Bug#945133: gcc-9: __has_attribute(ifunc) false positive on hurd and kfreebsd
Hi Samuel, I forwarded the bug to the GCC tracker and they said that your interpretation of the docs is correct. I doubt whether they are willing to change the behaviour, but we'll see. Best, Fabian
Bug#945133: gcc-9: __has_attribute(ifunc) false positive on hurd and kfreebsd
forwarded 945133 https://gcc.gnu.org/bugzilla/show_bug.cgi?id=93419
Bug#944299: ITP: phylonium -- Fast and Accurate Estimation of Evolutionary Distances
Hi all, I started packaging phylonium locally. However, I can't push to salsa because of some "default branch" issue. As I am only a "Developer" for that repo, I can't change it my self. Could someone fix that for me or make me a maintainer so that I can do it? Best Fabian https://salsa.debian.org/med-team/phylonium On 07.11.19 13:34, Fabian Kloetzl wrote: Package: wnpp Severity: wishlist Owner: Fabian Klötzl * Package name: phylonium Version : 1.1 Upstream Author : Fabian Klötzl * URL : https://github.com/evolbioinf/phylonium * License : GPL Programming Lang: C++ Description : Fast and Accurate Estimation of Evolutionary Distances This is the phylonium program for estimating the evolutionary distances between closely related genomes. It is much faster than alignment based approaches for phylogeny reconstruction and usually more accurate than competing alignment-free methods. This package will be co-maintained in the Debian Med Team.
Bug#936088: [Debian-med-packaging] Bug#936088: marked as done (libmurmurhash autopkg tests fail)
I saw that there was something wrong with the CI of libmurmurhash but didn't have the time to look into it, yet. Thanks to Matthias for the patch and to Andreas for releasing a new version so quickly. Best, Fabian
Bug#922010: RFS: libmurmurhash 1.3
On 11.02.19 22:24, Andreas Tille wrote: I had a look on the build logs[1] and at least mips and s390x keep on failing (some archs are not yet build). Sorry for keeping you busy with this That's fine, because it is entirely my fault; Wouldn't have happened if I had merged your automake suggestion. Pushed a new release to salsa. To quote another authority: "Everything should be made as simple as possible, but not simpler." (A. Einstein) I regard the simple Makefile as to simple for the intended purpose. Touché. Fabian
Bug#922010: RFS: libmurmurhash 1.3
Hi Andreas, On 11.02.19 15:41, Andreas Tille wrote: Furthermore, I added some man page links. I also wanted to remove some private functions from the .symbols file. However, that resulted in a lintian error. Could you be more verbose about what you did and what lintian error was issued? Normally you do not simply remove symbols vrom the .symbols file manually. You should rather declare the interface private inside the code and update the symbols file. Long Description: PMurHash comes with a few functions e.g. "PMurHash32_Process" which I use internally, but I don't want to support. The true API of libmurmurhash consists of six functions "prefixed with lmmh_ or MurmurHash3_. Only these functions appear in the header supplied by the -dev package. As they are the public interface, only they should appear in the symbols file, right? So my advise to upstream is: 1. Declare the private functions really private Got it; managed to define the PMurHash with visibility hidden. Will create a new upstream version with bumped soname some time. 2. Use Automake I leave it to Lennart Poettering to describe the madness that are the autotools: „Das ist ein Perlskript, das ein m4-Skript generiert, das ein Shellskript generiert, was ein Makefile generiert.“ [1] Even though I know automake, I am a bit reluctant to add it to libmurmurhash, because I think that for such a small project a simple makefile should suffice. (And it works just fine on Arch Linux *cough*) 3. Bump SONAME if the resulting lib has changed / removed symbols Please note: Bumping SONAME also means changing the package name and thus trying another round inside new queue. While currently ftpmaster is incredibly quick I've seen relion sitting there for longer than expected due to the same reason (admittedly way more complex code to review). In any case the tour via new queue has a non-predictable delay time and may be we wait until mash has migrated to testing before doing this. Fully agree on this one; Let's take one step after the other, first libmurmurhash, then mash, then our other packages, and, maybe if we want to and the API/ABI is stable, other debian packages. Best, Fabian 1: https://cre.fm/cre209-das-linux-system?t=15:53
Bug#919778: Bug#918566: Lost of code copies of MurmurHash3 (Was: Bug#918566: mash FTBFS on big endian: test failures)
Hi Andreas, On 07.02.19 14:58, Andreas Tille wrote: There are also build issues of libmurmurhash on some architectures[2] Any idea what to do next? [2] https://buildd.debian.org/status/package.php?p=libmurmurhash=sid I hope to have fixed the build issues upstream. Have pushed a new—and hopefully working—version to salsa. Could you sponsor another upload? I will take a further look at the package next week. Have a nice weekend Fabian
Bug#919778: Bug#918566: Lost of code copies of MurmurHash3 (Was: Bug#918566: mash FTBFS on big endian: test failures)
Hi, On 07.02.19 16:00, Andreas Tille wrote: > I've obviously missed that part of your mail. It is fixed now and I'll > re-upload. No worries. The alternative would have been to create a separate set of unit tests for the 32bit architectures. > > Meanwhile I've fixed the symbols file in Git. Please git pull. > While your at it, could you also push the tags? Thanks in advance Fabian
Bug#919778: Bug#918566: Lost of code copies of MurmurHash3 (Was: Bug#918566: mash FTBFS on big endian: test failures)
On 07.02.19 14:58, Andreas Tille wrote: Unfortunately the -DARCH32 flag (which is set according to the build log[1]) does not help on i386 architecture: ./mash info -d test/reads.msh > test/reads.json diff test/genomes.json test/ref/genomes.json 7c7 < "hashType" : "MurmurHash3_x86_32", --- "hashType" : "MurmurHash3_x64_128", mash uses two different hash functions depending on the architecture: MurmurHash3_x86_32 for 32 bit and MurmurHash3_x64_128 for 64 bit architectures; These produce different hash values. The tests compare the results of one run with a precomputed result. However, the tests check against the 64bit reference. Thus they are bound to fail on 32bit. Hence my suggestion to turn the tests off for 32bit. There are also build issues of libmurmurhash on some architectures[2] This is curious. One of the three hash functions is wrong, but at least consistently wrong. I'll look into that. Fabian
Bug#918566: Lost of code copies of MurmurHash3 (Was: Bug#918566: mash FTBFS on big endian: test failures)
Hi Andreas, On 07.02.19 08:10, Andreas Tille wrote: Unfortunately it does not pass its build time tests any more now that I rebuild it for uploading. I had a look and could trace the failure to two issues. 1) The test should run sequentially; can be fixed via a simple override. 2) The previous commit (ARCH32) doesn't work as expected [1]. Building on AMD64 will still have the -DARCH32 flags. This then leads to a different hash function being used and the tests failing. I tried to fix the conditional in the makefile but cannot figure out what is wrong with it in the first place. Also it should deactivate unit tests on 32bit while at it. Could you take another look at the conditional? Best Fabian 1: https://salsa.debian.org/med-team/mash/commit/42bf5484376d9b3e5ae4271f7d0e998ae0daac34
Bug#918566: Lost of code copies of MurmurHash3 (Was: Bug#918566: mash FTBFS on big endian: test failures)
Hi Andreas, So I improved the upstream libmurmurhash, adapted the package and filed an ITP (#921353). I even managed to locally build mash against the new package. So hereby I kindly ask you to fix the last lintian issue about NMU which I don't fully understand and then maybe sponsor an upload. Best Fabian
Bug#918566: Lost of code copies of MurmurHash3 (Was: Bug#918566: mash FTBFS on big endian: test failures)
As promised, I pushed my packaging attempt. However, I didn't manage to create a repository under med-team, thus it is under my account [1]. Best Fabian 1: https://salsa.debian.org/kloetzl-guest/libmurmurhash
Bug#918566: Lost of code copies of MurmurHash3 (Was: Bug#918566: mash FTBFS on big endian: test failures)
Hi Andreas, I started a new project `libmurmurhash` which should fix the problem of code duplication [1]. However, I could not yet check whether my code produces the correct result on big endian systems without crashing. On x64 it works fine and I also produced a working package locally. I could commit it to salsa tomorrow. The upstream project just needs a bit more polishing (documentation, better tests) before I would call it done. Have a nice Sunday, Fabian 1: https://github.com/kloetzl/libmurmurhash
Bug#918566: Lost of code copies of MurmurHash3 (Was: Bug#918566: mash FTBFS on big endian: test failures)
Hi, There are 162 packages in Debian containing the string MurmurHash. Some of them use an implementation called PMurHash which fixes the endianess issue. On 07.01.19 16:42, Andreas Tille wrote: > It seems to be time to package MurmurHash3 separately, isn't it? Yeah, I think it makes sense to create a libmurmurhash package and then have all "bad" implementations link against that. I will look at some oof the code and start a project. Best, Fabian
Bug#918566: [Debian-med-packaging] Bug#918566: mash FTBFS on big endian: test failures
forwarded 918566 https://github.com/marbl/Mash/issues/106 thanks
Bug#918566: [Debian-med-packaging] Bug#918566: mash FTBFS on big endian: test failures
mash internally uses MurmurHash 3 which is sensitive to the endianess. There is a note in the source [1], but no preventive measures are taken. I will forward this upstream and might even have a go at this myself. (In theory this should not be a big issue expect for slightly inaccurate/different results.) Fabian 1: https://github.com/marbl/Mash/blob/aabd5925e7cfc097a8d89e2d8691ac4af5b95d37/src/mash/MurmurHash3.cpp#L52
Bug#912235: Bug#912235: figtree FTBFS with OpenJDK 11
forwarded 912235 https://github.com/rambaut/figtree/issues/128 I agree, using Java 8 is the easy solution, not the nice one. Even with the hot-of-the-press version 1.4.4 the problem exists, so I opened an issue upstream [1]. I will continue looking into this even if Java is not my strength. Fabian 1: https://github.com/rambaut/figtree/issues/128
Bug#912235: [Debian-med-packaging] Bug#912235: figtree FTBFS with OpenJDK 11
Thank you for reporting. I added a fix to the repo. Will get resolved with the next upload. Best Fabian
Bug#908459: theseus FTBFS with gcc 8
On 11.09.2018 15:58, Adrian Bunk wrote: Control: reopen -1 Some builds were still running into #897876 due to the buildd chroots only regenerated twice per week (which is not something you should be worried about), but the armhf/i386 and ppc64el FTBFS look more like actual problems that need fixing in theseus. Unfortunately, fixing this will take a while longer. I first have to figure out how to build an arm vm because I don't want to debug remotely via the autobuilds. ☺ Best, Fabian
Bug#908459: theseus FTBFS with gcc 8
Hi Andreas, On 10.09.18 13:59, Andreas Tille wrote: > /usr/bin/gcc -O3 -ffast-math -fstrict-aliasing -funroll-loops > -fomit-frame-pointer -Wall -Werror -pedantic -std=c99 -Wno-unused-result > -Wformat-truncation=0 -pthread -c logistic_dist.c > logistic_dist.c: In function 'evallogisticML': > logistic_dist.c:172:1: error: 'reciptmp.16' is used uninitialized in this > function [-Werror=uninitialized] > evallogisticML(const double *x, const int n, > ^~ > cc1: all warnings being treated as errors > That is a compiler bug [1, 2]. Temporarily deactivating -ffast-math or -Werror should help to move on, nonetheless. Best, Fabian 1: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=86835 2: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=897876
Bug#908459: [Debian-med-packaging] Bug#908459: theseus FTBFS with gcc 8
Thanks for reporting. There were plenty of string related errors. Fixed in git repo.
Bug#908039: figtree: Crashes with NoClassDefFoundError
On 05.09.2018 16:13, Andreas Tille wrote: I commited the same change that helped for cgview. Not tested yet but setting tag pending to prevent others from spending time with this most probably solved problem. Tested and it works. Thank you very much. So apparently supplying a classpath via the commandline and the manifest are different things. Thanks for telling me, Java. You would make me very happy, if you were to upload at your leisure. Best, Fabian
Bug#908039: figtree: Crashes with NoClassDefFoundError
On 05.09.2018 14:46, Andreas Tille wrote: Probably same as #907559. Yeah, that looks related. Would you mind adding batik-constants.jar to CLASSPATH and try again? As far as I understand java, I already tried that. One can give additional paths to the java executable via the -cp parameter. That is what I did with the command given, above. Trying the shell variable CLASSPATH does not lead to any improvement either. That is whats bugging me. There is a XMLConstants in the batik-constants.jar. However, java just decides not to load it even though compilation was fine. Best, Fabian
Bug#887632: [Debian-med-packaging] Bug#887632: progressivemauve FTBFS with glibc 2.26
Hi all, This bug is easily fixed by forcing mauve to use the native getopt. A half-hearted fix is pushed. However, I have trouble removing the unnecessary files from the orig tarball, because the pristine-tar branch contains only a .delta and a .id file? Any help would be appreciated. Best Fabian
Bug#859202: warning: 'int readdir_r(DIR*, dirent*, dirent**)' is deprecated
Tags: patch Hi, Since version 3.6.2, there is a proper check for the availability of readdir_r. So we could leave things as they are and wait for libc to remove readdir_r at which point the warnings will also vanish. Or we could force dcmtk to no longer use readdir_r by disabling the check. I attached a patch for the latter. Best, Fabian From: Fabian KlötzlDate: Fri, 22 Dec 2017 12:55:35 + Subject: do not use readdir_r anymore --- CMake/GenerateDCMTKConfigure.cmake | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CMake/GenerateDCMTKConfigure.cmake b/CMake/GenerateDCMTKConfigure.cmake index dc1e920..924586a 100755 --- a/CMake/GenerateDCMTKConfigure.cmake +++ b/CMake/GenerateDCMTKConfigure.cmake @@ -616,7 +616,8 @@ ENDIF(WIN32 AND NOT CYGWIN) CHECK_FUNCTIONWITHHEADER_EXISTS("_fpclassf(0.0f)" "${HEADERS}" HAVE_PROTOTYPE__FPCLASSF) CHECK_FUNCTIONWITHHEADER_EXISTS("getgrnam_r((char*)0,(group*)0,(char*)0,0,(group**)0)" "${HEADERS}" HAVE_GETGRNAM_R) CHECK_FUNCTIONWITHHEADER_EXISTS("getpwnam_r((char*)0,(passwd*)0,(char*)0,0,(passwd**)0)" "${HEADERS}" HAVE_GETPWNAM_R) - CHECK_FUNCTIONWITHHEADER_EXISTS("readdir_r((DIR*)0,(dirent*)0,(dirent**)0)" "${HEADERS}" HAVE_READDIR_R) + #CHECK_FUNCTIONWITHHEADER_EXISTS("readdir_r((DIR*)0,(dirent*)0,(dirent**)0)" "${HEADERS}" HAVE_READDIR_R) + set(HAVE_READDIR_R 0) CHECK_FUNCTIONWITHHEADER_EXISTS(nanosleep "${HEADERS}" HAVE_PROTOTYPE_NANOSLEEP) CHECK_FUNCTIONWITHHEADER_EXISTS("::pw_gecos" "${HEADERS}" HAVE_PASSWD_GECOS)
Bug#780816: December: tophat
Hi Andreas, On 04.12.2017 17:33, Andreas Tille wrote: > On Mon, Dec 04, 2017 at 02:09:48PM +0100, Fabian Klötzl wrote: >> I just pushed some changes to build tophat with our version of libbam. >> Not sure if the previously mentioned issue in [1] is fixed; can't test, > > Thanks to the test suite we now know that the issue is not solved yet: > > $ sh run-unit-test That should be done with my recent commit; The new samtools version used a different set of arguments. That's an old one down for the advent calendar. ☺ Best Fabian
Bug#780816: [Debian-med-packaging] Bug#780816: December: tophat
On 04.12.2017 17:33, Andreas Tille wrote: > Thanks to the test suite we now know that the issue is not solved yet: > > $ sh run-unit-test > > [2017-12-04 17:28:54] Beginning TopHat run (v2.1.1) > --- > [2017-12-04 17:28:54] Checking for Bowtie > Bowtie version:2.3.3.1 > Error locating program: samtools_0.1.18 > > > Unfortunately a grep for this explicite string has several hits. I > have no idea what might happen if we replace it by /usr/bin/samtools. Ah, I took this as a build-only problem. Will look into it. Fabian
Bug#780816: December: tophat
Hi all, I just pushed some changes to build tophat with our version of libbam. Not sure if the previously mentioned issue in [1] is fixed; can't test, because my cowbuild just broke. :( Best, Fabian [1]: https://lists.debian.org/debian-med/2014/10/msg4.html
Bug#752860: bug 752860 is forwarded to https://github.com/Teuniz/EDFbrowser/issues/38
forwarded 752860 https://github.com/Teuniz/EDFbrowser/issues/38 thanks
Bug#866646: Any idea how to fix freebayes? [Was: Bug#866646: freebayes FTBFS with libhts-dev 1.4.1-2]
Hi Andreas, On 02.09.2017 14:54, Andreas Tille wrote: > The htslib issue remains the same but I have no idea how to fix it. The problem is that Allele.h defines a friend function called `json` residing in global namespace. However, hts.h already defined a value of an enum with the same name, thus the symbols clash. Basically, a sed -i 's/json/to_json/' src/Allele.* will fix the issue (also one call in Sample.cpp:267). However, in the long term hts should stop exporting such generic names. C++ invented namespaces and `enum class` exactly to avoid these problems. As htslib is pure C, they should prefix their symbols, as everyone else does it. Btw, I had to add -std=c++11 for a successful build. Best, Fabian
Bug#807486: ITP: INDELible -- A powerful and flexible simulator of biological evolution
Package: wnpp Severity: wishlist Owner: "Debian Med Team"* Package name: INDELible Version : 1.03 Upstream Author : William Fletcher * URL : http://abacus.gene.ucl.ac.uk/software/indelible/ * License : GPL Programming Lang: C++ Description : A powerful and flexible simulator of biological evolution INDELible is a new, portable, and flexible application for biological sequence simulation that combines many features in the same place for the first time. Using a length-dependent model of indel formation it can simulate evolution of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time. .. Nucleotide simulations may use the general unrestricted model or the general time reversible model and its derivatives, and amino-acid simulations can be conducted using fifteen different empirical rate matrices. Substitution rate heterogeneity can be modelled via the continuous and discrete gamma distributions, with or without a proportion of invariant sites. INDELible can also simulate under non-homogenous and non-stationary conditions where evolutionary models are permitted to change across a phylogeny. .. Unique among indel simulation programs, INDELible offers the ability to simulate using codon models that exhibit nonsynonymous/synonymous rate ratio heterogeneity among sites and/or lineages. This package will be maintained as part of the Debian Med packaging team.
Bug#800932: ITP: andi -- Efficient Estimation of Evolutionary Distances
Package: wnpp Severity: wishlist Owner: "Fabian Klötzl" <kloe...@evolbio.mpg.de> * Package name: andi Version : 0.9.4 Upstream Author : Fabian Klötzl <kloe...@evolbio.mpg.de> * URL : https://github.com/EvolBioInf/andi * License : GPL Programming Lang: C Description : Efficient Estimation of Evolutionary Distances This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes. I am the upstream author and think this program is useful for the scientific community to rapidly infer phylogenies. The Debian package will be maintained as part of the Debian Med team.
Bug#800932: ITP: andi -- Efficient Estimation of Evolutionary Distances
On 05.10.2015 10:55, Andreas Tille wrote: > I guess for non-German speakers andy might be a random 4 letter > combination and nobody will confuse it with the tyical nickname of > a German Andreas. :-) Great, I'll stick with "andi" then and continue packaging. Thanks for the quick advice Fabian
Bug#794729: [u...@debian.org: Bug#794729: libdivsufsort-dev: missing dependency on libdivsufsort3]
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi, On 06.08.2015 08:32, Andreas Tille wrote: Hi Fabian, I hope you read the mailing list debian-med-packag...@lists.alioth.debian.org or at least have subscribed this package in the Debian Package Tracker. If not please do either of one to receive the bug reports of your package. Done. BTW, using d-shlibs would prevent such kind of problems. You can find an example usage for instance here: git://anonscm.debian.org/debian-med/libmems.git Ok, I will have a look at it. Also, I included Thomasz in the conversation, as he is also interested in packaging libdivsufsort and has already committed some patches (which may or may not already fix the issue). Fabian - Forwarded message from Aaron M. Ucko u...@debian.org - Date: Wed, 05 Aug 2015 21:46:25 -0400 From: Aaron M. Ucko u...@debian.org To: Debian Bug Tracking System sub...@bugs.debian.org Subject: Bug#794729: libdivsufsort-dev: missing dependency on libdivsufsort3 X-Debian-PR-Message: report 794729 X-Debian-PR-Package: libdivsufsort-dev X-Debian-PR-Keywords: X-Debian-PR-Source: libdivsufsort Package: libdivsufsort-dev Version: 2.0.1-1 Severity: serious Justification: Policy 8.4 libdivsufsort-dev should depend on libdivsufsort3 to ensure that libdivsufsort.so won't dangle. $ ls -l /usr/lib/libdivsufsort.* lrwxrwxrwx 1 root root 22 Jul 28 10:59 /usr/lib/libdivsufsort.so - libdivsufsort.so.3.0.1 $ ls -lL /usr/lib/libdivsufsort.so ls: cannot access /usr/lib/libdivsufsort.so: No such file or directory Could you please fix that? While you're at it, you might also consider changing libdivsufsort3's section from science to libs, since it's not of direct end-user interest. Thanks! -- System Information: Debian Release: stretch/sid APT prefers testing APT policy: (500, 'testing'), (500, 'stable'), (300, 'unstable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.1.0-1-amd64 (SMP w/4 CPU cores) Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) -- no debconf information ___ Debian-med-packaging mailing list debian-med-packag...@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-pac kaging - End forwarded message - -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (GNU/Linux) iQIcBAEBAgAGBQJVwwquAAoJEA/ahZpWA3bB/SoP/3GOaVTIicl3UgikReOOm9Qu OvX4Upyv6oKqYHU707ecI9ChFDco9i1FVdIG61/rZhXtNkPb1lJIwp5YI/b5YcE4 wOcoPQZkQB3vgyGKHW473wr+cK4Cue7EzI1wwrs/t4OysE1H/ziAgbz1YDrskdeE qjnT6QPDLT7EomlJJ+yfts2Pq0YAjDihTyACZ6bT0XiVG02lP9QrftU5YbilSZta YneQqV3rbYqwbLeP9+/QWwm9VIoVkMspXPrCtH5Iwc4JZoUTKU1x1yWMGb+qj1nE 37aHA11wN9+ajw/w9SC09AlhauFqhQd4QyUaIDSpTWdmOk33KGP2zc/1BFPbKsAE GfFvYMny8Leic65yRXlikj3VyPK3blD4dOtMpE62OSqe/X2kdfzwmuHav9hsRaPT BVCQckbWVLl4GkzgRCMKWvFlfA/cXiyQEwGc3TTprF5uyVf/KoyKFDHDWuAtLv+P 13MD0GX1XbZzexh8wW9P3DvwZVrXr/azrcWk7lyv+5+QGeYnmsdQ5RpjIMPd2B3P lHCdXzTyjmQEQBLAlb4tD2JysVr6v8UxdWBNLvTOB2vT9B7/gQs5+vf4cMPgljz+ PJXwCa82ZVswwfk8VkNU2R3FUlaNDAQJvJysRVOrnMyEo9n4nHP3YyZH/kZNHaHw jIpTzwM5MfuB4I2brj2x =UjNQ -END PGP SIGNATURE- -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org