Wgsim stays in samtools.
Hello everyone, in conclusion, wgsim stays in samtools, where it will only get bug fixes, but no further developments. https://github.com/samtools/samtools/issues/429#issuecomment-129412846 Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan
Re: Please update from ITK v3 to v4 [Re: RM: insighttoolkit -- ROM; Obsoleted by insighttoolkit4]
On Wednesday 12 August 2015 22:01:36 Steve M. Robbins wrote: Could those package maintainers update to v4, please? First ITK-4 needs to be re-build for GCC-5 transition. At the moment ginkgocadx FTBFS in unstable (but not in testing) due to libstdc++6 : Breaks: libinsighttoolkit4.7 (= 4.7.2-2) but 4.7.2-2 is to be installed. -- Best wishes, Dmitry Smirnov. --- You have to start with the truth. The truth is the only way that we can get anywhere. Because any decision-making that is based upon lies or ignorance can't lead to a good conclusion. -- Julian Assange, 2010 signature.asc Description: This is a digitally signed message part.
Please update from ITK v3 to v4 [Re: RM: insighttoolkit -- ROM; Obsoleted by insighttoolkit4]
Hi, Previously on debian-med, I proposed that ITK v3 be dropped from the archive [1]. The only respondent agreed with that. So I filed for removal [2] and received notice that several packages still depend on ITK v3 (e.g. on libinsighttoolkit3-dev). Could those package maintainers update to v4, please? Thanks, -Steve [1] https://lists.debian.org/debian-med/2015/08/msg00010.html [2] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=795019 On August 12, 2015 11:54:07 AM you wrote: On Sunday, August 09, 2015 10:48:36 AM Steve M. Robbins wrote: Package: ftp.debian.org Severity: normal The package is already scheduled for autoremoval due to GCC 5 issues. But there is no need to wait: the code is several years old and will not be maintained. Successor package is insighttoolkit4. Has rdepends that need updating. Please remove the moreinfo tag once these are updated. Checking reverse dependencies... # Broken Depends: camitk: libcamitk3 fw4spl: fw4spl [amd64] ginkgocadx: ginkgocadx [amd64 armel armhf i386 mips mipsel powerpc ppc64el s390x] gofigure2: gofigure2 [amd64 armel armhf hurd-i386 i386 kfreebsd-amd64 kfreebsd- i386 mips mipsel powerpc ppc64el s390x] libgofigure0 [amd64 armel armhf hurd-i386 i386 kfreebsd-amd64 kfreebsd-i386 mips mipsel powerpc ppc64el s390x] igstk: libigstk4 [amd64 armel armhf hurd-i386 i386 kfreebsd-amd64 kfreebsd- i386 mips mipsel powerpc s390x] libigstk4-dev [amd64 armel armhf hurd-i386 i386 kfreebsd-amd64 kfreebsd-i386 mips mipsel powerpc s390x] itksnap: itksnap [armel armhf hurd-i386 kfreebsd-amd64 kfreebsd-i386 mips mipsel powerpc ppc64el s390x] nifti2dicom: nifti2dicom [armel armhf hurd-i386 kfreebsd-amd64 kfreebsd-i386 mips mipsel powerpc ppc64el s390x] qnifti2dicom [armel armhf hurd-i386 kfreebsd-amd64 kfreebsd-i386 mips mipsel powerpc ppc64el s390x] plastimatch: plastimatch [arm64 armel armhf kfreebsd-amd64 kfreebsd-i386 mips mipsel powerpc ppc64el s390x] vmtk/non-free: libvmtk1.0 python-vmtk # Broken Build-Depends: camitk: libinsighttoolkit3-dev (= 3.20) fw4spl: libinsighttoolkit3-dev ginkgocadx: libinsighttoolkit3-dev (= 3.20.0) gofigure2: libinsighttoolkit3-dev (= 3.20) igstk: libinsighttoolkit3-dev (= 3.20) itksnap: libinsighttoolkit3-dev Dependency problem found. signature.asc Description: This is a digitally signed message part.
Re: python-pbcore 1.2.2
On الأربعاء 12 آب 2015 00:37, Andreas Tille wrote: Hi, On Tue, Aug 11, 2015 at 07:45:02PM -0700, Afif Elghraoui wrote: Hi, team, I have prepared an update to this package, but had to drop the (apparently nonfunctional) Python 3 version that I created the first time. Python 3 is not supported upstream yet, but is planned in the future [1]. The package has to pass NEW again. Would someone please upload? Upload to unstable or experimental? (If it should stay in experimental I would not mind too much about some broken functionality of Python3.) I'm asking since you left UNRELEASED (which is fine) but last upload was to experimental. Oh, sorry-- unstable. The Python 3 package was failing almost all the tests. The porting is non-trivial and it doesn't appear upstream is willing to cooperate on this yet. Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/55caf909.20...@ghraoui.name
DebianMed policy error
Hi, there is an error in DebianMed policy page [0]: *svn-buildpackage* --svn-tag-only = --svn-only-tag [0] http://debian-med.alioth.debian.org/docs/policy.html Olivier
Re: DebianMed policy error
Le Wed, Aug 12, 2015 at 09:12:34AM +, olivier sallou a écrit : there is an error in DebianMed policy page [0]: *svn-buildpackage* --svn-tag-only = --svn-only-tag Bonjour Olivier, I just realised that svn-buildpackage accepts both (according to its manpage). Have a nice day, Charles -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150812095828.ga18...@falafel.plessy.net
Re: Help needed to update to latest fastqc
Hi Andreas and Olivier, I'm going to have a crack at the FastQC update. I've been poking at the HDF5 packages and here are my conclusions so far: --- We have 2 Free Java libraries for HDF5: 1) The NCSA lib distributed by hdfgroup.org with classes in namespace ncsa.hdf.hdf5lib, packaged on Debian as libjhdf5-java. 2) The CISD aka. SIS lib distributed by ethz.ch with classes in the namespace ch.systemsx, not currently packaged on Debian. The SIS library forks some Java code from the ncsa.hdf namespace, and also needs to link against the NCSA native library (via JNI) at runtime. So, trying to package sis-jhdf5: wget 'https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.1-r33502.zip?version=1modificationDate=1424599261225api=v2' # The source is in a zip within the zip... unzip sis-* mkdir sis-jhdf5-14.12.1 cd !$ unzip ../sis-jhdf5/src/sis-jhdf5-src.zip For compilation to succeed, we also need sis-base, not to be confused with the entirely separate project at sis.apache.org! wget http://bs-svn01.ethz.ch/repos/cisd/libraries/trunk/sis-base/sis-base-src.zip The code also depends on their own args4j library, but only for the CLI under ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java which we can simply leave out just now. So - can we exclude the ncsa.hdf.hdf5lib.* classes from sis-jhdf5 and compile it against the existing classes in /usr/share/java/jhdf5.jar? My conclusion is not, because... The version of ncsa/hdf/hdf5lib/exceptions/HDF5Exception.java supplied with the sis-jhdf5 code subclasses RuntimeException but the version in libhdf5-java does not. The result is that the code here does not need to declare the exceptions being thrown, and thus simply ignores them all. One can go through and add all throws declarations (there are a _lot_ of them!!), but then any client code using the library will also break unless it is likewise patched or the code is modified to handle the exceptions internally. I think we'd best just admit defeat here and use the code supplied with sis-jhdf5. So, I'm going to try rolling two new packages, and see if that allows me to compile the latest FastQC: libsis-base-java (should be simple) libsis-jhdf5-java (depends on libsis-base-java + existing libjhdf5-jni) I'll report back on progress and commit to SVN as usual. Let me know if you think I'm missing something. Cheers, TIM On Thu, 2015-06-25 at 09:37 +0200, Andreas Tille wrote: Hi Olivier, any news about this hdf5lib packaging? Kind regards Andreas. On Tue, May 05, 2015 at 09:25:23AM +0200, Olivier Sallou wrote: On 05/04/2015 10:52 PM, Andreas Tille wrote: Hi Olivier, On Mon, May 04, 2015 at 06:41:10PM +0200, Olivier Sallou wrote: File fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java imports HDFS5Factory from ch.systemsx.cisd.hdf5 but jhdf5.jar only contains files like: ncsa/hdf/hdf5lib/... and no HDF5Factory this jhdf5 is not the correctl lib (or an other one is needed). I guess its this one: https://svncisd.ethz.ch/doc/hdf5/hdf5-8.10/ch/systemsx/cisd/hdf5/package-summary.html seems that original code source is the same (https://svncisd.ethz.ch/repos/cisd/jhdf5/trunk/source/java/) (/ncsa/...) but that /ch/... has not been included for a reason In addition, in debian/patches/build.xml is missing commons-math3.jar to be added in pathelement for classpath. for duplicate classes, I don't yet, but hdf5 first need to be resolved. If I do not hear from you I'll try the URL above tomorrow (if nobody else might beat me which would for sure welcome as always). Kind regards Andreas. -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/55487063.1090...@irisa.fr -- http://fam-tille.de -- Nothing is inherently mysterious - nothing that actually exists, that is. If I am ignorant about a phenomenon, that is a fact about my state of mind, not a fact about the phenomenon; to worship a phenomenon because it seems so wonderfully mysterious, is to worship your own ignorance. - Eliezer Yudkowsky -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/1439376259.4466.21.ca...@wllt1771.nerc-wallingford.ac.uk
Re: DebianMed policy error
Hi, if anybody spots an error - the policy is in SVN and can be fixed by anybody. You can use make publish to push it online easily. Kind regards Andreas. On Wed, Aug 12, 2015 at 10:25:55AM +0100, Sascha Steinbiss wrote: Hi, Btw, in the same paragraph, I think it should additionally be '--svn-noautodch' instead of '--svn-no-autodch': [vagrant@debian-8:~] $ svn-buildpackage --help | grep autodch --svn-noautodch Don't add a new Debian changelog entry when done Cheers Sascha On 12/08/2015 10:12, olivier sallou wrote: Hi, there is an error in DebianMed policy page [0]: *svn-buildpackage* |--svn-tag-only| |= --svn-only-tag| | | |[0] http://debian-med.alioth.debian.org/docs/policy.html| | | |Olivier| -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/55cb1123.10...@tetrinetsucht.de -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150812100634.ga12...@an3as.eu
Re: DebianMed policy error
Hi, Btw, in the same paragraph, I think it should additionally be '--svn-noautodch' instead of '--svn-no-autodch': [vagrant@debian-8:~] $ svn-buildpackage --help | grep autodch --svn-noautodch Don't add a new Debian changelog entry when done Cheers Sascha On 12/08/2015 10:12, olivier sallou wrote: Hi, there is an error in DebianMed policy page [0]: *svn-buildpackage* |--svn-tag-only| |= --svn-only-tag| | | |[0] http://debian-med.alioth.debian.org/docs/policy.html| | | |Olivier| -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/55cb1123.10...@tetrinetsucht.de
Re: Help needed to update to latest fastqc
Hi Tim, from my *very* naive point of view your considerations make sense. Olivier might have some more educated opinion (and perhaps some code?). I'll be available vor sponsering as usual. Thanks for your work on this Andreas. On Wed, Aug 12, 2015 at 11:44:19AM +0100, Tim Booth wrote: Hi Andreas and Olivier, I'm going to have a crack at the FastQC update. I've been poking at the HDF5 packages and here are my conclusions so far: --- We have 2 Free Java libraries for HDF5: 1) The NCSA lib distributed by hdfgroup.org with classes in namespace ncsa.hdf.hdf5lib, packaged on Debian as libjhdf5-java. 2) The CISD aka. SIS lib distributed by ethz.ch with classes in the namespace ch.systemsx, not currently packaged on Debian. The SIS library forks some Java code from the ncsa.hdf namespace, and also needs to link against the NCSA native library (via JNI) at runtime. So, trying to package sis-jhdf5: wget 'https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.1-r33502.zip?version=1modificationDate=1424599261225api=v2' # The source is in a zip within the zip... unzip sis-* mkdir sis-jhdf5-14.12.1 cd !$ unzip ../sis-jhdf5/src/sis-jhdf5-src.zip For compilation to succeed, we also need sis-base, not to be confused with the entirely separate project at sis.apache.org! wget http://bs-svn01.ethz.ch/repos/cisd/libraries/trunk/sis-base/sis-base-src.zip The code also depends on their own args4j library, but only for the CLI under ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java which we can simply leave out just now. So - can we exclude the ncsa.hdf.hdf5lib.* classes from sis-jhdf5 and compile it against the existing classes in /usr/share/java/jhdf5.jar? My conclusion is not, because... The version of ncsa/hdf/hdf5lib/exceptions/HDF5Exception.java supplied with the sis-jhdf5 code subclasses RuntimeException but the version in libhdf5-java does not. The result is that the code here does not need to declare the exceptions being thrown, and thus simply ignores them all. One can go through and add all throws declarations (there are a _lot_ of them!!), but then any client code using the library will also break unless it is likewise patched or the code is modified to handle the exceptions internally. I think we'd best just admit defeat here and use the code supplied with sis-jhdf5. So, I'm going to try rolling two new packages, and see if that allows me to compile the latest FastQC: libsis-base-java (should be simple) libsis-jhdf5-java (depends on libsis-base-java + existing libjhdf5-jni) I'll report back on progress and commit to SVN as usual. Let me know if you think I'm missing something. Cheers, TIM On Thu, 2015-06-25 at 09:37 +0200, Andreas Tille wrote: Hi Olivier, any news about this hdf5lib packaging? Kind regards Andreas. On Tue, May 05, 2015 at 09:25:23AM +0200, Olivier Sallou wrote: On 05/04/2015 10:52 PM, Andreas Tille wrote: Hi Olivier, On Mon, May 04, 2015 at 06:41:10PM +0200, Olivier Sallou wrote: File fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java imports HDFS5Factory from ch.systemsx.cisd.hdf5 but jhdf5.jar only contains files like: ncsa/hdf/hdf5lib/... and no HDF5Factory this jhdf5 is not the correctl lib (or an other one is needed). I guess its this one: https://svncisd.ethz.ch/doc/hdf5/hdf5-8.10/ch/systemsx/cisd/hdf5/package-summary.html seems that original code source is the same (https://svncisd.ethz.ch/repos/cisd/jhdf5/trunk/source/java/) (/ncsa/...) but that /ch/... has not been included for a reason In addition, in debian/patches/build.xml is missing commons-math3.jar to be added in pathelement for classpath. for duplicate classes, I don't yet, but hdf5 first need to be resolved. If I do not hear from you I'll try the URL above tomorrow (if nobody else might beat me which would for sure welcome as always). Kind regards Andreas. -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/55487063.1090...@irisa.fr -- http://fam-tille.de -- Nothing is inherently mysterious - nothing that actually exists, that is. If I am ignorant about a phenomenon, that is a fact about my state of mind, not a fact about the phenomenon; to worship a phenomenon because it seems so wonderfully mysterious, is to worship your own ignorance. - Eliezer Yudkowsky -- http://fam-tille.de
Re: Help needed to update to latest fastqc
Hi, After a fair amount of struggling I conclude that I do not have all the code required to build this thing from source. The distribution of JHDF5 from https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=26609113 contains some Java source code and a bunch of pre-compiled JNI shared libs, eg.: sis-jhdf5/lib/native/jhdf5/amd64-Linux/libjhdf5.so The source for this file is not to be found anywhere that I can see it. One might assume (and the FAQ implies) that the file is equivalent to /usr/lib/jni/libjhdf5.so provided by the exiting package libjhdf5-jni but it isn't! Inspecting it with readelf shows it is full of symbols in the ETH SIS namespace: tbooth@balisaur[sis-jhdf5] readelf -sW ./sis-jhdf5/lib/native/jhdf5/amd64-Linux/libjhdf5.so | grep ch_systemsx | head 19: 00039a4058 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Scopy 31: 0002e930 181 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dchdir_1ext 35: 0003b590 918 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sget_1select_1bounds 40: 000387f045 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pcreate_1xfer_1abort 41: 0003882066 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1char_1encoding 46: 00034500 203 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Oopen 47: 00034ae0 363 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1version 52: 0003521066 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1layout 65: 0003c560 126 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1member_1name 68: 00032da058 FUNCGLOBAL DEFAULT 10 Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Idec_1ref ...and many more... So, this .so file is definitely specific to this library. It seems to be a superset of a fork of the upstream NCSA code. The only contact details I can find for the library are for Dr. Bernd Rinn who is the head of the whole division, but I shall contact him personally and see if he can pass the query on. If Bernd can't help, then unless I've missed a trick we will have to consider that this library and anything that depends on it (eg FastQC) are not fully open source :-( Cheers, TIM On Wed, 2015-08-12 at 15:00 +0200, Andreas Tille wrote: Hi Tim, from my *very* naive point of view your considerations make sense. Olivier might have some more educated opinion (and perhaps some code?). I'll be available vor sponsering as usual. Thanks for your work on this Andreas. On Wed, Aug 12, 2015 at 11:44:19AM +0100, Tim Booth wrote: Hi Andreas and Olivier, I'm going to have a crack at the FastQC update. I've been poking at the HDF5 packages and here are my conclusions so far: --- We have 2 Free Java libraries for HDF5: 1) The NCSA lib distributed by hdfgroup.org with classes in namespace ncsa.hdf.hdf5lib, packaged on Debian as libjhdf5-java. 2) The CISD aka. SIS lib distributed by ethz.ch with classes in the namespace ch.systemsx, not currently packaged on Debian. The SIS library forks some Java code from the ncsa.hdf namespace, and also needs to link against the NCSA native library (via JNI) at runtime. So, trying to package sis-jhdf5: wget 'https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.1-r33502.zip?version=1modificationDate=1424599261225api=v2' # The source is in a zip within the zip... unzip sis-* mkdir sis-jhdf5-14.12.1 cd !$ unzip ../sis-jhdf5/src/sis-jhdf5-src.zip For compilation to succeed, we also need sis-base, not to be confused with the entirely separate project at sis.apache.org! wget http://bs-svn01.ethz.ch/repos/cisd/libraries/trunk/sis-base/sis-base-src.zip The code also depends on their own args4j library, but only for the CLI under ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java which we can simply leave out just now. So - can we exclude the ncsa.hdf.hdf5lib.* classes from sis-jhdf5 and compile it against the existing classes in /usr/share/java/jhdf5.jar? My conclusion is not, because... The version of ncsa/hdf/hdf5lib/exceptions/HDF5Exception.java supplied with the sis-jhdf5 code subclasses RuntimeException but the version in libhdf5-java does not. The result is that the code here does not need to declare the exceptions being thrown, and thus simply ignores them all. One can go through and add all throws declarations (there are a _lot_ of them!!), but then any client code using the library will also break unless it is likewise patched or the code is modified to handle the exceptions internally. I think we'd best just admit defeat here and use the code supplied with sis-jhdf5. So, I'm going to try rolling two new
