. > > It makes sense. In that particular case though, after a bit of > reading and quite some testing, the resulting Cephes.pm > regenerated by swig fails the build time testing. I don't > exclude this is caused by a mishandling of mine with swig. > Here is the kind of command I was considering in d/rules: > > swig -perl5 -module Math::Cephes -I$(CURDIR)libmd/ \ > -o $(CURDIR)/lib/Math/Cephes.pm Cephes.i > > But I'm afraid to suspect manual modifications in Cephes.pm. > Maybe I'll leave these files as such for the moment. > > Anyway, thanks for the pointer! > I believe I learned something useful with swig. If I were you I would formally commit your try and ask on debian-mentors (may be adding some diff between the upstream version and the generated one). In case it does not trigger some help I agree that for the moment the upstream provided file might be OK. Sorry, but I can not help with swig. Kind regards Andreas. -- http://fam-tille.de
Re: Bug#961619: ITP: libmath-cephes-perl -- perl interface to the math cephes library
Hi Andreas, Andreas Tille, on 2020-05-26 21:50:13 +0200: > On Tue, May 26, 2020 at 07:10:49PM +0200, Étienne Mollier wrote: > > ... > > The package will be maintained under the umbrella of the Debian Perl Group. > > Thanks for packaging this. I guess sponsoring is no issue in Debian Perl > Group - please let us know if this assumption is wrong. So far I have a very positive impression of the Debian Perl Team; I guess things should go well. :) Should the package happen to be stuck at upload, then I would probably ping both teams through the existing mail thread. Thanks for your concern, 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: undefined vdb_mbed functions in ncbi-vdb2 library - ran out of ideas
On 26.05.20 21:55, Andreas Tille wrote: Hi Aaron, On Tue, May 26, 2020 at 01:41:41PM -0400, Aaron M. Ucko wrote: I think I finally have everything in order and on track to migrate, so please don't upload either ncbi-vdb or sra-sdk for non-urgent matters until that happens. (In particular, please hold off for now on updating sra-sdk to the new 2.10.7 point release that showed up along the way.) Thanks a lot for this. As far as it concerns me I'm super happy that some obviously competent maintainer picked up this set of packages and will not touch it without any big need. Same here. I already spammed Aaron with emails praising and thanking him. Best, Steffen
Re: RFS: prinseq-lite: added dependencies to fix autopkgtest failures
Hi Andreas, Andreas Tille, on 2020-05-26 22:01:41 +0200: > If I were you I would formally commit your try and ask on debian-mentors > (may be adding some diff between the upstream version and the generated > one). In case it does not trigger some help I agree that for the moment > the upstream provided file might be OK. Good idea, I subscribe! (to both the idea and the mailing list... :) Cheers, -- 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 2020-05-26 20:41, Étienne Mollier wrote: > It makes sense. In that particular case though, after a bit of > reading and quite some testing, the resulting Cephes.pm > regenerated by swig fails the build time testing. I don't > exclude this is caused by a mishandling of mine with swig. > Here is the kind of command I was considering in d/rules: > > swig -perl5 -module Math::Cephes -I$(CURDIR)libmd/ \ > -o $(CURDIR)/lib/Math/Cephes.pm Cephes.i > > But I'm afraid to suspect manual modifications in Cephes.pm. > Maybe I'll leave these files as such for the moment. This is an interesting data point. I have some experience with swig, and I could give it a look. I suggest opening a git branch with your attempt to rebuild swig bindings. Thus your attempt will not interfere with packaging and uploading Math::Cephes with upstream-provided bindings. Best, Andrius signature.asc Description: OpenPGP digital signature
