Bug#830681: trilinos-all-dev: Updating binutils breaks trilinos
I see your point, so what do I do? Should I file a bug report against binutils? -- debian-science-maintainers mailing list debian-science-maintainers@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#830681: trilinos-all-dev: Updating binutils breaks trilinos
Package: trilinos-all-dev Version: 12.6.3-1 Severity: grave Justification: renders package unusable Dear Maintainer, The latest update of binutils to version 2.26.1-1 makes it imopssible to compile against trilinos. The linker complains /usr/bin/ld: warning: libbfd-2.26-system.so, needed by /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libtrilinos_teuchoscore.so, not found (try using -rpath or -rpath-link) /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libtrilinos_teuchoscore.so: undefined reference to "bfd_openr" /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libtrilinos_teuchoscore.so: riferimento non definito a "bfd_map_over_sections" /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libtrilinos_teuchoscore.so: riferimento non definito a "bfd_close" /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libtrilinos_teuchoscore.so: riferimento non definito a "bfd_check_format" /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libtrilinos_teuchoscore.so: riferimento non definito a "bfd_check_format_matches" /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libtrilinos_teuchoscore.so: riferimento non definito a "bfd_init" collect2: error: ld returned 1 exit status The new target library is $apt-file search libbfd-2.26 binutils: /usr/lib/x86_64-linux-gnu/libbfd-2.26.1-system.so A similar problem was solved for PETSc package recently, see https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=828987 -- System Information: Debian Release: stretch/sid APT prefers testing APT policy: (500, 'testing') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.6.0-1-amd64 (SMP w/4 CPU cores) Locale: LANG=it_IT.UTF-8, LC_CTYPE=it_IT.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages trilinos-all-dev depends on: ii libtrilinos-amesos-dev 12.6.3-1 ii libtrilinos-amesos2-dev12.6.3-1 ii libtrilinos-anasazi-dev12.6.3-1 ii libtrilinos-aztecoo-dev12.6.3-1 ii libtrilinos-belos-dev 12.6.3-1 ii libtrilinos-epetra-dev 12.6.3-1 ii libtrilinos-epetraext-dev 12.6.3-1 ii libtrilinos-galeri-dev 12.6.3-1 ii libtrilinos-globipack-dev 12.6.3-1 ii libtrilinos-ifpack-dev 12.6.3-1 ii libtrilinos-ifpack2-dev12.6.3-1 ii libtrilinos-intrepid-dev 12.6.3-1 ii libtrilinos-isorropia-dev 12.6.3-1 ii libtrilinos-kokkos-dev 12.6.3-1 ii libtrilinos-komplex-dev12.6.3-1 ii libtrilinos-ml-dev 12.6.3-1 ii libtrilinos-moertel-dev12.6.3-1 ii libtrilinos-muelu-dev 12.6.3-1 ii libtrilinos-nox-dev12.6.3-1 ii libtrilinos-optipack-dev 12.6.3-1 ii libtrilinos-pamgen-dev 12.6.3-1 ii libtrilinos-phalanx-dev12.6.3-1 ii libtrilinos-pike-dev 12.6.3-1 ii libtrilinos-piro-dev 12.6.3-1 ii libtrilinos-pliris-dev 12.6.3-1 ii libtrilinos-rol-dev12.6.3-1 ii libtrilinos-rtop-dev 12.6.3-1 ii libtrilinos-rythmos-dev12.6.3-1 ii libtrilinos-sacado-dev 12.6.3-1 ii libtrilinos-shards-dev 12.6.3-1 ii libtrilinos-shylu-dev 12.6.3-1 ii libtrilinos-stokhos-dev12.6.3-1 ii libtrilinos-stratimikos-dev12.6.3-1 ii libtrilinos-teko-dev 12.6.3-1 ii libtrilinos-teuchos-dev12.6.3-1 ii libtrilinos-thyra-dev 12.6.3-1 ii libtrilinos-tpetra-dev 12.6.3-1 ii libtrilinos-trilinoscouplings-dev 12.6.3-1 ii libtrilinos-triutils-dev 12.6.3-1 ii libtrilinos-xpetra-dev 12.6.3-1 ii libtrilinos-zoltan-dev 12.6.3-1 ii libtrilinos-zoltan2-dev12.6.3-1 trilinos-all-dev recommends no packages. Versions of packages trilinos-all-dev suggests: pn trilinos-doc -- no debconf information -- debian-science-maintainers mailing list debian-science-maintainers@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#828987: libpetsc3.6-dev: Updating openmpi breaks usage of PETSc
Package: libpetsc3.6-dev Version: 3.6.4.dfsg1-2 Severity: grave Justification: renders package unusable Dear Maintainer, Every time package openmpi is updated PETSc is rendered unusable by an internal preprocessor directive, resulting in the error /usr/lib/petscdir/3.6.4/x86_64-linux-gnu-real/include/petscsys.h:133:6: error: #error "PETSc was configured with one OpenMPI mpi.h version but now appears to be compiling using a different OpenMPI mpi.h version" #error "PETSc was configured with one OpenMPI mpi.h version but now #appears to be compiling using a different OpenMPI mpi.h version" PETSc needs to be re-configured and re-built with the new openmpi version. Thanks for your help. -- System Information: Debian Release: stretch/sid APT prefers testing APT policy: (500, 'testing') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.6.0-1-amd64 (SMP w/4 CPU cores) Locale: LANG=it_IT.UTF-8, LC_CTYPE=it_IT.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages libpetsc3.6-dev depends on: ii libpetsc3.6.4-dev 3.6.4.dfsg1-2 libpetsc3.6-dev recommends no packages. libpetsc3.6-dev suggests no packages. -- no debconf information -- debian-science-maintainers mailing list debian-science-maintainers@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#787796: fenics fresh installation is broken
Package: fenics Version: 1:1.5.0.1 Severity: grave Justification: renders package unusable Dear Maintainer, a fresh install of fenics yields a broken environment. In fact, the command from dolfin import * in an ipython terminal returns the backtrace you can find in the attachment. The problem might be due to a version mismatch in one of the dependencies [I remember there was little mess during the migration from 1.4.0 to 1.5.0]. Best regards, Massimiliano Leoni -- System Information: Debian Release: stretch/sid APT prefers testing-updates APT policy: (500, 'testing-updates'), (500, 'testing-proposed-updates'), (500, 'stable-updates'), (500, 'proposed-updates'), (500, 'testing'), (500, 'stable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 3.16.0-4-amd64 (SMP w/4 CPU cores) Locale: LANG=it_IT.UTF-8, LC_CTYPE=it_IT.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages fenics depends on: ii dolfin-bin 1.5.0-2 ii dolfin-doc 1.5.0-2 ii libdolfin-dev 1.5.0-2 ii python-dolfin 1.5.0-2 ii python-ffc 1.5.0-3 ii python-fiat 1.5.0-1 ii python-instant 1.5.0-1 ii python-ufl 1.5.0-1 ii python-ufl-doc 1.5.0-1 Versions of packages fenics recommends: ii python-scitools 0.9.0-2 fenics suggests no packages. -- no debconf information In [1]: from dolfin import * --- ValueErrorTraceback (most recent call last) ipython-input-1-f9fe29351801 in module() 1 from dolfin import * /usr/lib/python2.7/dist-packages/dolfin/__init__.pyc in module() 14 15 # Import names from the compiled cpp modules --- 16 from . import cpp 17 from dolfin.cpp import * 18 from dolfin.cpp import __version__, __swigversion__, __pythonversion__ /usr/lib/python2.7/dist-packages/dolfin/cpp/__init__.py in module() 40 41 # Import the module --- 42 exec(from . import %s % module_name) 43 module = globals()[module_name] 44 string in module() /usr/lib/python2.7/dist-packages/dolfin/cpp/common.py in module() 108 __swigversion__ = %d.%d.%d%(tuple(map(int, [tmp[-5], tmp[-3], tmp[-2:]]))) 109 tmp = hex(dolfin_pythonversion()) -- 110 __pythonversion__ = %d.%d.%d%(tuple(map(int, [tmp[2], tmp[4], tmp[6]]))) 111 del tmp, dolfin_pythonversion, dolfin_swigversion 112 ValueError: invalid literal for int() with base 10: 'a' -- debian-science-maintainers mailing list debian-science-maintainers@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#766584: fenics: Fenics to be removed with recent dist-upgrade
Hi Ralf, Thanks for your answer, but you are necroposting this bug. The issue was solved long ago, it was related to a transition from 1.3 to 1.4. The situation you described is an issue in testing at the moment, as some of fenics packages are version 1.5 and others 1.4, breaking the whole fenics package collection, but has nothing to do with this bug. Massimiliano In data lunedì 4 maggio 2015 22:03:42, Ralf Treinen ha scritto: Hello, this seems to be due to the fact that fenics depends on libdolfin-dev (= 1.5.0), which currently only exists in experimental. The long-term solution would then be to upload libdolfin-dev 1.5.0-x to sid. A quick fix for a user should be to install libdolfin-dev 1.5.0-1 from experimental. -Ralf. -- debian-science-maintainers mailing list debian-science-maintainers@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#766584: fenics: Fenics to be removed with recent dist-upgrade
Ok, somehow the problem seems to be solved. I had to reinstall debian for external reasons, but then apt-get complained about some missing dependency and didn't let me install fenics. For other's reference, I solved installing fenics with aptitude, which all of a sudden seems to be smarter than apt-get in managing dependencies. Massimiliano In data martedì 28 ottobre 2014 09:13:24, Johannes Ring ha scritto: Hi Massimiliano, Do you still have this problem? If so, can you please give us some more information? For instance, what do you get when you run the following command? # apt-get -s dist-upgrade Johannes On Fri, Oct 24, 2014 at 8:29 AM, Massimiliano Leoni leoni.massimilia...@gmail.com wrote: Package: fenics Version: 1:1.4.0.1 Severity: normal Dear Maintainer, since about last week apt-get dist-upgrade proposes me a huge update involving 200+ packages, whose side effect is to have fenics - and all packages coming with it - removed from the system. I would guess it's a dependency issue, but of course I'm not sure. How can I recover this? Thanks for help, Massimiliano -- System Information: Debian Release: jessie/sid APT prefers testing-updates APT policy: (500, 'testing-updates'), (500, 'testing') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 3.16-2-amd64 (SMP w/4 CPU cores) Locale: LANG=it_IT.UTF-8, LC_CTYPE=it_IT.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Versions of packages fenics depends on: ii dolfin-bin 1.4.0+dfsg-4 ii dolfin-doc 1.4.0+dfsg-4 ii libdolfin-dev 1.4.0+dfsg-4 ii python-dolfin 1.4.0+dfsg-4 ii python-ffc 1.4.0-1 ii python-fiat 1.4.0-1 ii python-instant 1.4.0-1 ii python-ufl 1.4.0-1 ii python-ufl-doc 1.4.0-1 Versions of packages fenics recommends: ii python-scitools 0.9.0-1 fenics suggests no packages. -- no debconf information -- debian-science-maintainers mailing list debian-science-maintainers@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-mai ntainers -- debian-science-maintainers mailing list debian-science-maintainers@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#766584: fenics: Fenics to be removed with recent dist-upgrade
Hi Johannes, yes, I still have the problem. The output of apt-get -s dist-upgrade is long, so I attach it. I also provided basic translation in english [my locale is in italian]. Thanks, Massimiliano In data martedì 28 ottobre 2014 09:13:24, Johannes Ring ha scritto: Hi Massimiliano, Do you still have this problem? If so, can you please give us some more information? For instance, what do you get when you run the following command? # apt-get -s dist-upgrade Johannes On Fri, Oct 24, 2014 at 8:29 AM, Massimiliano Leoni leoni.massimilia...@gmail.com wrote: Package: fenics Version: 1:1.4.0.1 Severity: normal Dear Maintainer, since about last week apt-get dist-upgrade proposes me a huge update involving 200+ packages, whose side effect is to have fenics - and all packages coming with it - removed from the system. I would guess it's a dependency issue, but of course I'm not sure. How can I recover this? Thanks for help, Massimiliano -- System Information: Debian Release: jessie/sid APT prefers testing-updates APT policy: (500, 'testing-updates'), (500, 'testing') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 3.16-2-amd64 (SMP w/4 CPU cores) Locale: LANG=it_IT.UTF-8, LC_CTYPE=it_IT.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Versions of packages fenics depends on: ii dolfin-bin 1.4.0+dfsg-4 ii dolfin-doc 1.4.0+dfsg-4 ii libdolfin-dev 1.4.0+dfsg-4 ii python-dolfin 1.4.0+dfsg-4 ii python-ffc 1.4.0-1 ii python-fiat 1.4.0-1 ii python-instant 1.4.0-1 ii python-ufl 1.4.0-1 ii python-ufl-doc 1.4.0-1 Versions of packages fenics recommends: ii python-scitools 0.9.0-1 fenics suggests no packages. -- no debconf information -- debian-science-maintainers mailing list debian-science-maintainers@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-mai ntainers Lettura elenco dei pacchetti... # reading package list Generazione albero delle dipendenze... # generating dependency tree Lettura informazioni sullo stato... # reading status info I seguenti pacchetti sono stati installati automaticamente e non sono più richiesti: # The following packages were automatically installed and are not needed anymore gir1.2-gtk-2.0 libarpack2-dev libatk1.0-dev libavcodec-dev libavformat-dev libavresample-dev libavutil-dev libblacs-mpi-dev libblacs-openmpi1 libbtf1.2.0 libcairo-script-interpreter2 libcairo2-dev libcf0 libcgal-dev libcgal10 libcsparse3.1.2 libdc1394-22-dev libdolfin1.4 libfontconfig1-dev libfreetype6-dev libgdk-pixbuf2.0-dev libgl2ps-dev libglib2.0-dev libgmp-dev libgmpxx4ldbl libgtk2.0-dev libharfbuzz-dev libharfbuzz-gobject0 libhdf5-openmpi-8 libhypre-2.8.0b libhypre-dev libilmbase-dev libjasper-dev libjbig-dev libjpeg62:i386 libjpeg8:i386 libjpeg8-dev libklu1.2.1 libldl2.1.0 libllvm3.4 libllvm3.4:i386 liblzma-dev libmpfr-dev libmumps-4.10.0 libmumps-dev libnetcdf-dev libnetcdff5 libopencv-calib3d-dev libopencv-calib3d2.4 libopencv-contrib2.4 libopencv-features2d-dev libopencv-features2d2.4 libopencv-flann-dev libopencv-flann2.4 libopencv-gpu-dev libopencv-gpu2.4 libopencv-imgproc-dev libopencv-legacy2.4 libopencv-ml-dev libopencv-ml2.4 libopencv-objdetect2.4 libopencv-ocl2.4 libopencv-photo-dev libopencv-photo2.4 libopencv-stitching-dev libopencv-stitching2.4 libopencv-superres2.4 libopencv-ts-dev libopencv-ts2.4 libopencv-video-dev libopencv-video2.4 libopencv-videostab2.4 libopencv2.4-java libopencv2.4-jni libopenexr-dev libpango1.0-dev libparpack2 libpcre3-dev libpcrecpp0 libpetsc3.4.2 libpixman-1-dev libpng12-dev libptscotch-5.1 libptscotch-dev libraw1394-dev libraw1394-tools libscalapack-mpi-dev libscalapack-openmpi1 libscotch-5.1 libscotch-dev libslepc3.4.2 libspooles-dev libspooles2.2 libspqr1.3.1 libsuitesparse-dev libsuperlu-dev libsuperlu4 libswscale-dev libsystemd-journal0 libsystemd-login0 libtiffxx5 libvtk5.8 libvtk5.8-qt4 libwxbase2.8-0 libwxgtk2.8-0 libxcb-shm0-dev libxcomposite-dev libxcursor-dev libxft-dev libxi-dev libxinerama-dev libxrandr-dev libxrender-dev libxss-dev opencv-data python-ffc python-fiat python-instant python-ply python-pmw python-pyx python-scitools python-ufl python-ufl-doc swig swig2.0 tcl8.5-dev tk8.5-dev x11proto-composite-dev x11proto-randr-dev x11proto-render-dev x11proto-scrnsaver-dev x11proto-xinerama-dev Usare apt-get autoremove per rimuoverli. # use apt-get autoremove to remove them I seguenti pacchetti saranno RIMOSSI: # the following packages will be REMOVED dolfin-bin dolfin-doc fenics libcv-dev libcvaux-dev libdolfin-dev libhdf5-mpi-dev libhdf5-openmpi-dev libhighgui-dev libopencv-contrib-dev libopencv-dev libopencv-highgui-dev libopencv-legacy-dev libopencv-objdetect-dev libopencv-ocl-dev libopencv
Bug#766584: fenics: Fenics to be removed with recent dist-upgrade
Package: fenics Version: 1:1.4.0.1 Severity: normal Dear Maintainer, since about last week apt-get dist-upgrade proposes me a huge update involving 200+ packages, whose side effect is to have fenics - and all packages coming with it - removed from the system. I would guess it's a dependency issue, but of course I'm not sure. How can I recover this? Thanks for help, Massimiliano -- System Information: Debian Release: jessie/sid APT prefers testing-updates APT policy: (500, 'testing-updates'), (500, 'testing') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 3.16-2-amd64 (SMP w/4 CPU cores) Locale: LANG=it_IT.UTF-8, LC_CTYPE=it_IT.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Versions of packages fenics depends on: ii dolfin-bin 1.4.0+dfsg-4 ii dolfin-doc 1.4.0+dfsg-4 ii libdolfin-dev 1.4.0+dfsg-4 ii python-dolfin 1.4.0+dfsg-4 ii python-ffc 1.4.0-1 ii python-fiat 1.4.0-1 ii python-instant 1.4.0-1 ii python-ufl 1.4.0-1 ii python-ufl-doc 1.4.0-1 Versions of packages fenics recommends: ii python-scitools 0.9.0-1 fenics suggests no packages. -- no debconf information -- debian-science-maintainers mailing list debian-science-maintainers@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers
[Paraview on Jessie] Rescale over time feature broken, patch released
Hi everyone, I am on Jessie and I installed package Paraview from the official repos, but I found out that a very useful feature, rescale data range over all timesteps is broken in this version. However, a patch was created and is discussed on the official kitware forum, where it is claimed to solve the problem. http://review.source.kitware.com/#/c/14052/ Could you please apply it and update the debian package? This is a very fundamental feature and I wouldn't like to manually install or compile another version to have it working. Thanks in advance, Massimiliano Leoni P.s. Sorry if you received a blank email a moment ago, my bad. P.p.s Sorry if this isn't the appropriate way to report a bug; in this case, can you point me to the right place? -- debian-science-maintainers mailing list debian-science-maintainers@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#766406: paraview: Rescale to all timesteps feature broken, but patch released
Package: paraview Version: 4.1.0+dfsg-3+b2 Severity: normal Tags: patch Dear Maintainer, I am using package paraview on debian testing, but the (very handful) feaure rescale data over all timesteps is known to be broken. However, a patch was released on the official kitware forum, at http://review.source.kitware.com/#/c/14052/ Could you please apply the patch and update the debian package? You can confirm the bug by comparing the paraview package in the debian repos with the paraview binaries downloadable form paraview's website. Thanks Massimiliano Leoni -- System Information: Debian Release: jessie/sid APT prefers testing-updates APT policy: (500, 'testing-updates'), (500, 'testing') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 3.16-2-amd64 (SMP w/4 CPU cores) Locale: LANG=it_IT.UTF-8, LC_CTYPE=it_IT.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Versions of packages paraview depends on: ii libavcodec-extra-56 6:11-1 ii libavformat56 6:11-1 ii libavutil54 6:11-1 ii libc6 2.19-11 ii libexpat1 2.1.0-6 ii libfreetype6 2.5.2-2 ii libgcc1 1:4.9.1-16 ii libgl1-mesa-glx [libgl1] 10.2.8-1 ii libhdf5-8 1.8.13+docs-14 ii libjpeg8 8d1-1 ii libjsoncpp0 0.6.0~rc2-3 ii libogg0 1.3.2-1 ii libopenmpi1.6 1.6.5-8+b1 ii libpng12-01.2.50-2 ii libpython2.7 2.7.8-10 ii libqt4-help 4:4.8.6+git64-g5dc8b2b+dfsg-2 ii libqt4-network4:4.8.6+git64-g5dc8b2b+dfsg-2 ii libqtcore44:4.8.6+git64-g5dc8b2b+dfsg-2 ii libqtgui4 4:4.8.6+git64-g5dc8b2b+dfsg-2 ii libqtwebkit4 2.3.4.dfsg-2 ii libstdc++64.9.1-16 ii libswscale3 6:11-1 ii libtheora01.1.1+dfsg.1-3.2 ii libtiff5 4.0.3-10+b1 ii libx11-6 2:1.6.2-3 ii libxml2 2.9.1+dfsg1-4 ii libxt61:1.1.4-1 ii tcl8.58.5.16-1 ii zlib1g1:1.2.8.dfsg-2 Versions of packages paraview recommends: ii mpi-default-bin 1.0.2+nmu2 ii paraview-doc 4.1.0+dfsg-3 ii paraview-python 4.1.0+dfsg-3+b2 Versions of packages paraview suggests: pn h5utils none pn hdf5-tools none -- no debconf information -- debian-science-maintainers mailing list debian-science-maintainers@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers
