Bug#685316: ITP: molds -- semi-empirical electronic structure and molecular dynamics

2012-08-19 Thread Michael Banck
Package: wnpp Severity: wishlist Owner: debichem-de...@lists.alioth.debian.org * Package name: molds Version : no release yet Upstream Author : Mikiya Fujii * URL : http://en.sourceforge.jp/projects/molds/ * License : GPLv3+ Programming Lang: C++

Bug#683467: aces3: divide-by-zero error in many test cases when running on one core only

2012-07-31 Thread Michael Banck
package: aces3 severity: important tags: upstream version: 3.0.6-1 I now ran the full testsuite, and unfortunately I get a floating point exception in tran_rhf_ao_sv1.sio: | An instruction timer report will be printed | | Gather on company_rank succeeded. | Static pre-defined array #

Bug#683467: aces3: divide-by-zero error in many test cases when running on one core only

2012-07-31 Thread Michael Banck
On Wed, Aug 01, 2012 at 02:18:58AM +0200, Michael Banck wrote: Apparently this code is relevant, from , line 107: That was supposed to read , from main/worker_init.F, line 107: niocompany = 0 do i = 1, nprocs if (pst_get_company(i-1) .eq. io_company_id

Bug#683226: mpich2: Segfaults if ssh is not available

2012-07-30 Thread Michael Banck
Hi, On Mon, Jul 30, 2012 at 12:06:21AM -0500, Pavan Balaji wrote: Thanks for the bug report, Michael. This was already fixed in the MPICH2 trunk, but perhaps after 1.4.1p1 was released. In any case, it should appear in the next release -- mpich2-1.5. Indeed, but as Debian is frozen I think

Bug#683217: aces3: Test suite failure on MPICH architectures

2012-07-29 Thread Michael Banck
Package: aces3 Version: 3.0.6-5 Severity: normal On architectures which have MPICH as default MPI implementation, ACESIII segfaults during the test suite, see e.g. https://buildd.debian.org/status/fetch.php?pkg=aces3arch=s390xver=3.0.6-5stamp=1342695500 debian/rules override_dh_auto_test

Bug#683217: [Debichem-devel] Bug#683217: aces3: Test suite failure on MPICH architectures

2012-07-29 Thread Michael Banck
On Sun, Jul 29, 2012 at 11:23:37PM +0200, Michael Banck wrote: Package: aces3 Version: 3.0.6-5 Severity: normal On architectures which have MPICH as default MPI implementation, ACESIII segfaults during the test suite, see e.g. https://buildd.debian.org/status/fetch.php?pkg=aces3arch

Bug#683226: mpich2: Segfaults if ssh is not available

2012-07-29 Thread Michael Banck
Package: mpich2 Version: 1.4.1-4 Severity: important Tags: patch In a minimal unstable chroot, after installing mpich2 with --no-install-recommends: nighthawk:/tmp# mpirun /bin/true Segmentation fault nighthawk:/tmp# apt-get install --no-install-recommends openssh-client [...] nighthawk:/tmp#

Bug#683226: mpich2: Segfaults if ssh is not available

2012-07-29 Thread Michael Banck
On Mon, Jul 30, 2012 at 01:40:49AM +0200, Michael Banck wrote: nighthawk:/tmp# mpirun /bin/true Segmentation fault I forgot to mention the backtrace: #0 0x00421020 in HYDU_get_abs_wd () No symbol table info available. #1 0x0042127c in HYDU_find_in_path () No symbol table info available. #2

Bug#683226: mpich2: Segfaults if ssh is not available

2012-07-29 Thread Michael Banck
Hi, On Mon, Jul 30, 2012 at 02:02:50AM +0200, Michael Banck wrote: On Mon, Jul 30, 2012 at 01:40:49AM +0200, Michael Banck wrote: nighthawk:/tmp# mpirun /bin/true Segmentation fault I have rebuilt mpich2 with the patch I mentioned and now it no longer segfaults: Preparing to replace mpich2

Bug#680397: [Debichem-devel] Bug#680397: aces3: FTBFS: Times out

2012-07-06 Thread Michael Banck
Hi, On Thu, Jul 05, 2012 at 06:50:40PM +0200, Kurt Roeckx wrote: Source: aces3 Version: 3.0.6-4 Severity: serious Your package fails to build on a few arches, timing out in the test suite: (cd tests; OMPI_MCA_plm_rsh_agent=/bin/false csh ./runscript) Running 1.1.1.1 mpirun: killing

Bug#680397: [Debichem-devel] Bug#680397: Bug#680397: aces3: FTBFS: Times out

2012-07-06 Thread Michael Banck
Hi, On Fri, Jul 06, 2012 at 01:46:10PM +0200, Michael Banck wrote: On Thu, Jul 05, 2012 at 06:50:40PM +0200, Kurt Roeckx wrote: Source: aces3 Version: 3.0.6-4 Severity: serious Your package fails to build on a few arches, timing out in the test suite: (cd tests

Bug#676658: ITP: chemfp -- Cheminformatics fingerprints file formats and tools

2012-06-08 Thread Michael Banck
Package: wnpp Severity: wishlist Owner: Debichem Team debichem-de...@lists.alioth.debian.org * Package name: chemfp Version : 1.0 Upstream Author : Andrew Dalke da...@dalkescientific.com * URL : http://code.google.com/p/chem-fingerprints/ * License : MIT

Bug#676667: ITP: fmcs -- Find Maximum Common Substructure

2012-06-08 Thread Michael Banck
Package: wnpp Severity: wishlist Owner: Debichem Team debichem-de...@lists.alioth.debian.org * Package name: fmcs Version : 1.0 Upstream Author : Andrew Dalke da...@dalkescientific.com * URL : https://bitbucket.org/dalke/fmcs/overview * License : BSD

Bug#602126: Package ready

2012-06-01 Thread Michael Banck
Hi, On Fri, Jun 01, 2012 at 01:16:37AM +0200, Ask Hjorth Larsen wrote: Hi 2012/5/28 Michael Banck mba...@debian.org: On Mon, May 28, 2012 at 01:52:56PM +0200, Ask Hjorth Larsen wrote: 2012/5/27 Michael Banck mba...@debian.org: (...) 1. It might be a good idea to run testase on package

Bug#602126: Package ready

2012-05-28 Thread Michael Banck
Hi, On Mon, May 28, 2012 at 01:52:56PM +0200, Ask Hjorth Larsen wrote: 2012/5/27 Michael Banck mba...@debian.org: 1. The changelog entry should not refer to ppa, and should read unstable as distribution.  If the package was never in Ubuntu, I would also suggest to remove all prior

Bug#674626: [Debichem-devel] Bug#674626: wishlist: update package to cinfony 1.1

2012-05-26 Thread Michael Banck
Hi, Cinfony 1.1 has been released and supports CDK 1.4.x, which is requested to be sponsored for unstable, but blocked by being binary incompatible with Cinfony 1.0. Right, I forgot to upload cinfony after indigo got accepted. Will get to it. Michael -- To UNSUBSCRIBE, email to

Bug#602126: Package ready

2012-05-26 Thread Michael Banck
Hi, On Thu, May 24, 2012 at 12:30:27AM +0200, Ask Hjorth Larsen wrote: 2012/5/23 Michael Banck mba...@debian.org: On Mon, May 21, 2012 at 04:28:55PM +0200, Ask Hjorth Larsen wrote: We have a package now which is ready to be uploaded.  So we would like to have this bug promoted to an RFS

Bug#674135: ITP: spglib -- Crystal Symmetry Library

2012-05-23 Thread Michael Banck
Package: wnpp Severity: wishlist Owner: DebiChem Project debichem-de...@lists.alioth.debian.org * Package name: spglib Version : 1.0.8 Upstream Author : Atsushi Togo atz.t...@gmail.com * URL : http://spglib.sourceforge.net * License : BSDish Programming

Bug#602126: Package ready

2012-05-23 Thread Michael Banck
Hi, On Mon, May 21, 2012 at 04:28:55PM +0200, Ask Hjorth Larsen wrote: We have a package now which is ready to be uploaded. So we would like to have this bug promoted to an RFS. Great news! If you point me to a source package, I can review it and upload. Michael -- To UNSUBSCRIBE,

Bug#673150: RM: several -- ROP; outdated hurd-i386 binary package

2012-05-16 Thread Michael Banck
Package: ftp.debian.org Severity: normal The following list of source packages should have hurd-i386 binary packages which are outdated and can be removed from the archive. If you prefer a different format of the list, let me know. The list is: apachetop audacity bandwidthd cdcat cp2k

Bug#673150: RM: several -- ROP; outdated hurd-i386 binary package

2012-05-16 Thread Michael Banck
Hi, On Wed, May 16, 2012 at 07:30:12PM +0200, Alexander Reichle-Schmehl wrote: Hi Michael! * Michael Banck mba...@debian.org [120516 15:32]: The list is: [..] That results in: # Broken Depends: audacity: audacity-dbg dragonegg: llvm-gcc-4.5 iftop: iftop-dbg rrdcollect

Bug#671621: libopenmpi1.3: embedded-library usr/lib/openmpi/lib/libopen-pal.so.0.0.0: ltdl

2012-05-05 Thread Michael Banck
Package: libopenmpi1.3 Version: 1.4.3-2.1 Severity: important libopenmpi1.3 has the following lintian error: embedded-library usr/lib/openmpi/lib/libopen-pal.so.0.0.0: ltdl Michael -- System Information: Debian Release: 6.0.2 APT prefers stable APT policy: (500, 'stable') Architecture:

Bug#666110: pvbatch / openmpi refuses under chroot

2012-05-05 Thread Michael Banck
Hi, On Wed, May 02, 2012 at 01:15:46PM +0200, Michael Banck wrote: On Thu, Apr 19, 2012 at 12:27:43AM +0200, Michael Banck wrote: I could NMU the current unstable version with the patch if you agree. I have just uploaded an NMU to DELAYED/3-day. Let me know if I should move it to 0-day

Bug#671057: [Debichem-devel] Bug#671057: a fix of this bug

2012-05-03 Thread Michael Banck
Hi, On Thu, May 03, 2012 at 11:51:56PM +0800, 雨蒼 wrote: hi, I'm try to fix this bug. I added python in python-indigo depends, and add dh_python2 in rules. Please help me to check if it can work. Many thanks for the patch, but I have fixed it slightly differently now. It was enough to

Bug#666110: pvbatch / openmpi refuses under chroot

2012-05-02 Thread Michael Banck
tags 666110 +pending thanks Hi, On Thu, Apr 19, 2012 at 12:27:43AM +0200, Michael Banck wrote: On Tue, Apr 03, 2012 at 06:33:24PM +0200, Sylvestre Ledru wrote: On 03/04/2012 18:21, Julien Cristau wrote: On Thu, Mar 29, 2012 at 20:20:43 +0200, Sylvestre Ledru wrote: On 29/03/2012 20:06

Bug#625832: python-mpi4py: importing MPI fails

2012-05-02 Thread Michael Banck
severity 625832 important tags 625832 +unreproducible thanks Hi, On Sun, May 08, 2011 at 12:22:35PM +0100, Juha Jäykkä wrote: That result is independent of number of ranks and whether I start the program with or without orterun. The hello.c is very short: #include mpi.h #include stdio.h

Bug#671226: adun.app: Please consider splitting up into GUI and non-GUI packages

2012-05-02 Thread Michael Banck
Package: adun.app Severity: wishlist Adun.app seems to be a quite capable molecular dynamics (MD) program. If possible, it would be nice to split the package into a a text-only computational backend package, and a GUI frontend package; it might be that this is not feasable due to the GNUstep

Bug#670184: RM: kfreebsd-8 [hurd-i386] -- NVIU; blocks transition of 8.3-1

2012-04-25 Thread Michael Banck
Hi, On Mon, Apr 23, 2012 at 10:14:19PM +0200, Robert Millan wrote: The hurd-i386 buildd isn't keeping up, so 8.2-11 hurd-i386 builds haven't been replaced with 8.3-1. The hurd-i386 autobuilders are keeping up in general. About kfreebsd-8: 15:02 youpi azeem: I've put kfrebsd-8 non

Bug#670054: [Debichem-devel] Bug#670054: rdkit: FTFBS on powerpc / s390x / sparc (test suite failures)

2012-04-23 Thread Michael Banck
Hi Greg, On Mon, Apr 23, 2012 at 05:55:28AM +0200, Greg Landrum wrote: This is almost certainly a problem with byte-ordering and the RDKit's method of handling serialization. I'm sure it's not that tough to fix, and I will happily do the work, but I don't have access to a big-endian machine

Bug#666110: pvbatch / openmpi refuses under chroot

2012-04-18 Thread Michael Banck
Hi, On Tue, Apr 03, 2012 at 06:33:24PM +0200, Sylvestre Ledru wrote: On 03/04/2012 18:21, Julien Cristau wrote: On Thu, Mar 29, 2012 at 20:20:43 +0200, Sylvestre Ledru wrote: On 29/03/2012 20:06, Anton Gladky wrote: I have similar problem on liggghts/lammps packages, which are running

Bug#666110: [Debichem-devel] Bug#666110: mpqc: FTBFS on armel (tests hang?)

2012-03-29 Thread Michael Banck
tags 666110 +patch thanks On Thu, Mar 29, 2012 at 12:17:46AM +0200, Michael Banck wrote: Even if I just run /usr/bin/ompi-ps without arguments, it eats 100% cpu and spins at sched_yield() forever accordings to strace: socket(PF_INET, SOCK_STREAM, IPPROTO_IP) = 7 setsockopt(7, SOL_TCP

Bug#494046: openmpi-bin: Doesn't work in a chroot environment

2012-03-28 Thread Michael Banck
Hi, On Sun, Sep 11, 2011 at 05:34:35PM +0200, Michael Banck wrote: I think this bug is really quite important, there are a number of my packages where I cannot run the test suite during build because openmpi fails instantly in the buildd chroot. Did somebody test whether the 1.5 devlopment

Bug#666110: [Debichem-devel] Bug#666110: mpqc: FTBFS on armel (tests hang?)

2012-03-28 Thread Michael Banck
reassign 666110 openmpi-bin thanks On Wed, Mar 28, 2012 at 09:31:36PM +0200, Julien Cristau wrote: Source: mpqc Version: 2.3.1-14 Severity: serious Justification: fails to build from source (but built successfully in the past) Well, it built successfully cause openmpi was just crashing/not

Bug#664975: ITP: indigo -- Organic Chemistry Toolkit

2012-03-21 Thread Michael Banck
Package: wnpp Severity: wishlist Owner: Debichem Team debichem-de...@lists.alioth.debian.org * Package name: indigo Version : 1.0.0 Upstream Author : GGA Software Services LLC * URL : http://ggasoftware.com/opensource/indigo * License : GPLv3 Programming

Bug#663894: [Debichem-devel] Bug#663894: apbs: FTBFS on mips (hang in test suite)

2012-03-15 Thread Michael Banck
Hi, On Wed, Mar 14, 2012 at 09:21:36PM +0100, Julien Cristau wrote: Source: apbs Version: 1.3.0-1 Severity: serious Justification: fails to build from source (but built successfully in the past) apbs FTBFS on the mips buildds, see the last couple of logs on

Bug#663636: ITP: opsin -- Chemical name to structure converter

2012-03-12 Thread Michael Banck
Package: wnpp Severity: wishlist Owner: Debichem Team debichem-de...@lists.alioth.debian.org * Package name: opsin Version : 1.2.0 Upstream Author : Daniel Lowe, Peter Corbett and Peter Murray-Rust * URL : http://www-ucc.ch.cam.ac.uk/products/software/opsin * License

Bug#663153: ITP: automaton -- Finite-State Automaton for Regular Expressions

2012-03-08 Thread Michael Banck
Package: wnpp Severity: wishlist Owner: Debian Java Maintainers pkg-java-maintain...@lists.alioth.debian.org * Package name: automaton Version : 1.11-8 Upstream Author : Anders Møller * URL : http://www.brics.dk/automaton/ * License : BSD Programming Lang:

Bug#661976: [Debichem-devel] Bug#661976: rdkit-doc: Places docs in /usr/share/docs/ instead of /usr/share/doc/

2012-03-03 Thread Michael Banck
tags 661976 +pending thanks On Sat, Mar 03, 2012 at 06:54:19AM +0100, Guillem Jover wrote: This package installs its documentation into /usr/share/docs/ dir, while per the FHS, it should be placed under /usr/share/doc/. Thanks, fixed in subversion. Michael -- To UNSUBSCRIBE, email to

Bug#639465: RM: postgresql-9.0 -- RoM; Obsoleted by postgresql-9.1

2012-02-26 Thread Michael Banck
Hi, On Sat, Feb 25, 2012 at 11:36:49AM +0100, Martin Pitt wrote: Ansgar Burchardt [2012-01-24 0:04 +0100]: I guess that it would also be removed from backports after a short while or at least no longer receive updates? In that case it might be a good idea to upgrade d.o hosts using

Bug#660176: [Debichem-devel] Bug#660176: cp2k: FTBFS with long paths to source files

2012-02-17 Thread Michael Banck
Hi, On Thu, Feb 16, 2012 at 10:18:40PM -0500, Aaron M. Ucko wrote: Source: cp2k Version: 2.2.426-1 Severity: serious Justification: fails to build from source Thanks for addressing #641242! cp2k now fares better, but still fails to build when absolute path names are long, as they wind up

Bug#660176: [Debichem-devel] Bug#660176: cp2k: FTBFS with long paths to source files

2012-02-17 Thread Michael Banck
tags 660176 +pending thanks On Thu, Feb 16, 2012 at 10:18:40PM -0500, Aaron M. Ucko wrote: cp_common_uses.h suggests a couple of possible ways to accommodate line-length limits, of which arranging to build with relative paths would be ideal. Alternatively, it looks like you can eliminate the

Bug#641242: [Debichem-devel] Bug#641242: Bug #641242: cp2k: FTBFS anywhere but (linux-)i386

2012-02-12 Thread Michael Banck
tags 641242 +pending thanks Hi, On Fri, Jan 20, 2012 at 09:18:53PM +0800, Aron Xu wrote: Tail of logs for cp2k on ia64 (supported): /usr/bin/make -C /build/buildd-cp2k_2.1.637-2.1-ia64-ezcZn1/cp2k-2.1.637/makefiles/../obj/Linux-ia64-gfortran/popt -f

Bug#659048: [Debichem-devel] Bug#659048: avogadro: FTBFS on hurd-i386: missing .desktop file and its icon

2012-02-07 Thread Michael Banck
tags 659048 +pending thanks On Tue, Feb 07, 2012 at 07:19:21PM +0100, Pino Toscano wrote: currently[1], avogadro does not build on hurd-i386. The problem is that the .desktop file and its icon are not installed on Hurd, so dh_install fails to install them. Attached there is a patch which I

Bug#658299: RFP: madness -- Multiresolution Adaptive Numerical Environment for Scientific Simulation

2012-02-01 Thread Michael Banck
Package: wnpp Severity: wishlist * Package name: madness Version : None yet, really Upstream Author : Oak Ridge National Laboratory * URL : http://www.example.org/ * License : GPLv2+ Programming Lang: C++ Description : Multiresolution Adaptive

Bug#193616: link wfm with dft

2012-01-21 Thread Michael Banck
Hi, On Sat, Jan 21, 2012 at 01:35:25PM +0100, Julian Taylor wrote: the build system is a mess so I just made a minimal patch to fix ghemicals build with as-needed. I merged it into the 11_as_needed patch. See the attachment. It would be great if you can apply it to the debian package even

Bug#193616: [Debichem-devel] Bug#193616: progress?

2011-12-29 Thread Michael Banck
Hi, On Wed, Dec 28, 2011 at 05:18:03PM +0100, Julian Taylor wrote: user debian-...@lists.debian.org usertags 193616 + ld-as-needed thanks any progress on this? the missing links cause build failures with ld --as-needed [0] See e.g. ghemical build log in ubuntu:

Bug#640950: [Pkg-openmpi-maintainers] Bug#640950: libopenmpi1.3: unresolved symbols in libmpi_f90

2011-12-25 Thread Michael Banck
Hi, On Wed, Dec 21, 2011 at 02:26:42PM +0100, Manuel Prinz wrote: On Thu, Sep 08, 2011 at 09:38:44PM +0200, Michael Banck wrote: Adding libmpi_f77 to the library list fixed this problem, but I believe this is not the right fix, so filing as a bug. I tested this with the new version

Bug#653254: ITP: mesmer -- Chemical reactions dynamics solver

2011-12-25 Thread Michael Banck
Package: wnpp Severity: wishlist Owner: Debichem Team debichem-de...@lists.alioth.debian.org * Package name: mesmer Version : 0.2 Upstream Authors: Struan H. Robertson, David R. Glowacki, Chi-Hsiu Liang, Chris Morley and Michael J. Pilling * URL :

Bug#650192: RM: several -- ROP; outdated hurd-i386 binary package

2011-11-27 Thread Michael Banck
Package: ftp.debian.org Severity: normal The following list of source packages should have hurd-i386 binary packages which are outdated and can be removed from the archive. I can file distinct bugs for each if you prefer. Would it be more convenient to quote the binary package name? I could do

Bug#649381: mpqc: Please enable mp2r12

2011-11-21 Thread Michael Banck
Hi, On Mon, Nov 21, 2011 at 08:38:30AM +0100, Daniel Leidert wrote: Am Montag, den 21.11.2011, 01:46 +0100 schrieb Michael Banck: On Sun, Nov 20, 2011 at 03:26:08PM +0100, Michael Banck wrote: This is because libSCcints and (at least) libSCmbptr12 are not shipped in libsc7. Turns

Bug#649381: mpqc: Please enable mp2r12

2011-11-20 Thread Michael Banck
Package: mpqc Version: 2.3.1-10 Severity: wishlist Running mpqc on /usr/share/doc/mpqc/examples/mp2r12ah2o.in results in an error: nighthawk/tmp$ mpqc mp2r12ah2o.in Reading file /usr/share/mpqc/atominfo.kv. MPQC: Massively Parallel Quantum Chemistry

Bug#649382: libghemical: Not binNMUable

2011-11-20 Thread Michael Banck
Package: libghemical Version: 2.99.1-2 Severity: normal libghemical is not binNMU-ready: mba@hartree:~/build$ dpkg -I libghemical5_2.99.1-2+b1_amd64.deb | grep Depends Depends: libblas3gf | libblas.so.3gf | libatlas3gf-base, libc6 (= 2.2.5), libgcc1 (= 1:4.1.1), libgfortran3 (= 4.3),

Bug#649390: ITP: python-mdanalysis -- MDAnalysis is a Python library to analyze and manipulate molecular dynamics trajectories.

2011-11-20 Thread Michael Banck
Hi Sébastien, On Sun, Nov 20, 2011 at 04:30:08PM +0100, Sébastien Buchoux wrote: Package: wnpp Severity: wishlist Owner: Sébastien Buchoux sebastien.buch...@gmail.com * Package name: python-mdanalysis Version : 0.7.4 Upstream Author : Sébastien Buchoux

Bug#649381: [Debichem-devel] Bug#649381: mpqc: Please enable mp2r12

2011-11-20 Thread Michael Banck
On Sun, Nov 20, 2011 at 03:26:08PM +0100, Michael Banck wrote: This is because libSCcints and (at least) libSCmbptr12 are not shipped in libsc7. Turns out those are only enabled when libint is present: |AC_CHECK_HEADERS(libint/libint.h, | AC_CHECK_LIB(int,init_libint_base, |HAVE_LIBINT

Bug#642668: [Debichem-devel] Bug#642668: libghemical: FTBFS: eng1_qm_mpqc.h:37:44: fatal error: util/keyval/keyval.h: No such file or directory

2011-10-31 Thread Michael Banck
Hi, On Mon, Oct 31, 2011 at 01:38:32PM +0400, Ilya Barygin wrote: The problem is actually in libsc-dev which installs header files in /usr/include/include/sc and says they're in /usr/include/sc: $ find /usr/include -name keyval.h /usr/include/include/sc/util/keyval/keyval.h $ sc-config

Bug#642277: [Debichem-devel] Bug#642277: package ftbfs with ld --as-needed

2011-10-31 Thread Michael Banck
tags 642277 +pending thanks On Wed, Sep 21, 2011 at 03:26:46AM +0200, Matthias Klose wrote: Package: mpqc Version: 2.3.1-7 Severity: normal User: ubuntu-de...@lists.ubuntu.com Usertags: origin-ubuntu oneiric User: debian-...@lists.debian.org Usertags: ld-as-needed patch at

Bug#509631: [Debichem-devel] Bug#509631: mpqc FTBFS on armel

2011-10-31 Thread Michael Banck
fixed 509631 2.3.1-8 thanks Hi, On Wed, Dec 24, 2008 at 12:06:30AM +0200, Riku Voipio wrote: Package: mpqc Version: 2.3.1-5 Severity: important The new upload in experimental fails: At least the current version builds fine on armel according to buildd.debian.org. Michael -- To

Bug#466808: mpqc: MPQC does not support multiprocessor support?

2011-10-31 Thread Michael Banck
fixed 466808 2.3.1-5 thanks On Wed, Feb 20, 2008 at 09:18:44PM -0800, Jordan Mantha wrote: Package: mpqc Severity: normal Reported by Egon Willighagen to Ubuntu: $ export MESSAGEGRP='MPIMessageGrp:(n=2)' $ mpqc water.inp ClassDesc::load_class looking for ./classes

Bug#647050: ITP: cinfony -- python abstraction layer to cheminformatics pacakges

2011-10-29 Thread Michael Banck
Package: wnpp Severity: wishlist Owner: Debichem Team debichem-de...@lists.alioth.debian.org * Package name: cinfony Version : 1.0 Upstream Author : Noel O'Boyle * URL : http://code.google.com/p/cinfony/ * License : BSD Programming Lang: Python Description

Bug#644397: [Debichem-devel] Bug#644397: Bug#644397: gromacs: pdb2gmx, version 4.5.5, fails with 'Illegal instruction' on i686, 3.0.0.1-686-pae (testing)

2011-10-08 Thread Michael Banck
Hi, On Sat, Oct 08, 2011 at 09:17:25PM +0200, Steffen Möller wrote: Thank you for investing so much energy into this. Indeed! The chip is soon ten years old and indeed, if there are no other voices from the off coming up with similar issues, then there is little to be gained. And, hey, who

Bug#643310: [Debichem-devel] Bug#643310: mpqc cannot be started

2011-09-27 Thread Michael Banck
Hi, On Tue, Sep 27, 2011 at 09:02:50AM +0200, Georg wrote: Package: mpqc Version: 2.3.1-7 Severity: grave Tags: upstream Justification: renders package unusable Dear Maintainer, Whenever I try to start mpqc, whatever parameters I submit, mpqc 2.3.1-7 crashes with the same output to

Bug#643310: [Debichem-devel] Bug#643310: mpqc cannot be started

2011-09-27 Thread Michael Banck
Hi again, On Tue, Sep 27, 2011 at 09:02:50AM +0200, Georg wrote: Package: mpqc Version: 2.3.1-7 Severity: grave Tags: upstream Justification: renders package unusable Dear Maintainer, Whenever I try to start mpqc, whatever parameters I submit, mpqc 2.3.1-7 crashes with the same output

Bug#643310: [Debichem-devel] Bug#643310: Bug#643310: mpqc cannot be started

2011-09-27 Thread Michael Banck
retitle 64331 mpqc: Missing Depends on mpi-default-bin thanks On Tue, Sep 27, 2011 at 11:09:16AM +0200, Michael Banck wrote: Erm, can you try installing openmpi-bin, if you have that one not installed, and let me know if that fixes it? Yeah, that seems to be the problem, sorry about

Bug#642084: [Debichem-devel] Bug#642084: qutemol: Cannot start the program

2011-09-22 Thread Michael Banck
Hi, On Mon, Sep 19, 2011 at 11:20:51AM +0100, Manuel A. Fernandez Montecelo wrote: Package: qutemol Version: 0.4.1~cvs2008-1 Severity: important $ qutemol (qutemol:8256): Gdk-CRITICAL **: IA__gdk_drawable_get_size: assertion `GDK_IS_DRAWABLE (drawable)' failed (qutemol:8256):

Bug#642472: ITP: aces2 -- Advanced Concepts in Electronic Structure II

2011-09-22 Thread Michael Banck
Package: wnpp Severity: wishlist Owner: Michael Banck mba...@debian.org * Package name: aces2 Version : 2.8.0 Upstream Author : Quantum Theory Project, University of Florida * URL : http://www.qtp.ufl.edu/ACES * License : GPL Programming Lang: Fortran

Bug#639227: Bug#639227: gabedit: Typo in package description

2011-09-20 Thread Michael Banck
Hi, On Tue, Sep 20, 2011 at 04:42:36PM +0200, Daniel Leidert wrote: Am Donnerstag, den 25.08.2011, 23:13 +0200 schrieb Michael Banck: tags 639227 +pending thanks On Thu, Aug 25, 2011 at 08:07:58AM +0200, Simon Kainz wrote: There are some typos in the package description. Please see

Bug#641655: ITP: xtalopt -- Evolutionary Crystal Structure Prediction

2011-09-14 Thread Michael Banck
Package: wnpp Severity: wishlist Owner: Debichem Team debichem-de...@lists.alioth.debian.org * Package name: xtalopt Version : r8.0 Upstream Author : David Lonie * URL : http://xtalopt.openmolecules.net * License : GPLv2, LGPLv2 and BSD Programming Lang: C,

Bug#641474: [Debichem-devel] Bug#641474: psi3 fails using basis sets cc-pVNZ with N 5

2011-09-13 Thread Michael Banck
severity 641474 normal thanks Hi, On Tue, Sep 13, 2011 at 06:30:26PM +0200, Georg wrote: % SCF-Rechnung am Wasserstoffmolekül mit der pV7Z-Basis psi:( label = cc-pV7Z SCF H2 jobtype = sp wfn = scf reference = rhf num_threads = 8 memory = (3.072 GB) basis = cc-pV7Z units =

Bug#641470: [Debichem-devel] Bug#641470: psi3 fails optimizing geometry

2011-09-13 Thread Michael Banck
forwarded 641470 https://sourceforge.net/tracker/?func=detailaid=3408945group_id=127784atid=709454 thanks Hi, thanks for your report. On Tue, Sep 13, 2011 at 06:10:59PM +0200, Georg wrote: The contents of the input file, corresponding to the example in the user manual: % 6-31G** H2O Test

Bug#494046: openmpi-bin: Doesn't work in a chroot environment

2011-09-11 Thread Michael Banck
severity 494046 +important thanks Hi, I think this bug is really quite important, there are a number of my packages where I cannot run the test suite during build because openmpi fails instantly in the buildd chroot. Did somebody test whether the 1.5 devlopment series fixes this bug? Feel free

Bug#640950: libopenmpi1.3: unresolved symbols in libmpi_f90

2011-09-08 Thread Michael Banck
Package: libopenmpi1.3 Version: 1.4.2-4 Severity: normal Hi, I tried to link an Fortran90 project with libmpi_f90, but I got an error message: /usr/lib/gcc/i486-linux-gnu/4.6.1/../../../../lib/libmpi_f90.so: undefined reference to `mpi_testsome_' Indeed, libmpi_f90 does not NEED libmpi_f77,

Bug#640718: ITP: aces3 -- Advanced Concepts in Electronic Structure III

2011-09-06 Thread Michael Banck
Package: wnpp Severity: wishlist Owner: Michael Banck mba...@debian.org * Package name: aces3 Version : 3.0.6 Upstream Author : Quantum Theory Project, University of Florida * URL : http://www.qtp.ufl.edu/ACES/ * License : GPL Programming Lang: C, Fortran

Bug#602126: Proposing a package soon

2011-09-04 Thread Michael Banck
Hi, On Mon, Jun 13, 2011 at 12:36:08PM +0200, Yann Pouillon wrote: I'm still in contact with the upstream developers of ASE, and I think we can propose a package for Debian soon, very likely before September. Great! Let me know if you need sponsoring. Michael -- To UNSUBSCRIBE, email to

Bug#640118: ITP: rdkit -- Collection of cheminformatics and machine-learning software

2011-09-02 Thread Michael Banck
Package: wnpp Severity: wishlist Owner: Michael Banck mba...@debian.org * Package name: rdkit Version : 201106 Upstream Author : Greg Landrum and Julie Penzotti * URL : http://www.rdkit.org/ * License : BSD Programming Lang: C++, Python Description

Bug#628292: [Debichem-devel] Bug#628292: jmol: FTBFS: [javac] /build/user-jmol_12.0.40-1-amd64-wyLf4R/jmol-12.0.40/src/org/jmol/applet/JmolAppletRegistry.java:70: cannot find symbol

2011-09-01 Thread Michael Banck
tags 628292 +pending thanks Hi, On Sat, May 28, 2011 at 03:48:20PM +0200, Lucas Nussbaum wrote: During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part: [javac] /build/user-jmol_12.0.40-1-amd64-wyLf4R/jmol-12.0.40/src/JmolApplet.java:37:

Bug#639322: [Debichem-devel] Bug#639322: Bug#639322: ghemical: [INTL:de] Initial German translation

2011-08-29 Thread Michael Banck
Hi, On Mon, Aug 29, 2011 at 10:45:14PM +0200, Chris Leick wrote: Michael Banck wrote: Chris Leick wrote: Some comments again: BTW: You've received my answer to libghemical? Yeah, didn't get around answering yet though, sorry. #: ../src/gtk_app.cpp:120 msgid OrbitXY ; orbit

Bug#639322: [Debichem-devel] Bug#639322: ghemical: [INTL:de] Initial German translation

2011-08-29 Thread Michael Banck
Hi, On Thu, Aug 25, 2011 at 11:55:38PM +0200, Chris Leick wrote: Package: ghemical Version: 2.99.2 Severity: wishlist Tags: l10n please find attached the inital German translation of ghemical. #: ../src/gtk_oglview_wnd.cpp:42 msgid Import other file formats using libopenbabel msgstr

Bug#639322: [Debichem-devel] Bug#639322: ghemical: [INTL:de] Initial German translation

2011-08-27 Thread Michael Banck
Hi, On Thu, Aug 25, 2011 at 11:55:38PM +0200, Chris Leick wrote: Package: ghemical Version: 2.99.2 Severity: wishlist Tags: l10n please find attached the inital German translation of ghemical. Great! Some comments again: #: ../src/custom_app.cpp:100 msgid Added global light. msgstr

Bug#639321: [Debichem-devel] Bug#639321: ghemical: Patch fixes 3 typos

2011-08-27 Thread Michael Banck
Hi, On Thu, Aug 25, 2011 at 11:52:15PM +0200, Chris Leick wrote: diff -ru ghemical-2.99.2.orig//src/res_gtk/gtk_moldyn_dialog.glade ghemical-2.99.2//src/res_gtk/gtk_moldyn_dialog.glade --- ghemical-2.99.2.orig//src/res_gtk/gtk_moldyn_dialog.glade 2009-04-01 10:18:58.0 +0200 +++

Bug#639227: [Debichem-devel] Bug#639227: gabedit: Typo in package description

2011-08-25 Thread Michael Banck
tags 639227 +pending thanks On Thu, Aug 25, 2011 at 08:07:58AM +0200, Simon Kainz wrote: There are some typos in the package description. Please see the attached patch. Applied, thanks. Michael -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of

Bug#637012: [Debichem-devel] Bug#637012: libghemical: [INTL:de] Initial German translation

2011-08-07 Thread Michael Banck
Hi, On Sun, Aug 07, 2011 at 08:25:20PM +0200, Chris Leick wrote: please find attached the German translation of libghemical. Wow! Did you consider submitting it upstream? Not sure there will be a nother ghemical release, though. Some comments: #: ../src/bond.cpp:33 msgid Conjugated

Bug#628826: [Debichem-devel] Bug#628826: Bug#628826: pdb2pqr: FTBFS on i386: collect2: ld terminated with signal 6

2011-06-11 Thread Michael Banck
Hi, On Thu, Jun 09, 2011 at 03:36:38PM +0200, Manuel Prinz wrote: I can build pdb2pqr without problems in i386 unstable chroots on two different amd64 host. Can you please give details on your build setup? FWIW, I could reproduce the crash on my machine (the i386) after I updated the upgraded

Bug#626362: [Debichem-devel] Bug#626362: Fails to build from source if libghemical is recompiled from source

2011-05-11 Thread Michael Banck
Hi, On Wed, May 11, 2011 at 12:31:42PM +0200, Moritz Muehlenhoff wrote: I've tried to rebuild ghemical for Univention Corporate Server, a Debian derived distribution based on Debian stable (currently Lenny, our next release will be based on Squeeze). Oh, any particular reason you include

Bug#553808: libreadline5-dev removal pending, please update to readline6

2011-04-27 Thread Michael Banck
On Wed, Apr 27, 2011 at 07:12:29PM +, Matthias Klose wrote: The package still build-depends on libreadline5-dev. Which package? I can look up the bug number myself, but this looks like a mass-ping, so consider including the package name next time (hrm, should be in the bug title anyway, I

Bug#623945: dpkg-dev: Please add option to tell dpkg-source 3.0 (quilt) to skip diffing source tree

2011-04-24 Thread Michael Banck
Package: dpkg-dev Version: 1.15.8.10 Severity: wishlist Hi, I have a 90 mb source tarball, which is 528 mb unpacked. Running dpkg-buildpackage -S on it takes ages (657 seconds, to be exact) on my notebook, as it checks whether there are changes in the original source to put into

Bug#623075: [Debichem-devel] Bug#623075: Please package jmol 12.1 into experimental

2011-04-17 Thread Michael Banck
Hi, On Sun, Apr 17, 2011 at 09:41:35AM +0200, Vincent Fourmond wrote: I'm currently packaging jalview, Cool! Getting jalview packages was actually one of the major points why I wanted to get jmol into the archive. who relies on jmol internally. Unfortunately, it embeds the newer jmol

Bug#619712: opensync-plugin-evolution: synchronization fails due to change in evolution-backend

2011-03-27 Thread Michael Banck
On Sat, Mar 26, 2011 at 12:58:11PM +0100, Andreas Mueck wrote: Synchronization fails with messages like Cannot get cal from factory. The problem was solved by downloading the source and building a new binary for wheezy. Which source exactly? Michael -- To UNSUBSCRIBE, email to

Bug#618971: Please remove some outdated hurd-i386 binary packages

2011-03-20 Thread Michael Banck
On Sun, Mar 20, 2011 at 08:42:14AM +0100, Svante Signell wrote: On Sun, 2011-03-20 at 00:55 +0100, Michael Banck wrote: Package: ftp.debian.org I saw that netspeed is still on the list. It has been fixed, see #618745. Then it will just be getting built again once the fix is uploaded

Bug#611456: Why wishlist?

2011-03-20 Thread Michael Banck
On Sun, Mar 20, 2011 at 12:48:08PM +0100, Svante Signell wrote: On Sat, 2011-03-19 at 13:14 +, Mark Brown wrote: severity 611456 wishlist kthxbye OK, lets keep is as wishlist as you propose. Will it be hanging around for another three years as bug #468696? Please stop this. The

Bug#611456: Why wishlist?

2011-03-19 Thread Michael Banck
On Sat, Mar 19, 2011 at 01:14:22PM +, Mark Brown wrote: severity 611456 wishlist kthxbye On Thu, Mar 17, 2011 at 11:17:44PM +0100, Svante Signell wrote: Why downgrading this bug report to a wishlist? Due to lack of support for multiple cores?? Take a look at the output of x86info

Bug#618971: Please remove some outdated hurd-i386 binary packages

2011-03-19 Thread Michael Banck
Package: ftp.debian.org Hi, I ran a query on merkel which retrieves all outdated (by more than 60 days) binary packages on hurd-i386 and looked at which of those are leaf packages (no complaints from `dak rm --rdep-check') and then removed a couple which look useful (debfoster and traceroute,

Bug#602126: ITP: python-ase -- Atomic Simulation Environment

2011-02-13 Thread Michael Banck
Hi, On Mon, Nov 01, 2010 at 08:10:30PM +0100, Yann Pouillon wrote: * Package name: python-ase Version : 3.4.1 Upstream Author : Ask Hjorth Larsen a...@fysik.dtu.dk * URL : https://wiki.fysik.dtu.dk/ase/ * License : GPL, LGPL Programming Lang: Python

Bug#612625: ITP: libtecla -- a command-line editing library

2011-02-11 Thread Michael Banck
Hi, On Wed, Feb 09, 2011 at 10:18:15AM -0600, Scott Christley wrote: Description : Tecla is a command-line editing library The tecla library provides UNIX and LINUX programs with interactive command line editing facilities, similar to those of the UNIX tcsh shell. In addition to simple

Bug#438694: gabedit: Crashes when loading any XYZ format file

2011-02-11 Thread Michael Banck
Hi, On Tue, Feb 08, 2011 at 03:50:33PM +0100, Daniel Leidert wrote: [crash reading XYZ file] Can this issue still be reproduced with gabedit? If yes: - which version of gabedit? - can you provide a new backtrace? I'm sorry, but I still cannot reproduce this crash and we are now at

Bug#611142: [Debichem-devel] Bug#611142: Processed: tagging 611142

2011-02-02 Thread Michael Banck
On Wed, Feb 02, 2011 at 03:54:24PM +0100, Julien Cristau wrote: On Wed, Feb 2, 2011 at 15:47:25 +0100, Filippo Rusconi wrote: On Tue, Feb 01, 2011 at 10:30:21PM +0100, Julien Cristau wrote: On Tue, Feb 1, 2011 at 17:54:09 +, Debian Bug Tracking System wrote: Processing commands for

Bug#611142: [Debichem-devel] Bug#611142: Processed: tagging 611142

2011-02-02 Thread Michael Banck
On Wed, Feb 02, 2011 at 04:27:51PM +0100, Julien Cristau wrote: On Wed, Feb 2, 2011 at 16:19:43 +0100, Filippo Rusconi wrote: care to explain ? http://www.debian.org/Bugs/Developer#tags adding the squeeze tag means the bug doesn't affect any other suite. Well, it's fixed in unstable

Bug#611142: [Debichem-devel] Bug#611142: Processed: tagging 611142

2011-02-02 Thread Michael Banck
Hi, On Wed, Feb 02, 2011 at 04:49:32PM +0100, Julien Cristau wrote: It's fixed in unstable because unstable has a version which is marked as fixed, not because it's unstable. Version tracking can handle that. The tag is necessary in the few cases where whether a bug affects a release depends

Bug#611436: pymol: fails to start

2011-01-29 Thread Michael Banck
Package: pymol Version: 1.1-1 ---BeginMessage--- Hello; i have installed (apt-get install ...) on Debian amd64 lenny package pymol 1.1-1, which also installs apbs blt freeglut3 libmaloc1 python-pmw python-tk tk8.4. The executable is in /usr/bin/pymol. As it can be seen below, dpkg reports

Bug#611142: [Debichem-devel] Bug#611142: massxpert: Program crashes when clicking left of first monomer vignette

2011-01-26 Thread Michael Banck
Hi, On Tue, Jan 25, 2011 at 11:23:22PM +0100, Filippo Rusconi wrote: Package: massxpert Version: 2.4.1-1 Severity: grave Tags: upstream Justification: renders package unusable Sending bug report to myself. When clicking left of the first monomer vignette the program crashes. Presumably

Bug#610894: opensync-plugin-syncml: Unable to configure syncml plugin

2011-01-25 Thread Michael Banck
Hi, On Mon, Jan 24, 2011 at 09:49:30PM +0100, Hendrik Sattler wrote: Am Montag 24 Januar 2011, 17:50:00 schrieb Michael Banck: Also note that the syncml plugin has been sort of orphaned upstream, if you need this for some bigger project, I suggest getting involved upstream

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