Re: Problems with libmtj-java and new version of beast-mcmc
On 09/04/2015 08:04 AM, Andreas Tille wrote: > On Fri, Sep 04, 2015 at 05:09:45AM +, olivier sallou wrote: >>> Do you want me to work on the todo list (which looks a bit scary to me - >>> but I might try to have a look). >> Nope, for the moment I will continue. >> But will take time. It needs intensive patching because netlib-java classes >> do not use the same namespace than embeded/used library. >> So patches are *easy* but many files to patch with different class >> namespaces >> >> There is also a dependency not available in debian. I will check but it >> seems they use a small part of something really bigger. I may patch the >> code to remove this dependency. >> >> I will let you know when I get something. I have fixed most of issues. Remains missing dependency *lombok* which seems a bit difficult to build (eclipse dependencies and others) There are a few other issues we should be able to manage with patches once lombok is available, if possible... Olivier > Thanks a lot > > Andreas. > > > -- > gpg key id: 4096R/326D8438 (keyring.debian.org) > Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Re: Trinityrnaseq status
On 08/22/2015 09:34 PM, Michael Crusoe wrote: On Sat, Aug 22, 2015 at 6:49 AM Andreas Tille andr...@an3as.eu mailto:andr...@an3as.eu wrote: Hi, On Sat, Aug 22, 2015 at 12:57:20AM +, Michael Crusoe wrote: trinityrnaseq: waiting on libjung-free-java, rsem, express, and jaligner. Otherwise all the tests run successfully for me. I really hope that jaligner will make it soon - no idea why several packages later in the queue made it way faster. On the upside it is now the second oldest package in queue so hopefully it will get some attention soon. libjung-free-java package: in NEW queue courtesy Olivier https://ftp-master.debian.org/new/libjung-free-java_2.0.1-1.html rsem: waiting for r-bioc-ebseq; needs manpages, patch descriptions, add new patches to add hardening flags Usually it is related to CFLAGS/CXXFLAGS/ etc... not being extended but replaced in makefiles: example: CFLAGS = -O3 instead of CFLAGS += -O3 and oflen LDFLAGS not being used at ld step r-bioc-ebseq: ready for sponsoring now that r-cran-blockmodeling is in the archive Uploaded. Thanks! Any and all assistance you and the group can provide for the above would be greatly appreciated! Please be more verbose if you see tasks I could do to support this. Do have experience in what incantations it takes to add the hardening build flags to recalcitrant packages? -- Michael R. Crusoe: Programmer Bioinformatician cru...@ucdavis.edu mailto:cru...@ucdavis.edu The lab for Data Intensive Biology; University of California, Davis https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Re: Help needed to update to latest fastqc
On 08/22/2015 03:35 PM, Andreas Tille wrote: Hi, On Sat, Aug 22, 2015 at 08:27:39AM +, olivier sallou wrote: As libsis-base-java and libsis-jhdf5-java are in our git repo and seem to be fine, you may want to build/install them locally to test your fastqc update ? As it makes use of the libraries, it would also be a good additional test for those libs before uploading them Since I personally have bo proper test case I'd vote for starting to upload the first link in the chain of dependencies. There might be pretty much time to fix things while its hanging in the new queue (hopefully less time). ok, I have uploaded libsis-base-java (the first one in chain) Thanks for your work on this Andreas. -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Re: libsis-base-java switched to git
libsis-jhdf5 is on git: Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/libsis-jhdf5-java.git Vcs-Git: git://anonscm.debian.org/debian-med/libsis-jhdf5-java.git I have updated DEP3 patches headers and a few things. Should we for upload of sis-base and sis-jhdf5 ? Olivier On 08/21/2015 05:13 PM, Tim Booth wrote: Hi Olivier, I'd say jhdf5 is ready, so go ahead. Since I got all the testng tests to run I'm confident that all the JNI stuff is now linking up properly, and I've tested the get-orig-source too. Cheers, TIM On Fri, 2015-08-21 at 14:31 +, olivier sallou wrote: Hi, I have fixed a few things (pure Debian) and moved to switch. Now repo is: git://anonscm.debian.org/debian-med/libsis-base-java.git Now I propose that: 1) you validate on your side the jhdf5 librarry 2) once ready ping me and I move it to git and check for cleanup. 4) when both have moved to git, I upload them. Is it ok for you? Olivier -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Re: Lena licensing, how to patch?
On 08/20/2015 10:05 PM, Ghislain Vaillant wrote: On 20/08/15 20:54, olivier sallou wrote: Hi, I have a colleague who have the lena image licensing issue in his package. He tried to patch it but get fuzzing issue when building the package. As it is a binary file and never patched a binary file, has anyone an idea on how to correctly patch this file ? As it is not a new upstream release, we cannot simply exclude it from orig.tar Thanks Olivier Hi Olivier, You can submit a new stripped orig.tar with a +dfsg1 suffix and bump the dversion of the source package with that suffix too. Would be a solution, thanks Olivier No ? Ghis -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Re: python-cobra seems to resist backporting :-( [python-cobra_0.4.0b2-1~bpo8+1_amd64.changes REJECTED]
On 08/17/2015 01:39 PM, Andreas Tille wrote: I've never seen this. :-( Any idea Andreas. - Forwarded message from Debian FTP Masters ftpmas...@ftp-master.debian.org - Date: Mon, 17 Aug 2015 09:22:57 + From: Debian FTP Masters ftpmas...@ftp-master.debian.org To: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org, Afif Elghraoui a...@ghraoui.name, ti...@debian.org Subject: python-cobra_0.4.0b2-1~bpo8+1_amd64.changes REJECTED python-cobra_0.4.0b2-1~bpo8+1.dsc: Invalid size hash for python-cobra_0.4.0b2.orig.tar.gz: According to the control file the size hash should be 2264579, but python-cobra_0.4.0b2.orig.tar.gz has 2231532. maybe try to get orig.tar.gz from Debian web site and use it for your build. Maybe your local orig.tar.gz is not the same (compression timestamp...) If you did not include python-cobra_0.4.0b2.orig.tar.gz in your upload, a different version might already be known to the archive software. === Please feel free to respond to this email if you don't understand why your files were rejected, or if you upload new files which address our concerns. ___ Debian-med-packaging mailing list debian-med-packag...@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging - End forwarded message - -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Re: Help needed to update to latest fastqc
On 08/14/2015 10:48 AM, Tim Booth wrote:
Hi Olivier,
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libsis-base-java/
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libsis-jhdf5-java/
I've not modified FastQC at all. Or rather, I tried patching out the
FAST5 support but I just did that within the vanilla source; I'm not
playing with the package from GIT at this point.
Ok, libsis-base-java sounds good (except a few remaining polishing).
However, you can take code from svn and build package. autotests are fine.
I have updated libsis-jhdf5-java in svn too to generate native libs,
java lib (what you already did) and launch tests.
Libraries compilation is ok (.so and .jar), but tests fail when using
native libs (load is ok). I don't know why and am struggling with it, as
error message does not help (failed to instanciate). If you want to have
a look I gonna continue ot investiguate.
Olivier
Cheers,
TIM
On Fri, 2015-08-14 at 08:16 +0200, olivier.sal...@codeless.fr wrote:
On 08/13/2015 05:20 PM, Tim Booth wrote:
Hi Olivier,
Looks like Bernd Rinn is making positive noises regarding a DFSG version
of the library, so hopefully once he provides code you can take what I
have done and make use of it. I committed to SVN because it's so much
easier than pushing to GIT and I'm lazy, sorry.
what do you mean by commit to SVN ?
I looked at SVN repo for fastqc but it is empty, referring to git repo
[0]
Where is you code ?
[0] http://anonscm.debian.org/viewvc/debian-med/trunk/packages/fastqc/
Olivier
In my libsis-jhdf5-java package I created a small test
ReadWriteTest.java which I confirmed works correctly when used with
the binary libhdf5.so supplied by upstream. Also my patches
fix_dodgy_cast.patch and remove_ch_rinn_imports.patch should be sound
but the others are junk caused by me trying to kick the code into
submission.
If for some reason we can't get this working then you could very easily
patch out FAST5 support in FastQC for now. My impression is that it's
something of an alpha feature in any case. I can't even find a .fast5
format file to test with!
PATCH for FASTQC
This patch disables support for FAST5 format until we get the library built.
Most users won't need this anyway, and those that do can convert the file
to FASTQ using other tools.
Note you also need to completely remove the file
uk/ac/babraham/FastQC/Sequence/Fast5File.java, which I can't do in a quilt
patch.
Tim Booth - 13th Aug 2015
--- a/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
+++ b/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
@@ -100,7 +100,8 @@
return new BAMFile(file,false);
}
else if (file.getName().toLowerCase().endsWith(.fast5)) {
- return new Fast5File(file);
+ //return new Fast5File(file);
+ throw new SequenceFormatException(Support for FAST5
files has not been enabled in this build of FastQC.);
}
else {
return new FastQFile(config,file);
PATCH
I'm done with this for now. Off to debug some Python code.
Best,
TIM
--
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
--
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Re: Help needed to update to latest fastqc
On 08/13/2015 05:20 PM, Tim Booth wrote:
Hi Olivier,
Looks like Bernd Rinn is making positive noises regarding a DFSG version
of the library, so hopefully once he provides code you can take what I
have done and make use of it. I committed to SVN because it's so much
easier than pushing to GIT and I'm lazy, sorry.
what do you mean by commit to SVN ?
I looked at SVN repo for fastqc but it is empty, referring to git repo [0]
Where is you code ?
[0] http://anonscm.debian.org/viewvc/debian-med/trunk/packages/fastqc/
Olivier
In my libsis-jhdf5-java package I created a small test
ReadWriteTest.java which I confirmed works correctly when used with
the binary libhdf5.so supplied by upstream. Also my patches
fix_dodgy_cast.patch and remove_ch_rinn_imports.patch should be sound
but the others are junk caused by me trying to kick the code into
submission.
If for some reason we can't get this working then you could very easily
patch out FAST5 support in FastQC for now. My impression is that it's
something of an alpha feature in any case. I can't even find a .fast5
format file to test with!
PATCH for FASTQC
This patch disables support for FAST5 format until we get the library built.
Most users won't need this anyway, and those that do can convert the file
to FASTQ using other tools.
Note you also need to completely remove the file
uk/ac/babraham/FastQC/Sequence/Fast5File.java, which I can't do in a quilt
patch.
Tim Booth - 13th Aug 2015
--- a/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
+++ b/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
@@ -100,7 +100,8 @@
return new BAMFile(file,false);
}
else if (file.getName().toLowerCase().endsWith(.fast5)) {
- return new Fast5File(file);
+ //return new Fast5File(file);
+ throw new SequenceFormatException(Support for FAST5
files has not been enabled in this build of FastQC.);
}
else {
return new FastQFile(config,file);
PATCH
I'm done with this for now. Off to debug some Python code.
Best,
TIM
--
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Re: Help needed to update to latest fastqc
On 08/12/2015 08:43 PM, Tim Booth wrote: 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. I will have a look on my side. I think that I found some code some times ago, but this packaging is definitly quite hard. could you make what you made available (sis-hdf5, sis-base etc.) so that I avoid losing time doing the same thing to test compilation. Olivier 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
Re: Help needed to update to latest fastqc
On 08/12/2015 12:44 PM, 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: I already had a look and started some work. In fact I expected to progress on it during Debconf, but if you started it... --- 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! Is it all ? In my previous check, it seemed (but not sure, it was quite some time ago) that there were multiple dependencies (or sis-base itself depending on other libs to package in sis repo) 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. I think that we should indeed keep the copied code from original, as I think they adapted it for their needs. Makihng modifications to use completly nca would make it unmaintainable in later updates I think. 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 -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Re: python-cobra 0.4.0b2 ready for upload
On 08/10/2015 02:50 PM, Andreas Tille wrote: On Mon, Aug 10, 2015 at 09:16:26PM +0900, Charles Plessy wrote: Le Mon, Aug 10, 2015 at 02:28:37AM -0700, Afif Elghraoui a écrit : Hi, Andreas, I've completed packaging the latest upstream release of python-cobra. Would you be able to upload to unstable, please? Hi Andreas, I am on it, if you do not mind :) Cool. I never mid if anybody else beats me in doing some work. Uploading from train to DebConf is also not a good idea. I am uploading it. Please update changelog to set to unstable instead of UNRELEASED (I made it locally for upload). There are also 2 warnings with lintian on timestamped gzip, might worth having a look next time. Olivier Greatings to all Andreas. -- 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/55c8b63c.8060...@codeless.fr
Re: python-cobra 0.4.0b2 ready for upload
On 08/10/2015 02:50 PM, Andreas Tille wrote: On Mon, Aug 10, 2015 at 09:16:26PM +0900, Charles Plessy wrote: Le Mon, Aug 10, 2015 at 02:28:37AM -0700, Afif Elghraoui a écrit : Hi, Andreas, I've completed packaging the latest upstream release of python-cobra. Would you be able to upload to unstable, please? Hi Andreas, I am on it, if you do not mind :) Cool. I never mid if anybody else beats me in doing some work. Uploading from train to DebConf is also not a good idea. sorry, I just released someone did it before. Greatings to all Andreas. -- 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/55c8b698.4020...@codeless.fr
Re: fastq status?
On 05/14/2015 06:22 PM, Andreas Tille wrote: On Thu, May 14, 2015 at 08:57:43AM +0200, olivier.sal...@codeless.fr wrote: Debian Science team. In other words: While you stated that what we need is probably a different code base than we need for fastqc the package might need some love independently. I may package it independently but how should we do that ? It would in a way conflict with official hdf5 lib. How should we name /describe it ? Or should it be a kinda libjava-fastq-hdf5 package ? I do not think that fastqc is the important point but may be libjava-hdf5-ethz since it was developed at ethz. Does this sound logical? Sounds logical. I will have a look but it will certainly require quite a lot of time. I had a look at library source code and it requires other libs (from some source) that should be packaged too, plus C stuff to compile (java calls native C). so it will be I think a complex package. Olivier Kind regards Andreas. -- 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/d714.50...@codeless.fr
Fwd: Re: fastq status?
CC'ing list... Forwarded Message Subject:Re: fastq status? Date: Thu, 14 May 2015 08:57:43 +0200 From: olivier.sal...@codeless.fr olivier.sal...@codeless.fr To: Andreas Tille andr...@an3as.eu On 05/13/2015 10:43 AM, Andreas Tille wrote: Hi Olivier, On Wed, May 13, 2015 at 05:58:41AM +, olivier sallou wrote: could you fix/get info about the hdf5 lib issue (not being complete s needed one in fastq) to get fastq build? No response from the libjhdf5-java maintainers. :-( This does not come unexpected since Sylvestre officially resigned from Debian Science team. In other words: While you stated that what we need is probably a different code base than we need for fastqc the package might need some love independently. I may package it independently but how should we do that ? It would in a way conflict with official hdf5 lib. How should we name /describe it ? Or should it be a kinda libjava-fastq-hdf5 package ? Olivier Hope you will be able to sort things out. Kind regards Andreas. -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Re: DebianMed Sprint network issue
On 12/11/2014 05:48 PM, Sebastian Hilbert wrote: Am Donnerstag, 11. Dezember 2014, 17:33:44 schrieb Karsten Hilbert: On Thu, Dec 11, 2014 at 04:09:34PM +0100, Andreas Tille wrote: I just talked with the hotel and they still have wifi access issues (though it was supposed to be solved). So it is almost plain sure that wifi won't be accessible. : :-( No Wifi or not even internet (via LAN) ? Since the (try to) provide Wifi access on their premises they must have some other means to get connectivity into their hotel in the first place. Might it be possible to persuade them to let you guys plug in your own wlan repeater or even route a very long LAN cable from their inhouse hub to your switch in the conference room ? If it helps I can send you a pair of PowerLAN adapters. I tried to propose this solution but it seems that their box is too far from the room for a cable. I did not think about powerlans, it may be a solution, though I should test this. I gonna investigate this point Thanks Olivier Sebastian -- 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/548aabc0.4060...@codeless.fr
Re: DebianMed Sprint network issue
On 12/11/2014 04:09 PM, Andreas Tille wrote: Hi Olivier, On Thu, Dec 11, 2014 at 12:29:12PM +, olivier sallou wrote: Hi, I just talked with the hotel and they still have wifi access issues (though it was supposed to be solved). So it is almost plain sure that wifi won't be accessible. :-( No Wifi or not even internet (via LAN) ? One solution could be a 3G / Wifi router with a 3G data card, has anyone experienced this ? I'm using a http://www.amazon.de/Huawei-E5220-WLAN-Router-WLAN-Zug%C3%A4nge-Boot-Zeit-wei%C3%9F/dp/B00DI7HPAU/ref=sr_1_1 quite frequently (tested with three clients connected at the same time). I can bring this but I have no French SIM card to use. I can get one (at least mine, but I can see to get an other one). I could buy a card with 4Go of data. Though I gonna investigate any other solution, can you please come with your router, at least as a backup solution. I will manage the SIM card. Thanks Kind regards Andreas. -- 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/548aac2f.9040...@codeless.fr
Re: DebianMed Sprint network issue
On 12/12/2014 11:36 AM, Andreas Tille wrote: Hi, On Fri, Dec 12, 2014 at 09:48:00AM +0100, olivier.sal...@codeless.fr wrote: If it helps I can send you a pair of PowerLAN adapters. I tried to propose this solution but it seems that their box is too far from the room for a cable. ??? Can they specify too far in numbers of meters? I can not really believe this. I think the issue is not the length but where is the internet box to pull a cable (if upstairs...) I talked with the owner, and I will go to the hotel to try to setup a wifi router myself and check connectivity in the room we will use (as well as power lan if I can get one for a try). Olivier I did not think about powerlans, it may be a solution, though I should test this. I gonna investigate this point Sounds good. And as I incidently send only in PM: I'll bring my UMTS hub in any case. Kind regards Andreas. -- 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/548ae10f.3030...@codeless.fr
Re: Licensing terms for data derived from ARB/SILVA data
On 11/28/2014 04:48 PM, Frank Oliver Glöckner wrote: Dear Sascha Steinbiss, thanks for the information. We discussed it and in general we agree that the HMM profiles derived from LSURef_115_tax_silva_full_align_trunc.fasta can be distributed. But we would like to ask you to clearly indicate that the profiles are only free for non-commercial usage, commercial users need a licence. The easiest approach is to add a reference to the SILVA terms of license assigned to the software/profile. Argghh! this will prevent from being in free section. And I suppose those profiles are mandary for software usage ? Have a nice weekend Frank Oliver Glöckner Am 26.11.2014 20:28, schrieb Sascha Steinbiss: On 26/11/2014 17:56, Frank Oliver Glöckner wrote: Dear Sascha Steinbeiss, Dear Prof. Gloeckner, thanks for your prompt reply. Before we can answer your question may I ask you to provide us with some more information about the: 1. name of the tool The software in question is barrnap (http://www.vicbioinformatics.com/software.barrnap.shtml) written by Torsten Seemann. 2. functionality of the tool, e.g. does it just detect rRNAs, and/or does it classify sequences? The main functionality is to detect rRNAs and to output their locations in an input sequence as GFF3 features. As far as classification goes, it does distinguish between the individual rRNAs for a given kingdom (5S,23S,16S for bacteria; 5S,5.8S,28S,18S for eukaryotes, etc.) but does not taxonomically classify them as being close to a particular species. You can see example output on the web page given above. It is basically a wrapper around nhmmer searching for a relatively general rRNA pHMM, meant for de novo annotation. All the best Frank Oliver Glöckner Best wishes from a former 'Nordlicht' (I think we met once when I still was at the ZBH Hamburg) Sascha Steinbiss Am 26.11.2014 12:34, schrieb Sascha Steinbiss: Dear ARB/SILVA team, I am writing to inquire about a special case regarding your data licensing terms. I am involved with the Debian Med project (https://www.debian.org/devel/debian-med/), whose goal it is to provide software from the medical and bioinformatics fields to users of the Debian Linux distribution. Currently I am working on packaging a piece of free (GPL) software for prediction of rRNA genes in sequences. This software requires (and would be bundled with) a set of nucleotide profile HMMs (built with HMMER) based on several individual data sources. One of the data sources used to build these HMMs was the file LSURef_115_tax_silva_full_align_trunc.fasta, available from your database. Since your licensing terms (http://www.arb-silva.de/silva-license-information/) are not clear about how derivatives of your data are to be licensed, I would like to ask whether it would be OK for us to package and redistribute these HMMs under a free license, for both academic and non-academic users. I wish to make it clear here that the original file LSURef_115_tax_silva_full_align_trunc.fasta will NOT be included in the package, only HMMs built from it (and other free sources). I am looking forward to your response. Best regards Sascha Steinbiss -- 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/54798abd.7090...@codeless.fr
Re: Licensing terms for data derived from ARB/SILVA data
On 11/29/2014 12:29 PM, Sascha Steinbiss wrote: Hi all, But we would like to ask you to clearly indicate that the profiles are only free for non-commercial usage, commercial users need a licence. The easiest approach is to add a reference to the SILVA terms of license assigned to the software/profile. Argghh! this will prevent from being in free section. And I suppose those profiles are mandary for software usage ? To ensure that the Debian version and the upstream version produce the same results, yes, they are necessary. I guess there are two choices now: 1. Put barrnap in non-free. What consequences would that have for a 'regular' academic user -- they would have to enable non-free on a default install, right? Yeap, they need to add non-free to apt sources 2. Use an alternative set of pHMMs in the Debian version of barrnap, only including those which are built from Rfam alignments only (Rfam has a free license (CC0)). However, that would strongly limit the functionality of barrnap as whole rRNA families could end up being missing from the output of the dfsg compliant version. I guess to have a usable barrnap version, 1. is the only viable solution. Any comments? I agree Thanks Sascha -- 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/5479b2c0.20...@codeless.fr
Next sprint proposal
Hi, sorry if mail is a duplicate, I had an issue when I sent my previous mail. After our nice sprint in Stonehaven, I come with a proposal (well ideas in fact) for the next sprint in France. There are several options: 1) in Brittany, in Saint Malo [0]. This is a really nice place (old town from pirates and corsairs) with beautiful beach. It needs however a 3 hours train ride from Paris (TGV). There is an airport near (Dinard, with RyanAir) but with no bus connection (though I could make the shuttle with my car). There are also train and bus connections from Rennes, itself connected with Paris by train or plane. 2) Deauville [1], the place where people from Paris goes for the week-end. There is a small airport for connection with London (fridayt and sunday), but mainly there are many train connections with Paris (2 hours ride) at a cheap price. There are several hotels near the beach at affordable price. [0] https://www.google.fr/maps/preview/place/Saint-Malo/@48.646282,-2.006653,12z/data=!3m1!4b1!4m2!3m1!1s0x480e81102126bf5d:0xf8e97dadb22be12d [1] https://www.google.fr/maps/preview/place/Deauville/@49.3539409,0.075006,13z/data=!3m1!4b1!4m2!3m1!1s0x47e1d4bac4578671:0x40c14484fbcf150 We have time to decide, but I want your opinions, ideas and preferences, for the easiest access for you. If we find a place that matches for everyone, then we could agree for a sprint in France. Please forward the email to anyone interested and not in the list. Olivier -- 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: http://lists.debian.org/52f7a3ae.5020...@codeless.fr
Re: Need some help for Java package
On 02/09/2014 12:57 AM, Andreas Tille wrote: Hi, On Sat, Feb 08, 2014 at 06:12:07PM +0100, olivier.sal...@codeless.fr wrote: I found some reference here: http://bioinf.hutton.ac.uk/tablet/svn.txt which belongs to the BSD licensed http://bioinf.hutton.ac.uk/tablet/ which might be interesting as well and it claims to be BSD licensed but I can not find a source download nor the SVN where the log above is from. I'll send a mail to upstream about this I've got response from upstream that the code is available at http://ics.hutton.ac.uk/svn/tablet means an other package dependency packaging and may be others. I had a quick look at svn, and it contains too other jar files (flamingo, scri-commons) that may need themselves packaging. Olivier Anyway, giira have this code (at least the one class they use), to compile their program. They should include the code or link to the used libraries. It seems to be a different codebase anyway - so my suggested fallback to ask upstream remains. Kind regards Andreas. -- 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: http://lists.debian.org/52f87cdc.6040...@codeless.fr
Re: Need some help for Java package
On 02/08/2014 04:54 PM, Andreas Tille wrote: Hi Olivier, On Sat, Feb 08, 2014 at 09:11:15AM +0100, olivier.sal...@codeless.fr wrote: I've gone furher, remove cplex, but there is still an issue. Code references: CigarParser.extractAllAlignDiffs() but there is no import in the code that would import CigarParser from a library or local code! and I cannot find on Internet any CigarParser class. This is related in a way or an other to samtools, but I do not see any CigarParser in libsam-java. I wonder how the source code is stable Any way, does anyone has an idea where this CigarParser may come from? I found some reference here: http://bioinf.hutton.ac.uk/tablet/svn.txt which belongs to the BSD licensed http://bioinf.hutton.ac.uk/tablet/ which might be interesting as well and it claims to be BSD licensed but I can not find a source download nor the SVN where the log above is from. I'll send a mail to upstream about this Anyway, giira have this code (at least the one class they use), to compile their program. They should include the code or link to the used libraries. Olivier Kind regards Andreas. -- 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: http://lists.debian.org/52f66567.9090...@codeless.fr
Re: Chances for cooperation between OSDDLinux and Debian
On 11/21/2013 02:00 PM, Andreas Tille wrote: Hi Raghava, On Thu, Nov 21, 2013 at 04:40:52PM +0530, G P S Raghava wrote: Dear Andreas Thanks for your email and detail response to my quiries. We have created debian package for our number of software, though they are not perfect but works. It is great to start with a set of packages which are somehow working and finalise them by polishing. Mean time I have a request from members of this community, please have a look on our repository and suggestions. I mean, what is required to make them official package of Debian. Surely I have looked into your repository - that's actually the reason why I considered contacting you in the first place. The requirements are: 1. (DFSG) free software 2. somebody who does the maintenance Since you are just building Debian packages you can most probably commit the packaging code into the Debian Med VCS (as described in our team policy[1]) and we will sponsor the packages to the official mirror. This is probably a successive process because we will have problems to do this for all packages in one rush. If packages are numerous, we can split the sponsoring work among a few of us (DebianMed team). Olivier Mean time, we are reading about conditions required to make a package debian package. You are best advised to read our team policy - specifically the hints for newcomers[2]. We will try to attend the conference you suggested, all depend on finance. I can not promise to much but team sprints are supported by Debian to some extent. Usually this means covering the costs of official Debian developers but we do not have a final calculation. In any case if this might help for your decision I'd volunteer to hand over my share (~250Eur) to somebody of your team if this might fill a needed gap. Developers from my group also joining mailing list. Do we have any person on this mailing list who has expertise in packaging, belong to our region (India). Joining the mailing list makes perfectly sense. There are several experienced packagers lurking on this list. I have no idea what you mean by belong to $any region. We have an i18n team in Debian if there are any country specific things but from a first view on your list I do not see any specifics for India. But apropos India: We have written a paper[3] which was originally intended to be published in an Indian journal (see the discussion here [4]) but I have not heard from the person who asked me to write this article and I think it is a nice reading anyway. So we should look for a proper place to publish the text once it is written at some more reasonable / prominent place than here[3] - but for the moment it might help you understanding what we finally are approaching and in how far this is in line with your goals. Kind regards Andreas. [1] http://debian-med.alioth.debian.org/docs/policy.html [2] http://debian-med.alioth.debian.org/docs/policy.html#packagingguidelines [3] http://debian-med.alioth.debian.org/docs/debian-med-healthcafe.pdf [4] https://lists.debian.org/debian-med/2013/02/msg00129.html From: Andreas Tille andr...@an3as.eu Subject:Re: Chances for cooperation between OSDDLinux and Debian Date: 21 November 2013 3:12:04 AM GMT+05:30 To: G P S Raghava ragh...@imtech.res.in Hi Raghava, please feel free to quote me fully on Debian Med mailing list - I'd prefer open discussion since other team members are definitely interested. On Thu, Nov 21, 2013 at 12:38:21AM +0530, G P S Raghava wrote: Dear Andreas Sorry for late response. One of the reason, I have not written to you earlier is that OSDDlinux is not fully finished. Well, is there any software that is finished at all? ;-) IMHO this is no reason at all. The point is that we really want to help you reaching your goals - thus getting stronger contact right now would be better than doing this later. We are are expert in biological science but we have limited knowledge in the filed of system software. So that would be a perfect match with Debian Med team. While there are also a couple of biologists we also have people wo are more into system questions. This mix has been quite successful as I wanted to point out in my initial mail. Our group http://www.imtech.res.in/raghava/ have developed large number of web-based service (more than 150) related to bioinformtics/chemoinformatics/vaccineinformatics. Thus for us major challenge is to make our web-services available to public in form of standalone software and integration with workflow GALAXY. We achieved it successfully, we develop standalone software and Galaxy-compaitable software, thus our first phase is nearly complete. Now , we are learning to develop debian-packages, soon all software packages our own and third party will be available in form of debian-package. Since I realised this from your web page I approached you
Re: (Java-)Help with ne version of igv needed
On 09/13/2013 08:57 PM, Andreas Tille wrote: Hi Olivier, On Fri, Sep 13, 2013 at 05:02:14PM +0200, Olivier Sallou wrote: hi, I just updated the git repo on my computer and tried a build, and it works fine, I could build the package. However, I had to download the upstream tar with get-orig-source, it is not set in pristine-tar branch (bu this is not theissue) Hmmm, I guess I should just have `git push --tags` to make it visible. Whatever, you have obviously solved it so that is fine. Are you sure you have a Java (openjdk) compiler installed? Hmmm, when building in pbuilder with git-buildpackage all preconditions should be fullfilled, shouldn't it? right! so it is quite strange. I could not build in pbuilder though due to an issue with pbuilder itself on my computer. As it did not change dependencies since previous builds, I though that this would be fine. Since recently, pbuilder fails with an error on dpkg-source (Can't locate strict.pm: permission denied), though I am running it on root and updated pbuilder (package and chroot). Do you have any idea of what could be wrong? Olivier Kind regards Andreas. -- 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: http://lists.debian.org/52340134.9050...@codeless.fr
bugs about crashed with exit code 139
Hi, you all have seen many many bugs from forallsecure, getting all the same crash exit code. Does anymore has a hint on the root cause of this? I can't imagine this does not come from the same root cause considering the numerous bugs found. Olivier -- 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: http://lists.debian.org/51cc3b56.6030...@codeless.fr
IGV package ready
Hi Andreas, the package libbc-prov dependency update I was waiting for has been done. I have made a few updates on IGV and it should be ok now for non-free. However, dependency has been pushed to experimental. As IGV will go to non-free, it will have to be pushed to non-free/experimental too. Do you want to upload the package and have a look? (as you made most of the packaging) Olivier -- 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: http://lists.debian.org/516122f6.6040...@codeless.fr
Re: [z...@debian.org: Availability of Debian official cloud images from debian.org]
Le 3/16/13 6:40 AM, Charles Plessy a écrit : Le Fri, Mar 15, 2013 at 09:25:55AM +0100, olivier.sal...@codeless.fr a écrit : Le 3/15/13 8:13 AM, Andreas Tille a écrit : Hi, any volunteer to join this effort to create such images featuring med-cloud packages? What would be a med-cloud image ? (but an image containing med-cloud packages) Hi all, the idea behind med-cloud is to install as much tools as possible, while limiting the size of the image. Hence it is limited to tools that do not depend on graphical environments, but if some command-line tools would pull hundreds of megabytes of packages just for themselves, I think that they would not be fit for the med-cloud metapackage. Other from this, it should be a standard installation. Ideally we should improve the support for Blends in tasksel, so that making a med-cloud image would be only the matter of one parameter when creating an image. Alternatively, a user running a standard image and installing med-cloud should have everything he needs (except data !) to run simple analysis, including the analysis of large quantities of sequence reads. Further usage will show us what adjustment we need. For instance, if /tmp is in the virtual memory, I expect that some workflow will not work when for instance sorting multi-gigabyte BED files, etc. In complemnt with this, it would be great to have tutorials explaining how to fetch data and make it ready for use with the tools that we distribute. One solution I know is 'getdata', but did not pass beyond the proof-of-principle stage. Can biomaj be used on the command line ? yes, web interface is only an additional tool for easier administration. Alternatively or in complement, we can also design a standard file hierarchy and configure our tools to use it, so that one could prepare separately some data repositories ready for being used from Debian Med images. Have a nice week-end, -- 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: http://lists.debian.org/51444a9b.7060...@codeless.fr
Re: [z...@debian.org: Availability of Debian official cloud images from debian.org]
Le 3/15/13 8:13 AM, Andreas Tille a écrit : Hi, any volunteer to join this effort to create such images featuring med-cloud packages? What would be a med-cloud image ? (but an image containing med-cloud packages) I would gladly help such thing with debian-cloud team when debian-cloud team have procedures to build such images. For raw/qcow2/ovh, it can be quite easy to build (you can transform between each other). Difficulty is more related to EC2 and specific setups per cloud. Olivier Kind regards Andreas. - Forwarded message from Thomas Goirand z...@debian.org - Date: Fri, 15 Mar 2013 14:28:07 +0800 From: Thomas Goirand z...@debian.org To: Debian Developers debian-de...@lists.debian.org, debian-cl...@lists.debian.org debian-cl...@lists.debian.org Subject: Availability of Debian official cloud images from debian.org Hi, Multiple times, in the debian-cloud@l.d.o, we've came to the conclusion that Debian should be release images of the stable release (and probably testing as well) to be run in the cloud. I'm bringing this topic to -devel, as I'm convince it is a topic which should be debated with everyone in Debian. There is enough software in Debian itself which can support such images: - Openstack - Eucalyptus - XCP - etc. Currently, we have semi-official images which, thanks to the nice work of the people in debian-cl...@lists.debian.org, are uploaded to both AWS and Azure. While it's nice that we have these, and while I believe such initiatives should be encouraged and generalize to other hosting providers, it is now clear that we need a channel to be able to provide Debian cloud images. Please have a look to what they do at Ubuntu: https://cloud-images.ubuntu.com/releases/ and more specifically, when you click on one of them: https://cloud-images.ubuntu.com/releases/precise/release/ they provide both the images for all Ubuntu releases. Also, please notice that there are multiple format available: - .ovf, which is an open format - disk1.img qcow2 format: can be uploaded to Openstack, or booted directly using kvm, and many more - .img, +kernel and ramdisk: can be used on EC2, Eucalyptus, or Openstack Plus there are links to EC2 so that you can just launch such instances. [in debian.org, we should allow anyone to add information about Debian images in any company though, and not focus only on one major vendor, otherwise it is anti-competitive] So, put in simple words: we need something like this. Question is, where can this be uploaded? To me, cdimage.debian.org seem to be the natural place. Does it make sense to everyone else? Could we, in a near future, imagine having these images creation, included in the official release build process, together with the CDs, DVDs, etc.? Cheers, Thomas -- 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: http://lists.debian.org/5142db13.9000...@codeless.fr
Re: FWD Next BioPerl release
Le 2/6/13 5:43 AM, Charles Plessy a écrit : Hi all, for your information, there is a new BioPerl release scheduled soon. I a still very busy at work and may not be able to push it in Debian quickly. Also, we need to ensure compatibility with the reverse dependancies. What do you propose ? Push it to experimental but build test then try to build all reverse dependants? I think there are many packages that depend on BioPerl, how can we test them all ? (one by one on our computer? or is there a Debian tool/way to do so?) I am committed to keep BioPerl in shape in Debian, but if somebody wants to step in and take the lead, I would be pleased. I can take the lead on BioPerl if you want. Cheers, -- Charles - Forwarded message from Fields, Christopher J cjfie...@illinois.edu - Date: Tue, 5 Feb 2013 21:53:29 + From: Fields, Christopher J cjfie...@illinois.edu To: BioPerl List bioper...@lists.open-bio.org Subject: [Bioperl-l] Next BioPerl release Message-ID: 118f034cf4c3ef48a96f86ce585b94bf6ce18...@chimbx5.ad.uillinois.edu All, I am scheduling the next BioPerl CPAN release tentatively for March 1. Any help in triaging bug reports would be greatly appreciated! Amongst all other changes, as mentioned in a separate thread we will remove Bio::FeatureIO, now developed in a separate repository: https://github.com/bioperl/Bio-FeatureIO Feedback, suggestions, etc are greatly appreciated. chris ___ Bioperl-l mailing list bioper...@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l - End forwarded message - -- 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: http://lists.debian.org/51120b2a.7000...@codeless.fr
please upgrade libbio-graphics-perl
Hi Charles, could you please upgrade libbio-graphics-perl? New GBrowse needs at least v2.31. If you do not have time, please tell me and I 'll try to update it myself. Thanks Olivier -- 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: http://lists.debian.org/50cc31bf.1040...@codeless.fr
Re: please upgrade libbio-graphics-perl
Le 12/15/12 9:37 AM, Charles Plessy a écrit : Le Sat, Dec 15, 2012 at 09:15:59AM +0100, olivier.sal...@codeless.fr a écrit : could you please upgrade libbio-graphics-perl? New GBrowse needs at least v2.31. If you do not have time, please tell me and I 'll try to update it myself. Hi Olivier, thank you for the offer. I caught cold and have a bit of difficulty to focus, so I would be grateful if you would updated it. May I ask you to import version 2.30 in the Git repository before version 2.31, Version 2.32 is available now, I need to upgrade with each intermediate version? and to either send the build logs or commit them to the meta branch ? sure Bon week-end, -- 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: http://lists.debian.org/50cc375a.2070...@codeless.fr
Re: please upgrade libbio-graphics-perl
Le 12/15/12 9:37 AM, Charles Plessy a écrit : Le Sat, Dec 15, 2012 at 09:15:59AM +0100, olivier.sal...@codeless.fr a écrit : could you please upgrade libbio-graphics-perl? New GBrowse needs at least v2.31. If you do not have time, please tell me and I 'll try to update it myself. Hi Olivier, thank you for the offer. I caught cold and have a bit of difficulty to focus, so I would be grateful if you would updated it. May I ask you to import version 2.30 in the Git repository before version 2.31, and to either send the build logs or commit them to the meta branch ? Bon week-end, package has been updated to version 2.31, with logs in meta. I will update to 2.32 later on. Olivier -- 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: http://lists.debian.org/50cc4e64.5000...@codeless.fr
Re: Fwd: RFS: scscp-imcce/0.7.0+ds-1 [ITP] -- IMCCE SCSCP C Library
Le 8/28/12 10:54 PM, Jerome BENOIT a écrit : Hello: On 28/08/12 12:16, olivier.sal...@codeless.fr wrote: Le 8/28/12 12:12 PM, Steffen Möller a écrit : Hello, I am totally swamped, but also like seeing so many astronomers now surfacing on Debian. I would like to introduce you to Olivier on the cc line, who I have some hope to be located (relatively speaking) close to you. Should Olivier (unexpectedly as I experienced to know him) not be available, and nobody else on debian-science show up, then contact me again, please. Hi, I won't be able to look at this before 2 weeks. But I would be glad to help after this. I am glad to read that. Hi, I am now available to have a look at your package. Is it still needeed? I will go through the review of the package and send you my comments so that you update the package. If package is to be in debian-science, you should ask to be added on Alioth to the debian-science team so that you put the debian code in the repository. Or should it be put in debian-med repository? Nevertheless, please observe that this package concerns a library that implements the SCSCP protocol. This protocol is meant for communication between CAS (Computer Algebraic Systems) as Maple, Mathematica, GAP, ... Actually is is already implemented in Maple and the last GAP (not yet available in Debian). So to speak, it is this package does not target astronomers in particular. Personally, I am not an astronomer. I have in main to write an ad hoc CAS to deals with polygonal knots which can be called by softwares used in protein biology as GROMACS, PyMOL, ... I guess that I should made this point clearer before. Olivier Cheers, Steffen On 08/28/2012 03:12 AM, Jerome BENOIT wrote: Original Message Subject: RFS: scscp-imcce/0.7.0+ds-1 [ITP] -- IMCCE SCSCP C Library Date: Tue, 28 Aug 2012 03:03:08 +0200 From: Jerome Benoitcalcu...@rezozer.net To: Debian Bug Tracking Systemsub...@bugs.debian.org Package: sponsorship-requests Severity: normal Dear mentors, I am looking for a sponsor for my package scscp-imcce * Package name: scscp-imcce Version : 0.7.0+ds-1 Upstream Author : Mickael Gastineaugastin...@imcce.fr * URL : http://www.imcce.fr/trip/scscp/ * License : CeCILL v2.0 Section : math It builds those binary packages: libscscp-doc - IMCCE SCSCP C Library -- reference manual libscscp0 - IMCCE SCSCP C Library -- library package libscscp0-dbg - IMCCE SCSCP C Library -- debug symbols package libscscp0-dev - IMCCE SCSCP C Library -- development package To access further information about this package, please visit the following URL: http://mentors.debian.net/package/scscp-imcce Alternatively, one can download the package with dget using this command: dget -x http://mentors.debian.net/debian/pool/main/s/scscp-imcce/scscp-imcce_0.7.0+ds-1.dsc More information about scscp can be obtained from http://www.imcce.fr/trip/scscp/ First upload. Best wishes, Jerome BENOIT -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- 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: http://lists.debian.org/5056bf75.8090...@codeless.fr
please upgrade libbio-graphics-perl
Hi Charles, would you mond upgrading libbio-graphics-perl to latest version? I need at least version 2.28 (current 2.29) for gbrowse. Thanks Olivier -- 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: http://lists.debian.org/504b33fd.3010...@codeless.fr
Bug#686938: ITP: libvm-ec2-perl
Package: wnpp Severity: wishlist Owner: Olivier Sallou osal...@debian.org X-Debbugs-Cc: debian-med@lists.debian.org * Package name: libvm-ec2-perl Version : 1.17 Upstream Author : Lincoln D. Stein lincoln.st...@gmail.com * URL : http://search.cpan.org/~lds/VM-EC2-1.02/ * License : Artistic 1 and GPL-1 Programming Lang: Perl Description : limited interface to Amazon EC2 REST tools This is an interface to Amazon EC2 REST tools that follows the 2011-05-15 API. Author created it because he needed access to the Tag and TagSet interfaces. The core Amazon API is supported, but support for VPC, clusters, spot instances and reserved instances is incomplete. This package is a dependency for gbrowse package. -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Re: libsnappy1.0.3 and picard-tools ok
Le 9/6/12 6:59 AM, Charles Plessy a écrit : Le Mon, Sep 03, 2012 at 08:53:39AM +0200, Olivier Sallou a écrit : I have just uploaded libsnappy1.0.3-java_1.0.3-rc3~dfsg-3 which does not conflict anymore on maven repo. I use it against picard-tools, with additiona patches for jbzip2 usage and classpath issue and it seems to work. Charles, follows test output. I do not know if it is ok (at least no error). Git repo is up-to-date if you want to build the package. If ok, do you upload the package or do you want I do it? Hi Olivier, I tested picard-tools further and found no problem. Do you think you would have time to upload it ? Done! Many thanks again. Picard-tools has a couple of unique functionalities, and it is good to have it up to date in Debian. Cheers, -- 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: http://lists.debian.org/50484d53.3030...@codeless.fr
Re: snappy uploaded and picard-tools can be build against it
Le 8/29/12 7:07 AM, Charles Plessy a écrit : Le Tue, Aug 28, 2012 at 12:49:59PM +0200, olivier.sal...@codeless.fr a écrit : Hi, I have uploaded libsnappy1.0.3-java package for picard-tools. I could successfully build picard-tools with this package. picard-tools still need to be updated to get latest release and use snappy1.0.3-java.jar file (update of the patch) Hi Olivier, many thanks for all of this. I built and installed libsnappy1.0.3-java. It will need to conflict with libsnappy-java, or the maven information will need to be renamed: I think maven info should be renamed, does not need to conflict. I will update package. Maven info should be: /usr/share/maven-repo/org/xerial/snappy/snappy1.0.3-java/debian/snappy1.0.3-java-debian.pom Selecting previously unselected package libsnappy1.0.3-java. (Reading database ... 312719 files and directories currently installed.) Unpacking libsnappy1.0.3-java (from libsnappy1.0.3-java_1.0.3-rc3~dfsg-1_all.deb) ... dpkg: error processing libsnappy1.0.3-java_1.0.3-rc3~dfsg-1_all.deb (--install): trying to overwrite '/usr/share/maven-repo/org/xerial/snappy/snappy-java/debian/snappy-java-debian.pom', which is also in package libsnappy-java 1.0.4.1~dfsg-1 Errors were encountered while processing: libsnappy1.0.3-java_1.0.3-rc3~dfsg-1_all.deb On the source pakcage side, can you push the pristine-tar branch that contain the version 1.0.3-rc3~dfsg ? I will have a look. I updated the code Andreas put in git repo. I did not check for pristine etc... as I just updated the debian directory. I then build and installed picard tools, but all the command I try to run fail with an errror like the following. $ picard-tools EstimateLibraryComplexity I=testdata/net/sf/samtools/compressed.bam O=/dev/stdout [Wed Aug 29 14:06:35 JST 2012] net.sf.picard.sam.EstimateLibraryComplexity INPUT=[testdata/net/sf/samtools/compressed.bam] OUTPUT=/dev/stdout MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=50 CREATE_INDEX=false CREATE_MD5_FILE=false [Wed Aug 29 14:06:35 JST 2012] Executing as charles@anx191 on Linux 3.2.0-2-amd64 amd64; OpenJDK 64-Bit Server VM 1.6.0_24-b24; Picard version: 1.75(exported) [Wed Aug 29 14:06:35 JST 2012] net.sf.picard.sam.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=189071360 FAQ: http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page Exception in thread main java.lang.NoClassDefFoundError: org/apache/tools/bzip2/CBZip2OutputStream at net.sf.picard.sam.EstimateLibraryComplexity.doWork(EstimateLibraryComplexity.java:217) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177) at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119) at net.sf.picard.sam.EstimateLibraryComplexity.main(EstimateLibraryComplexity.java:208) Caused by: java.lang.ClassNotFoundException: org.apache.tools.bzip2.CBZip2OutputStream at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) ... 4 more Installing libjbzip2-java did not solve the problem. Do you have an idea ? Strange, I did not face this issue. libjbzip2-java should indeed solve CBZip2OutputStream. Have a nice day, -- 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: http://lists.debian.org/503db9f7.4070...@codeless.fr
Re: snappy uploaded and picard-tools can be build against it
Le 8/29/12 7:07 AM, Charles Plessy a écrit : Le Tue, Aug 28, 2012 at 12:49:59PM +0200, olivier.sal...@codeless.fr a écrit : Hi, I have uploaded libsnappy1.0.3-java package for picard-tools. I could successfully build picard-tools with this package. picard-tools still need to be updated to get latest release and use snappy1.0.3-java.jar file (update of the patch) Hi Olivier, many thanks for all of this. I built and installed libsnappy1.0.3-java. It will need to conflict with libsnappy-java, or the maven information will need to be renamed: Selecting previously unselected package libsnappy1.0.3-java. (Reading database ... 312719 files and directories currently installed.) Unpacking libsnappy1.0.3-java (from libsnappy1.0.3-java_1.0.3-rc3~dfsg-1_all.deb) ... dpkg: error processing libsnappy1.0.3-java_1.0.3-rc3~dfsg-1_all.deb (--install): trying to overwrite '/usr/share/maven-repo/org/xerial/snappy/snappy-java/debian/snappy-java-debian.pom', which is also in package libsnappy-java 1.0.4.1~dfsg-1 Errors were encountered while processing: libsnappy1.0.3-java_1.0.3-rc3~dfsg-1_all.deb On the source pakcage side, can you push the pristine-tar branch that contain the version 1.0.3-rc3~dfsg ? I then build and installed picard tools, but all the command I try to run fail with an errror like the following. $ picard-tools EstimateLibraryComplexity I=testdata/net/sf/samtools/compressed.bam O=/dev/stdout [Wed Aug 29 14:06:35 JST 2012] net.sf.picard.sam.EstimateLibraryComplexity INPUT=[testdata/net/sf/samtools/compressed.bam] OUTPUT=/dev/stdout MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=50 CREATE_INDEX=false CREATE_MD5_FILE=false [Wed Aug 29 14:06:35 JST 2012] Executing as charles@anx191 on Linux 3.2.0-2-amd64 amd64; OpenJDK 64-Bit Server VM 1.6.0_24-b24; Picard version: 1.75(exported) [Wed Aug 29 14:06:35 JST 2012] net.sf.picard.sam.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=189071360 FAQ: http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page Exception in thread main java.lang.NoClassDefFoundError: org/apache/tools/bzip2/CBZip2OutputStream at net.sf.picard.sam.EstimateLibraryComplexity.doWork(EstimateLibraryComplexity.java:217) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177) at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119) at net.sf.picard.sam.EstimateLibraryComplexity.main(EstimateLibraryComplexity.java:208) Caused by: java.lang.ClassNotFoundException: org.apache.tools.bzip2.CBZip2OutputStream at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) ... 4 more Installing libjbzip2-java did not solve the problem. Do you have an idea ? Sorry, I also face the issue, I did not see you talked of runtime error. As it is a runtime dependency, the libjbzip2-java should be in classpath. Maybe this jar file should be added in jar manifest (and added as Depends of course) Olivier Have a nice day, -- 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: http://lists.debian.org/503dbbd5.8010...@codeless.fr
snappy uploaded and picard-tools can be build against it
Hi, I have uploaded libsnappy1.0.3-java package for picard-tools. I could successfully build picard-tools with this package. picard-tools still need to be updated to get latest release and use snappy1.0.3-java.jar file (update of the patch) Olivier -- 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: http://lists.debian.org/503ca257.6050...@codeless.fr
fixed picard-tools
Hi, I have updated picard-tools on Debian git to use libsnappy1.0.3. I updated the patches and files to use version 1.75 (latest). Package build correctly, however it would be fine to test the package (I do not know picard-tools) before uploading it. Charles, could you have a look? Thanks Olivier -- 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: http://lists.debian.org/503cbac3.5070...@codeless.fr
Re: snappy uploaded and picard-tools can be build against it
Le 8/28/12 2:36 PM, Andreas Tille a écrit : On Tue, Aug 28, 2012 at 12:49:59PM +0200, olivier.sal...@codeless.fr wrote: Hi, I have uploaded libsnappy1.0.3-java package for picard-tools. I could successfully build picard-tools with this package. Cool. Thanks a lot. picard-tools still need to be updated to get latest release and use snappy1.0.3-java.jar file (update of the patch) Charles, will you step in here? I have updated git to use snappy 1.0.3 and few fixes. I expect Charles to control/test the package from git repo. Kind regards Andreas. PS: I did not changed my mind that we should advise picard-tools upstream to not use unmaintained outdated code. I asked them for this but they are reluctant because they had difficulties to use it and faced many usage issues with different user/config. Now that library changed its API they are not really enthusiast to change their code. -- 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: http://lists.debian.org/503ced2f.8070...@codeless.fr
Re: status on picard-tools and issue with libsnappy-java
Le 8/14/12 10:57 AM, Andreas Tille a écrit : Hi, On Tue, Aug 14, 2012 at 09:06:46AM +0200, olivier.sal...@codeless.fr wrote: Le 8/13/12 1:35 PM, Andreas Tille a écrit : On Mon, Aug 13, 2012 at 08:07:22PM +0900, Charles Plessy wrote: For libsnappy-java, since it still only has 10 Popcon users, of which I already contribute 2 or 3 points because I develop on multiple machines, we can also do something very dark side, that is a) downgrade libsnappy-java to 1.0.3 using an epoch, and b) request its removal from Wheezy. Its dirty but probably solves the problem in a way that causes the least work for us currently. However, I think the popcon count is anyway alarming enough to assume that we might leave some unhappy users behind. I'd rather like avoiding a removal. I'd still prefer packaging a v1.0.3 ( with an epoch) I agree that this is also my prefered solution but if the package say libsnappy1.0.3-java should be maintained in addition to libsnappy-java ... but without an epoch IMHO, because these are distinct packages without a common history. Or am I missing something? Nope, youre right. that conflicts with the current version I do not see any reason for a conflict if the file names are different. and a picard-tools that recomments 1.0.3. If 1.0.3 is not present, it does not matter, picard-tools will work. It is only mandatory for picard-tools building. IMHO the only thing what we need to do in picard-tools is changing the class dependencies from snappy.jar to snappy1.0.3.jar which should do the trick. I tried something along this path and created git://git.debian.org/debian-med/snappy1.0.3-java.git However, when doing so I noticed that all downloadable versions snappy-java-1.0.3.[1-3].tar.gz are unfortunately NOT featuring our target class LoadSnappy. I wonder whether somebody could contact picard-tools upstream again what exact version they are using (and perhaps nagging again that finally using unmaintained code is definitely not a good idea - beeing angry about ABI changes or not.) They refer to snappy 1.0.3-rc3 [0]. LoadSnappy is available there. [0] http://code.google.com/p/snappy-java/source/browse/?name=snappy-java-1.0.3-rc3#hg%2Fsrc%2Fmain%2Fjava%2Forg%2Fxerial%2Fsnappy Kind regards Andreas. -- 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: http://lists.debian.org/502b53b7.2020...@codeless.fr
Re: status on picard-tools and issue with libsnappy-java
Le 8/14/12 10:57 AM, Andreas Tille a écrit : Hi, On Tue, Aug 14, 2012 at 09:06:46AM +0200, olivier.sal...@codeless.fr wrote: Le 8/13/12 1:35 PM, Andreas Tille a écrit : On Mon, Aug 13, 2012 at 08:07:22PM +0900, Charles Plessy wrote: For libsnappy-java, since it still only has 10 Popcon users, of which I already contribute 2 or 3 points because I develop on multiple machines, we can also do something very dark side, that is a) downgrade libsnappy-java to 1.0.3 using an epoch, and b) request its removal from Wheezy. Its dirty but probably solves the problem in a way that causes the least work for us currently. However, I think the popcon count is anyway alarming enough to assume that we might leave some unhappy users behind. I'd rather like avoiding a removal. I'd still prefer packaging a v1.0.3 ( with an epoch) I agree that this is also my prefered solution but if the package say libsnappy1.0.3-java should be maintained in addition to libsnappy-java ... but without an epoch IMHO, because these are distinct packages without a common history. Or am I missing something? that conflicts with the current version I do not see any reason for a conflict if the file names are different. and a picard-tools that recomments 1.0.3. If 1.0.3 is not present, it does not matter, picard-tools will work. It is only mandatory for picard-tools building. IMHO the only thing what we need to do in picard-tools is changing the class dependencies from snappy.jar to snappy1.0.3.jar which should do the trick. I tried something along this path and created git://git.debian.org/debian-med/snappy1.0.3-java.git However, when doing so I noticed that all downloadable versions snappy-java-1.0.3.[1-3].tar.gz are unfortunately NOT featuring our target class LoadSnappy. I wonder whether somebody could contact picard-tools upstream again what exact version they are using (and perhaps nagging again that finally using unmaintained code is definitely not a good idea - beeing angry about ABI changes or not.) By the way, do you plan to package it and update picard-tools or do you want I take this in charge. I can do it if you want, it is only a matter of time. Thanks Olivier Kind regards Andreas. -- 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: http://lists.debian.org/502b5466.9040...@codeless.fr
Re: status on picard-tools and issue with libsnappy-java
Le 8/13/12 1:35 PM, Andreas Tille a écrit : On Mon, Aug 13, 2012 at 08:07:22PM +0900, Charles Plessy wrote: For libsnappy-java, since it still only has 10 Popcon users, of which I already contribute 2 or 3 points because I develop on multiple machines, we can also do something very dark side, that is a) downgrade libsnappy-java to 1.0.3 using an epoch, and b) request its removal from Wheezy. Its dirty but probably solves the problem in a way that causes the least work for us currently. However, I think the popcon count is anyway alarming enough to assume that we might leave some unhappy users behind. I'd rather like avoiding a removal. I'd still prefer packaging a v1.0.3 ( with an epoch) that conflicts with the current version and a picard-tools that recomments 1.0.3. If 1.0.3 is not present, it does not matter, picard-tools will work. It is only mandatory for picard-tools building. Olivier Note to the other readers: this is really something that usually should not be done. Please forget what you read ! What did you wrote? Probably need to start reading from top because I forgot what was written there. ;-) What do you think ? I have a slight preference for Oliviers suggestion and I'd be fine with waiting once he is back from holidays. We should keep the dirtier method (which was in some mail I need to reread because I forgot) in mind if something might cause any problem. There might be a third way that also qualifies as dirty solution: As I said we could inject LoadSnappy.java as patch and by doing so build the package successfully. Then we could *Conflict* picard-tools with libsnappy-java to make sure that the class is not found at execution time. Could you please exlpain again the advantage of having libsnappy for the picard-tools user? Kind regards Andreas. -- 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: http://lists.debian.org/5029f906.8030...@codeless.fr
Re: Ping: Help for non-technical task needed (Was: License of colt [colt_1.2.0~dfsg-1_amd64.changes REJECTED)
Le 8/10/12 2:18 PM, Andreas Tille a écrit : Hi Olivier (or whoever else might lurk un FB) On Wed, Aug 01, 2012 at 11:07:53AM +0200, Olivier Sallou wrote: Perhaps I'm wrong but I found the following: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libcolt-java/trunk/debian/copyright?view=markup I have sent a message via Facebook to one of the author but I am afraid that it will be complicated Any answer from colt author? No, no answer. :-( Kind regards Andreas. -- 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: http://lists.debian.org/5028a9a3.2000...@codeless.fr
status on picard-tools and issue with libsnappy-java
I copy below the answer from upstream team. They will not go to latest snappy version. Seems it was quite difficult to integrate it and faced issues. The problem is snappy-java 1.0.4 breaks its API and is not compatible with version 1.0.3 used by picard-tools. At runtime, picard-tools tries to detect snappy. If not present, it will be ok. However we still face the problem for Debian for compilation Olivier Message original Sujet: Re: [Samtools-help] support of snappy-1.0.4 Date : Thu, 09 Aug 2012 10:27:11 -0400 De :Alec Wysoker al...@broadinstitute.org Pour : olivier.sallou olivier.sal...@laposte.net Copie à : samtools-h...@lists.sourceforge.net Hi Olivier, I assume you are referring to Picard library rather than samtools, because I don't think samtools uses Snappy. I am reluctant to fiddle with Snappy or get a new version, because we had lots of problems when we released it, some of which did not happen on our configuration but only for other users, which made it difficult to test and debug. It took several iterations for this to settle down. Could you try one of the following alternatives to using latest snappy-java: * Use the same version Picard uses, i.e. 1.0.3-rc3 * Omit snappy-java classes completely. net.sf.samtools.util.SnappyLoader is written so that if org.xerial.snappy.SnappyInputStream and org.xerial.snappy.SnappyOutputStream are not found on the classpath, then the code should work without using Snappy. -Alec On 8/8/12 10:02 AM, olivier.sallou wrote: Hi, I am part of the DebianMed team, we package some programs for Debian. When trying to compile sam-tools, we got an issue because current snappy version is 1.0.4 and it is not compatible with previous ones. Indeed, LoadSnappy class is not present anymore, and has been replaced by SnappyLoader (same name as one of your classes). Furthermore, public method load is not present anymore. With hacks, I could get it compile, but I do not know if my hacks are correct (if needed I can send you what I did). Do you plan to support new snappy version ? Thanks Olivier -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Samtools-help mailing list samtools-h...@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
Re: status on picard-tools and issue with libsnappy-java
Le 8/13/12 11:08 AM, Andreas Tille a écrit : On Mon, Aug 13, 2012 at 09:27:50AM +0200, olivier.sal...@codeless.fr wrote: I copy below the answer from upstream team. They will not go to latest snappy version. Seems it was quite difficult to integrate it and faced issues. The problem is snappy-java 1.0.4 breaks its API and is not compatible with version 1.0.3 used by picard-tools. This is what we also learned (the hard way). At runtime, picard-tools tries to detect snappy. If not present, it will be ok. However we still face the problem for Debian for compilation Message original Sujet: Re: [Samtools-help] support of snappy-1.0.4 Date : Thu, 09 Aug 2012 10:27:11 -0400 De : Alec Wysoker al...@broadinstitute.org Pour : olivier.sallou olivier.sal...@laposte.net Copie à :samtools-h...@lists.sourceforge.net ... Could you try one of the following alternatives to using latest snappy-java: * Use the same version Picard uses, i.e. 1.0.3-rc3 It somehow came to my mind to package this older version. Finally we started packaging libsnappy-java for the only purpose to support picard ... and currently this purpose is not fullfilled. Too bad We could indeed package a libsnappy1.0.3-java (with a conflict on libsnappy-java, and a recommends on picard-tools) and make picard-tools depend on this version. I am on holiday for the moment and won't have much time to manage this. However, if adding such library (1.0.3) can fix the issue, I could do this in a few weeks. * Omit snappy-java classes completely. net.sf.samtools.util.SnappyLoader is written so that if org.xerial.snappy.SnappyInputStream and org.xerial.snappy.SnappyOutputStream are not found on the classpath, then the code should work without using Snappy. Hmmm, I do not know the advantage we would liked to reach and whether this is acceptable. However, it seems to make sense to do not only a check whether the class is available but also to verify the version if there are incompatible versions known. I have no idea whether this is possible - but if yes this would be a reasonable hint to upstream. Incompatible versions should also be detected as expected class will not be found. But this does not fix our compilation issue as snappy is still required for build (with correct version) Kind regards Andreas. -- 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: http://lists.debian.org/5028d734.6090...@codeless.fr
Re: Ping: Help for non-technical task needed (Was: License of colt [colt_1.2.0~dfsg-1_amd64.changes REJECTED)
Le 8/13/12 10:58 AM, Andreas Tille a écrit : On Mon, Aug 13, 2012 at 09:15:47AM +0200, olivier.sal...@codeless.fr wrote: I have sent a message via Facebook to one of the author but I am afraid that it will be complicated Any answer from colt author? No, no answer. :-( Is it possible to obtain any valid e-mail address at least? Not via facebook. I can only send message via facebook, but I don't have his address. And did not find other valid address. Thanks for your effort Andreas. -- 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: http://lists.debian.org/5028d77b.7010...@codeless.fr
netlib-java not moving to testing
Hi, package netlib-java remains in unstable and has not moved to testing due to: libnetlib-java/i386 unsatisfiable Depends: f2j f2j, in non-free, is available as binary only on amd64. But I wonder why package does not move to testing if amd64 is available. Any idea of I should do to get it in testing? I could try to build the i386 binary and upload it, but I wonder if i386 will be the only issue (and not all other archs) Thanks Olivier -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Re: use of json.org in biojava3-ws
Le 5/29/12 6:30 PM, Steffen Möller a écrit : On 05/29/2012 02:23 PM, Mehdi Dogguy wrote: On 29/05/12 14:17, Andreas Tille wrote: On Tue, May 29, 2012 at 02:03:27PM +0200, Niels Thykier wrote: On 2012-05-29 13:59, Olivier Sallou wrote: Hi, biojava3 makes use of json.org library. this library is not packaged in Debian. After a google, I saw old posts saying that library is (was?) not compliant regarding its license [0]. Though, after a quick look on their web site I do not see any restriction. Can anyone tell me is something wrong with their code for not being packaged? [0] http://www.json.org/license.html Olivier The Software shall be used for Good, not Evil. Fails DFSG#5 or DFSG#6. Not to mention evil is not defined, so it makes it hard to figure out whether we are doing evil or not. I'd call this an over-picky interpretation of something that rather qualifies as a joke rather than a license which can be dealt with in court (disclaimer: I'm not a lawyer, just try to apply common sense.) FWIW, FTP-masters already rejected packages because their license had the to be used for good, not evil bit. So there is at least one side that it is not taking it as a joke. Upstream should remove that clause to comply with the DFSG terms. intentionally evil might save it. Anyway, libjson-java is not possibly it, is it? Well ... that has its home in http://json-lib.sourceforge.net/ and there it reads JSON-lib is a java library for transforming beans, maps, collections, java arrays and XML to JSON and back again to beans and DynaBeans. It is based on the work by Douglas Crockford in http://www.json.org/java; Anyway, I would not have a problem with biojava in contrib. Would be too bad I expect that upstream will take into account my request to use a free one. In the meanwhile, I could deliver biojava without the library biojava3-ws (web service) which is the only one impacted by json lib. Olivier Cheers, Steffen -- 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: http://lists.debian.org/4fc5bbd3.9020...@codeless.fr
Re: use of json.org in biojava3-ws
Le 5/30/12 9:33 AM, Alexandre Rossi a écrit : Hi, I've already seen this library, but it is not a compatible API. I gonna ask to biojava team if they would go to using such library instead of org.json one... For what it's worth, from the work I've begun doing on GWT, which had the same problem among others, I settled using json-simple and my patch is available[2] (though the packaging work is not finished). [1] http://code.google.com/p/json-simple/ [2] http://sousmonlit.dyndns.org/~niol/repositories.git/gwt-debian.git/debian/patches/use-json-simple I gonna use simple_json and patch accordingly, thanks for the hint Olivier And there IS software in Debian using json.org libraries, I know of at least one popular package that uses it. Cheers, Alex -- 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: http://lists.debian.org/4fc5ec39.6080...@codeless.fr
Re: [Debichem-devel] Where to maintain pdb2pqr
Le 5/18/12 5:56 PM, Andreas Tille a écrit : On Fri, May 18, 2012 at 12:16:04PM +0200, Michael Banck wrote: I believe it is best kept at team maintenance, either in the debian-med or the debichem repository, I do not particularly care which one, and as it is already in debian-med, it might be easier to keep it there and just change the maintainer (back?). Are you a member of either? Olivier is DD and in Debian Med team. I'm fine with setting the maintainer to Debian Med team (back) and Olivier as Uploader. Packaging should be a straightforeward upgrade - but if I'm not missleaded Manuel just gave an answer that he might do it. I guess he will not mind if somebody else is faster doing the job. (I also remember that Manuel voted against moving to debichem SVN because keeping the history is hard for partial checkouts.) I gonna update and upload package for Debian Med. Olivier Kind regards Andreas (today and on weekand basically offline). -- 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: http://lists.debian.org/4fb6b76a.7020...@codeless.fr
pdb2pqr
Hi all, I tried to get pdb2pqr to build and upload it. However, new version does not build at all (failure at install time). I think I will need Manuel help to get the package ready. I see that Makefile.in contains lots of options (@with_propka@,...), and as I do not know the program, I do not know if some options should be disabled. By default, install target tries to create dirs and files in /usr instead of debian dir. I tried to fix this , skipping install target to use debian files (.install, .links etc...), but I have other issues with missing files (propka library and binary). As I have no iead of what propka is... Additional stuff is needed as they had a web server, /var/www content should be moved, but this can be done easilly with a new directive in install file Olivier -- 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: http://lists.debian.org/4fb6c665.6090...@codeless.fr
Bug#657832: ITP: mmtk -- Python molecular modelling toolkit
Package: wnpp Severity: wishlist Owner: Olivier Sallou olivier.sal...@irisa.fr X-Debbugs-Cc: debian-med@lists.debian.org * Package name: mmtk Version : 2.6.1 Upstream Author : Konrad Hinsen hin...@cnrs-orleans.fr * URL : https://sourcesup.cru.fr/projects/mmtk/ * License : CeCILL C Programming Lang: C, Python Description : Python molecular modelling toolkit The Molecular Modelling Toolkit (MMTK) is an Open Source program library for molecular simulation applications. In addition to providing ready-to-use implementations of standard algorithms, MMTK serves as a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular simulations. MMTK is a package consisting of various modules, most of them written in Python, and some in C. -- gpg key id: 4096R/326D8438 (pgp.mit.edu) 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: http://lists.debian.org/4f251955.5030...@codeless.fr
Need someone to upload Chado
Hi, I have finished the Chado package, ready in SVN for a first upload and a volunteer to do so. There are several Lintian warnings raised. I added some explanation in Debian.source, especially regarding warning on non trap errors in postinst step (which are trapped in fact, but differently). Tested with pbuilder. Thanks Olivier -- gpg key id: 4096R/326D8438 (pgp.mit.edu) 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: http://lists.debian.org/4f23e9ae.2080...@codeless.fr
