Re: Bug#896483: beast-mcmc FTBFS with TeX Live 2018

Control: tags -1 help Hi On Sat, Apr 21, 2018 at 05:57:50PM +0300, Adrian Bunk wrote: > > Fix is attached. I tried this patch in Git[1] but when I build the packag I'm running into ... This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)

cmake packages fail to build since yesterday even if package has build before

Hi, since yesterday packages using cmake are failing. Example: libbpp-core has build yesterday according to https://buildd.debian.org/status/package.php?p=libbpp-core but it fails if I build today in current pbuilder (just not building the build target). A very similar package libbpp-seq

Re: Different symbols files on different architectures

Hi Bas, On Fri, Apr 06, 2018 at 02:18:03PM +0200, Sebastiaan Couwenberg wrote: > On 04/06/2018 02:08 PM, Andreas Tille wrote: > > after adding a symbols file to libbpp-core all other architectures are > > failing due to different symbols (see below for ppc64el[1]) but others

Different symbols files on different architectures

Hi, after adding a symbols file to libbpp-core all other architectures are failing due to different symbols (see below for ppc64el[1]) but others are failing as well. What is the correct way to fix this? Kind regards Andreas. On Fri, Apr 06, 2018 at 11:04:02AM +0200, Julien Yann Dutheil

Re: Testsuite of package squizz fails for d/compat > 9

On Sun, Feb 18, 2018 at 04:00:48PM +0100, Sebastiaan Couwenberg wrote: > The parallel option is enabled by default for compat level >= 10, try > setting `dh --no-parallel` to disable the parallel option again. I confirm that running only build time tests with --no-parallel is sufficient. I'm a

Testsuite of package squizz fails for d/compat > 9

trol b/debian/control index c543fc7..46b86f0 100644 --- a/debian/control +++ b/debian/control @@ -4,8 +4,7 @@ Uploaders: Olivier Sallou <osal...@debian.org>, Andreas Tille <ti...@debian.org> Section: science Priority: optional -Build-Depends: debhelper (>= 9), -

Re: Problem with Qt progam bandage

On Mon, Feb 12, 2018 at 01:01:28PM +0500, Andrey Rahmatullin wrote: > On Sun, Feb 11, 2018 at 06:51:45PM +0100, Andreas Tille wrote: > > I'm currently mentoring Cédric Lood to package bandage[1]. > > Unfortunately we both failed to get the package building inside > > a

Problem with Qt progam bandage

Hi folks, I'm currently mentoring Cédric Lood to package bandage[1]. Unfortunately we both failed to get the package building inside a pbuilder chroot while it builds on Cédric's local machine. I remember that there was a magic way to know how to add the needed Build-Depends but I forgot how to

How to sensibly announce a finalised packaging if I do not intend to upload myself (Was: packjpg packaging: C++ help needed)

Hi Juhani, On Wed, Jan 31, 2018 at 07:35:47PM +0200, Juhani Numminen wrote: > > The compilation succeeds if I modify the patch not to define DEV_INFOS: > > $ git diff -U0 > diff --git a/debian/patches/dev.patch b/debian/patches/dev.patch > index 02869a1..415ebda 100644 > ---

packjpg packaging: C++ help needed

Hi, I stumbled upon unfinished packaging for packjpg in collab-maint SVN[1]. I intended to save the current packaging state to Git before SVN will be closed down and consiered pkg-phototools a better place than collab-maint. So I updated the packaging to latest upstream and pushed the packaging

Re: r-cran-git2r uses private header files of libgit2 (Was: Help with libgit2 needed to strip code copy from r-cran-git2r)

Hi Dirk, On Thu, Jan 11, 2018 at 10:51:45AM -0600, Dirk Eddelbuettel wrote: > > I had some friendly emails with Stefan (git2r upstream) when he started the R > package git2r (as I needed some features in my drat R package) and he > expressed quite some frustration at working with libgit2 as it

r-cran-git2r uses private header files of libgit2 (Was: Help with libgit2 needed to strip code copy from r-cran-git2r)

Hi again, On Thu, Jan 11, 2018 at 08:34:09AM +0100, Andreas Tille wrote: > > # Add include paths for git2r > > -CPPFLAGS="-I. -Ilibgit2/src -Ilibgit2/include -Ilibgit2/deps/http-parser > > ${CPPFLAGS}" > > -+CPPFLAGS="-I. -I/usr/include/git2 ${CPPFLAG

Re: Help with libgit2 needed to strip code copy from r-cran-git2r

On Thu, Jan 11, 2018 at 12:58:16AM +0100, Jose Luis Rivero wrote: > dah .. I sent the reverse patch sorry: > > diff --git a/debian/patches/use_debian_packaged_libgit2.patch > b/debian/patches/use_debian_packaged_libgit2.patch > index c716773..ab603cd 100644 > ---

Re: Help with libgit2 needed to strip code copy from r-cran-git2r

Hi Aaron, On Wed, Jan 10, 2018 at 06:37:17PM -0500, Aaron M. Ucko wrote: > Andreas Tille <andr...@an3as.eu> writes: > > > Hi, > > Hi, Andreas. > > > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include/git2 > > -DGIT_ARCH_64 -D_GNU_SOUR

Help with libgit2 needed to strip code copy from r-cran-git2r

Hi, r-cran-git2r was rejected by ftpmaster[1] due to the code copy of libgit2. I intended to fix this by removing the code copy and linking against the Debian packaged libgit2. The attempt to do so can be found in Git[2]. Unfortunately that seems to be not as simple as I was hoping for since

[Help] How to relace PADDED define (Was: Bug#884236: fis-gtm FTBFS with linux-libc-dev 4.14.2-1)

Control: tags -1 help Any hint how to replace this define? Thanks for any help Andreas. - Forwarded message from Adrian Bunk - Date: Tue, 12 Dec 2017 22:28:40 +0200 From: Adrian Bunk To: Debian Bug Tracking System

What to do if arch:all package is lacking arch:any package on specific architecture

Hi, there is a series of bugs filed about missing Build-Depends python-pbcore on i386. The problem is that the Arch:all package python-pbcore Depends the Arch:any package python-pysam which is not available on all architectures. I wonder whether the issue would be more transparent when adding

Test failure due to C++ error

control: reopen -1 While the header that was formerly missing is provided the C++ file used for testing has syntax errors: khmer/src/oxli(master) $ c++ -o test-prog-static -static -std=c++11 -I/usr/local/include -I/usr/include/oxli/smhasher test-compile.cc -L/usr/local/lib -loxli -lbz2 -lz

Suspected change in test dependencies - where is "discover" (Was: [Help] Re: Bug#884040: python-matplotlib-venn FTBFS: test failure)

Hi again, On Mon, Dec 11, 2017 at 09:27:57AM +0100, Andreas Tille wrote: > > On Sun, Dec 10, 2017 at 09:05:07PM +0200, Adrian Bunk wrote: > > === warnings summary > > === > > None > > [pytest] section in

Re: [Help] How to fix type issue on 32bit archs in C++ (Was: Bug#852839: baitfisher: FTBFS (32-bit): mixes ::size_t and faststring::size_t)

On Mon, Dec 11, 2017 at 03:23:49PM +0200, Juhani Numminen wrote: > This is not related to the FTBFS, but your and James' messages made me > take a look at the package. I found its makefile could be improved to > accept {CPP,CXX,LD}FLAGS. So if you're also interested in getting > hardening to work

[Help] How to fix type issue on 32bit archs in C++ (Was: Bug#852839: baitfisher: FTBFS (32-bit): mixes ::size_t and faststring::size_t)

control: tags -1 help Hi, I admit I have to poor C++ knowledge to fix this possibly very simple issue. Any help would be welcome. Kind regards Andreas. On Fri, Jan 27, 2017 at 01:23:40PM -0500, Aaron M. Ucko wrote: > Source: baitfisher > Version: 1.0+dfsg-1 > Severity: important >

Re: cc1plus: error: -Wformat-security ignored without -Wformat (Re: CMake help needed to enable hdf5 for gatb-core)

On Sun, Dec 10, 2017 at 12:59:30PM +0100, Gert Wollny wrote: > In summary, Debian flags set -Wformat and -Werror=format-security, but > the package also sets -Wno-format which overrides the former and > results in the error message.  > > Pushed another patch. Cool. Thanks a lot! > Now it seems

cc1plus: error: -Wformat-security ignored without -Wformat (Re: CMake help needed to enable hdf5 for gatb-core)

Hi again, On Mon, Dec 04, 2017 at 05:59:28PM +0100, Andreas Tille wrote: > some problems with gatb[1]. With the new upstream version, I get: > > cc1plus: error: -Wformat-security ignored without -Wformat > [-Werror=format-security] > cc1plus: error: -Wformat-security ignored w

Re: [Debian-med-packaging] C++ help needed for lamarc

Hi Gert, thanks for your hint. On Mon, Dec 04, 2017 at 07:32:42PM +0100, Gert Wollny wrote: > > make_pair doesn't require the explicite type specification, i.e. the > following should work: > > - return make_pair(eigvals, eigvecs); > + return make_pair(eigvals,

Re: CMake help needed to enable hdf5 for gatb-core (Was: [MoM] Re: gatb-core packaging)

Hi again some problems with gatb[1]. With the new upstream version, I get: cc1plus: error: -Wformat-security ignored without -Wformat [-Werror=format-security] cc1plus: error: -Wformat-security ignored without -Wformat [-Werror=format-security] Any idea how to fix this? Kind regards

C++ help needed for lamarc

Hi, I intend to package lamarc[1] and hit the following C++ issue: ... g++ -DHAVE_CONFIG_H -I. -I./config -Wdate-time -D_FORTIFY_SOURCE=2 -DLAMARC_COMPILE_LINUX -DNDEBUG -Wall -Wextra -Wno-unused -I ./config -I ./config -I ./src/bayeslike -I ./ src/control -I ./src/conversion

Help to get Qt GUI of clonalorigin needed

Hi, I intend to package ClonalOrigin and the packaging is ready in Debian Med Git[1] in principle. I needed to apply some patches to migrate the code from Qt4 to Qt5[2] which enabled to **build** the package. However, my totally Qt uneducated simply web search inspired patches only enable to

Re: Bug#882349: sra-sdk FTBFS with glibc 2.25

control: tags -1 help Hi, is there any hint how to fix this issue? On Tue, Nov 21, 2017 at 07:34:09PM +0200, Adrian Bunk wrote: > Source: sra-sdk > Version: 2.8.1-2+dfsg-2 > Severity: serious > Tags: buster sid > Forwarded: https://github.com/ncbi/sra-tools/issues/67 > >

Re: CMake help needed to enable hdf5 for gatb-core (Was: [MoM] Re: gatb-core packaging)

On Tue, Nov 28, 2017 at 10:00:48PM +0100, Christian Seiler wrote: > Hi Andreas, > > On 11/28/2017 11:52 AM, Andreas Tille wrote: > > it turned out hat the cmake issue is a bit tricky for a MoM project so I > > gave it a try myself. The current state of gatb-core packaging

CMake help needed to enable hdf5 for gatb-core (Was: [MoM] Re: gatb-core packaging)

Hi, it turned out hat the cmake issue is a bit tricky for a MoM project so I gave it a try myself. The current state of gatb-core packaging is in Git[1]. I went as far as my poor cmake knowledge permits to replace the cmake hdf5 code to use the Debian packaged code after the internal code copy

Re: C++ help needed for centrifuge

Hi, On Sat, Nov 25, 2017 at 01:39:03PM -0800, Walter Landry wrote: > > In file included from centrifuge_build.cpp:27:0: > > bt2_idx.h: In static member function 'static std::pair > Ebwt*> Ebwt::fromStrings(const > > EList&, bool, int, int, bool, > >

C++ help needed for centrifuge

Hi, I started packaging centrifuge[1] and hit a build error which is most probably caused by gcc-7 incompatibility: ... In file included from centrifuge_build.cpp:27:0: bt2_idx.h: In static member function 'static std::pair Ebwt::fromStrings(const EList

Re: Trying to get rid of code copy of jsoncpp in seqtools

Hi Gert, On Wed, Oct 25, 2017 at 05:47:01PM +0200, Gert Wollny wrote: > This looks like > > #include > > was missing in that file (fix pushed). Thanks. > In addition the include is not found. For that a  > "pkg-config jsoncpp" and the according flag setting should be added. > > If you

Trying to get rid of code copy of jsoncpp in seqtools

Hi, I try to package seqtools[1] which originally contained a code copy of jsoncpp which I removed. Unfortunately the build fails with the Debian packaged jsoncpp and I'm lacking the necessary C++ knowledge to get this fixed. Does anybody have an idea how to fix ... gbtoolsTrackhub.cpp: In

Re: C++ help needed (Was: Help with cmake / Qt5 migration needed)

Hi Juhani, thanks a lot for your help. On Fri, Oct 20, 2017 at 08:41:35PM +0300, Juhani Numminen wrote: > > I think that's the build system sorted, even though the compilation still > fails. Now you probably need to add some includes. I was able to add the said includes but somehow this

Re: C++ help needed (Was: Help with cmake / Qt5 migration needed)

Hi Juhani, On Fri, Oct 20, 2017 at 06:14:02PM +0300, Juhani Numminen wrote: > > I think I fixed this by removing the code copy of CImg.h and using the > > Debian packaged version instead. But the QDebug issue came back and > > may be I need another trick to tweak src/qtbeads/CMakeLists.txt that

C++ help needed (Was: Help with cmake / Qt5 migration needed)

Hi again, On Fri, Oct 20, 2017 at 11:55:22AM +0200, Wout B wrote: > It looks like the initial #include was actually correct and that > it indeed doesn't find it somehow. Manually adding Qt5::Core and > Qt5::Widgets to target_link_libraries seems to work though. I can confirm that this helps -

Re: Help with cmake / Qt5 migration needed

ere to seek for the qt5 includes. I'm afraid that the cmake configuration was not fully successful. Any further hints? Kind regards Andreas. > Op 19 okt. 2017 10:41 p.m. schreef "Andreas Tille" <andr...@an3as.eu>: > > On Thu, Oct 19, 2017 at 07:18:45PM +02

Re: Help with cmake / Qt5 migration needed

On Thu, Oct 19, 2017 at 07:18:45PM +0200, Wout B wrote: > Have you added the LinguistTools component too? I think it depends on that. Ahhh, another step forward and I fixed some more in [1]. Now the configuration seems to be finalised but I get: ... cd

Re: Help with cmake / Qt5 migration needed

Hi Andrey, On Thu, Oct 19, 2017 at 07:16:47PM +0500, Andrey Rahmatullin wrote: > On Thu, Oct 19, 2017 at 04:11:49PM +0200, Andreas Tille wrote: > > The FIND_PACKAGE line was patched by me where I naively did > > > >s/Qt4 REQUIRED/Qt5 REQUIRED/ > find_package(Qt5

Help with cmake / Qt5 migration needed

Hi, I'd like to package beads[1] which is Qt4 but since Qt4 will be droped soon my goal is to port it to Qt5. With my current packaging attempt[1] I get: CMake Error at src/CMakeLists.txt:4 (FIND_PACKAGE): Found package configuration file:

Bug#877196: Please fix lintian warnings

Hi Ghislain Please fix the following issues: W: nfft source: unnecessary-testsuite-autopkgtest-header W: libnfft3-2: transitional-package-should-be-oldlibs-optional oldlibs/extra W: libnfft3-doc: embedded-javascript-library usr/share/doc/libnfft3-doc/html/jquery.js please use libjs-jquery

Bug#878086: Please fix "appstream-metadata-in-legacy-location usr/share/appdata/pyzo.appdata.xml"

Hi Ghislain, please fix W: pyzo: appstream-metadata-in-legacy-location usr/share/appdata/pyzo.appdata.xml N: N:AppStream metadata file was found in /usr/share/appdata/. The AppStream N:XML files should be placed in /usr/share/metainfo/. N: N:Refer to

Re: Help with watchfile to Gitlab clone needed (Was: Source code of altree vanished)

On Fri, Oct 06, 2017 at 06:59:30PM +0800, Paul Wise wrote: > On Fri, Oct 6, 2017 at 6:50 PM, Andreas Tille wrote: > > > Any hint how to fix this? > > If you run uscan with --debug Nice hint! > (or look at the HTML) you can see that > the URLs are domain absolute rath

Help with watchfile to Gitlab clone needed (Was: Source code of altree vanished)

Hi, I migrated the altree package from SVN to Git[1]. I tried to adapt the suggested template for watch files to Gitlab to the gitlab instance running at inria.fr: $ cat debian/watch version=4 opts=filenamemangle=s/.*\.tar\.gz\?ref=v?(\d\S*)/ALTree-$1\.tar\.gz/g \

Re: C++ help needed for new version of tifffile

On Thu, Oct 05, 2017 at 09:56:39PM +0200, Sven Joachim wrote: > On 2017-10-05 21:00 +0200, Andreas Tille wrote: > > It seems that the definition of GET_NEXT_CODE is just wrong - but > > what would be correct? > > Remove the last backslash, or include a blank line after

C++ help needed for new version of tifffile

Hi, I migrated the Debian packaging of tifffile from SVN to Git[1]. After upgrading to the latest upstream version (dated 2017-09-14) I get: ... x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2

fseeko() on reference file: Invalid argument (Was: Bug#876840: staden-io-lib FTBFS on non-i386 32bit: FAIL: java)

control: tags -1 help Hi, I need to admit I have no idea why fseeko() on reference file: Invalid argument is happening on some architectures. Any help is welcome Andreas. On Tue, Sep 26, 2017 at 12:28:38PM +0300, Adrian Bunk wrote: > Source: staden-io-lib > Version: 1.14.9-2 >

Re: Bug#876839: staden-io-lib FTBFS on big endian: error: invalid operands to binary

control: tag -1 help Hi, it seems this problem happens in bgzip interface. Is there any known change to the compression library that is incompatible since staden-iu-lib was successfully uploaded and built (at least on several architectures) yesterday. Any help is welcome Andreas. On

Is there any sensible way to know what qt5 devel packages might be needed as build-depends

Hi, I try to port clonalframe[1] to Qt5 and I somehow wild-guessed what Build-Depends might be needed. Anyway I got qmake: could not find a Qt installation of '' I've got this totally unhelpful message in another package - what is a sensible approach to find the needed packages? Kind

Bug#872652: Problems building package

Hi Ghislain, On Sun, Sep 24, 2017 at 06:54:34PM +0100, Ghislain Vaillant wrote: > > On 24/09/17 11:19, Andreas Tille wrote: > > > > BTW, the issue happens inside the clean target which is run *before* > > chrooting into cowbuilder chroot. > > I have pushe

Re: Bowtie segfaults in pbuilder chroot at build time (Was: Issue with new version of Bowtie)

Hi Phil, On Thu, Sep 21, 2017 at 11:47:40PM +0100, Phil Wyett wrote: > At this current time on a pbuilder sid created using: > > sudo pbuilder create --distribution sid --debootstrapopts --variant=buildd > > I cannot reproduce seg faults at all. I have tracked back through the med list > and

Bug#872652: Problems building package

On Sun, Sep 24, 2017 at 08:39:02AM +0100, Ghislain Vaillant wrote: > > Are you sure your cowbuilder setup is ok? This is usually not a good sign: BTW, the issue happens inside the clean target which is run *before* chrooting into cowbuilder chroot. Kind regards Andreas. --

Bug#872652: Problems building package

On Sun, Sep 24, 2017 at 08:39:02AM +0100, Ghislain Vaillant wrote: > > > $ gbp-build > > gbp:info: Tarballs 'python-pymeasure_0.4.6.orig.tar.gz' not found at > > '../tarballs/' > > gbp:info: Exporting 'WC' to > >

Bug#872652: Problems building package

On Sat, Sep 23, 2017 at 10:39:35AM +0100, Ghislain Vaillant wrote: > > Frederic gave a hint to bug #873921. > > Now that the situation with pandas / statsmodels is resolved, the package > builds fine [1]. > > [1] >

Re: Bowtie segfaults in pbuilder chroot at build time (Was: Issue with new version of Bowtie)

On Thu, Sep 21, 2017 at 07:00:27PM +0200, Steffen Möller wrote: > > That looks pretty similar and no visible missing. > > You have cowdancer - but you are right. Hm. Just because it works for me > without pbuilder - I know the build process takes a while but would you > mind much to confirm the

Re: Bowtie segfaults in pbuilder chroot at build time (Was: Issue with new version of Bowtie)

Hi Phil, thanks for your attempt to help. On Thu, Sep 21, 2017 at 12:15:50PM +0100, Phil Wyett wrote: > 1. Parallel build. > > // Diff starts on line below. > diff --git a/debian/rules b/debian/rules > index 7919361..b536ce7 100755 > --- a/debian/rules > +++ b/debian/rules > @@ -11,7 +11,7 @@

Re: Bowtie segfaults in pbuilder chroot at build time (Was: Issue with new version of Bowtie)

Hi Steffen, On Wed, Sep 20, 2017 at 10:52:55PM +0200, Steffen Möller wrote: > > ... > > Error testing example > > --- tests/example6.out 2017-09-20 13:07:01.0 + +++ example6.out > > 2017-09-20 13:13:53.186064608 + @@ -1 +1,5 @@ - > > gi|110640213|ref|NC_008253.1| 2852852 8:T>A

Bowtie segfaults in pbuilder chroot at build time (Was: Issue with new version of Bowtie)

[switching back to list discussion also involving debian-mentors. Please see the gdb output below I get when installing gdb inside the pbuilder chroot.] Hi Steffen, On Wed, Sep 20, 2017 at 02:26:20PM +0200, Steffen Möller wrote: > >> /build/bowtie-1.2.1.1+dfsg# ./bowtie -a -v 2 e_coli

Re: Nanopolish: gcc-7 issue solved, but immintrin.h missing on most architectures

Hi Gert, On Mon, Sep 18, 2017 at 02:58:32PM +0200, Gert Wollny wrote: > Am Montag, den 18.09.2017, 13:54 +0200 schrieb Andreas Tille: > >  #include > >   ^ > > compilation terminated. > > ... > > > > > > On amd64 t

Nanopolish: gcc-7 issue solved, but immintrin.h missing on most architectures

control: tags -1 help Hi, the gcc-7 issue of nanopolish described in latest upstream (0.8.1) which is now in unstable but according to the build logs[1] on most architecture the build fails with ... cc -o src/thirdparty/scrappie/scrappie_common.o -c -g -O2 -fdebug-prefix-map=/<>=.

Re: Help to add synctex to new version of texmaker

Hi again, On Wed, Sep 13, 2017 at 02:21:25PM +0200, Sebastian Ramacher wrote: > > > > > > Remove the synctex file from HEADERS and SOURCES and add -lsynctex to LIBS > > > > Synctex files are not mentioned in HEADERS nor SOURCES. > > % grep -n synctex texmaker.pro > 111:synctex_parser.h \ >

Re: Help to add synctex to new version of texmaker

Hi Sebastian, On Wed, Sep 13, 2017 at 01:08:54PM +0200, Sebastian Ramacher wrote: > > not sure why you CC me, but … Since the patch for the previous version[1] was crafted by you. :-) > On 2017-09-13 12:46:40, Andreas Tille wrote: > > > > I tried to upgrade TeXMaker t

Help to add synctex to new version of texmaker

Hi, Debian Science team had no answer to my question below. So how can I add synctex library to a qmake project? Any help would be welcome Andreas. - Forwarded message from Andreas Tille <andr...@an3as.eu> - Date: Sun, 10 Sep 2017 20:38:11 +0200 From: Andreas Tille

Re: Is there any chance to easily find out Qt5 Build-Depends (Was: Bug#874851: [clustalx] Future Qt4 removal from Buster)

Hi Andrey, On Mon, Sep 11, 2017 at 01:10:50PM +0500, Andrey Rahmatullin wrote: > That's not enough, you also need > export QT_SELECT=qt5 OK, so I did: $ git diff diff --git a/debian/rules b/debian/rules index 75d1955..d4f697f 100755 --- a/debian/rules +++ b/debian/rules @@ -2,6 +2,8 @@

Is there any chance to easily find out Qt5 Build-Depends (Was: Bug#874851: [clustalx] Future Qt4 removal from Buster)

Hi, I tried to port clustalx[1] to Qt5 by the following patch: diff --git a/debian/control b/debian/control index 569d145..efee27b 100644 --- a/debian/control +++ b/debian/control @@ -6,7 +6,9 @@ Uploaders: Steffen Moeller , Section: science Priority: optional

Please help switching edfbrowser to Qt5

Hi, I tried to switch edfbrowser[1] from Qt4 to Qt5 since upstream confirmed that it builds with Qt5. I tried the following patch: diff --git a/debian/control b/debian/control index b5f9eec..a24d609 100644 --- a/debian/control +++ b/debian/control @@ -5,8 +5,8 @@ Uploaders: Bas Zoetekouw

Re: Gcc-7 help needed to upgrade r-cran-igraph

Hi On Thu, Sep 07, 2017 at 01:32:59PM +0200, Fabian Klötzl wrote: > On 07.09.2017 12:06, Andreas Tille wrote: > > Uhmm, yes, I missed this. Adding Build-Depends libxml2-dev helped ... > > > > Thanks for helping me reading > > It is always the little things.

Re: Gcc-7 help needed to upgrade r-cran-igraph

On Thu, Sep 07, 2017 at 11:00:44AM +0200, Fabian Klötzl wrote: > Note that GRAPHML_NAMESPACE_URI is only defined if > > #if HAVE_LIBXML == 1 > > see src/foreign-graphml.c:37. Maybe hoisting it out of that block might > help? Uhmm, yes, I missed this. Adding Build-Depends libxml2-dev helped ...

Gcc-7 help needed to upgrade r-cran-igraph

Hi I intended to upgrade r-cran-igraph[1] to the latest upstream version but I stumbled upon a strange issue where a #define statement seems to be ignored by the C prepocessor. At first I assumed that some printf format statement would be the cause which I tried to fix in a patch[2] but it seems

Bug#872652: Problems building package

Hi Ghislain, On Mon, Sep 04, 2017 at 11:47:09AM +0200, Ghislain Vaillant wrote: > Hi Andreas, how are you doing? Fine thank you. > On 04/09/17 11:27, Andreas Tille wrote: > > I just ran a test build on debomatic, and it is now riddled with "undefined > symbol: PyFPE_jbu

Bug#872652: Problems building package

Hi Ghislain, when using gbp buildpackage I get gbp:info: Tarballs 'python-pymeasure_0.4.6.orig.tar.gz' not found at '../tarballs/' gbp:info: Exporting 'WC' to '/home/andreas/debian-maintain/alioth/debian-science/git/packages/build-area/python-pymeasure-tmp' gbp:info: Moving

No idea how to fix abs arguments in nanopolish

Hi, to fix bug #853568 I tried a patch (gcc-7.patch) to fix abs() arguments in nanopolish[1] but I have no idea how to deal with this: ... g++ -o src/hmm/nanopolish_pore_model_set.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security

Re: Help needed with gcc-7 error

Hi James, On Sun, Aug 27, 2017 at 02:58:34PM +0100, James Cowgill wrote: > > g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time > > -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools > > -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o > >

Help needed with gcc-7 error

Hi, when trying to build sga it results in an error: ... g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall -Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o libutil_a-VariantIndex.o `test -f

C++ help needed (Was: Bug#853375: disulfinder: ftbfs with GCC-7)

Hi, I moved disulfinder to Git[1] and tried to track down this issue with my limited C++ knowledge but failed. The issue is ... make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/disulfinder-1.2.11=.

Re: How to replace throw exceptions in C++11

Hi, On Fri, Aug 25, 2017 at 11:57:25AM +0200, Christian Seiler wrote: > > The patch in the bug report already disables -Werror - and that should > definitely be what you should use to build the package even after those > warnings have gone. Thanks for the long explanation which is helpful for

How to replace throw exceptions in C++11

Hi, I try to fix #872262 and while I've read that dynamic exception specifications are deprecated in C++11 I have not found a sensible replacement for the affected code. Any hint what to do here? Kind regards Andreas. -- http://fam-tille.de

Re: C++ help needed with new version of phyml

Hi Thomas, On Sat, Jun 24, 2017 at 03:29:56PM +0200, Thomas Schmitt wrote: > i wrote: > > https://anonscm.debian.org/cgit/debian-med/phyml.git/tree/src/lk.c > > has > > ... > > double branch_lens[1] = { len }; > > Duh. That's already how i think it should be. > > The git code has in

C++ help needed with new version of phyml

Hi, I'd like to package the latest version of phyml[1]. Unfortunately I get ... gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -march=native -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o lk.o lk.c utilities.c: In

Help needed for bcl2fastq

Hi folks, I have not even checked whether bcl2fastq EULA is fit for non-free but since we need it locally on more than one box I intend to at least inject the packaging into our Git[1] - may be its useful for somebody else or we can try to convince Illumina to use a free license. Anywaxy I have

Re: Problem backporting libhmsbeagle

Hi James and Gunter, On Sat, Jun 17, 2017 at 12:08:21PM +0100, James Cowgill wrote: > > ++i; > > i &= 3; > > > > Perhaps the c compiler is as unsure which assignment should have the > > precedence as I am. > > Or "i = (i + 1) & 0x3" which I think looks better. > > The original code invokes

Problem backporting libhmsbeagle

Hi, I want to upgrade the backport of libhmsbeagle from 2.1.2+20150609-1~bpo8+1 to 2.1.2+20160831-5. When trying to build the latter I get ... == libhmsbeagle 2.1.2: examples/tinytest/test-suite.log

Droping v5 extension to library names

Hi, when libraries were build with gcc 5 'v5' was added to the soversion inside the library name. Should this extension be kept even if there is a new soversion. For instance for the package libbpp-core2v5 which has now soversion=3. Should the new package be named libbpp-core3v5 or

Bug#864014: Pristine tar for python-pydap is missing

Hi Ghislain, see subject. Kind regards Andreas. -- http://fam-tille.de

Re: Bug#861754: libpll: FTBFS on non-x86: x86intrin.h: No such file or directory

Hi Aaron, On Mon, May 15, 2017 at 10:01:53AM -0400, Aaron M. Ucko wrote: > > Alas, non-x86 builds are still failing, with the immediate cause of > failure being either an uncompilable cpuid call Hmmm, I'm a bit clueless about this. > or (in the case of > powerpc[spe] and ppc64[el]) the use of

Re: Bug#861281: rnahybrid: FTBFS on armel

Hi Gianfranco, On Thu, Apr 27, 2017 at 07:23:20AM +, Gianfranco Costamagna wrote: > > rnahybrid FTBFS on armel: > > the warning above is somewhat important > (too many nested loops), and this usually relates badly with > high optimization levels > > gcc -DHAVE_CONFIG_H -I. -I..

Re: Bug#861281: rnahybrid: FTBFS on armel

tags 861281 help thanks Hi, I admit I have no idea what the problem might be and the build log (see below) does not enable me to spot the issue. Any help would be welcome since otherwise the only solution I could imagine is to ask ftpmaster to remove the armel port of this package. Kind

Re: C++ help needed for psortb

Hi Bastien, On Wed, Apr 19, 2017 at 01:32:43PM +, Bastien Roucaries wrote: > > Le 19 avril 2017 08:09:11 GMT+02:00, Andreas Tille <andr...@an3as.eu> a écrit > : > > > >Psortb[1] was using header files from biosquid[2] and hmmer2[3] but did > >not shipped the

Re: Bug#860652: snap-aligner: FTBFS on i386: SNAPLib/SortedDataWriter.cpp:338:70: error: no matching function for call to 'max(long unsigned int, _int

Hi Lucas, On Wed, Apr 19, 2017 at 11:33:11AM +0200, Lucas Nussbaum wrote: > On 19/04/17 at 09:19 +, Gianfranco Costamagna wrote: > > Can you please fix your script? :) > > rmadison -u debian snap-aligner > > snap-aligner | 1.0~beta.18+dfsg-1 | testing| source, amd64, arm64, > >

Re: Bug#860690: crac: FTBFS on i386: build-dependency not installable: libjellyfish-2.0-dev

Hi Lucas, could you please be more verbose why this is a RC bug? Crac was never Build on i386 (neither was it on any other arch than amd64) exactly because this not installable Build-Dependency. As far as I know there is no point in restricting the Build-Architectures explicitly since once the

Re: Bug#860652: snap-aligner: FTBFS on i386: SNAPLib/SortedDataWriter.cpp:338:70: error: no matching function for call to 'max(long unsigned int, _int64)'

Hi, some hours ago the Debian Med team was flooded with lots of bugs regarding build on i386 - I guess this is not the only team. I need to admit I'm a bit astonished about this kind of bugs that are showing up right now ... may be autobuilding on i386 started right now? Anyway. I try to

Re: C++ help needed for psortb

Hi Christian, On Tue, Apr 18, 2017 at 11:07:03PM +0200, Christian Seiler wrote: > > > > which is probably due to the fact that I did not changed hmmer2 to > > create a shared rather than a static library and lhmmer is not compiled > > with -fPIC. What might be the less stressful way to solve

Re: C++ help needed for psortb

Hi Walter, On Tue, Apr 18, 2017 at 01:26:58PM -0700, Walter Landry wrote: > > hmm-binding.cpp: In member function ‘void HMM::init(char*, int, int)’: > > hmm-binding.cpp:245:20: error: ‘CUT_NONE’ was not declared in this scope > >thresh.autocut = CUT_NONE; > > ^~~~ > >

C++ help needed for psortb

Hi, I intend to package psortb in Debian Med team[1]. To successfully build this package I needed to re-arrange the package layout of biosquid and hmmer2 since psortb is using code from those project but only provides the according header files. This was solved by proper -dev packages -

Re: Sigrok packages review/mentoring

On Wed, Mar 29, 2017 at 11:09:20PM +0200, Zoltan Gyarmati wrote: > Ok, as you might saw i requested (and got) the Debian Science team > membership, and now i'm able to SSH into alioth.debian.org. > Just to make sure i don't mess up anything: > So now i'm supposed to create the the git repos under

Re: After upgrading pbuilder jessie-backports pbuilder stopped working

Hi Mattia, On Tue, Mar 28, 2017 at 05:48:18PM +0200, Mattia Rizzolo wrote: > > Yes, we have a regression. > > I've been told one "solution" is to recreate the chroot using the > jessie-bpo debootstrap. This works. I saved my previous chroot in case testers are needed. > otherwise please

Re: After upgrading pbuilder jessie-backports pbuilder stopped working

Hi Gianfranco, On Tue, Mar 28, 2017 at 01:29:03PM +, Gianfranco Costamagna wrote: > >I: Generated dsc will be overwritten by build result; not generating changes > >file > >I: Copying COW directory > >I: forking: rm -rf /var/cache/pbuilder/build/cow.7226 > >I: forking: cp -al

After upgrading pbuilder jessie-backports pbuilder stopped working

Hi, yesterday I upgraded pbuilder from jessie-backports on a Jessie machine: $ grep pbuilder /var/log/dpkg.log | grep " installed" 2017-03-16 11:02:36 status installed pbuilder:all 0.228.5~bpo8+1 2017-03-27 09:22:52 status installed pbuilder:all 0.228.6~bpo8+1 Since then I get for any build:

Help needed for pandas bug: Could anybody verify the suspicion that tzdata might have some influence?

tags 858260 help thanks Hi, I admit that when reading the bug report I have no idea how to fix it. I can confirm that I can reproduce the issue in a recent unstable chroot. I have added maintainers of tzdata, Debian Science and Debian mentors in CC - just hoping for any helpful hint. Kind

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