Hi guys, At the moment, I would only be able to do work on this package in my spare time. IVA is building properly with the locally injected python3-pysam, fastaq-1.6, kmc+dfsg-2.0, plus all the already accepted debian packages dependencies.
I can say that at the moment, I do feel motivated to keep working on python-pysam on my own time, but I have to be very honest and say that this motivation might quickly disapear in a couple of days. Main reason for this is that I have several other RT tickets to work on for the Sanger Pathogens Informatics group. To work on this package on the weekend or when I get home after a day's work might really not be what I would like to do. Would be great if python-pysam could be accepted as is, since it is building, and there are no lintian Warnings, nor Errors. Only Infos. Regards, Jorge On Mon, Dec 8, 2014 at 2:57 PM, Jorge Sebastião Soares <j.s.soa...@gmail.com > wrote: > Hi Andreas, > > If I run lintian with -i -I I get this: > > vagrant@debian:~/deb-alioth/current/pysam_packaging/python-pysam$ lintian > -i -I ../python3-pysam_0.8.1-1_amd64.deb > I: python3-pysam: hardening-no-fortify-functions > usr/lib/python3/dist-packages/pysam/ > TabProxies.cpython-34m-x86_64-linux-gnu.so > N: > N: This package provides an ELF binary that lacks the use of fortified > libc > N: functions. Either there are no potentially unfortified functions > called > N: by any routines, all unfortified calls have already been fully > validated > N: at compile-time, or the package was not built with the default Debian > N: compiler flags defined by dpkg-buildflags. If built using > N: dpkg-buildflags directly, be sure to import CPPFLAGS. > N: > N: NB: Due to false-positives, Lintian ignores some unprotected > functions > N: (e.g. memcpy). > N: > N: Refer to https://wiki.debian.org/Hardening and > N: http://bugs.debian.org/673112 for details. > N: > N: Severity: normal, Certainty: wild-guess > N: > N: Check: binaries, Type: binary, udeb > N: > I: python3-pysam: spelling-error-in-binary > usr/lib/python3/dist-packages/pysam/ > calignmentfile.cpython-34m-x86_64-linux-gnu.so explicitely explicitly > N: > N: Lintian found a spelling error in the given binary. Lintian has a > list > N: of common misspellings that it looks for. It does not have a > dictionary > N: like a spelling checker does. > N: > N: If the string containing the spelling error is translated with the > help > N: of gettext or a similar tool, please fix the error in the > translations > N: as well as the English text to avoid making the translations fuzzy. > With > N: gettext, for example, this means you should also fix the spelling > N: mistake in the corresponding msgids in the *.po files. > N: > N: You can often find the word in the source code by running: > N: > N: grep -rw <word> <source-tree> > N: > N: This tag may produce false positives for words that contain non-ASCII > N: characters due to limitations in strings. > N: > N: Severity: minor, Certainty: wild-guess > N: > N: Check: binaries, Type: binary, udeb > N: > I: python3-pysam: spelling-error-in-binary > usr/lib/python3/dist-packages/pysam/ > calignmentfile.cpython-34m-x86_64-linux-gnu.so auxilliary auxiliary > I: python3-pysam: hardening-no-fortify-functions > usr/lib/python3/dist-packages/pysam/ > calignmentfile.cpython-34m-x86_64-linux-gnu.so > I: python3-pysam: spelling-error-in-binary > usr/lib/python3/dist-packages/pysam/ctabix.cpython-34m-x86_64-linux-gnu.so > preceeding preceding > I: python3-pysam: hardening-no-fortify-functions > usr/lib/python3/dist-packages/pysam/ctabix.cpython-34m-x86_64-linux-gnu.so > I: python3-pysam: spelling-error-in-binary > usr/lib/python3/dist-packages/pysam/cvcf.cpython-34m-x86_64-linux-gnu.so > tEH the > I: python3-pysam: extended-description-is-probably-too-short > N: > N: The extended description (the lines after the first line of the > N: "Description:" field) is only one or two lines long. The extended > N: description should provide a user with enough information to decide > N: whether they want to install this package, what it contains, and how > it > N: compares to similar packages. One or two lines is normally not > enough to > N: do this. > N: > N: Refer to Debian Developer's Reference section 6.2.1 (General > guidelines > N: for package descriptions) and Debian Developer's Reference section > 6.2.3 > N: (The long description) for details. > N: > N: Severity: minor, Certainty: possible > N: > N: Check: description, Type: binary, udeb > N: > > which is different from what you get. > > I will work on changing the setup.py and make this into a +dfsg package, > but was wondering why the difference. > > Regards, > > Jorge > > On Sun, Dec 7, 2014 at 9:03 PM, Andreas Tille <andr...@an3as.eu> wrote: > >> Hi Jorge, >> >> On Sun, Dec 07, 2014 at 04:51:11PM +0000, Jorge Sebastião Soares wrote: >> > > It looks like the pysam source package contains the source code for an >> > > older samtools and tabix version. >> > > >> > Should I just turn this package into +dfsg, and implement dependency on >> the >> > new samtools and tabix? >> >> This would perfectly fit the Debian philosophy. If the test suite works >> with the Debian packaged versions this would be really great. >> >> Kind regards >> >> Andreas. >> >> -- >> http://fam-tille.de >> >> >> -- >> To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org >> with a subject of "unsubscribe". Trouble? Contact >> listmas...@lists.debian.org >> Archive: https://lists.debian.org/20141207210356.gk22...@an3as.eu >> >> >
