Re: Bug#728797: ITP: python-mne -- Python modules for MEG and EEG data analysis
Hi, On Wed, Nov 27, 2013 at 11:12:51PM +0100, Alexandre Gramfort wrote: Since I just uploaded this now only depends from ftpmaster accepting the package (sorry, currently this simply takes about one month for accepting new packages). As the owner of the ITP bug you will be notified automatically. perfect. btw we'll have a 0.7.1 release early next week due to a few issues spotted by our early adopters... That's OK. Once python-mne has passed NEW we will update immediately to whatever version is current at this pointin time. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131128081635.gb12...@an3as.eu
Re: QIIME 1.7 - any users in debian-testing/unstable ?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Am 2013-11-27 14:27, schrieb Andreas Tille: Hi Steffen, On Wed, Nov 27, 2013 at 01:33:32PM +0100, Steffen Möller wrote: Hello, qiime in stable is (expectedly) outdated with version 1.4. Now, I had my colleague using the Debian package of 1.7 rather than installing it all by himself, but, well, all_tests.py fails miserably. We quickly hacked the missing packages for rtax Simon ITPed rtax #724280 and he claimed that the package is close to be finished. Simon, if it might speed up things I'd volunteer to create the according Vcs repository (please tell me your preference between Git and SVN). In case you might consider this helpful just provide the needed stuff somewhere online. As you see there are testers waiting for it. Hello! Wel, yes please, i woulde really appreciate that. I would prefer git over svn. My current work is available here: http://www.familiekainz.at/projekte/linux/rtax/rtax-0.984-all.tgz This includes the upstream source and my work so far. d ebuild -uc -us runs fine. I removed the VCS-Entries from the control file, as i'm currently not sure what the vcs location is. I hopefully made it Debian-Med policy compliant. I don't want to drop work on you, but yes, please help me getting starting with this the right way. Thank you very much. Simon and qcli together, installed R packages I never heard of before, and then ... well ... decided to just experiment with the virtualbox image that upstream provides. We need to do something to improve our users' experience. I know Tim to care for the package. Who else? Among our users anyone? Well, you know how this magical we works. :-) Make a proper list what needs to be done - rtax: #724280 - qcli: what homepage, did you startet some packaging - R packages I never heard of before: we neither have heard about these - you at least are knowing the names Than we might tackle your list step by step - the more you can personally do the faster we will finish your list and can fullfill your requirement. Kind regards Andreas. -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQIcBAEBAgAGBQJSlwO8AAoJEBy08PeN7K/pXMwP/0nk5T/PjtrMSuuumaNsAO3T guu5wvwLuLyFYRowj0c6UtNyKJPspwLjltecpuraGwpDyob0lJE834Au0xCvG/d5 Gghc97bPZvJ9Lo+cAhc+k5heeBp5Toe+1ui1ZMx/OLVtPg/UdXHXchwotJOJngkb Z7vIgLVlCsVnnI34w8OQnFDsw7kh1V35xUxwnVCWKeLoWibGhnmOIVlca7rBtQAi bpJ3rkfTCvFztYbMn6q5+7aI1qQYLTOkvbX/GwApPaTGEEh+FslmcCkHRWR7L9jO ApWjjCmi+2ROKYzl7akmMIIu5zrJv0eFDQEfd4A0hY0Iu3xjrL1UOoH49IH2sQnk 2/K1+pXlhc0b3fpA0lHMzX+5bKpnKElP7paY/7Q0erotgRgDA60Smo21S/zF7NSM fWuGo1eqKKk73k/Ro0YdL4d7UV6iPGPIuBkUnmLHXMONFkfRCuu9GFeYxuTbhxbX 9UoyODu/2mzsy837YybZX1dBPDmoZr7E6wWM/15Aw8FlL+G2WL2RrolD1fwt9WAw 37Sp4FTYnSapXoKJshNx+YmDHvz4xGb71S5md0QY+gvaHkjmwv6DHrnx4rTQN5fW Q8XD8wKetxCYIFTF/ScTXudZxel++gyRCdvymWuriUeAV+15MqPLlv+V38wmGwhs ysY9G461c5768edQUtI1 =A7w8 -END PGP SIGNATURE- -- 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/529703c2.9090...@familiekainz.at
Re: Advent calendar
Hi everyone, Furthermore I would like to mention another page[3] with lots of information about Debian Med packages. Besides the list of RC bugs you can also see packages that can not be built on a Debian architecture, packages that are not allowed to migrate from unstable to testing (and thus won't be included in the next release) and packages with a new upstream version. I think those packages need some care as well. +1 I am trying to understand the mechanism of the excuses given for the package CamiTK that is in the list of blocked packages in [1]. As I am a very inexperienced in debian packaging, I am not sure what action can be taken. In the great page [2], the excuses for CamiTK point to a problem with insightoolkit, which itself mention gdcm which now mention not yet built on sparc and ia64 (which I suppose are the show stoppers). But a while ago gdcm excuses were about the fact gdcm was part of a transition (itself mentioning mono or something). What can be done concretely to fix this problem? If there is anything in my reach, I will try to help (might not be for the advent calendar, but maybe for the spring cleaning!). Another question, may be more addressed to the itk/vtk/gdcm specialists: is it time to switch the dependencies from insighttoolkit to insighttoolkit4? And as Andreas always encouraged me to ask question even if they looked silly, here it is: More generally, where can I see what lib version are deprecated or which version is advocated in Jessie/next stable? For instance the CamiTK package depends on huge libs such as qt, vtk, insighttoolkit and gdcm. When is the best time to try a transition to Qt5, Vtk6, itk4 and gdcm2.4? Kind regards and thanks for all the efforts, Mahnu [1] http://udd.debian.org/dmd.cgi?email=debian-med-packag...@lists.alioth.debian.org [2] http://release.debian.org/migration/testing.pl?package=camitk smime.p7s Description: S/MIME Cryptographic Signature
Re: Advent calendar
On Thu, Nov 28, 2013 at 8:27 AM, Emmanuel Promayon emmanuel.proma...@imag.fr wrote: Hi everyone, Furthermore I would like to mention another page[3] with lots of information about Debian Med packages. Besides the list of RC bugs you can also see packages that can not be built on a Debian architecture, packages that are not allowed to migrate from unstable to testing (and thus won't be included in the next release) and packages with a new upstream version. I think those packages need some care as well. +1 I am trying to understand the mechanism of the excuses given for the package CamiTK that is in the list of blocked packages in [1]. As I am a very inexperienced in debian packaging, I am not sure what action can be taken. In the great page [2], the excuses for CamiTK point to a problem with insightoolkit, which itself mention gdcm which now mention not yet built on sparc and ia64 (which I suppose are the show stoppers). But a while ago gdcm excuses were about the fact gdcm was part of a transition (itself mentioning mono or something). What can be done concretely to fix this problem? #730700 Thanks for the report ! -- 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/ca+7wusyqq8f5xw6b8qyrxwhrgyjbbvzuxe__6u28_jhz8jw...@mail.gmail.com
Sponsoring request: new upstream mia-2.0.12
Dear all, I prepared the packages for the latest MIA upstream release and pushed it to the git repro. The Debian changelog reads: * New upstream release * correct entries for maintainers and uploaders * correct application of linker flag -Wl,--as-needed * remove CXXFLAGS in rules since this is now taken care of in the build system I've has a look into creating a symbols file but ran into the problem that I would have to define one for each architecture, since they are different for 64 bit and 32 bit - not only because of changed standard types that could be handled by the pkgkde-gensymbols, but also because certain templates are only instantiated in the 64 bit version. Therefore, I leave the lintian warning no-symbols-control-file open for now. Many thanks, Gert signature.asc Description: This is a digitally signed message part
Re: QIIME 1.7 - any users in debian-testing/unstable ?
On Thu, Nov 28, 2013 at 09:50:10AM +0100, Simon Kainz wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Am 2013-11-27 14:27, schrieb Andreas Tille: Hi Steffen, On Wed, Nov 27, 2013 at 01:33:32PM +0100, Steffen Möller wrote: Hello, qiime in stable is (expectedly) outdated with version 1.4. Now, I had my colleague using the Debian package of 1.7 rather than installing it all by himself, but, well, all_tests.py fails miserably. We quickly hacked the missing packages for rtax Simon ITPed rtax #724280 and he claimed that the package is close to be finished. Simon, if it might speed up things I'd volunteer to create the according Vcs repository (please tell me your preference between Git and SVN). In case you might consider this helpful just provide the needed stuff somewhere online. As you see there are testers waiting for it. Hello! Wel, yes please, i woulde really appreciate that. I would prefer git over svn. My current work is available here: http://www.familiekainz.at/projekte/linux/rtax/rtax-0.984-all.tgz This includes the upstream source and my work so far. d ebuild -uc -us runs fine. I removed the VCS-Entries from the control file, as i'm currently not sure what the vcs location is. I hopefully made it Debian-Med policy compliant. I don't want to drop work on you, but yes, please help me getting starting with this the right way. Thank you very much. Simon and qcli together, installed R packages I never heard of before, and then ... well ... decided to just experiment with the virtualbox image that upstream provides. We need to do something to improve our users' experience. I know Tim to care for the package. Who else? Among our users anyone? Well, you know how this magical we works. :-) Make a proper list what needs to be done - rtax: #724280 - qcli: what homepage, did you startet some packaging - R packages I never heard of before: we neither have heard about these - you at least are knowing the names Than we might tackle your list step by step - the more you can personally do the faster we will finish your list and can fullfill your requirement. Kind regards Andreas. -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQIcBAEBAgAGBQJSlwO8AAoJEBy08PeN7K/pXMwP/0nk5T/PjtrMSuuumaNsAO3T guu5wvwLuLyFYRowj0c6UtNyKJPspwLjltecpuraGwpDyob0lJE834Au0xCvG/d5 Gghc97bPZvJ9Lo+cAhc+k5heeBp5Toe+1ui1ZMx/OLVtPg/UdXHXchwotJOJngkb Z7vIgLVlCsVnnI34w8OQnFDsw7kh1V35xUxwnVCWKeLoWibGhnmOIVlca7rBtQAi bpJ3rkfTCvFztYbMn6q5+7aI1qQYLTOkvbX/GwApPaTGEEh+FslmcCkHRWR7L9jO ApWjjCmi+2ROKYzl7akmMIIu5zrJv0eFDQEfd4A0hY0Iu3xjrL1UOoH49IH2sQnk 2/K1+pXlhc0b3fpA0lHMzX+5bKpnKElP7paY/7Q0erotgRgDA60Smo21S/zF7NSM fWuGo1eqKKk73k/Ro0YdL4d7UV6iPGPIuBkUnmLHXMONFkfRCuu9GFeYxuTbhxbX 9UoyODu/2mzsy837YybZX1dBPDmoZr7E6wWM/15Aw8FlL+G2WL2RrolD1fwt9WAw 37Sp4FTYnSapXoKJshNx+YmDHvz4xGb71S5md0QY+gvaHkjmwv6DHrnx4rTQN5fW Q8XD8wKetxCYIFTF/ScTXudZxel++gyRCdvymWuriUeAV+15MqPLlv+V38wmGwhs ysY9G461c5768edQUtI1 =A7w8 -END PGP SIGNATURE- -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131128123526.ge14...@an3as.eu
Re: QIIME 1.7 - any users in debian-testing/unstable ?
[Sorry for my last empty mail ...] Hi On Thu, Nov 28, 2013 at 09:50:10AM +0100, Simon Kainz wrote: Wel, yes please, i woulde really appreciate that. I would prefer git over svn. My current work is available here: http://www.familiekainz.at/projekte/linux/rtax/rtax-0.984-all.tgz I turned this into ssh://git.debian.org/git/debian-med/rtax.git which you can checkout. Please `git log` to visit my changes. I hopefully made it Debian-Med policy compliant. As I said I did some changes. I don't want to drop work on you, but yes, please help me getting starting with this the right way. The workload was OK given your preparation. I guess you do not mind that I just sponsored the package. Regarding qiime: I was tunning all_tests again and I wonder why Steffen thinks rtax might have any influence on this test. The installed package did neither good nor bad for the test - it simply had the same result and rtax was not mentioned in any of the logs except in the form cogent/app/rtax.py ... but that's python-cogent and not rtax. Steffen, please be a bit more verbose about what you think might be helpful for a better qiime support. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131128123938.gf14...@an3as.eu
Bits from Debian Med team
Hi, some of these bits are a bit outdated but there is no point in hiding this information just because it is old. 1. FOSDEM talk 2. Jabber interview about Debian Med 3. Article about Debian Med 4. Yearly sprint of Debian Med team 5. DebConf 13 in Vaumarcus 6. Codefest of the Open Bioinformatics Foundation 7. Reupload unattended packages (** might be of general interest **) 8. Debian Med Bug Squashing Advent Calendar 2013 1. FOSDEM talk == Andreas Tille had a talk at FOSDEM[1a] which is also Video recorded. A quite similar but updated talk was held at DebConf 13[5a] (see below). [1a] http://people.debian.org/~tille/talks/201302_fosdem_distro/ 2. Jabber interview by reporter from India == There was an interesting interview between Rajeev Nair and Andreas Tille at So, 17.02.2013 Rajeev Nair is Business head of an health care journal in India[2a] held via jabber. Since this might serve as some nice FAQ about Debian Med here is a complete log of this interview[2b] (permission to publish it was granted). [2a] http://www.healthcafe.in [2b] http://anonscm.debian.org/viewvc/debian-med/trunk/community/interview/interview_r.nair-a.tille.log?view=markup 3. Article about Debian Med === As a consequence of the interview above[2b] the Debian Med team has assembled an article which was originally intended to be published in the Health Cafe journal[2a] but somehow this never happened. So we ended up with a nice article targeting at interested readers about Free Software in medicine with not necessarily informatics background. Since the article is considered to be of good quality and has consumed some time of several team members we are seeking for ideas for relevant places where to publish it. It is available as PDF[3a] as well as in SVN[3b]. [3a] http://debian-med.alioth.debian.org/docs/debian-med-healthcafe.pdf [3b] http://anonscm.debian.org/viewvc/debian-med/trunk/community/papers/13_healthcafe/ 4. Yearly sprint of Debian Med team === This year we had our third sprint of the Debian Med team and all participants consider it a great success again. The sprint was in end of February and the individual reports are linked from the according wiki page[4a]. Since Andreas Tille was able to prove the nice effect of having face to face meetings in Debian teams in the team metrics graphs presented in his talks at DebConf[5a,5b] we will keep on with this good tradition. The next sprint[4b] is scheduled for Friday 31st January until Sunday 2nd February in Stonehaven near Aberdeen. If you are interested to meet the people behind Debian Med and want to join us in developing packages which are helpful in health care and bioinformatics you are invited to join us. [4a] https://wiki.debian.org/DebianMed/Meeting/Kiel2013 [4b] https://wiki.debian.org/DebianMed/Meeting/Aberdeen2014 5. DebConf 13 in Vaumarcus == Andreas Tille had two talks with specific influence to Debian Med development[5a,5b]. For those who want to read a full (and lengthy) report about DebConf 13 by Andreas Tille this is online as well[5c]. [5a] http://people.debian.org/~tille/talks/20130812_blend [5b] http://people.debian.org/~tille/talks/20130815_mom [5c] http://debianmed.blogspot.de/2013/09/debconf-13-report-by-andreas-tille.html 6. Codefest of the Open Bioinformatics Foundation = Ivo Maintz and Steffen Möller organised the Codefest of the Open Bioinformatics Foundation[6a] in Berlin. About 40 contributors from all over the world attended, connecting the Debian community strongly with upstream. The event triggered a joint paper of participants to Sprints, Codefests and Hackathons alike, presented at the Nettab conference on Semantic, Social, and Mobile Applications for Bioinformatics and Biomedical Laboratories in Venice[6b]. [6a] http://www.open-bio.org/wiki/Codefest_2013 [6b] http://www.nettab.org/2013/ 7. Reupload unattended packages === Andreas Tille has mentored the GSoC student Emmanouil Kiagias[7a] and as a byproduct some Blends metadata were now kept in UDD. This has inspired some new tools and one of this was an UDD query[7b] to return all packages in the interest of the Blend ordered by date when they were uploaded. It has shown that there were packages hanging around in the package pool since five years. So some effort was done to check those packages which were not necessarily buggy according to BTS entries and so we were able to fix the following issues in about 20-30 packages: - Remove DM-Upload-Allowed fields - hardening - canonical Vcs fields - checking homepages / watch files - checking policy 3.9.4 (cme fix dpkg-control) - profit from xz compression in binary packages which makes perfectly sense in some of our packages - DEP5 - DEP3 - use dh consequently to simplify
Re: QIIME 1.7 - any users in debian-testing/unstable ?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Am 2013-11-27 13:33, schrieb Steffen Möller: Hello, qiime in stable is (expectedly) outdated with version 1.4. Now, I had my colleague using the Debian package of 1.7 rather than installing it all by himself, but, well, all_tests.py fails miserably. We quickly hacked the missing packages for rtax and qcli together, installed R packages I never heard of before, and then ... well ... decided to just experiment with the virtualbox image that upstream provides. We need to do something to improve our users' experience. I know Tim to care for the package. Who else? Among our users anyone? Best, Steffen Hi, sorry for the late reply. We also run (well, i *installed* it for some users) qiime 1.7.0+dfsg-1 from unstable. So i could also eventually try to run some tests. So contact me, just in case i should try out something. Regards, Simon -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQIcBAEBAgAGBQJSlz+VAAoJEBy08PeN7K/pf/sP/RWizsfXJ7XvWHXBLT2HYWHz sP197i/4EUV1cCEkqRON9FXcBQ43/nff7G+AztuWk8+z6nQi99soBY0A/TTs1cBv 2FXIn0WneD1pgTma14U6Kx0D4TyHamkaGQxqycw+/1pwiyTbnsrDNFXu9EGpj0E/ z8T7ZjRjNNlHlXsp5W61xBYyqGyRHGooRGPdOgMnYgtUg2HfD3A2VdvUpw97RH8o kJQbXyDLA4x5b34/L8RUDfKmarzW7LX28tmiAPuUbmrL0Ouf0NEqt2KYfMmcF9ck PZ2c8o3cq4CbQ/rOT6EM+ivqOdOiN/7ru8G38HO+ZhcI2/aU/7BbeF4ZnH5A7Ewc iHkfXETDVWyTUUdFdPgFC5NhLxtqeNfYHLCIuR+KLOJWVfyXYbgHE362sLUepht7 HFtfGKs/X9dAoyPLly//QQd/Rc+Kkw5toGZ08n6ij9vkgGHZpi638uBXSJVq93bn Y2zA72IYjEI3qBLtg1hnI3XChDMwQLxR1jk7UGgWeL9uPYCdrwN9uymFlyHIG2V4 uq99GdmD3dBxNUGkXaIsGKOaDFRCWdV7TU4AKGzjlXR/bfoyay7IKPGvvQkhvzMH E7axDEXfbXOSXLQMZxMgm8/zDt31MIeROk3fEuQT/nH+WDbdLptdvFbIt6rR0xk4 /KTZh0WRuYjsEA8gZlUi =uV1O -END PGP SIGNATURE- -- 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/52973f9a.5050...@familiekainz.at
Re: QIIME 1.7 - any users in debian-testing/unstable ?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Am 2013-11-28 13:39, schrieb Andreas Tille: [Sorry for my last empty mail ...] Hi On Thu, Nov 28, 2013 at 09:50:10AM +0100, Simon Kainz wrote: Wel, yes please, i woulde really appreciate that. I would prefer git over svn. My current work is available here: http://www.familiekainz.at/projekte/linux/rtax/rtax-0.984-all.tgz I turned this into ssh://git.debian.org/git/debian-med/rtax.git which you can checkout. Please `git log` to visit my changes. I hopefully made it Debian-Med policy compliant. As I said I did some changes. I don't want to drop work on you, but yes, please help me getting starting with this the right way. The workload was OK given your preparation. I guess you do not mind that I just sponsored the package. WOW, thank you! Thank you very much. Regarding qiime: I was tunning all_tests again and I wonder why Steffen thinks rtax might have any influence on this test. The installed package did neither good nor bad for the test - it simply had the same result and rtax was not mentioned in any of the logs except in the form cogent/app/rtax.py ... but that's python-cogent and not rtax. Steffen, please be a bit more verbose about what you think might be helpful for a better qiime support. I also contacted Steffen, as we also have soem users running qiime 1.7. maybe we can improve the package a bit. Thank you again! Kind regards Andreas. -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQIcBAEBAgAGBQJSl0dpAAoJEBy08PeN7K/pxZcP+gOhunLN3brXQHWIA3Mm8Bcn 8SAL5aeg6AMWE4ilBg3dy5SDdR6wDliQUioFQlM6LYOE7hAC3v2czUpi893mGXQJ TOqlQZOey52ke+pnB5pMfB/DxpNgb2gAiD2fZJKvIcb/xO3h33SCzSzIKej1n3nZ XTNKUZx8PWdDtXS7eFte3+DdLPFhHqCPSB+kNQ7zVIWnriP8TV/glhZ2fdRQpmA5 4puPH6IAMey/Ygxkmbr+7KPPg3+UscL4Kx9aXhljElVYEswhCGEMD4BBlBSRzJ+R bOjjgHxt7SMQaGX5VC8ukyB3UhUZe13b827U3uPmGUlzK6TqhMM02k/NEEQ8SBx5 8yaHopU/KXAbGVizKBiwneIo6yqjDGWJrPYL6ZrrpQ5jNcSRZr4pj5mByKlX9gcc dD0qEuPKYj9EUg8vzcZqUg+i/1jB9Pal/3VgRNainpL6fOMPuqYm8xmJgUjZuq5w ZcZN2+LAs4EF5ElyOLOjRfI9+uaLxUDRT49T6+C+Td/iMhXU+v6Y2bMwsCYbIIME vGzelbmOPlpAcwTE2YgDDdCkye1UZ073tuK+z2cwuc5UorcE1Bk4cpF+zkyLYz8z ewFwK4dgT4ma09L2SlzKarDTIImyemEZANxzJpdI0ynquWbPWcNhaq4NjFUDO6Xd m0yrJM/Pt5dlw/JTaPNI =NHvV -END PGP SIGNATURE- -- 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/5297476f.2030...@familiekainz.at
Re: Sponsoring request: new upstream mia-2.0.12
On Thu, Nov 28, 2013 at 01:10:38PM +0100, Gert Wollny wrote: I prepared the packages for the latest MIA upstream release and pushed it to the git repro. The Debian changelog reads: Uploaded. Thanks for the preparation Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131128135004.ga21...@an3as.eu
Re: Advent calendar
Regarding ITK4, Being close to the ITK development team, I will be happy to help with the process of transitioning to ITK4. If anything needs to be coordinated with ITK upstream, we will be glad to collaborate. Best Luis On Thu, Nov 28, 2013 at 2:27 AM, Emmanuel Promayon emmanuel.proma...@imag.fr wrote: Hi everyone, Furthermore I would like to mention another page[3] with lots of information about Debian Med packages. Besides the list of RC bugs you can also see packages that can not be built on a Debian architecture, packages that are not allowed to migrate from unstable to testing (and thus won't be included in the next release) and packages with a new upstream version. I think those packages need some care as well. +1 I am trying to understand the mechanism of the excuses given for the package CamiTK that is in the list of blocked packages in [1]. As I am a very inexperienced in debian packaging, I am not sure what action can be taken. In the great page [2], the excuses for CamiTK point to a problem with insightoolkit, which itself mention gdcm which now mention not yet built on sparc and ia64 (which I suppose are the show stoppers). But a while ago gdcm excuses were about the fact gdcm was part of a transition (itself mentioning mono or something). What can be done concretely to fix this problem? If there is anything in my reach, I will try to help (might not be for the advent calendar, but maybe for the spring cleaning!). Another question, may be more addressed to the itk/vtk/gdcm specialists: is it time to switch the dependencies from insighttoolkit to insighttoolkit4? And as Andreas always encouraged me to ask question even if they looked silly, here it is: More generally, where can I see what lib version are deprecated or which version is advocated in Jessie/next stable? For instance the CamiTK package depends on huge libs such as qt, vtk, insighttoolkit and gdcm. When is the best time to try a transition to Qt5, Vtk6, itk4 and gdcm2.4? Kind regards and thanks for all the efforts, Mahnu [1] http://udd.debian.org/dmd.cgi?email=debian-med-packaging@ lists.alioth.debian.org [2] http://release.debian.org/migration/testing.pl?package=camitk
Re: Advent calendar
On Thu, Nov 28, 2013 at 8:27 AM, Emmanuel Promayon emmanuel.proma...@imag.fr wrote: For instance the CamiTK package depends on huge libs such as qt, vtk, insighttoolkit and gdcm. When is the best time to try a transition to Qt5, Vtk6, itk4 and gdcm2.4? This is a long debate ;) Technically this is up to the maintainers to request a transition slot: https://wiki.debian.org/OngoingTransitions In any case you are simply *using* those libs, everything should occur without you noticing anything (well if it is going smoothly). Within a sid/schroot (or any virtual machine) you can try out if compilation goes smoothy. For example you could add `experimental` to your `/etc/apt/sources.list`, pull gdcm2.4 and try to rebuild CamITK using GDCM 2.4. That will help once the GDCM transition kicks in. In any case the next freeze period has already been annonced so read carefully about what is allowed during the freeze period and what's not ;) 2cts -- 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/CA+7wUsw7k6YUZ67mpnewpVJ4oF8=8fjqnnneodx1ck6b8m9...@mail.gmail.com
Re: Bug#728797: ITP: python-mne -- Python modules for MEG and EEG data analysis
On Wed, 27 Nov 2013, Alexandre Gramfort wrote: Let me know when we can advertise debian packaging. Since I just uploaded this now only depends from ftpmaster accepting the package (sorry, currently this simply takes about one month for accepting new packages). As the owner of the ITP bug you will be notified automatically. perfect. btw we'll have a 0.7.1 release early next week due to a few issues spotted by our early adopters... cool -- please update packaging whenever you update: - upload of fixed up version to NEW will avoid us needing to reupload it later on so that sid will get a fixed up version right away - I will upload it to NeuroDebian without waiting for it to pass through NEW thanks guys! -- Yaroslav O. Halchenko, Ph.D. http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org Senior Research Associate, Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik -- 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/20131128145231.gz6...@onerussian.com
Re: Bug#728797: ITP: python-mne -- Python modules for MEG and EEG data analysis
Hi Yaroslav, On Thu, Nov 28, 2013 at 09:52:31AM -0500, Yaroslav Halchenko wrote: btw we'll have a 0.7.1 release early next week due to a few issues spotted by our early adopters... cool -- please update packaging whenever you update: +1 - upload of fixed up version to NEW will avoid us needing to reupload it later on so that sid will get a fixed up version right away H, this information is new to me. If I have understood NEW queue correctly than it is better not to touch packages which are in the queue. Otherwise you might confuse ftpmaster or influence the position of your package to get handled later. Do you have any reference that I#m wrong in assuming this? - I will upload it to NeuroDebian without waiting for it to pass through NEW That's perfectly OK. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131128153153.gb21...@an3as.eu
Re: Bug#728797: ITP: python-mne -- Python modules for MEG and EEG data analysis
On Thu, 28 Nov 2013, Andreas Tille wrote: Hi Yaroslav, On Thu, Nov 28, 2013 at 09:52:31AM -0500, Yaroslav Halchenko wrote: btw we'll have a 0.7.1 release early next week due to a few issues spotted by our early adopters... cool -- please update packaging whenever you update: +1 - upload of fixed up version to NEW will avoid us needing to reupload it later on so that sid will get a fixed up version right away H, this information is new to me. If I have understood NEW queue correctly than it is better not to touch packages which are in the queue. Otherwise you might confuse ftpmaster or influence the position of your package to get handled later. Do you have any reference that I#m wrong in assuming this? sorry -- I would not even try to look up the reference atm (need to work on turkey) but just trust me on this one -- IIRC position would not change and ftpmasters will be just fine. I have done that many times (upload a new one, -2 without .orig.tar.gz even) -- they I believe would just review the last one available since that would be the one entering archive look e.g. at debmake in http://ftp-master.debian.org/new.html ;) - I will upload it to NeuroDebian without waiting for it to pass through NEW That's perfectly OK. cool -- Yaroslav O. Halchenko, Ph.D. http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org Senior Research Associate, Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik -- 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/20131128160633.gb6...@onerussian.com
Re: Bug#728797: ITP: python-mne -- Python modules for MEG and EEG data analysis
Hi, On Thu, Nov 28, 2013 at 11:06:33AM -0500, Yaroslav Halchenko wrote: - upload of fixed up version to NEW will avoid us needing to reupload it later on so that sid will get a fixed up version right away H, this information is new to me. If I have understood NEW queue correctly than it is better not to touch packages which are in the queue. Otherwise you might confuse ftpmaster or influence the position of your package to get handled later. Do you have any reference that I#m wrong in assuming this? sorry -- I would not even try to look up the reference atm (need to work on turkey) but just trust me on this one -- IIRC position would not change and ftpmasters will be just fine. I have done that many times (upload a new one, -2 without .orig.tar.gz even) -- they I believe would just review the last one available since that would be the one entering archive look e.g. at debmake in http://ftp-master.debian.org/new.html ;) Thanks for the clarification which is definitely helpful. - I will upload it to NeuroDebian without waiting for it to pass through NEW That's perfectly OK. cool I personally would like to give Alexandre the chance to verify his issues with the Git repository on Alioth and will not touch it for the moment since it does not seem that urgent to me for now since we just reserved the position for python-mne inside the new queue. Alexandre, please let us know if your trouble to update the repository remains. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131128163420.ge21...@an3as.eu
Re: Bug#728797: ITP: python-mne -- Python modules for MEG and EEG data analysis
hi guys, FYI I just tagged v0.7.1 on github. For some obscure reasons I still depend on Andreas to update the package on debian.org... thanks Alex On Thu, Nov 28, 2013 at 3:52 PM, Yaroslav Halchenko y...@debian.org wrote: On Wed, 27 Nov 2013, Alexandre Gramfort wrote: Let me know when we can advertise debian packaging. Since I just uploaded this now only depends from ftpmaster accepting the package (sorry, currently this simply takes about one month for accepting new packages). As the owner of the ITP bug you will be notified automatically. perfect. btw we'll have a 0.7.1 release early next week due to a few issues spotted by our early adopters... cool -- please update packaging whenever you update: - upload of fixed up version to NEW will avoid us needing to reupload it later on so that sid will get a fixed up version right away - I will upload it to NeuroDebian without waiting for it to pass through NEW thanks guys! -- Yaroslav O. Halchenko, Ph.D. http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org Senior Research Associate, Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik -- 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/cadeotzom6ihbp8_pberft0cc1xvgiamud8rzkpnrhjyuqef...@mail.gmail.com
Re: Bug#728797: ITP: python-mne -- Python modules for MEG and EEG data analysis
Hi Alexandre, On Thu, Nov 28, 2013 at 06:59:10PM +0100, Alexandre Gramfort wrote: FYI I just tagged v0.7.1 on github. Fine. For some obscure reasons I still depend on Andreas to update the package on debian.org... Can you please post here the actuall command line and the error message you tried and failed. We should find out the problem now to enable you working properly. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131128190936.ga30...@an3as.eu
Aw: Re: QIIME 1.7 - any users in debian-testing/unstable ?
Hi Simon, Hi Simon, We also run (well, i *installed* it for some users) qiime 1.7.0+dfsg-1 from unstable. So i could also eventually try to run some tests. So contact me, just in case i should try out something. I suggest you try the lines below. Best, Steffen $ apt-get source qiime $ sudo apt-get install qiime $ cd qiime-1.7.0+dfsg/tests/ $ ./all_tests.py In no particular order * ApplicationNotFoundError: Cannot find blat. Is it installed? Is it in your path? * == ERROR: test_call_infernal_test1 (__main__.InfernalAlignerTests) InfernalAligner: functions as expected when returing objects -- * Testing /homeStorage/moeller/git/a/qiime-1.7.0+dfsg/tests/test_alpha_diversity.py: /usr/lib/python2.7/dist-packages/cogent/util/progress_display.py:28: UserWarning: Not using MPI as mpi4py not found from cogent.util import parallel, terminal * Testing /homeStorage/moeller/git/a/qiime-1.7.0+dfsg/tests/test_assign_taxonomy.py: test_call_alt_input_types (__main__.BlastTaxonAssignerTests) BlastTaxonAssigner.__call__ functions w alt input types ... ERROR test_call_existing_blast_db (__main__.BlastTaxonAssignerTests) BlastTaxonAssigner.__call__ functions w existing db ... ERROR test_call_logs_run (__main__.BlastTaxonAssignerTests) BlastTaxonAssigner.__call__ logs the run when expected ... ERROR test_call_on_the_fly_blast_db (__main__.BlastTaxonAssignerTests) BlastTaxonAssigner.__call__ functions w creating blast db ... ERROR test_call_output_to_file (__main__.BlastTaxonAssignerTests) BlastTaxonAssigner.__call__ functions w output to file ... ERROR ERROR test_get_blast_hits (__main__.BlastTaxonAssignerTests) BlastTaxonAssigner._get_blast_hits functions w existing db ... ERROR test_get_first_blast_hit_per_seq (__main__.BlastTaxonAssignerTests) Extracting the first blast hit for each seq functions as expected ... ok test_init (__main__.BlastTaxonAssignerTests) * RuntimeError: BLAST cannot run if the BLASTMAT environment variable is not set. Usually, the BLASTMAT environment variable points to the NCBI data directory, which contains matrices like PAM30 and PAM70, etc. Alternatively, you may create a .ncbirc file to define these variables. * ApplicationNotFoundError: Cannot find mothur. Is it installed? Is it in your path? * == ERROR: test_call_result_to_file (__main__.RdpTaxonAssignerTests) RdpTaxonAssigner should save results to file -- Traceback (most recent call last): File /homeStorage/moeller/git/a/qiime-1.7.0+dfsg/tests/test_assign_taxonomy.py, line 850, in test_call_result_to_file log_path=None) File /usr/lib/python2.7/dist-packages/qiime/assign_taxonomy.py, line 447, in __call__ max_memory=max_memory, fixrank=fix_ranks, tmp_dir=tmp_dir) File /usr/lib/python2.7/dist-packages/qiime/pycogent_backports/rdp_classifier.py, line 394, in assign_taxonomy app = RdpClassifier(**app_kwargs) File /usr/lib/python2.7/dist-packages/cogent/app/util.py, line 165, in __init__ self._error_on_missing_application(params) File /usr/lib/python2.7/dist-packages/qiime/pycogent_backports/rdp_classifier.py, line 141, in _error_on_missing_application JAR file not found in current directory and the RDP_JAR_PATH ApplicationNotFoundError: JAR file not found in current directory and the RDP_JAR_PATH environment variable is not set. Please set RDP_JAR_PATH to the full pathname of the JAR file. * == ERROR: test_call_paired_result (__main__.RtaxTaxonAssignerTests) -- Traceback (most recent call last): File /homeStorage/moeller/git/a/qiime-1.7.0+dfsg/tests/test_assign_taxonomy.py, line 449, in test_call_paired_result actual = p(self.input_seqs_fp) File /usr/lib/python2.7/dist-packages/qiime/assign_taxonomy.py, line 748, in __call__ log_path=log_path,base_tmp_dir=get_qiime_temp_dir()) File /usr/lib/python2.7/dist-packages/cogent/app/rtax.py, line 239, in assign_taxonomy app_result = app() File /usr/lib/python2.7/dist-packages/cogent/app/util.py, line 251, in __call__ open(errfile).read()) ApplicationError: Unacceptable application exit status: 127 Command: cd /homeStorage/moeller/git/a/qiime-1.7.0+dfsg/tests/; rtax -a /tmp/RtaxTaxonAssignerTests_MDgLQe2McLs9Ot4pN314.fasta -b /tmp/RtaxTaxonAssignerTests_kyEYQV06DwNu0ZFZgeTc.fasta -m /tmp/rtax_GBTCHi2iW0iZQGIBZNy5 -l /tmp/rtax_GBTCHi2iW0iZQGIBZNy5/ampliconIdsToClassify -o /tmp/RtaxAssignments_2jFt94.txt -i '\S+\s+(\S+?)\/' -t /tmp/RtaxTaxonAssignerTests_gWd250r71OsFfVONnP1r.txt -r /tmp/RtaxTaxonAssignerTests_7O10fQ04as0vKxnVtI0i.fasta /tmp/tmpubkVBs7fhz6anXxcuKy0.txt 2
Re: Bug#728797: ITP: python-mne -- Python modules for MEG and EEG data analysis
Hi Yaroslav, On Thu, 28 Nov 2013, Andreas Tille wrote: H, this information is new to me. If I have understood NEW queue correctly than it is better not to touch packages which are in the queue. Otherwise you might confuse ftpmaster or influence the position of your package to get handled later. Do you have any reference that I#m wrong in assuming this? sorry -- I would not even try to look up the reference atm (need to work on turkey) but just trust me on this one -- IIRC position would not change and ftpmasters will be just fine. in case an ftp trainee has checked the -1 version and now sees a new one, he would not be delighted by this, as his previous work would be just a waste of time. look e.g. at debmake in http://ftp-master.debian.org/new.html ;) This seems to be one of the oldest packages in the queue ... Thorsten -- 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/pine.lnx.4.64.1311282223140.3...@tor.gallien.in-chemnitz.de
Re: [fis-gtm] ready for upload - needs sponsor
Hi Andreas, I had the time to install and quickly play with the installed GT.M, and it worked fine. I've not done deep testing, but I'd say more of a smoke test. If I hit any issue down the road, I'll let the list know. Thanks, Laurent On Mon, Nov 25, 2013 at 8:19 AM, Andreas Tille andr...@an3as.eu wrote: Hi, On Mon, Nov 25, 2013 at 08:13:06AM -0500, Laurent Parenteau wrote: Unfortunately no; other things took priority over this. That said, I should have time for testing it this week, so if all goes well, I'll be able to give some feedback by the end of the week. I have updated the packages at http://people.debian.org/~tille/packages/fis-gtm/ to the recently uploaded ones. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131125131925.gh8...@an3as.eu
Re: Bug#728797: ITP: python-mne -- Python modules for MEG and EEG data analysis
On Thu, 28 Nov 2013, Thorsten Alteholz wrote: Hi Yaroslav, On Thu, 28 Nov 2013, Andreas Tille wrote: H, this information is new to me. If I have understood NEW queue correctly than it is better not to touch packages which are in the queue. Otherwise you might confuse ftpmaster or influence the position of your package to get handled later. Do you have any reference that I#m wrong in assuming this? sorry -- I would not even try to look up the reference atm (need to work on turkey) but just trust me on this one -- IIRC position would not change and ftpmasters will be just fine. in case an ftp trainee has checked the -1 version and now sees a new one, he would not be delighted by this, as his previous work would be just a waste of time. is that from personal experience? debdiff between the two would quickly show what was changed/fixed thus possibly addressing already enlisted concerns which trainee would need to deal upon resubmission anyways, thus imho the situation would be a win-win mne is so early in the queue that it is doubtful anyone is looking at it atm anyways look e.g. at debmake in http://ftp-master.debian.org/new.html ;) This seems to be one of the oldest packages in the queue ... and not the only one with multiple versions... so far your concern is the first one I ever heard in regard of reuploads to NEW -- Yaroslav O. Halchenko, Ph.D. http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org Senior Research Associate, Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik -- 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/20131128215406.gm6...@onerussian.com
