Yet another list statistics for debian-mentors
Hi, as you can read in my lightning talk at DebConf http://people.debian.org/~tille/talks/200808_lightning/ I did some investigation on who is frequently posting on our mailing lists. I now created graphs until end of last year and write a short summary for those lists I regard worth a comment. I'm not CCed to all of this list so if you want to discuss something please keep me in CC. If you want to discuss the results in general just write to debian-project. All graphs and the code that was used to create the graphs are available at http://people.debian.org/~tille/liststats/ If you are interested in a mailing list which was not analysed, just tell me. I was running the scripts on those lists I personally had some interest and those with more than 1000 subscribers. I plan to clean up code and write some doc about it but this will not happen in the next couple of weeks. The graph for this specific list is --- start of mailing list specific part -- http://people.debian.org/~tille/liststats/authorstat_mentors.pdf Guessing from the graph this is a nice list with very active mentors (guessing that people who are frequently posting are mentoring instead or asking questions to mentors ;-)). Keep on the good work! Kind regards Andreas -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
How to debug problems in postinst using debconf / dbconfig common
Hi, I try to build a package from mlstdbnet for Debian Med. The packaging stuff is available here: Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mlstdbnet/trunk/?rev=0sc=0 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mlstdbnet/trunk/ and you can obtain the orig.tar.gz via make -f debian/rules get-orig-source If I build the package I get an error message but failed to track down the problem: ~ sudo dpkg -i mlstdbnet_2.0.0-1_all.deb (Reading database ... 341999 files and directories currently installed.) Preparing to replace mlstdbnet 2.0.0-1 (using mlstdbnet_2.0.0-1_all.deb) ... Unpacking replacement mlstdbnet ... Setting up mlstdbnet (2.0.0-1) ... dpkg: error processing mlstdbnet (--install): subprocess post-installation script returned error exit status 128 Errors were encountered while processing: mlstdbnet You get the preconfiguration I used on the machine in question if you copy debian/more_examples/cdif.xml to /etc/mlstdbnet I'm probably blind for the problem but this exit status 128 without any debug information is quite less. What are the best strategies to track down the problematic line of code which causes the problem. Kind regards and thanks for any help Andreas. PS: I'm not subscribed to debian-mentors so a CC would be nice but I might read the archive. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Re: debian OID / dicom3tools packaging
On Tue, 27 Jan 2009, Mathieu Malaterre wrote: $ echo med | od -b 000 155 145 144 012 1.3.6.1.4.1.9586.155.145.144 This would be the toplevel (root) of all UID generated from the dicom3tools package. Hmm, I'm not sure whether this helps. May be I missunderstood the problem but is the UID per *package* or per *installation*. IMHO assigning a UID to a Debian package makes not much sense because it is finally interesting for the organisation which *installs* this package. So rather than generating the UID in the build process it should be created in the postinst and the admin who is installing the package should register this UID at IANA. So we should find a way how to find some reasonable means to *generate* a UID which was not registered yet. Asking for an Organisation name per debconf and perhaps using a part of the MD5 sum or something like that and *combining* it with a *template* for the package comes to mind. Did I missed something? Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Re: MUMmer patches and Artistic license.
On Sun, Jul 12, 2009 at 10:50:10PM +0900, Charles Plessy wrote: This patch is a good idea -- fixed length buffers are rarely considered user-friendly. However, it is executed poorly; it's not ready for upstream in its current state. Hi, thank you for the comment. I will stop to apply this patch until a better solution is found. Quite late comment after working down my batch of unread mail: The patch was *not* *only* to avoid fixed length buffers - it was invented to stop mummer from *crashing*. I do not remember the case exactly nor do I find the data any more but I *clearly* remember that we actually had example data which were causing mummer to crash without the patch. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
How to detect 32 or 64 bit at build time?
Hi, the new version of arb I want to package requires to set a variable ARB_64=0/11=compile 64 bit version to specify whether it will be compiled on 32 or 64 bit architecture. Is there any safe way to set this variable automatically from environment? I expected dpkg-architecture to provide this information but it does not. Am I missing something? Kind regards Andreas. PS: I'm not subscribed to this list so CC would be nice. -- http://fam-tille.de Klarmachen zum Ändern! -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Re: How to detect 32 or 64 bit at build time?
On Mon, Sep 07, 2009 at 10:50:54AM +, Bart Martens wrote: I guess that you're looking for: dpkg --print-architecture No. The result is equivalent to dpkg-architecture | grep -w DEB_BUILD_ARCH I'm locking for something that responds with 0 for 32 bit architectures and 1 for 64 bit architectures. With the suggestion above I would have to implement a case statement for all existing architectures and would have to keep this up to date. Kind regards Andreas. -- http://fam-tille.de Klarmachen zum Ändern! -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Re: How to detect 32 or 64 bit at build time?
On Mon, Sep 07, 2009 at 12:58:59PM +0200, Sven Joachim wrote: How about DEB_HOST_ARCH_BITS? This needs dpkg 1.15.4, though. Sorry, that should have been DEB_BUILD_ARCH_BITS. Cool, the version in unstable is the key. Thanks for the hint Andreas. -- http://fam-tille.de Klarmachen zum Ändern! -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
How exactly can I use add_command_options to prevent compressing pdfs
Hi, I found in the log of #543392 that there is now a way implemented since debhelper 7.3.16 to prevent dh_compress from zipping everything in the doc directory (especially I want to do an --exclude=.pdf). But I have actually no idea how to *use* this command. Is there any example syntax in a rules file? Kind regards Andreas. PS: It would be nice if you could CC me because I'm not subscribed. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Re: MUMmer patches and Artistic license.
On Sun, Jul 12, 2009 at 10:50:10PM +0900, Charles Plessy wrote: Hi, thank you for the comment. I will stop to apply this patch until a better solution is found. Charles, could you please give an update of the status of mummer package? Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Re: dpkg-shlibdeps: couldn't find library [...]
On Fri, 2 Nov 2007, David Paleino wrote: ... dpkg-shlibdeps: failure: couldn't find library libvtkpxRegistrationTCL.so (note: only packages with 'shlibs' files are looked into). I think you reached a point were I personally would consider asking in debian-devel list (in case there would be no response from debian-mentors). I had not yet to deal with this because my packages use libtool which seems to handle private libraries nicely enough that dpkg-shlibdeps does not complain. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: RFS: mustang, btk-core
On Wed, 9 Jan 2008, Morten Kjeldgaard wrote: Upstream does not build shared libraries, so there is no need for it. I learned that Debian users sooner or later ask for it (even if neither upstream nor yourself thought there would be a need for it). So at least be prepared. :) I have chosen not to build shared libraries, because I would have to choose a soname, and if upstream at some point decides to offer a shared library, we could be in trouble. Choosing a low (0.0) soversion might be safe and if upstream decides to offer a shared library you might send a patch that keeps you out of trouble. Just a thought Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: RFS: mustang, btk-core
Hi, I just took the freedom to really upload the Debian packaging stuff of mustang and btk-core to our SVN: http://cia.vc/stats/project/Debian-Med/.message/51b9d Morten, feel free to revert the group maintainance things I added in a separate check in if you don't feel happy about this. If there is nobody who would like to sponsor the packages until tomorrow I'll go for it (will not make it today). Kind regards and thanks for your work on the packages which helps Debian-Med Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: RFS: adun.app (updated package):wq
On Mon, 21 Jan 2008, Charles Plessy wrote: For biology-related packages, do not hesitate to CC [EMAIL PROTECTED] PS: maybe we (debia-med) should adopt the package ? Definitely. If the package is orphaned we can easily do this without stepping on someones shoes. So I'd be in favour of adding the debian-med-packaging group as Maintainer before finally uploading the package. Moreover I would do the following steps: - Adding a watch file - Adding packaging to Debian-Med SVN - Adding XS-DM-Upload-Allowed, Vcs-Browser, Vcs-Svn tags to debian/control Yavor, do you agree with these steps before an upload? Are you specifically interested in biology related programs or did you just a perfect QA job with your long changelog entry? Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: BALLView - a molecular viewer and modeling tool
On Fri, 26 Jan 2007, Andreas Moll wrote:
I have uploaded a new version of the package.
Well, I checked your work offline and my comments are concerning
the version from tomorrow morning. So feel free to ignore issues
that might be voided by your new version.
I have changed the control file again, to support the ppc arch.
If there is no reason to exclude a certain architecture you should
always use Architecture: all in your package. It is not necessarily
your problem if it fails running on this architecture. Your task
is to deal with the bug reports of users of this architecture later.
In the end this will lead to better upstream code (or to the fact
that one architecture has *really* to be excluded if there is no
way out).
Looks interesting, but I can't play with it, as it requires python 2.3.
Huh, where does this 2.3 dependency come from? Builded on a
not upt to date machine?
This issue is fixed in the new version, I have set the build dependency to
python-dev instead of python2.4-dev.
OK - that's right.
1. I would repack the tarball and leave out the Mac OSX and Windows
directory. It is useless burden to the ftp archive
I tried, but failed miserably ;)
I deleted these folders in the extracted upstream package, but build-package
just printed some warnings that it will ignore the missing directories.
Do I have to manually create a new orig.tar.gz without the mentioned folders?
Yes. Building a new tarball means unpacking the upstream tarball,
removing things you want to remove and build a new tarball that
replaces the original one.
2. The debian-upstream directory is a really interesting
alternative to something we do not really like if upstream
provides a debian directory. I have to clear up my mind
whether I wil like it or not. ;-)
*g* Well, I like the idea, since our upstream authors, can develop install
routines, that can be used by future downstream authors as well.
So if you like it - just keep it (and perhaps add a README as suggested
below.
Bug#407665: ITP: ballview -- Molecular viewer and modeling tool
Changed Bug title.
I got this email from the Debian bug tracking system and I am not really
sure what it means? Did someone tagged my package for usage in the med-bio
project?
Yes, I did so. Just to keep it in focus of our project - nothing
else.
Now for the text I prepared offline:
Please note: The first things I write are *recomendations* in
the direction I *personally* would do the packaging. If you
have reasons to keep it as is - feel free to do so.
1. As I said I would remove the directories MacOSX and
Windows.
2. To the debian-upstream directory: I often elaborated
on the drawbacks if upstream provided a debian packaging
directory (if needed I try to find some links). The
debian-upstream directory might show the fact that
upstream is aware of these problems and provides this
directory just as a nice comfort for the Debian
maintainer. An additional README explaining this would
be nice.
What I would definitely remove from the tarball in any
case are the files that would have been cleaned after
make -f debian/rules clean
like
debian-upstream/{deb-ball-source,ballview.substvars,files}
This is just waste.
3. debian/ballview.doc-base
Quote:
This manual describes what ballview is and how it
can be used.
Uhmmm, I guess the packaging is not really finished, right?
;-))
4. debian/compat
The current debhelper version is 5.x. So if you have no
certain reason (like backporting to Sarge for instance),
I would recommend to use debhelper 5 here.
Now for the package builded. It is lintian free which is good,
However I guess lintian is not perfect in detecting everything -
perhaps we should write a lintian bug report. The problem:
In /usr/share/BALL/bin and /usr/share/BALL/lib there are binary
architecture dependant files. This is forbidden. The solution
would be as follows:
/usr/share/BALL/lib/* /usr/lib/BALL
/usr/share/BALL/bin/* /usr/lib/BALL
These files have to go onto a architecture dependant package.
You also have to adapt the shell script in /usr/bin according
to the changed pathes. This is absolutely required and the
package has no chance to pass ftpmaster in the current form.
So if I would be the maintainer of the project I would build
the following packages:
ballview_1.2-1_arch.deb
/usr/bin/BALLView (Shell-script wrapper)
/usr/lib/BALL/BALLView (real binary)
/usr/share/man/man1
ballview-data_1.2-1_all.deb
/usr/share/BALL/data
/usr/share/BALL/PYTHON (I don't think that you have
a big deal with Python policy
here because they are simple
scripts no reusable
Re: BALLView - a molecular viewer and modeling tool
On Fri, 26 Jan 2007, Kevin B. McCarty wrote: I'm pretty sure you meant to say Architecture: any here. (For anyone who might need clarification: an Architecture: any package must Yes, Thanks for the hint. I hope this didn't come across as nitpicky, just wanted to make sure things were clear for anyone new to Debian packaging who might be reading the lists. I don't know nitpicking. If there is a mistake it should be corrected. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: BALLView - a molecular viewer and modeling tool
On Sun, 28 Jan 2007, Andreas wrote: 4. debian/compat The current debhelper version is 5.x. So if you have no certain reason (like backporting to Sarge for instance), I would recommend to use debhelper 5 here. I used the version 4 because otherwise I could not build the package on the Edgy Ubuntu. The package works fine with the older version of debhelper. So if you aware of this fact and have reasons to keep version 4 it is fine. perhaps we should write a lintian bug report. The problem: In /usr/share/BALL/bin and /usr/share/BALL/lib there are binary architecture dependant files. This is forbidden. The solution would be as follows: I fixed the used directories as you suggested. Fine. In case the binary expects the doc files at a certain location put symlinks into this place. This is still a problem, I tried to create the symlinks, such that they will be created in the debian/ballview folder, but when the package is finished, the links are disappeared and instead there are real folders under /usr/share/BALL/doc. Do I have to create the links in the ballview.postinst.debhelper file? Have a look into man dh_link For the moment I would dislike splitting up the package because I guess it would complicate thinks further. Is there a serious problem with the current packaging form? Yes. You should definitely use a binary _any_ package with the binary dependant part and a binary _all_ package with all files that work under all architectures (except man pages who are usually shipped with the binary in one package). The rationale behind is to keep the ftp archive (and especially bandwidth and space of the mirrors all over the world) clean of duplicated files that do not need to be duplicated. There is probably no need to split up doc and data if the doc is used as online help and is needed anyway. So this can be put into a ballview-common package, but using such a package is really high recommended. It depends a little bit from the ratio of the size of binary and independant files to make ftpmaster force you to split the package but IMHO splitting ballview is necessary. And for the BALL library: I have thought about creating either an extra development package with the full BALL library or a header and static lib dev package. My guess is that both would not be too useful for the following reason: The library has around 20 different configure options and thus can be adapted to differing needs, e.g. by switching features on and off. Therefore I guess that for every developer that wants to seriously use the library, it would be better to configure and build the library from the sources. This also allows to compile and run the tests and benchmarks. Well, you are the expert and I have no idea how this optional features are used. I also wonder if you decide for a certain set of options whether it will not be possible to provide a development package with the very same set of options and add a README that if you need different options you have to compile the development library on your own. But as I said the developmen package is a bonus and there is no need to provide it for the first shot. On the other hand I guess people will ask you for it (I just realized it for the WOrdNet package where I never expected people to ask for it). Maybe I am wrong? Maybe I'm wrong as well. ;-) I have changed the control file yet an other time to support any arch. Fine. By the way, Andreas Moll, the PPC architecture name in Debian is powerpc and not ppc, as in foo_1.0-3_powerpc.deb, just in case there was some doubt... Where is this name used, except for the control file? I personally have no idea. Kind regards and thanks for your work on ballview Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: BALLView: new package version
On Sun, 28 Jan 2007, Andreas Moll wrote: there is a now a new improved package version available. Got it and builded the package. My main concerns are solved and I would regard the package nearly ready for upload. There is just one issue if I run the demo I get the following output: Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/BALL/index.html' for reading Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/BALL/index.html reading PDB file... Read 454 atoms from file /usr/share/BALL/data/structures/bpti.pdb applying molecular properties ... normalized names generated missing bonds Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo01.html' for reading Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo01.html Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo02.html' for reading Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo02.html Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo03.html' for reading Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo03.html Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo04.html' for reading Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo04.html Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo05.html' for reading Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo05.html Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo06.html' for reading Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo06.html Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo07.html' for reading Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo07.html Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo08.html' for reading Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo08.html Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo09.html' for reading Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo09.html Calculated 15 H-bonds Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo10.html' for reading Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo10.html Could not delete Representation while update is running! Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo11.html' for reading Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo11.html Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo12.html' for reading Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo12.html Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo13.html' for reading Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo13.html Set up the force field for 892 atoms with parameters from /usr/share/BALL/data/Amber/amber96.ini. Minimizing 892 of 892 atoms. final RMS gradient: 25.544510 kJ/(mol A) after 20 iterations Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo14.html' for reading Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo14.html Canonical MD simulation System has potential energy -8454.06 kJ/mol at time 0 ps Canonical MD simulation System has temperature 0 at time 0 ps final RMS gradient: 31.285550 kJ/(mol A) after 30 iterations Warning: QTextBrowser: Cannot open 'file:///usr/share/BALL/data/../doc/internal/demo15.html' for reading Warning: QTextBrowser: No document for file:///usr/share/BALL/data/../doc/internal/demo15.html FDPB: creating array of charged atoms... FDPB: creating bounding box... FDPB::setup: grid border: 5 FDPB::setup: grid:(-11.0954 64.6133 -13.4265)/(38.7545 114.463 36.4234) grid dimensions: 50x50x50 Boundary points: 4639 creating phi grid... creating charge grid... creating boundary... Debye length = 3.40282e+38 m ionic strength = 0 calculating effective dipole... assigned negative charge: -89.9301 at (13.0115/88.8805/9.14098) assigned positive charge: 95.9301 at (13.0568/88.4927/9.57466) setting up xy-planes... setting up xz-planes... setting up yz-planes... setting up some arrays... calculating charged grid points... number of charged grid points: 2792 (2.10477%) starting iterations. Iteration 10 RMS: 0.0109379 MAX: 0.301846 Iteration 20 RMS: 0.00386107 MAX: 0.10198 Iteration 30 RMS: 0.00139456 MAX:
Re: RFS: libsbml
On Mon, 29 Jan 2007, Steffen Moeller wrote: Dear Moriyoshi and dear Changyan, please get in contact with each other for an exchange of ideas for the package. Whoever wishes to go forward with the maintenance should do so. A SVN-based group maintenance would be preferable from my point of view as it does not harm and is much fun if it works out nicely. It is in no way required, though. Andreas? There is nothing to add from my side (and also no need to ask me in person - I will never stop anybody from doing reasonable things ;-) ) Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: BALLView: new package version
On Mon, 29 Jan 2007, Andreas Moll wrote: Your welcome, it is in my own interest to get this package in perfect shape as soon as possible. :) To stop the cross-list posting I include only mentors (please CC me, I'm not subscribed): Did I understand current freeze state right that uploads to unstable will not be moved to testing automatically any more only by manual intervention of ftpmaster or should we rather continue with the upload to experimental target which would be really boring, thought. I just would like to go for an upload to unstable. Thank you again for your help! Well, the Debian-Med project has interest in such nice programs as well. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: BALLView: new package version
On Mon, 29 Jan 2007, Andreas Moll wrote: This may mean that this code has to be reimplemented... OK. Just keep me informed if you are ready and keep on the good work. (Thanks to Margarita for the hint about uploading.) Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: RFS: libsbml
On Mon, 5 Feb 2007, Changyan Xie wrote: I have looked over all the patch stuff! Your work are excellent! But I have a little opinion on the libsbml-doc package and the build dependence to latex2html: the upstream offer a seperated libsbml-doc source package,which contained compiled html and pdf document. So, why not just use this source rather than to compile it? from my side, I think the dependence to latex is evitable and this will save a lot of compiling time. Well, in a Debian source package we provide the *source*. The rationale is if you need to patch something in the docs you will have problems to modify a PDF. So compiling the docs is really a good idea and the compile time should not really be an argument here. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: RFS: libsbml
On Tue, 6 Feb 2007, Changyan Xie wrote: Ok, I admit that the real problem is that the dependence to latex2html require tetex-extra and a lot of other packages,and after this additional dependence, my system require another 100 M disk space. If it is about bloating your production system I would suggest to use pbuilder which installs all this stuff into a chroot and will remove it afterwards. This does not really make the build process faster but keeps your system clean and has other additional advantages (like beeing sure that all build-dependencies are mentioned and ensures more or less that auto-builders will probably work). I'm unsure but there is a chance that an alternative build-dependency to texlive that is known to be packages more fine grainded might be possible with less disk space than you mentioned. I don't like installing a lot of packages just because an unnecessary package. Well, whether something is unnecessary depends from the point of view. To build libsmbl from source it seems to be necessary. I believe other people may feel the same like me. Why not just left this an option to user? I mean, in the upstream source, to build the doc is optional, we can just left this like the original source. If you ask me I would rather leave the compiled docs out of the source tarball because these ar not necessary. Another reason, we have an analogue: this package support matlab binding too. Of course, we will not enable this binding by default. but user can simply apt-get source and add this support. This is just like the doc package's situation, we can disable it by default, but easily enable it. Not really. Docs are always welcome and if they are free they should be packaged. Matlab is neither free nor exist a package so this support would be not reasonable. Further more, I think there will be few people want to patch doc package, Ahh, really? You will be astonished how many reasons might be or how many bug reports you might gather for a pretended simple doc package. I can asure you that the package maintainer of a doc package has good chances to be forced to patch the docs. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: RFS: libsbml
On Tue, 6 Feb 2007, Charles Plessy wrote: What is happening to a source package with build-dependancies on a non-free package. Can it produce a binary packages for main, with only a -doc package going in contrib? Do the Debian buildds have non-free enabled? (I doubt...) It is quite a sloppy issue. The reaosn is that the resulting binary doc package does not even need any non-free stuff so there is no real reason to move it to contrib. This is quite a difficult topic and might be either discussed here or on debian-legal (perhaps on debian-devel). In this special case I wrote in private mail to Changyan Xie that I would rethink my request for compiling html from source because we are perfectly able to patch HTML documents (in contrast to PDFs) and would avoid serious and quite boring licensing issues. In the other hand Do you think that there are other converters around which can to the same job ? I have just read that there are two other free converters. I would give these a chance before continue thinking about nasty licensing issues. If we decide to keep latex2html, maybe we can try to add texlive-latex-recommended and texlive-fonts-recommended to the build-dependancies, so that it would avoid to use tetex-extra? If there is an alternative dependency on a package you need in your build dependencies you could list it in you build dependencies as well as an alternative (if I'm not completely wrong). Either the build dependency is fullfilled on your machine or in a chroot the first alternative is choosen (not tested but guessed). Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Meshlab and Qutemol
On Tue, 24 Apr 2007, Teemu Ikonen wrote: ... I could go on and package Meshlab with a static copy of VCG included, but if there's someone with suitable hardware, time and interest to package Qutemol, then maybe VCG should be in a separate package. Sounds good. I personally would prefer if you would split VCG in any case because I'm a big fan of modularized packaging. Anybody interested? Well, do you want to know whether somebody is interested or whether somebody would like to start real work on it. Interest on my side yes, but these projects would definitely not on top of my todo list. Sponsoring is no problem. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Meshlab and Qutemol
On Sun, 3 Jun 2007, Teemu Ikonen wrote: I've made packages of Meshlab with the relevant parts of the VCG library included in the source (separate packaging does not make much sense ATM, since VCG upstream does not even have a build system). The source package is at http://www.helsinki.fi/~tpikonen/meshlab/ I've found /usr/lib/meshlab/plugins.txt containing Put in this folder your DLL plugin and restart MeshLab Is this really a file that is parsed by the runtime or should this rather be a documentation file? In general I really think there is a bit less documentation (not to mention the missing man pages). For instance what is the sense behind /usr/bin/meshlabserver. From a users point of view I would have no idea where to start with this package. So, if any DD interested in this software is reading this, please help close bug #426581 and sponsor an upload to the archive. Any comments or suggestions for improving the packaging are very much welcome as well. Sponsoring would be no problem, if my brain dead users perspective could be at least a little bit liftet. Thanks for working on this package that seems quite useful obtained from the screen shots from the web page (even if the shots show a strange window manager ;-)). Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Sofa-framework: Again QT help needed
On Sat, Dec 31, 2011 at 12:41:11PM +0200, Boris Pek wrote: Hi Andreas, There is typo here. Try correct string: QT += qt3support While I have no experience with cmake I'm not sure about the difference between += and *= I guess the vraiant with '*' was intended. In any case I can confirm that both results in the very same build failure. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120101112231.gb18...@an3as.eu
Re: Sofa-framework: Again QT help needed / Re: [Sofa-devel] Debian packaging
Hi Eric, to give an update of this issue I uploaded the latest status of packaging to http://people.debian.org/~tille/packages/sofa-framework/ It shows problems building the plugins as you have noticed. As I said in my latest (private) mail I really needed to add LIBS *= -lQt3Support -lQtGui -lQtCore When I tried without the build was broken (and I've got the explicite hint to add these libraries. Even if this should not be needed in theorie as you said when using QT *= qt3support it just did not worked as intended. If nobody has an idea how to solve the problem in the end of the build log http://people.debian.org/~tille/packages/sofa-framework/sofa-framework_1.0~rc1-1_amd64.build I will probably apply pluginsample.patch and build the package without this part. However, any hint is welcome. Kind regards Andreas. On Mon, Jan 02, 2012 at 05:57:41PM +0100, Eric Maeker wrote: Le 2 janvier 2012 15:40, Francois Jourdes francois.jour...@inria.fr a écrit : Hi, Thank you for your interest for SOFA. I applied your patches (except for pluginsample.patch) to my sofa-rc1.0 directory and managed to compile successfully. However I did not encounter the errors you reported on my first attempts. I am compiling with qt 4.6.2 installed on my machine, but I suspect versions of qt = 4.5 are ok as well. The build failed with Qt4.7.4 on Ubuntu 11.10 and Debian testing. The build log can be found here http://people.debian.org/~tille/packages/sofa-framework/sofa-framework_1.0~rc1-1_amd64.build Regarding PluginExample I attached a patch which excludes the classes which requires qt from compilation if the SOFA_QT4 compilation flag is not present. Ok I'll check as soon as possible. François Jourdes. Thanks -- Eric Maeker, MD (FR) http://www.freemedforms.com/ http://www.ericmaeker.fr/ http://wiki.debian.org/DebianMed -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120103182548.gb13...@an3as.eu
Help with java package (beast-mcmc) needed
Hi, I tried building a package from beast and uploaded for simlicity this stuff to http://people.debian.org/~tille/packages/beast-mcmc-help-wanted/ It contains six executable files in /usr/bin. Three of them are starting nicely. These are beast-mcmc, beauti and loganalyser. However, the other three executables are failing for a reason I do not understand: $ logcombiner Exception in thread main java.lang.NoClassDefFoundError: jam/console/ConsoleApplication at dr.app.tools.LogCombiner.main(Unknown Source) Caused by: java.lang.ClassNotFoundException: jam.console.ConsoleApplication 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) ... 1 more The executable treeannotator fails with the very same error message and for treestat I get: $ treestat Exception in thread main java.lang.NoClassDefFoundError: jam/framework/SingleDocApplication at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:634) ... I checked that /usr/share/java/jam.jar is installed and contains the relevant classes. Any idea what might went wrong here? Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120108204258.ga18...@an3as.eu
Re: Bug#653799: FTBFS: CMake Error at cmake_modules/FindOpenCV.cmake:77 (file): file STRINGS file /usr/include/opencv/cvver.h cannot be read.
Hi, On Fri, Dec 30, 2011 at 07:08:09PM -0600, Steve M. Robbins wrote: Source: sitplus Version: 1.0.1-2 Severity: serious Justification: fails to build from source Package failed to build in a clean sid chroot: -- checking for one of the modules 'glib-2.0' -- Found GLib2: glib-2.0 /usr/include/glib-2.0;/usr/lib/x86_64-linux-gnu/glib-2.0/include -- Looking for include files HAVE_GLIB_GREGEX_H -- Looking for include files HAVE_GLIB_GREGEX_H - found The old build log continued like this: -- OpenCV_FOUND. true -- OpenCV_LIBS. /usr/lib/libcxcore.so;/usr/lib/libcv.so;/usr/lib/libml.so;/usr/lib/libhighgui.so;/usr/lib/libcvaux.so -- OpenCV_INCLUDE_DIR. /usr/include/opencv CMake Error at cmake_modules/FindOpenCV.cmake:77 (file): file STRINGS file /usr/include/opencv/cvver.h cannot be read. Call Stack (most recent call first): src/creavision/CMakeLists.txt:57 (FIND_PACKAGE) CMake Error at cmake_modules/FindOpenCV.cmake:78 (string): string sub-command REGEX, mode REPLACE needs at least 6 arguments total to command. I noticed that the new version of libcv-dev in unstable is lacking the header file in question. So I'm CCing the maintainer as well as debian-mentors in case I can get any other help how to fix this problem. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120109094322.ga1...@an3as.eu
Re: Help with java package (beast-mcmc) needed
Hi Sylvestre, On Tue, Jan 10, 2012 at 06:09:53AM +0100, Sylvestre Ledru wrote: Exception in thread main java.lang.NoClassDefFoundError: jam/console/ConsoleApplication Usually, this kind of problem is due to the CLASSPATH not containing jam.jar $ grep jam debian/rules export CLASSPATH := $(DEBJAR)/itext.jar:lib/beagle.jar:lib/mpj.jar:lib/org.boehn.kmlframework_20090320.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:lib/options.jar:lib/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar As far as I understood you do not need to explicitely set CLASSPATH at runtime (and it would not explain why the other executables are perfectly finding the needed jars. Any further hints? Kind regards and thanks anyway Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120110095920.ge28...@an3as.eu
Re: Help with java package (beast-mcmc) needed
On Tue, Jan 10, 2012 at 12:01:57PM +0100, Olivier Sallou wrote: Usually, this kind of problem is due to the CLASSPATH not containing jam.jar $ grep jam debian/rules export CLASSPATH := $(DEBJAR)/itext.jar:lib/beagle.jar:lib/mpj.jar:lib/org.boehn.kmlframework_20090320.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:lib/options.jar:lib/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar As far as I understood you do not need to explicitely set CLASSPATH at runtime (and it would not explain why the other executables are perfectly finding the needed jars. For classpath, at runtime, all depends on how jar is generated. If it contains a MANIFEST file with the classpath defined, it will be able to find the JARS (supposing that libraries path are the same). If it dies not contains the classpath in the MANIFEST file, classpath must be set explicitly to each jar file in the command line (usually via a wrapper shell) Apropos MANIFEST: I formerly fiddled around with packaging using jh_manifest and there is also some alternative packaging method at http://people.debian.org/~tille/packages/beast-mcmc-help-wanted/manifest/ featuring a debian/beast-mcmc.manifest file. Believe it or not it shows the very same behaviour. The most strange fact for me is that the two executables loganalyser and logcombiner are very similar but only one of them runs and the other fails. Do you think I should simply add a CLASSPATH variable to those scripts that are failing without understanding why the others are working? Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120110131155.ga1...@an3as.eu
Help with architecture not supporting SSE (Was: Bug#656755: libhmsbeagle FTBFS on everything except amd64)
Hi, I have to admit that I do not have any experience with SSE issues. Any advise what to do in cases like this (see build logs linked below)? The error message starts with libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/build/buildd-libhmsbeagle_1.0-3-hurd-i386-sfmc4g/libhmsbeagle-1.0 -I/build/buildd-libhmsbeagle_1.0-3-hurd-i386-sfmc4g/libhmsbeagle-1.0 -O3 -c BeagleCPUSSEPlugin.cpp -fPIC -DPIC -o .libs/libhmsbeagle_cpu_sse_la-BeagleCPUSSEPlugin.o In file included from /build/buildd-libhmsbeagle_1.0-3-hurd-i386-sfmc4g/libhmsbeagle-1.0/libhmsbeagle/CPU/SSEDefinitions.h:37:0, from /build/buildd-libhmsbeagle_1.0-3-hurd-i386-sfmc4g/libhmsbeagle-1.0/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.hpp:44, from /build/buildd-libhmsbeagle_1.0-3-hurd-i386-sfmc4g/libhmsbeagle-1.0/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:240, from BeagleCPUSSEPlugin.cpp:9: /usr/lib/gcc/i486-gnu/4.6/include/emmintrin.h:32:3: error: #error SSE2 instruction set not enabled In file included from /build/buildd-libhmsbeagle_1.0-3-hurd-i386-sfmc4g/libhmsbeagle-1.0/libhmsbeagle/CPU/SSEDefinitions.h:39:0, from /build/buildd-libhmsbeagle_1.0-3-hurd-i386-sfmc4g/libhmsbeagle-1.0/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.hpp:44, from /build/buildd-libhmsbeagle_1.0-3-hurd-i386-sfmc4g/libhmsbeagle-1.0/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:240, from BeagleCPUSSEPlugin.cpp:9: /usr/lib/gcc/i486-gnu/4.6/include/xmmintrin.h:32:3: error: #error SSE instruction set not enabled In file included from /build/buildd-libhmsbeagle_1.0-3-hurd-i386-sfmc4g/libhmsbeagle-1.0/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.hpp:44:0, from /build/buildd-libhmsbeagle_1.0-3-hurd-i386-sfmc4g/libhmsbeagle-1.0/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:240, from BeagleCPUSSEPlugin.cpp:9: /build/buildd-libhmsbeagle_1.0-3-hurd-i386-sfmc4g/libhmsbeagle-1.0/libhmsbeagle/CPU/SSEDefinitions.h:52:10: error: '__m128d' does not name a type /build/buildd-libhmsbeagle_1.0-3-hurd-i386-sfmc4g/libhmsbeagle-1.0/libhmsbeagle/CPU/SSEDefinitions.h:80:2: error: 'V_Real' does not name a type In file included from /build/buildd-libhmsbeagle_1.0-3-hurd-i386-sfmc4g/libhmsbeagle-1.0/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:240:0, from BeagleCPUSSEPlugin.cpp:9: Any help is welcome Andreas. On Sat, Jan 21, 2012 at 09:50:16PM +, Adam D. Barratt wrote: On Sat, 2012-01-21 at 17:16 +0100, Andreas Tille wrote: On Sat, Jan 21, 2012 at 03:00:25PM +, peter green wrote: It seems things are a little more complex than they first appeared. In particular it seems libhmsbeagle has a specific sse2 plugin which can only be built with sse2 enabled and that is built even if --enable-sse=no is passed (which seems like a bug in the upstream build system to me). Therefore disabling -msse2 has caused the package to FTBFS everywhere except amd64. For non pc architectures I would think the sse2 plugin should simply be disabled. Do you have any hint how I could find this plugin which should be disabled. [...] A failed build log would probably be helpful. I also have included upstream whether they might be able to give any hint about this issue: Predictably, https://buildd.debian.org/status/package.php?p=libhmsbeagle has several - the hurd-i386, powerpc and s390x logs all look like they fail whilst building libhmsbeagle_cpu_sse_la-BeagleCPUSSEPlugin.lo. Regards, Adam -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120122133150.ga23...@an3as.eu
Re: Help with architecture not supporting SSE (Was: Bug#656755: libhmsbeagle FTBFS on everything except amd64)
On Wed, Jan 25, 2012 at 01:37:59AM +, peter green wrote: Andreas Tille wrote: Hi, I have to admit that I do not have any experience with SSE issues. Any advise what to do in cases like this (see build logs linked below)? From looking at the build logs it looks like it is trying to build a plain CPU plugin and a CPU with SSE plugin, presumablly the plugins are different peices of code that can be used to perform the core computations. It looks like you will need to modify the build system so that it is possible to disable building the CPU with SSE plugin. Yes, that's also what I guessed from the logs and the code. But thats only my gut feeling from looking at the build logs and package discriptions, this really needs to be confirmed by someone who actually knows the internals of the package in question. Upstream was in CC in all these mails. I'm urgently hoping for some answer. If you can't handle this then I don't think you are competant to be maintaining this package in debian. Knowing how the components of the software they are packaging fit together and how to fix the build systems to produce packages suitable for debian is IMO a pretty key part of a maintainers job. While I really agree to this statement I think there is few chance that somebody else will step in. We are just needing to maintain this as a predependency for two important packages of the Debian Med team. As you know RFP bugs are really rarely resolved and thus we try to drain the competence to handle this from upstream which is IMHO the fallback for maintainers in any case. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120125072326.gh8...@an3as.eu
Re: Help with architecture not supporting SSE (Was: Bug#656755: libhmsbeagle FTBFS on everything except amd64)
Hi Peter, many thanks for the patch which was in fact helpful to solve the problem. On Wed, Jan 25, 2012 at 11:04:13AM +, peter green wrote: Ok I took pity on you and took a look at the Makefile.am in that directory, turns out it wasn't that hard to disable building of the CPU with SSE plugin. You should really be able to do this kind of build-system modification yourself though, it's not like the package is using an exotic build system it's bog standard autotools. I agree that this was not to hard. However, I did not understand your motivation to work behind a perfectly working clean target which was fully functional by using autotools-dev, dh-autoreconf. So I deleted your part of debian/rules changes. I have tested that the resulting package builds on i386, I have not tested whether it actually works. I noticed that now the plugin for amd64 is not builded and needed to tweak debian/rules a bit by detecting the build architecture. Hope this will work now for all archs. The attatched patch makes the aforementioned change and also makes debian/rules clean actually work. As I said, this was unnecessary. Thanks in any case for your help Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120125135028.gw8...@an3as.eu
Re: Bug#653799: FTBFS: CMake Error at cmake_modules/FindOpenCV.cmake:77 (file): file STRINGS file /usr/include/opencv/cvver.h cannot be read.
Hi Nobuhiro, On Thu, Feb 02, 2012 at 04:06:12AM +0900, Nobuhiro Iwamatsu wrote: tags 653799 patch thanks ... I checked this bug. Because /usr is set to OpenCV_DIR, /usr/share/OpenCV/OpenCVConfig.cmake file has not been read. Moreover, when there is no /usr/OpenCVConfig.cmake, another checking is executed, but only old opencv corresponds. The problem in which the check of OpenCV fails is solved by specifying OpenCV_DIR. I attach a patch. Thanks for the patch - unfortunately this does not change anything at my site. :-( But if you will apply this patch, it becomes an error in other portions. - [ 55%] Building CXX object src/mod_camera/tests/CMakeFiles/test_mod_camera_gui.dir/test_mod_camera_gui.cpp.o Linking CXX executable ../../../bin/test_mod_camera_gui ../../../bin/libmod_camera.so: undefined reference to `cvLoadImage' ../../../bin/libmod_camera.so: undefined reference to `cvConvertImage' ../../../bin/libmod_camera.so: undefined reference to `cvReleaseImage' ../../../bin/libmod_camera.so: undefined reference to `cvReleaseImageHeader' ../../../bin/libmod_camera.so: undefined reference to `cvSetZero' ../../../bin/libmod_camera.so: undefined reference to `cvLine' ../../../bin/libmod_camera.so: undefined reference to `cvGetRawData' ../../../bin/libmod_camera.so: undefined reference to `cvGetErrStatus' ../../../bin/libmod_camera.so: undefined reference to `cvSaveImage' ../../../bin/libmod_camera.so: undefined reference to `cvCopy' ../../../bin/libmod_camera.so: undefined reference to `cvFlip' ../../../bin/libmod_camera.so: undefined reference to `cvNamedWindow' ../../../bin/libmod_camera.so: undefined reference to `cvCircle' ../../../bin/libmod_camera.so: undefined reference to `cvShowImage' ../../../bin/libmod_camera.so: undefined reference to `cvRectangle' ../../../bin/libmod_camera.so: undefined reference to `cvResize' ../../../bin/libmod_camera.so: undefined reference to `cvCreateData' ../../../bin/libmod_camera.so: undefined reference to `cvCreateImageHeader' collect2: ld returned 1 exit status - I could only wild guess here, but when using libopencv-core-dev the according strings appear in the installed *.a / *.so files. Unfortunately I can not check this because my build does not reach this point. Any further help (Luis, do you have an idea?) Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120201211852.gg10...@an3as.eu
Re: Bug#653799: FTBFS: CMake Error at cmake_modules/FindOpenCV.cmake:77 (file): file STRINGS file /usr/include/opencv/cvver.h cannot be read.
Hi Nobuhiro,
On Thu, Feb 02, 2012 at 12:17:36PM +0900, Nobuhiro Iwamatsu wrote:
Oh, sorry. I forgot to write important infomation.
You need to check with opencv 2.3.1-7.
Because this version fixed #658196. I just upload.
...
Could you check with opencv 2.3.1-7?
This version is not yet available on the mirror I'm using. Once
it is there I will test the following changes:
diff --git a/debian/changelog b/debian/changelog
index 912f835..6cf7db6 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,12 @@
+sitplus (1.0.1-3) UNRELEASED; urgency=low
+
+ * debian/rules: Apply patch kindly provided by Nobuhiro Iwamatsu
+iwama...@debian.org (thanks)
+Closes: #653799
+ * debian/control: Build-Depends: libcv-dev (= 2.3.1-7)
+
+ -- Andreas Tille ti...@debian.org Mon, 09 Jan 2012 10:10:13 +0100
+
sitplus (1.0.1-2) unstable; urgency=low
* debian/patches/as-needed.patch: Fix FTBFS with --as-needed linker option.
diff --git a/debian/control b/debian/control
index 9d52ede..cc18cb8 100644
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,12 @@ Maintainer: Debian Med Packaging Team
debian-med-packaging@lists.alioth.debian.
DM-Upload-Allowed: yes
Uploaders: Luis Rivas Vañó lui...@gmail.com,
Andreas Tille ti...@debian.org
-Build-Depends: debhelper (= 8), cmake, libpoco-dev, libboost-dev,
libboost-program-options-dev, libboost-thread-dev, libboost-system-dev,
wx2.8-headers, libwxbase2.8-dev, libbluetooth-dev, libconfig8-dev,
libsdl1.2-dev, libcv-dev, libcvaux-dev, libhighgui-dev, libv4l-dev,
libportmidi-dev, libboost-filesystem-dev, asciidoc, libsdl-gfx1.2-dev,
libsdl-image1.2-dev, libwxgtk2.8-dev
+Build-Depends: debhelper (= 8), cmake, libpoco-dev, libboost-dev,
+ libboost-program-options-dev, libboost-thread-dev, libboost-system-dev,
+ wx2.8-headers, libwxbase2.8-dev, libbluetooth-dev, libconfig8-dev,
libsdl1.2-dev,
+ libcv-dev (= 2.3.1-7), libcvaux-dev, libhighgui-dev, libv4l-dev,
libportmidi-dev,
+ libboost-filesystem-dev, asciidoc, libsdl-gfx1.2-dev, libsdl-image1.2-dev,
+ libwxgtk2.8-dev
Standards-Version: 3.9.2
Homepage: http://sitplus.crea-si.com
Vcs-Git: git://git.debian.org/debian-med/sitplus.git
diff --git a/debian/rules b/debian/rules
index 3a77152..277f0c0 100755
--- a/debian/rules
+++ b/debian/rules
@@ -8,12 +8,12 @@
#export DH_VERBOSE=1
override_dh_auto_configure:
- dh_auto_configure -- -DCMAKE_BUILD_TYPE=Release
-DCMAKE_INSTALL_RPATH=/usr/lib/sitplus -DCMAKE_EXE_LINKER_FLAGS=-lboost_system
+ dh_auto_configure -- -DCMAKE_BUILD_TYPE=Release
-DCMAKE_INSTALL_RPATH=/usr/lib/sitplus -DCMAKE_EXE_LINKER_FLAGS=-lboost_system
-DOpenCV_DIR=/usr/share/OpenCV/
override_dh_auto_install:
dh_auto_install
rm -f
${CURDIR}/debian/tmp/usr/share/sitplus/graphics/pictures/License.txt
Thanks for your help
Andreas.
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Re: Bug#653799: FTBFS: CMake Error at cmake_modules/FindOpenCV.cmake:77 (file): file STRINGS file /usr/include/opencv/cvver.h cannot be read.
Hi, On Thu, Feb 02, 2012 at 08:00:20AM +0100, Andreas Tille wrote: This version is not yet available on the mirror I'm using. Once it is there I will test the following changes: I can confirm that I was able to build after adding to opencv libs explicitely to the linker flags which now looks like: -DCMAKE_EXE_LINKER_FLAGS=-lboost_system -lopencv_core -lopencv_highgui It would be more fun if cmake would be able to detect this automagically but I'm no cmake expert and I'll leave this to upstream. Kind regards and thanks for the patch in the first place Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120202141608.gi2...@an3as.eu
Re: Bug#639995: epigrass does not start on GNOME
Hi Davide, thanks for using EpiGrass and I hope to get it up and running for your study. On Thu, Feb 02, 2012 at 12:21:27PM +0100, erB@rilloo wrote: Hello Jakub, I still have the error reported into bug 639995 (epigrass: missing dependency on python-pkg-resources): Traceback (most recent call last): File /usr/bin/epigrass, line 5, in module from pkg_resources import load_entry_point File /usr/lib/python2.7/dist-packages/pkg_resources.py, line 2676, in module parse_requirements(__requires__), Environment() File /usr/lib/python2.7/dist-packages/pkg_resources.py, line 552, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: distribute I urgently need EPIGRASS for my study so pls give me any advice to bypass this error. how can I get this missing dependency (it seems a python module) I'm using Ubuntu 11.10. I admit I never used Ubuntu and I'm just wild guessing. So please take this advise with a grain of salt because there will be a chance to break your system when doing so. If I understood things correctly the bug was not in epigrass but rather in python-networkx. It was fixed in python-networkx package version 1.6-1. So you can try to install this very package version on top of your Ubuntu system. I repeat my warning: There are chances to crash several things by mixing packages from different distributions - just ask an Ubuntu expert for more detailed advise. Another option would be to install Debian and upgrade to testing - it just depends *how* urgently you need EpiGrass. I also could give backporting EpiGrass a try to backports.debian.org if you confirm that you prefer to run a Debian stable system. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120203073316.gf...@an3as.eu
Proable multiarch related problem in finding header file (Was: Problem finding posix_types_32.h when using pbuilder on the fis-gtm package)
Hi, just a comment on this: I suspect a multiarch issue and http://lists.debian.org/debian-devel-announce/2011/06/msg2.html Multiarch handling of header files (/usr/include) will require more per-package attention, ... so Luis is asking for some hints how to deal with this like the need to specify explicite header search path via -I options or something like this. Any more detailed hint than the above would be helpful. Kind regards Andreas. On Sun, Feb 12, 2012 at 05:14:47PM -0500, Luis Ibanez wrote: Debian-mentors, I'm working on packaging fis-gtm, The configuration files that I'm using are here: svn+ssh://svn.debian.org/svn/debian-med/trunk/packages/fis-gtm/fis-gtm/trunk/debian http://anonscm.debian.org/viewvc/debian-med/trunk/packages/fis-gtm/fis-gtm/trunk/debian/ These are setup to get the tarball by using: uscan --verbose --force-depends I manage to build the package locally by using debuild, but, when I use the pdebuild command, I get the following output: - Start the build - Linux Host 32 Linux Host linux i386 x86_regs Source Directory List: sr_linux sr_i386 sr_x86_regs sr_unix_gnp sr_unix_cm sr_unix_nsb sr_unix sr_port_cm sr_port make[2]: Entering directory `/tmp/buildd/fis-gtm-5.4-002B' mkdir -p /tmp/buildd/fis-gtm-5.4-002B/pro/map tcsh -f /tmp/buildd/fis-gtm-5.4-002B/sr_unix/gen_gtm_threadgbl_deftypes.csh /tmp/buildd/fis-gtm-5.4-002B sr_port pro/obj sr_linux sr_i386 sr_x86_regs sr_unix_gnp sr_unix_cm sr_unix_nsb sr_unix sr_port_cm sr_port Entering gen_gtm_threadgbl_deftypes.csh to build gtm_threadgbl_deftypes.h ~/fis-gtm-5.4-002B/pro/obj ~/fis-gtm-5.4-002B Replacing /tmp/buildd/fis-gtm-5.4-002B/sr_linux/gtm_threadgbl_deftypes.h ~/fis-gtm-5.4-002B Exiting gen_gtm_threadgbl_deftypes.csh make -C /tmp/buildd/fis-gtm-5.4-002B/pro/obj -I/tmp/buildd/fis-gtm-5.4-002B/pro/obj -I/tmp/buildd/fis-gtm-5.4-002B/sr_linux -I/tmp/buildd/fis-gtm-5.4-002B/sr_i386 -I/tmp/buildd/fis-gtm-5.4-002B/sr_x86_regs -I/tmp/buildd/fis-gtm-5.4-002B/sr_unix_gnp -I/tmp/buildd/fis-gtm-5.4-002B/sr_unix_cm -I/tmp/buildd/fis-gtm-5.4-002B/sr_unix_nsb -I/tmp/buildd/fis-gtm-5.4-002B/sr_unix -I/tmp/buildd/fis-gtm-5.4-002B/sr_port_cm -I/tmp/buildd/fis-gtm-5.4-002B/sr_port -f /tmp/buildd/fis-gtm-5.4-002B/sr_unix/comlist.mk CURRENT_BUILDTYPE=pro all Linux Host 32 Linux Host linux i386 x86_regs Source Directory List: sr_linux sr_i386 sr_x86_regs sr_unix_gnp sr_unix_cm sr_unix_nsb sr_unix sr_port_cm sr_port make[3]: Entering directory `/tmp/buildd/fis-gtm-5.4-002B/pro/obj' cc1: note: obsolete option -I- used, please use -iquote instead /usr/include/i386-linux-gnu/asm/posix_types.h:2:30: fatal error: posix_types_32.h: No such file or directory compilation terminated. cc1: note: obsolete option -I- used, please use -iquote instead cc1: note: obsolete option -I- used, please use -iquote instead /usr/include/i386-linux-gnu/asm/posix_types.h:2:30: fatal error: posix_types_32.h: No such file or directory compilation terminated. ... and goes on an on, repeating the error about posix_types_32.h. BTW: Please disregard the message: cc1: note: obsolete option -I- used, please use -iquote instead This is a known issue, and probably not related to the problem with posix_types_32.h. I get the same cc1 warnings when building with dbuild and yet in that case the build is successful. I'm doing this in a Virtual Machine, in which uname -a returns: Linux debian-med 2.6.32-5-686 #1 SMP Mon Jan 16 16:04:25 UTC 2012 i686 GNU/Linux The host of this VM, returns for uname -a: Linux macondo 2.6.32-38-generic #83-Ubuntu SMP Wed Jan 4 11:12:07 UTC 2012 x86_64 GNU/Linux Login into pbuilder, it was possible to verify that the header file is actually there, under: ls ./usr/include/i386-linux-gnu/asm/posix* -l -rw-r--r-- 1 root root 92 Feb 6 01:32 ./usr/include/i386-linux-gnu/asm/posix_types.h -rw-r--r-- 1 root root 1316 Feb 6 01:32 ./usr/include/i386-linux-gnu/asm/posix_types_32.h -rw-r--r-- 1 root root 1306 Feb 6 01:32 ./usr/include/i386-linux-gnu/asm/posix_types_64.h I'm having trouble understanding why is that the build process finds: ./usr/include/i386-linux-gnu/asm/posix_types.h but fails to find posix_types_32.h Any suggestions will be appreciated, Thanks Luis -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/cabauzprbxvinepvnkjtgcobgobf83ukuy8dvxcy8a7i4yj5...@mail.gmail.com -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120213124209.gg24...@an3as.eu
Re: Proable multiarch related problem in finding header file (Was: Problem finding posix_types_32.h when using pbuilder on the fis-gtm package)
On Tue, Feb 14, 2012 at 09:47:23AM +0100, Mathieu Malaterre wrote: Andreas, Doing a quick check on packages.d.o I can see the file your are talking about. However: http://packages.debian.org/search?suite=sidarch=anymode=pathsearchon=contentskeywords=posix_types.h returns an empty list. Are you sure your pbuilder is up to date ? Hmm good point. I can only see it on testing http://packages.debian.org/search?suite=testingarch=anymode=pathsearchon=contentskeywords=posix_types_32.h I need to check this out later. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120214091012.gd25...@an3as.eu
Any hint for help2man if programm does not accept help option
Hi, I would like to add man pages to a program which does not accept any help option but if you call it without any option it outputs the help information which would be needed to create the man page. Is there any trick to convince help2man to work on this anyway? Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120401193703.gb25...@an3as.eu
Re: Any hint for help2man if programm does not accept help option
Hi, On Mon, Apr 02, 2012 at 07:45:46AM +0200, Gergely Nagy wrote: help2man -h $program will probably do the trick. No: $ help2man -h help2man help2man: can't get `' info from help2man That happens because help2man without arguments will output to stderr. Add --no-discard-stderr, and it will just work. Or try with a program that outputs to stdout. It does do the trick. Seems the combination of both `-h ` AND `--no-discard-stderr` . $ reportbug help2man may help to make it work one day. Or you can read the full output of the command you pasted: | algernon@luthien:~$ help2man -h help2man | help2man: can't get `' info from help2man | Try `--no-discard-stderr' if option outputs to stderr I admit I would prefer if help2man would have a more simple way to specify this. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120402081302.gb7...@an3as.eu
Help writing a watch file for rnahybrid
Hi, I tried to write a watch file for rnahybrid package: version=3 http://bibiserv.techfak.uni-bielefeld.de/download/tools/rnahybrid.html RNAhybrid-(.*)-src\.tar\.gz The first question is: Why does it not find a new version at all: $ uscan --verbose -- Scanning for watchfiles in . -- Found watchfile in ./debian -- In debian/watch, processing watchfile line: http://bibiserv.techfak.uni-bielefeld.de/download/tools/rnahybrid.html RNAhybrid-(.*)-src\.tar\.gz uscan warning: In debian/watch, no matching hrefs for watch line http://bibiserv.techfak.uni-bielefeld.de/download/tools/rnahybrid.html RNAhybrid-(.*)-src\.tar\.gz -- Scan finished The second question will probably follow because I guess this web-magic-radio-button will not enable automatic download. If you don't know a reasonable solution I might need to negotiate with upstream about a more friendly download option. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120419064044.gq13...@an3as.eu
Re: Help writing a watch file for rnahybrid
Hi Paul, On Thu, Apr 19, 2012 at 02:54:42PM +0800, Paul Wise wrote: On Thu, Apr 19, 2012 at 2:40 PM, Andreas Tille wrote: The first question is: Why does it not find a new version at all: uscan relies solely on links and since there are no links to the tarballs, it cannot find any tarballs. Thanks for the explanation. you don't know a reasonable solution I might need to negotiate with upstream about a more friendly download option. Yes, please cluebat upstream. :-) OK, I'll do so. By chance I ran into another watch file problem: version=3 http://www.bioconductor.org/packages/release/bioc/html/qvalue.html \ ../src/contrib/qvalue_([\d\.]+)\.tar\.gz runs into -- Downloading updated package qvalue_1.30.0.tar.gz uscan warning: In directory ., downloading http://www.bioconductor.org/../src/contrib/qvalue_1.30.0.tar.gz failed: 400 Bad Request Upstream hides their source directory somehow and a wget http://www.bioconductor.org/packages/release/src/contrib/qvalue_1.30.0.tar.gz ends up in 404 (so even if the relative URL would be properly resolved a download might fail). So while we at least can find out the proper new version number it requires manual download. Any idea? Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120419093432.gb1...@an3as.eu
Parsing single debian/control file using python-debian
Hi,
I'm unsure whether this might be the proper mailing list to ask
questions like this - but I have no better idea.
I intend to parse some machine readable files in some team maintained
packages. When trying something like
ctrl = open('debian/control','r')
for ctrlstanza in deb822.Packages.iter_paragraphs(ctrl):
print ctrlstanza
I get the full text of debian/control (same if I try
deb822.Sources.iter_paragraphs instead) - so there is no chance to parse
the single paragraphs in the Sources and Binary packages section. I
might be stupid because I'd regard this as a basic use case for
python-debian but I did not found a way to approach this. Any hint how
to do this properly?
Kind regards and thanks for any hint
Andreas.
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Help needed to fix g++ 4.7 error [Was: Bug#667120: bowtie: ftbfs with GCC-4.7]
Hi, similarly to the plink case I can not found an easy solution for this problem. Kind regards Andreas. - Forwarded message from Matthias Klose d...@debian.org - Date: Tue, 03 Apr 2012 23:08:03 + From: Matthias Klose d...@debian.org To: mainto...@bugs.debian.org Subject: Bug#667120: bowtie: ftbfs with GCC-4.7 X-Debian-PR-Message: report 667120 X-Debian-PR-Package: bowtie X-Debian-PR-Keywords: sid wheezy X-Debian-PR-Source: bowtie Package: bowtie Version: 0.12.7-1 Severity: important Tags: sid wheezy User: debian-...@lists.debian.org Usertags: ftbfs-gcc-4.7 The package fails to build in a test rebuild on at least amd64 with gcc-4.7/g++-4.7, but succeeds to build with gcc-4.6/g++-4.6. The severity of this report may be raised before the wheezy release. alphabet.h:48:3: error: 'reverseInPlace' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] The full build log can be found at: http://people.debian.org/~lucas/logs/2012/03/29-clang-gcc47/unstable-gcc47/bowtie_0.12.7-1_unstable-gcc47.log The last lines of the build log are at the end of this report. Some hints on fixing these issues can be found at http://gcc.gnu.org/gcc-4.7/porting_to.html To build with GCC 4.7, either set CC=gcc-4.7 CXX=g++-4.7 explicitly, or install the gcc, g++, gfortran, ... packages from experimental. [...] In file included from ebwt.h:24:0, from ebwt_build.cpp:11: alphabet.h: In instantiation of 'void reverseComplementInPlace(TStr, bool) [with TStr = seqan::Stringseqan::SimpleTypeunsigned char, seqan::_Dna5, seqan::Allocvoid ]': hit.h:97:45: required from here alphabet.h:48:3: error: 'reverseInPlace' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] alphabet.h:74:20: note: 'templateclass TStr void reverseInPlace(TStr)' declared here, later in the translation unit In file included from SeqAn-1.1/seqan/sequence.h:57:0, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConstsconst seqan::Stringseqan::SimpleTypeunsigned char, seqan::_Dna, seqan::Packed ': SeqAn-1.1/seqan/sequence/string_packed.h:906:131: required from 'typename seqan::Positionconst seqan::IterTContainer, seqan::PackedTHostspec ::Type seqan::position(const seqan::IterTContainer, seqan::PackedTHostspec ) [with TContainer = const seqan::Stringseqan::SimpleTypeunsigned char, seqan::_Dna, seqan::Packed ; THostspec = seqan::Allocvoid; typename seqan::Positionconst seqan::IterTContainer, seqan::PackedTHostspec ::Type = long unsigned int]' SeqAn-1.1/seqan/sequence/string_packed.h:1237:40: required from 'typename seqan::Differenceseqan::IterTContainer, seqan::PackedTHostspec ::Type seqan::operator-(const seqan::IterTContainer, seqan::PackedTHostspec , const seqan::IterTContainer, seqan::PackedTHostspec ) [with TContainer = const seqan::Stringseqan::SimpleTypeunsigned char, seqan::_Dna, seqan::Packed ; THostspec = seqan::Allocvoid; typename seqan::Differenceseqan::IterTContainer, seqan::PackedTHostspec ::Type = long int]' SeqAn-1.1/seqan/sequence/string_base.h:181:51: required from 'typename seqan::Sizeconst seqan::StringTValue, TSpec ::Type seqan::length(const seqan::StringTValue, TSpec) [with TValue = seqan::SimpleTypeunsigned char, seqan::_Dna; TSpec = seqan::Packed; typename seqan::Sizeconst seqan::StringTValue, TSpec ::Type = long unsigned int]' blockwise_sa.h:354:32: required from here SeqAn-1.1/seqan/sequence/string_packed.h:291:2: warning: comparison between 'enum seqan::BitsPerValueseqan::SimpleTypeunsigned char, seqan::_Dna ::anonymous' and 'enum seqan::BitsPerValueunsigned int::anonymous' [-Wenum-compare] SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConstsseqan::Stringseqan::SimpleTypeunsigned char, seqan::_Dna, seqan::Packed ': SeqAn-1.1/seqan/sequence/string_packed.h:731:94: required from 'typename seqan::Sizeseqan::StringTValue, seqan::PackedTHostspec ::Type seqan::reserve(seqan::StringTValue, seqan::PackedTHostspec , _TSize, seqan::TagTUsage) [with TValue = seqan::SimpleTypeunsigned char, seqan::_Dna; TSpec = seqan::Allocvoid; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Sizeseqan::StringTValue, seqan::PackedTHostspec ::Type = long unsigned int]' ebwt.h:3891:2: required from 'static TStr EbwtTStr::join(std::vectorFileBuf*, std::vectorRefRecord, uint32_t, const RefReadInParams, uint32_t) [with TStr = seqan::Stringseqan::SimpleTypeunsigned char, seqan::_Dna, seqan::Packed ; uint32_t = unsigned int]' ebwt_build.cpp:463:9: required from 'void driver(const string, std::vectorstd::basic_stringchar , const string, bool) [with TStr = seqan::Stringseqan::SimpleTypeunsigned char, seqan::_Dna, seqan::Packed ;
Help needed [Was: Bug#667325: plink: ftbfs with GCC-4.7]
Hi, I tried to follow the hints to fix this problem but failed. Any more skilled C++ programmer than me who might have a clue? Kind regards Andreas. - Forwarded message from Matthias Klose d...@debian.org - Date: Tue, 03 Apr 2012 23:11:40 + From: Matthias Klose d...@debian.org To: mainto...@bugs.debian.org Subject: Bug#667325: plink: ftbfs with GCC-4.7 X-Debian-PR-Message: report 667325 X-Debian-PR-Package: plink X-Debian-PR-Keywords: sid wheezy X-Debian-PR-Source: plink Package: plink Version: 1.07-1 Severity: important Tags: sid wheezy User: debian-...@lists.debian.org Usertags: ftbfs-gcc-4.7 The package fails to build in a test rebuild on at least amd64 with gcc-4.7/g++-4.7, but succeeds to build with gcc-4.6/g++-4.6. The severity of this report may be raised before the wheezy release. sets.cpp:771:37: error: redeclaration of 'std::vectorIndividual*::iterator i' The full build log can be found at: http://people.debian.org/~lucas/logs/2012/03/29-clang-gcc47/unstable-gcc47/plink_1.07-1_unstable-gcc47.log The last lines of the build log are at the end of this report. Some hints on fixing these issues can be found at http://gcc.gnu.org/gcc-4.7/porting_to.html To build with GCC 4.7, either set CC=gcc-4.7 CXX=g++-4.7 explicitly, or install the gcc, g++, gfortran, ... packages from experimental. [...] sets.cpp:317:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:323:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:329:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:332:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:367:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:370:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'void Set::initialiseSetMapping()': sets.cpp:412:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:413:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'void Set::empiricalSetPValues()': sets.cpp:618:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:619:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:631:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:632:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:642:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:643:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'vector_t Set::profileTestScore()': sets.cpp:703:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:713:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:771:37: error: redeclaration of 'std::vectorIndividual*::iterator i' sets.cpp:703:12: error: 'int i' previously declared here sets.cpp: In member function 'vector_t Set::fitLDSetTest(vector_t, bool)': sets.cpp:905:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp:975:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] sets.cpp: In member function 'vector_t Set::fitStepwiseModel()': sets.cpp:1042:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] make[1]: *** [sets.o] Error 1 make[1]: Leaving directory `/??PKGBUILDDIR??' make: *** [build-stamp] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ___ 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 - -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120422194542.ga2...@an3as.eu
Help needed to fix gcc 4.7 bug in jellyfish package
Hi,
I tried to fix the problem in the jellyfish package but the general
hints given did not helped me really. Any more precise help to fix
this problem:
parse_dna.cc:97:3: error: narrowing conversion of '-3' from 'int' to 'const
uint_t {aka const long unsigned int}' inside { } is ill-formed in C++11
[-Werror=narrowing]
My first idea was to do
--- jellyfish.orig/jellyfish/parse_dna.cc
+++ jellyfish/jellyfish/parse_dna.cc
@@ -57,7 +57,7 @@
}
}
- const uint_t parse_dna::codes[256] = {
+ const int parse_dna::codes[256] = {
-3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -2, -3, -3, -3, -3, -3,
-3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3,
-3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -1, -3, -3,
--- jellyfish.orig/jellyfish/parse_dna.hpp
+++ jellyfish/jellyfish/parse_dna.hpp
@@ -55,7 +55,7 @@
static uint64_t mer_string_to_binary(const char *in, uint_t klen) {
uint64_t res = 0;
for(uint_t i = 0; i klen; i++) {
-const uint_t c = parse_dna::codes[(uint_t)*in++];
+const int c = parse_dna::codes[(int)*in++];
if(c CODE_NOT_DNA)
return 0;
res = (res 2) | c;
because it makes no sense to initialise uint with negative numbers but
this did not changed the error message which sounds totally strange to
me.
Kind regards
Andreas.
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Re: Help needed to fix gcc 4.7 bug in jellyfish package
Hi,
On Wed, May 02, 2012 at 07:32:50AM +, Sune Vuorela wrote:
On 2012-05-02, Andreas Tille andr...@an3as.eu wrote:
Hi,
I tried to fix the problem in the jellyfish package but the general
hints given did not helped me really. Any more precise help to fix
this problem:
parse_dna.cc:97:3: error: narrowing conversion of '-3' from 'int' to 'const
uint_t {aka const long unsigned int}' inside { } is ill-formed in C++11
[-Werror=narrowing]
--- jellyfish.orig/jellyfish/parse_dna.cc
+++ jellyfish/jellyfish/parse_dna.cc
@@ -57,7 +57,7 @@
It looks like you aren't the right place. It complains about line 97 and
you have edits in line 60 ?
Huh? The file has only 78 lines and the build log says the problem is
in line 77 - which is consistent with my try to fix the problem because
it concerns a field of integers which starts in line 60 and ends in line
77. No idea where this 97 came from - but the patch is done at the
right place. Any other ideas?
Kind regards
Andreas.
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Re: Help needed to fix gcc 4.7 bug in jellyfish package
Hi Guillaume,
in the Debian bug tracking system
http://bugs.debian.org/667214
a build problem when using gcc-4.7 was reported. Below you can read
some discussion about a possible fix.
Michael, I can confirm that I also tried to s/uint_t/int/ in
parse_dna.hpp with the same result (same error message) after I did my
initial posting (that's why I did not felt a real need to send another
mail).
And yes, I agree that assigning negative values to unsigned variables
smells like done with some purpose which might stay hidden from the
first look and I would have definitely asked upstream about any problem
my suggested patch might have caused. I just felt like doing some
investigation into the problem might make sense. However, it seems
that this does not lead to any progres.
Guillaume, could you enlighten us a bit about this trick?
Kind regards
Andreas.
On Thu, May 03, 2012 at 09:52:09AM +0200, Michael Wild wrote:
On 05/02/2012 08:33 AM, Andreas Tille wrote:
Hi,
I tried to fix the problem in the jellyfish package but the general
hints given did not helped me really. Any more precise help to fix
this problem:
parse_dna.cc:97:3: error: narrowing conversion of '-3' from 'int' to 'const
uint_t {aka const long unsigned int}' inside { } is ill-formed in C++11
[-Werror=narrowing]
My first idea was to do
--- jellyfish.orig/jellyfish/parse_dna.cc
+++ jellyfish/jellyfish/parse_dna.cc
@@ -57,7 +57,7 @@
}
}
- const uint_t parse_dna::codes[256] = {
+ const int parse_dna::codes[256] = {
-3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -2, -3, -3, -3, -3, -3,
-3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3,
-3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -1, -3, -3,
--- jellyfish.orig/jellyfish/parse_dna.hpp
+++ jellyfish/jellyfish/parse_dna.hpp
@@ -55,7 +55,7 @@
static uint64_t mer_string_to_binary(const char *in, uint_t klen) {
uint64_t res = 0;
for(uint_t i = 0; i klen; i++) {
-const uint_t c = parse_dna::codes[(uint_t)*in++];
+const int c = parse_dna::codes[(int)*in++];
if(c CODE_NOT_DNA)
return 0;
res = (res 2) | c;
because it makes no sense to initialise uint with negative numbers but
this did not changed the error message which sounds totally strange to
me.
Kind regards
Andreas.
You missed the declaration of parse_dna::codes in parse_dna.hpp.
diff --git a/jellyfish/parse_dna.cc b/jellyfish/parse_dna.cc
index ab3ec64..9ea5ae1 100644
--- a/jellyfish/parse_dna.cc
+++ b/jellyfish/parse_dna.cc
@@ -57,7 +57,7 @@ namespace jellyfish {
}
}
- const uint_t parse_dna::codes[256] = {
+ const int parse_dna::codes[256] = {
-3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -2, -3, -3, -3, -3, -3,
-3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3,
-3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -1, -3, -3,
diff --git a/jellyfish/parse_dna.hpp b/jellyfish/parse_dna.hpp
index 0435ae2..7ef8afd 100644
--- a/jellyfish/parse_dna.hpp
+++ b/jellyfish/parse_dna.hpp
@@ -46,7 +46,7 @@ namespace jellyfish {
* '\n': map to -2. ignore
* Other ASCII: map to -3. Skip to next line
*/
-static const uint_t codes[256];
+static const int codes[256];
static const uint_t CODE_RESET = -1;
static const uint_t CODE_IGNORE = -2;
static const uint_t CODE_COMMENT = -3;
@@ -55,7 +55,7 @@ namespace jellyfish {
static uint64_t mer_string_to_binary(const char *in, uint_t klen) {
uint64_t res = 0;
for(uint_t i = 0; i klen; i++) {
-const uint_t c = parse_dna::codes[(uint_t)*in++];
+const int c = parse_dna::codes[(uint_t)*in++];
if(c CODE_NOT_DNA)
return 0;
res = (res 2) | c;
That said, assigning -3 to an unsigned int seems to be a pretty
conscious choice to me, so it might have been done on purpose to create
a wrap-around. Also, the same pattern shows up many other places (e.g.
parse_dna::CODE_RESET, parse_dna::CODE_IGNORE, ...). IMHO bad practice,
but plausible. Probably it's best to contact upstream about this and ask
what their original intention was.
Michael
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[Help] New version of ImageJ does not build in pbuilder because of lacking DISPLAY variable
Hi, I just commited packaging stuff for the latest ImageJ version to SVN[1] but I failed in building when using pdebuild: build: [copy] Copying 1 file to /tmp/buildd/imagej-1.46o/build [copy] Copying 1 file to /tmp/buildd/imagej-1.46o/build [copy] Copying 1 file to /tmp/buildd/imagej-1.46o/build [copy] Copying 1 file to /tmp/buildd/imagej-1.46o/build [copy] Copying 1 file to /tmp/buildd/imagej-1.46o/build [copy] Copying 1 file to /tmp/buildd/imagej-1.46o/build [copy] Copying 16 files to /tmp/buildd/imagej-1.46o/build/macros [jar] Building jar: /tmp/buildd/imagej-1.46o/ij.jar run: [copy] Copying 1 file to /tmp/buildd [java] No protocol specified [java] Exception in thread main java.lang.InternalError: Can't connect to X11 window server using ':0.0' as the value of the DISPLAY variable. [java] at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method) [java] at sun.awt.X11GraphicsEnvironment.access$200(X11GraphicsEnvironment.java:62) [java] at sun.awt.X11GraphicsEnvironment$1.run(X11GraphicsEnvironment.java:178) [java] at java.security.AccessController.doPrivileged(Native Method) [java] at sun.awt.X11GraphicsEnvironment.clinit(X11GraphicsEnvironment.java:142) [java] at java.lang.Class.forName0(Native Method) [java] at java.lang.Class.forName(Class.java:186) [java] at java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment.java:82) [java] at java.awt.Window.init(Window.java:424) [java] at java.awt.Window.init(Window.java:477) [java] at java.awt.Frame.init(Frame.java:419) [java] at ij.ImageJ.init(ImageJ.java:132) [java] at ij.ImageJ.main(ImageJ.java:657) I can confirm that debuild works fine because there is a properly setup X environment. Any clue? The hint from Steve[2] did not ring a bell when I was looking at the lines of code where the problem occured. Kind regards Andreas. [1] svn://svn.debian.org/debian-med/trunk/packages/imagej/trunk/ or `debcheckout imagej` [2] http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-June/015823.html -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120604102731.ge9...@an3as.eu
Ruby help needed (Was: Bug#676114: wordnet: FTBFS: debian/wn-for-goldendict.rb:465: invalid multibyte char (US-ASCII))
Hi, Dmitry E. Oboukhov un...@debian.org has added some Ruby code to wordnet packaging (debian/wn-for-goldendict.rb) which worked for two years and at least up to Fri, 01 Jun 2012 13:45:40 +0200 when I did the last upload. Yesterday I wanted to try to fix two (unrelated) open bugs and realised the FTBFS problem and asked Dmitry for help. My guess is that this is connected to the Ruby migration and most probably simple to fix for a Ruby coder. The only way *I* could fix the problem would be droping the goldendict-wordnet binary package again which would definitely not be the best solution. Any better hint? Kind regards Andreas. On Tue, Jun 05, 2012 at 12:33:49AM +0200, Lucas Nussbaum wrote: Source: wordnet Version: 1:3.0-27 Severity: serious Tags: wheezy sid User: debian...@lists.debian.org Usertags: qa-ftbfs-20120604 qa-ftbfs User: debian-r...@lists.debian.org Usertags: default19 Justification: FTBFS on amd64 Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part: make[3]: Entering directory `/«PKGBUILDDIR»' make[3]: Leaving directory `/«PKGBUILDDIR»' make[2]: Leaving directory `/«PKGBUILDDIR»' make[1]: Leaving directory `/«PKGBUILDDIR»' touch debian/stamp-makefile-build DEB_MAKE_CHECK_TARGET unset, not running checks set -e; \ if dpkg-architecture -qDEB_BUILD_ARCH|grep -q 'mips\|arm\|s390'; then \ if test $FORCE_GOLDENDICT_BUILD -gt 0; then \ ruby debian/wn-for-goldendict.rb goldendict-wordnet.dsl; \ else \ echo Building of goldendict-wordnet dictionary was skipped; \ echo to build this package use environment variable; \ echo FORCE_GOLDENDICT_BUILD=1 ; \ touch goldendict-wordnet.dsl; \ fi; \ else \ ruby debian/wn-for-goldendict.rb goldendict-wordnet.dsl; \ fi debian/wn-for-goldendict.rb:465: invalid multibyte char (US-ASCII) debian/wn-for-goldendict.rb:465: invalid multibyte char (US-ASCII) debian/wn-for-goldendict.rb:465: syntax error, unexpected $end, expecting ')' print_array(@words, 'Syn', [c blue]•[/c]) ^ make: *** [goldendict-wordnet.dsl] Error 1 The full build log is available from: http://people.debian.org/~lucas/logs/2012/06/04/wordnet_3.0-27_unstable.log A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! About the archive rebuild: The rebuild was done on EC2 VM instances from Amazon Web Services, using a clean, minimal and up-to-date chroot. Every failed build was retried once to eliminate random failures. -- debian-science-maintainers mailing list debian-science-maintain...@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120605140851.gg10...@an3as.eu
Re: Ruby help needed (Was: Bug#676114: wordnet: FTBFS: debian/wn-for-goldendict.rb:465: invalid multibyte char (US-ASCII))
Hi Sam, On Tue, Jun 05, 2012 at 11:26:42AM -0400, Sam Ruby wrote: On 06/05/2012 10:08 AM, Andreas Tille wrote: debian/wn-for-goldendict.rb:465: invalid multibyte char (US-ASCII) debian/wn-for-goldendict.rb:465: invalid multibyte char (US-ASCII) debian/wn-for-goldendict.rb:465: syntax error, unexpected $end, expecting ')' print_array(@words, 'Syn', [c blue]•[/c]) Probable fix: add the following at the top of the file (as first line if there is no #! line, or immediately after that): # encoding: utf-8 OK, sounds quite reasonable and leads to a next (different) error: ruby debian/wn-for-goldendict.rb goldendict-wordnet.dsl; \ fi WARNING: sentidx.vrb format error: [pet%2:35:00::] debian/wn-for-goldendict.rb:300:in `initialize': undefined method `times' for \x01:String (NoMethodError) from debian/wn-for-goldendict.rb:158:in `new' from debian/wn-for-goldendict.rb:158:in `get_data' from debian/wn-for-goldendict.rb:648:in `block (2 levels) in main' from debian/wn-for-goldendict.rb:647:in `each' from debian/wn-for-goldendict.rb:647:in `block in main' from debian/wn-for-goldendict.rb:644:in `foreach' from debian/wn-for-goldendict.rb:644:in `main' make: *** [goldendict-wordnet.dsl] Error 1 Any further hint? Thanks for your quick reply anyway Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120605165338.ga24...@an3as.eu
Re: Bug#676114: Ruby help needed (Was: Bug#676114: wordnet: FTBFS: debian/wn-for-goldendict.rb:465: invalid multibyte char (US-ASCII))
Hi Steve, On Tue, Jun 05, 2012 at 06:10:55PM +0100, Steve McIntyre wrote: Any better hint? It sounds like you should replace the functionality of the script in a more suitable language, specifically: * one you (and other maintainers) understand * one that's stable and supported on all the platforms in Debian At the moment, that doesn't sound like Ruby. :-( Yes. I asked Dmitry to choose a different language when he introduced this into the packaging to create an additional binary package. However, at this time Dmitry volunteered to care for this (and up to know he did so). If this support would stop my solution would be to drop the additional binary package (and thus goldendict support) because I (as the only active maintainer out of the team) can not support this. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120605172400.gb24...@an3as.eu
Re: Bug#676114: Ruby help needed (Was: Bug#676114: wordnet: FTBFS: debian/wn-for-goldendict.rb:465: invalid multibyte char (US-ASCII))
On Tue, Jun 05, 2012 at 06:35:28PM +0100, Steve McIntyre wrote: Sounds like you made a mistake, I'm afraid. :-( My barrier to revert this mistake is low. If there is no simple solution in three days (OK, I'll be offline weekend+Monday - so there is some additional delay) - I'll kick the binary and the problem is solved. This is a general problem that might be shared usefully with a wider audience - developers should try hard to *not* write build scripts or maintainer scripts in their favourite language-of-the-week. It makes packages that much harder to maintain in general, whether within the existing team, replacement maintainers, the QA team, etc... Fully ACK. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/2012060517.ga27...@an3as.eu
Re: Ruby help needed (Was: Bug#676114: wordnet: FTBFS: debian/wn-for-goldendict.rb:465: invalid multibyte char (US-ASCII))
Hi, On Wed, Jun 06, 2012 at 10:08:24AM +0400, Dmitry E. Oboukhov wrote: I see you have already patched the script. At first thanks to thsoe people who quickly provided patches. Hoewever, I decided to follow the hint to Build-Depend on ruby 1.8 because in this case we not only know that the script works without errors but we also can quite safely assume that the result is the same as we had before. Otherwise some more intensive tests would have been needed. Sorry for my later response: I'm very busy these days: I'm trying to change my job. I will able to do something in week or two. Please don't drop packages in the time :) I just uploaded 3.0-28 which fixes all important bugs. IMHO there is no real pressure to update it before freeze (rather the contrary - I'd like to see this package migrating to testing before another upload is done). In general I would really prefer a script written in Perl or Python in other words: I fully subscribe what Steve said about favourite language-of-the-week. If this is not possible in a reasonable time frame please update it to the new default ruby version and test it carefully. Please be aware that in similar future cases I might always consider droping the goldendict package as a fallback solution. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120606075742.ge12...@an3as.eu
Re: [Help] New version of ImageJ does not build in pbuilder because of lacking DISPLAY variable
Hi Vincent, On Mon, Jun 04, 2012 at 12:37:45PM +0200, Vincent Fourmond wrote: I can confirm that debuild works fine because there is a properly setup X environment. Any clue? The hint from Steve[2] did not ring a bell when I was looking at the lines of code where the problem occured. I had similar problems that I solved using xvfb, that provides a dummy well-behaved X11 server. Just wrap the call to the build system with xvfb. Could you please name the package in question to let me have a look and make sure that I understand correctly. Hope this helps, Thanks for the hint Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120606083805.gh12...@an3as.eu
uscan ends up with 500 Can't connect host:443 (certificate verify failed)
Hi, at svn://svn.debian.org/svn/debian-med/trunk/packages/camitk/trunk I did some preparation for a package including a watch file. Unfortunately I get: $ uscan --verbose --force-download -- Scanning for watchfiles in . -- Found watchfile in ./debian -- In debian/watch, processing watchfile line: http://camitk.imag.fr/download_source.xml https://forge.imag.fr/frs/download.php/[\d]+/camitk-([\d.]+)-Source\.tar\.gz -- Found the following matching hrefs: https://forge.imag.fr/frs/download.php/238/camitk-3.0.0-Source.tar.gz Newest version on remote site is 3.0.0, local version is 3.0.0 = Package is up to date Newest version on remote site is 3.0.0, local version is 3.0.0 = Forcing download as requested -- Downloading updated package camitk-3.0.0-Source.tar.gz uscan warning: In directory ., downloading https://forge.imag.fr/frs/download.php/238/camitk-3.0.0-Source.tar.gz failed: 500 Can't connect to forge.imag.fr:443 (certificate verify failed) -- Scan finished Any idea how to successfully get the upstream source using uscan? Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120709152803.gc18...@an3as.eu
Re: Bug#681230: RFS: gtkdataboxmm/0.9.1-1 [ITP]
Hi Daniele, most certainly you know that libgtkdatabox (without mm) is maintained in the Debian Science team. I admit it is not maintained at the standards I would like to apply usually and I'm one of the a bit lazy uploaders (the other one seems to have vanished at all). I used your ITP as a reason to do something again (currently in SVN - there is some remaining issue with multiarch I need to sort out). I would volunteer to check and sponsor your package and I would be really happy if you could also have some look into libgtkdatabox to enhance maintenance. In case you are intereested in beeing sponsored by me I woudl really like if you could commit your packaging to Debian Science team maintenance (either SVN or Git at your personal preference - in case you agree to my suggestion above I'd move libgtkdatabox from SVN to Git if this is your prefered VCS). Kind regards Andreas. PS: I'll be on travel in some hours from LSM / Geneva back home - so my responsiveness is a bit reduced for the next two days. On Wed, Jul 11, 2012 at 05:15:21PM +0200, Daniele E. Domenichelli wrote: Package: sponsorship-requests Severity: wishlist Dear mentors, I am looking for a sponsor for my package gtkdataboxmm * Package name: gtkdataboxmm Version : 0.9.1-1 Upstream Author : Daniele E. Domenichelli daniele.domeniche...@iit.it * URL : https://sourceforge.net/projects/gtkdataboxmm/ * License : LGPL Section : libs It builds those binary packages: libgtkdataboxmm-0.9-0 - C++ bindings for GtkDatabox - shared library libgtkdataboxmm-dev - C++ bindings for GtkDatabox - development files libgtkdataboxmm-doc - C++ bindings for GtkDatabox - documentation and examples To access further information about this package, please visit the following URL: http://mentors.debian.net/package/gtkdataboxmm Alternatively, one can download the package with dget using this command: dget -x http://mentors.debian.net/debian/pool/main/g/gtkdataboxmm/gtkdataboxmm_0.9.1-1.dsc More information about gtkdataboxmm can be obtained from https://sourceforge.net/projects/gtkdataboxmm/ Changes since the last upload: * Initial release. (Closes: #681199) Regards, Daniele E. Domenichelli -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120711151521.16297.92646.report...@murena.aquarius.home -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120712145245.gh11...@an3as.eu
Re: Bug#681230: RFS: gtkdataboxmm/0.9.1-1 [ITP]
Hi, On Fri, Jul 13, 2012 at 11:39:02AM +0200, Daniele E. Domenichelli wrote: On 12/07/12 16:52, Andreas Tille wrote: I would volunteer to check and sponsor your package and I would be really happy if you could also have some look into libgtkdatabox to enhance maintenance. Thanks!! I'm not really expert in packaging but I can try ;) :-) In case you are intereested in beeing sponsored by me I woudl really like if you could commit your packaging to Debian Science team maintenance (either SVN or Git at your personal preference - in case you agree to my suggestion above I'd move libgtkdatabox from SVN to Git if this is your prefered VCS). I just applied to join the Debian Science project on alioth, I'll be happy to host gtkdataboxmm there (I prefer git, if that is not a problem for you) If it would be a problem for me I would not have written either SVN or Git at your personal preference. :-) Just tell me if you are accepted to Debian Science team (I'm not admin) and you have commited the packaging. Meanwhile I have uploaded libgtkdatabox and I might consider moving the current state to Git to maintain some consistency. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120714203955.gb26...@an3as.eu
Re: Bug#681230: RFS: gtkdataboxmm/0.9.1-1 [ITP]
Hi Daniele, On Mon, Jul 16, 2012 at 10:50:29AM +0200, Daniele E. Domenichelli wrote: On 14/07/12 22:39, Andreas Tille wrote: Just tell me if you are accepted to Debian Science team (I'm not admin) and you have commited the packaging. Meanwhile I have uploaded libgtkdatabox and I might consider moving the current state to Git to maintain some consistency. I was accepted in the debian-science team, and I uploaded it here: http://anonscm.debian.org/gitweb/?p=debian-science/packages/gtkdataboxmm.git I checked out this but I did not found a pristine-tar branch: $ git branch * debian master This should actually look like: $ git branch * master pristine-tar upstream and according to http://debian-science.alioth.debian.org/debian-science-policy.html#idp6771792 you can reach this by doing $ git import-orig --pristine-tar path_ro_your_orig_tar_gz Could you try to implement this to enable me building with git-buildpackage easily? BTW, as promised I moved libgtkdatabox packaging to Vcs-Git: git://anonscm.debian.org/debian-science/packages/libgtkdatabox.git Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120716141522.gm4...@an3as.eu
Help needed in gcc-4.7 - cython issue
Hi, I did run into some trouble with a fresh package which is prepared in SVN at Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/python-biom-format/trunk/ You can obtain the source via `uscan --force-download` or `make -f debian/rules get-orig-source` . The package builds nicely when leaving out cython as Build-Depends but upstream recommended strongly to use cython which results in trying to build a C++ file which unfortunately fails when using gcc-4.7. I stripped down the command line which fails to the minimum and here is the comparison between gcc-4.7 and gcc-4.6 $ gcc-4.7 -I/usr/include/python2.6 -c python-code/support-code/_sparsemat.cpp -std=c++0x python-code/support-code/_sparsemat.cpp: In function ‘void __Pyx_RaiseArgtupleInvalid(const char*, int, Py_ssize_t, Py_ssize_t, Py_ssize_t)’: python-code/support-code/_sparsemat.cpp:5164:95: error: unable to find string literal operator ‘operator PY_FORMAT_SIZE_T’ python-code/support-code/_sparsemat.cpp: In function ‘void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t)’: python-code/support-code/_sparsemat.cpp:5424:52: error: unable to find string literal operator ‘operator PY_FORMAT_SIZE_T’ python-code/support-code/_sparsemat.cpp: In function ‘void __Pyx_RaiseTooManyValuesError(Py_ssize_t)’: python-code/support-code/_sparsemat.cpp:5430:73: error: unable to find string literal operator ‘operator PY_FORMAT_SIZE_T’ $ gcc-4.6 -I/usr/include/python2.6 -c python-code/support-code/_sparsemat.cpp -std=c++0x I did some giggling and noticed that the error above occured in some threads were some solution was promised with cython 0.16. So I also tried cython from experimental and can confirm that the problem above remains identical - so cython 0.16 does not seem to be the solution. However, in some way I would like to blame cython for the problem anyway because the problematic lines do seem to be injected by the cython preprocessing (the file python-code/support-code/_sparsemat.cpp is automatically created when calling python setup.py ... unfortunately I have no idea about cython internals). In other words: The problem might be relevant also for other packages using cython in connection with gcc-4.7. Any hint how to fix this would be welcome. Kind regards Andras. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120724070230.gc14...@an3as.eu
[k...@roeckx.be: Bug#680436: sra-sdk: FTBFS: gcc/i386/atomic32.h:125:5: error: impossible constraint in 'asm']
Hi, I tagged this bug help because I admit I do not have any clue about assembler programming and atomic operations. I did also forewarded the problem upstream. Any hint would be welcome Andreas. - Forwarded message from Kurt Roeckx k...@roeckx.be - Date: Thu, 5 Jul 2012 22:34:41 +0200 From: Kurt Roeckx k...@roeckx.be To: sub...@bugs.debian.org Subject: Bug#680436: sra-sdk: FTBFS: gcc/i386/atomic32.h:125:5: error: impossible constraint in 'asm' Source: sra-sdk Version: 2.1.7a-1 Severity: important Hi, It seems your packages uses i386 assembler unconditionally. I understand this is about atomic operations. gcc includes support for atomic operations. There is also atomic support in C11 / C++11. I suggest you use one of those. Kurt - End forwarded message - -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120724185734.gd28...@an3as.eu
Help with gcc-4.7 needed (Was: poco: FTBFS with multiarch libmysqlclient-dev)
Hi, I tried to apply the patch that is supposed to solve the problem below but I was running in another problem which sounds quite familiar from other gcc-4.7 issues. I tried to fix the problem in Git git+ssh://git.debian.org/git/collab-maint/poco.git and created a branch NMU/1.3.6p1-1.1 where I created a dpatch file debian/patches/gcc-4.7.dpatch which unfortunately just reiterates the original problem and ends up in /tmp/buildd/poco-1.3.6p1/Foundation/include/Poco/String.h: In instantiation of 'S Poco::replace(const S, const typename S::value_type*, const typename S::value_type*, typename S::size_type) [with S = std::basic_stringchar; typename S::value_type = char; typename S::size_type = long unsigned int]': src/X509Certificate.cpp:175:55: required from here /tmp/buildd/poco-1.3.6p1/Foundation/include/Poco/String.h:448:2: error: 'replaceInPlace' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] /tmp/buildd/poco-1.3.6p1/Foundation/include/Poco/String.h:480:4: note: 'templateclass S S Poco::replaceInPlace(S, const S, const S, typename S::size_type)' declared here, later in the translation unit Unfortunately my C++ knowledge is to limited to find an easy clue how to fix this and would be more than happy if somebody could provide some fix. BTW, it seems to me that libpoco development only happens in experimental and unstable does not deserve the attention it would need. Please help fixing the problem to make sure the reverse depends can stay in testing. Kind regards Andreas. - Forwarded message from Andreas Tille andr...@an3as.eu - Date: Thu, 26 Jul 2012 14:23:26 +0200 From: Andreas Tille andr...@an3as.eu To: Mathieu Malaterre mathieu.malate...@gmail.com, 680...@bugs.debian.org, Krzysztof Burghardt krzysz...@burghardt.pl, 650...@bugs.debian.org Subject: Re: Bug#680798: sitplus: FTBFS: build-dependency not installable: Hi Krzysztof, there is a long standing (6 month) RC bug filed against poco including a patch for this problem. When applying the patch and trying to build the package I realised another FTBFS problem when building with gcc-4.7. I'm currently trying to fix this problem and if I succeede I will upload to DELAYED/2. Otherwise I'll ask for help on debian-mentors and will NMU-upload once the problem is solved. Kind regards Andreas. On Thu, Jul 26, 2012 at 11:52:33AM +0200, Mathieu Malaterre wrote: 'lo On Thu, Jul 26, 2012 at 11:47 AM, Andreas Tille ti...@debian.org wrote: On Thu, Jul 26, 2012 at 11:38:24AM +0200, Mathieu Malaterre wrote: I believe this is because libpoco-dev was removed from testing: http://packages.qa.debian.org/p/poco/news/20120619T163916Z.html I came to the same conclusion but I have no idea how we (in terms of sitplus maintainers) could solve this. The patch looks straighfoward to apply but for some reason was never applied. So I simply ping'd the maintainers again: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=650059#16 We'll see. -- Mathieu -- http://fam-tille.de - End forwarded message - -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120726124502.gk27...@an3as.eu
Re: Help with gcc-4.7 needed (Was: poco: FTBFS with multiarch libmysqlclient-dev)
On Thu, Jul 26, 2012 at 04:55:02PM +0200, Michael Wild wrote: Hi Andreas Reading the error message, it seems that there is a forward-declaration of replaceInPlace(...) is missing before it is used in String.h:448. It seems like simply reversing the order of declaration should fix the problem: See the attached (modified) dpatch. This was my impression as well and so I reverted the order of some somehow competing declarations (with different numbers of arguments). After my try only the line numbers of the error and the note changed (to reflect the reverse order). Than I gave up ... Any other hint? Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120726172602.gp27...@an3as.eu
Need help for watch file
Hi, the watch file for the mriconvert package[1] is obviosely not working because http://lcni.uoregon.edu/~jolinda/MRIConvert/ upstream does not mind numbering its mriconvert_sources.zip sources. However, there should be some chance to drain the current version from other files on this page. Any help would be welcome because I failed terribly trying to use some mangling options. Kind regards Andreas. [1] Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mriconvert/trunk/ -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120827154738.gf3...@an3as.eu
Re: Need help for watch file
Hi, On Tue, Aug 28, 2012 at 12:12:08AM +0800, Paul Wise wrote: Best ask them to fix that and point them at our upstream guide while you are at it: http://wiki.debian.org/UpstreamGuide Right, but I guess chances are low ... However, there should be some chance to drain the current version from other files on this page. Any help would be welcome because I failed terribly trying to use some mangling options. This would work but uscan doesn't like the file that gets downloaded: I fixed this[1] in connection with the proposed uscan changes to enable deletion of files (see bug #685787). version=3 opts=downloadurlmangle=s/MRIConvert_.*/mriconvert_sources.zip/ \ http://lcni.uoregon.edu/~jolinda/MRIConvert/MRIConvert_x86-([\d\.]+-r\d+)\.tar\.gz Hmmm, I tried this opts=dversionmangle=s/([\d.]+)\.(\d+)/$1-r$2/,downloadurlmangle=s/MRIConvert_.*/mriconvert_sources.zip/ \ http://lcni.uoregon.edu/~jolinda/MRIConvert/MRIConvert_x86-([\d\.]+-r\d+)\.tar\.gz which ends up with version 2.0-r235. I know that dversionmangle is the wrong approach and it rather should be uversionmangle=s/([\d.]+)-r(\d+)/$1.$2/ but if I try this I do not get a match on the given download page. Kind regards Andreas. [1] http://anonscm.debian.org/gitweb/?p=users/tille/devscripts.git;a=commit;h=cc44217883219e7c9bb0875f75aebc4ecec59e63 -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120828092728.ga27...@an3as.eu
Bug#681230: [ftpmas...@ftp-master.debian.org: libgtkdatabox_0.9.1.3-1_amd64.changes ACCEPTED into experimental, experimental]
Hi Daniele, it took a bit longish that ftpmaster accepted latest libgtkdatabox due to the freeze. Would you like to check gtkdataboxmm against this and are you fine with an upload to experimental? Kind regards Andreas. - Forwarded message from Debian FTP Masters ftpmas...@ftp-master.debian.org - Date: Fri, 31 Aug 2012 19:00:16 + From: Debian FTP Masters ftpmas...@ftp-master.debian.org To: Debian Science Maintainers debian-science-maintain...@lists.alioth.debian.org, Andreas Tille ti...@debian.org Subject: libgtkdatabox_0.9.1.3-1_amd64.changes ACCEPTED into experimental, experimental X-Spam_score: -2.5 Accepted: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Wed, 11 Jul 2012 15:02:19 +0200 Source: libgtkdatabox Binary: libgtkdatabox-0.9.1-3-dev libgtkdatabox-0.9.1-3 libgtkdatabox-0.9.1-3-glade libgtkdatabox-0.9.1-3-libglade Architecture: source amd64 Version: 1:0.9.1.3-1 Distribution: experimental Urgency: low Maintainer: Debian Science Maintainers debian-science-maintain...@lists.alioth.debian.org Changed-By: Andreas Tille ti...@debian.org Description: libgtkdatabox-0.9.1-3 - Gtk+ library to display large amounts of numerical data libgtkdatabox-0.9.1-3-dev - Gtk+ library to display large amounts of numerical data libgtkdatabox-0.9.1-3-glade - Gtk+ library to display large amounts of numerical data libgtkdatabox-0.9.1-3-libglade - Gtk+ library to display large amounts of numerical data Closes: 640004 Changes: libgtkdatabox (1:0.9.1.3-1) experimental; urgency=low . * Upload to experimental because of freeze * New upstream version - Refreshed remaining patches - Deleted 02_deprecated_GTK.patch which was applied upstream * Incorporated patch from Ubuntu version below Closes: #640004 * debian/README.source: removed because redundant * debian/control: - Standards-Version: 3.9.3 - Updated versioned package names - Fixed Vcs fields - Dropped Build-Depends cdbs, quilt - Do not repeat Section field in binary packages if not required by d-shlibs * debhelper 9 (control+compat) * debian/rules: - cdbs - dh - enable building twice in a row by creating a copy of original docs/reference which differs drastically from the doc created in the build process - implement some dh_install, dh_link calls directly in rules instead of helper files to reduce the number of cases where you need to change the package name due to version number changes * libgtkdatabox-0.9.1-3.lintian-overrides: Use override because the symlink check seems to be a false positive here Checksums-Sha1: fbcaf3341d3f89f0d3f7dbe301fcb7d72e2d47b1 1837 libgtkdatabox_0.9.1.3-1.dsc 02380eeb755b885856253a1a71dd3e8109c201df 453125 libgtkdatabox_0.9.1.3.orig.tar.gz 3fe660379e59a2b61b4db60a0999f9bccbf23322 9316 libgtkdatabox_0.9.1.3-1.debian.tar.gz d57de74b188ca2b5409b6d3a29f6304307a85fda 116622 libgtkdatabox-0.9.1-3-dev_0.9.1.3-1_amd64.deb 68dbc20559f47a81ae00657736c2bed07ee6275b 49324 libgtkdatabox-0.9.1-3_0.9.1.3-1_amd64.deb fb1e7700b8058dc80a20e70bc66943bc0d09f5bd 18468 libgtkdatabox-0.9.1-3-glade_0.9.1.3-1_amd64.deb 125153c0eefeb8798b95e5b28d50767010bc288b 17772 libgtkdatabox-0.9.1-3-libglade_0.9.1.3-1_amd64.deb Checksums-Sha256: 038786aeffadc3882ac8a6eb6978e3c8807445f656054b19a4e71b117be7be41 1837 libgtkdatabox_0.9.1.3-1.dsc 90ff9fc20ea1541dfe75ae04ff98e02c3aa7ad1735d8f0e3b3352910a3f7427c 453125 libgtkdatabox_0.9.1.3.orig.tar.gz 74aa92b9f3ee8a860eecc9eed2f68d77903dd78f2085d728770f2f65d48b3cd6 9316 libgtkdatabox_0.9.1.3-1.debian.tar.gz 605b370bf2aed902e98def4e981f239cb97319f6409fcb0a7cdba6c9cdbb072d 116622 libgtkdatabox-0.9.1-3-dev_0.9.1.3-1_amd64.deb ff42d19809802eb290b8b7f784c6ee98deccb173a20641fd58a8c8d021c598f6 49324 libgtkdatabox-0.9.1-3_0.9.1.3-1_amd64.deb 7d504a8b41763bff9ba3bf730e9f53066892dad05a711f2edfcfc25e05cb16c1 18468 libgtkdatabox-0.9.1-3-glade_0.9.1.3-1_amd64.deb 68ea0716aa2e3fc68cb44e5f680f6f505889c97873026b28779b110bf534f24d 17772 libgtkdatabox-0.9.1-3-libglade_0.9.1.3-1_amd64.deb Files: 801777ee0ac80123480ab56d5c95c73e 1837 libs extra libgtkdatabox_0.9.1.3-1.dsc 60a3eebd61a4ca36879d7e60d1aca727 453125 libs extra libgtkdatabox_0.9.1.3.orig.tar.gz c48ae2af63a19efd95d999b020413227 9316 libs extra libgtkdatabox_0.9.1.3-1.debian.tar.gz 173734f28b277c66631c83e43a10a22d 116622 libdevel extra libgtkdatabox-0.9.1-3-dev_0.9.1.3-1_amd64.deb a7b3636c78659b5e92483dc806bdae96 49324 libs extra libgtkdatabox-0.9.1-3_0.9.1.3-1_amd64.deb fb1f3b1a4edc7674a48d778a5b5e7853 18468 libs extra libgtkdatabox-0.9.1-3-glade_0.9.1.3-1_amd64.deb d3c281720550683ba0680119c42f3c18 17772 libs extra libgtkdatabox-0.9.1-3-libglade_0.9.1.3-1_amd64.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) iEYEARECAAYFAlAv8PwACgkQYDBbMcCf01ryLwCeKi2+FhY9qhdW+ys6JqKlOw5p 12YAn2A5BzGndbHTJr/iHezRS8uH0afy =KS3F
Need help for watch file
Hi, to enable properly downloading the volview sources I tried the following watch file: version=3 opts=\ dversionmangle=s/[~\+]dfsg//,\ downloadurlmangle=s/VolView-([\d\.]+)-Linux-x86_64.sh/VolViewSrc.tar.gz/,\ filenamemangle=s/VolView(-[\d\.]+)-Linux-x86_64.sh/VolViewSrc$1.tar.gz/ \ http://www.kitware.com/products/vvdownload.html \ http://www.kitware.com/VolView/files/VolView-([\d\.]+)-Linux-x86_64.sh $ /usr/bin/uscan --verbose --force-download -- Scanning for watchfiles in . -- Found watchfile in ./debian -- In debian/watch, processing watchfile line: opts=dversionmangle=s/[~\+]dfsg//,downloadurlmangle=s/VolView-([\d\.]+)-Linux-x86_64.sh/VolViewSrc.tar.gz/,filenamemangle=s/VolView(-[\d\.]+)-Linux-x86_64.sh/VolViewSrc$1.tar.gz/ http://www.kitware.com/products/vvdownload.html http://www.kitware.com/VolView/files/VolView-([\d\.]+)-Linux-x86_64.sh -- Found the following matching hrefs: http://www.kitware.com/VolView/files/VolView-3.4-Linux-x86_64.sh http://www.kitware.com/VolView/files/VolView-3.4-Linux-x86_64.sh http://www.kitware.com/VolView/files/VolView-3.4-Linux-x86_64.sh Newest version on remote site is 3.4, local version is 3.4+dfsg (mangled local version number 3.4) = Package is up to date Newest version on remote site is 3.4, local version is 3.4+dfsg (mangled local version number 3.4) = Forcing download as requested -- Downloading updated package http://www.kitware.com/VolView/files/VolViewSrc-3.4.tar.gz uscan warning: ../http://www.kitware.com/VolView/files/VolViewSrc-3.4.tar.gz does not appear to be a compressed file; the file command says: ERROR: cannot open `../http://www.kitware.com/VolView/files/VolViewSrc-3.4.tar.gz' (No such file or directory) Not processing this file any further! -- Scan finished If I leave out the filenamemangle option the correct file is downloaded - but it is named *.sh which is a bit stupid for a tar.gz. Any hint (besides bothering upstream ... somebody from kitware in CC - Luis it would help if you could care for a properly numbered downloadable tarball.) Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120914142133.ga14...@an3as.eu
Another watch file problem
Hi, I stumbled upon another watch file problem for package visad which is available via ftp. I considered the following watch file a good idea opts=downloadurlmangle=s?$?/visad_src.jar?,filenamemangle=s?$?/visad_src.jar? \ ftp://ftp.ssec.wisc.edu/pub/visad-([\d\.]+) but got the following warning: uscan warning: downloadurlmangle option invalid for ftp sites, so it seems there is no real chance to obtain an unversioned file from a versioned ftp directory. As always I can confirm: I know that asking upstream is most probably the better way to fix this but in this case the chances to get a quick fix are low. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120914190728.ga19...@an3as.eu
Bug#689041: RFS: orthanc/0.2.1-3 [ITP] -- Lightweight, RESTful DICOM server for healthcare and medical research
Hi Sébastien, On Sun, Sep 30, 2012 at 06:29:33PM +0200, Mathieu Malaterre wrote: Salut Sébastien, Have you thought of maintaining your package within the debian-med umbrella org ? http://www.debian.org/devel/debian-med/ Just back from vacation I read your conversation about orthanc packaging. Besides the obvious helpful technical hints I would like to come back to the initial hint from Mathieu to join the Debian Med team. You would profit from several advantages - for instance you could bypass the uploads to mentors and commit your packaging to a VCS (either Git or SVN at your choice) where potential sponsors of the team could drop changes with helpful comments directly which might make the process much more smooth. To learn about the workflow in Debian Med team you might like to read our policy document[1]. Feel free to ask if you have some remaining questions. Kind regards Andreas. [1] debian-med.alioth.debian.org/docs/policy.html -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121006214945.gd18...@an3as.eu
Bug#673087: RFS: the-powder-toy/78.1-1 [ITP] -- Physics sandbox game
Hi Aditya, not that I would specifically interested in this very package (just stumbled upon it because of the physics keyword) I think you could enhance your chances to find a sponsor if you would more closely join the pkg-games team (by for instance following the group packaging policy and commit the packaging to VCS). Kind regards Andreas. On Mon, Sep 24, 2012 at 05:24:34PM -0500, Aditya Vaidya wrote: Hello, I've updated the package with the latest upstream release and uploaded it to Debian Mentors. The DSC file is at http://mentors.debian.net/debian/pool/main/t/the-powder-toy/the-powder-toy_83.0-1.dsc So, you can run dget -x http://mentors.debian.net/debian/pool/main/t/the-powder-toy/the-powder-toy_83.0-1.dsc to download the latest release. Please review this package version instead of the one mentioned earlier. This one should be lintian and pbuilder clean (with the exception of a watch file, which can't be done here). Thanks for your consideration! Sincerely, Aditya Vaidya -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121012080014.gb12...@an3as.eu
Help needed to download source via sf.net redirector
Hi, I try to write a watch file for pcalendar which is available at http://sourceforge.net/projects/linuxorg/files/PeriodicCalendar/pcalendar-3.3/ Unfortunately neither http://sf.net/pcalendar/pcalendar-src-(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))) nor http://sf.net/PeriodicCalendar/pcalendar-src-(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))) are working - I always get 404. Any help is welcome Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121016091902.ge15...@an3as.eu
Any idea how to write watch file for codeplex hosted sources?
Hi, I have spent some time into writing a watch file for https://csb.codeplex.com/releases/ but failed and some research on mailing lists revealed some other failures. Any idea whether a clever mangling might help anyway? And yes, I will ask my sponsee to teach upstream to find more easy ways to download their sources. Thanks for any help Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121105142302.ga12...@an3as.eu
Re: Any idea how to write watch file for codeplex hosted sources?
Hi, On Mon, Nov 05, 2012 at 08:29:24PM +0600, Andrey Rahmatullin wrote: On Mon, Nov 05, 2012 at 03:23:02PM +0100, Andreas Tille wrote: I have spent some time into writing a watch file for https://csb.codeplex.com/releases/ but failed and some research on mailing lists revealed some other failures. Any idea whether a clever mangling might help anyway? No, as you can't get a direct link to sources without JavaScript at all. All you can get is a list of name-version strings with links to individual download pages, and that won't help uscan. Sorry, but that's not true. The source of the https response above contains https://csb.codeplex.com/downloads/get/466454 as direct link and it delivers the tarball in question after some seconds of delay. The line of html code that contains this link also contains the version number as link content so finally some mangling should work. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121105184011.gb12...@an3as.eu
Re: jquery.js from Doxygen in documentation, what to do about it
On Fri, Nov 23, 2012 at 12:01:05PM -0800, Russ Allbery wrote: For right now, I think the best thing for the Doxygen *clients* to do is just ignore this issue. It may need a bug against doxygen, though (and possibly some help for the Doxygen maintainer). I'm just wild-guessing that the new version of doxygen that would solve Gert's problem is in experimental because of current freeze. Wouldn't it be the most simple way to upload to unstable and in the unlikely case that there will be any RC bug in testing upload a fix to testing-proposed-updates? I guess Gert is not the only maintainer facing this problem. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121124172321.ga13...@an3as.eu
How to specify a = X Y Depends (Was: Packaging GNU Health)
Hi Emilien, On Sat, Nov 24, 2012 at 11:54:59AM +0100, Emilien Klein wrote: ... As a general question: If package A depends on a specific set of releases (like in this case Tryton 2.4.X), how do we usually handle the case where the libraries are updated before the package depending on the library? Should I depend on Tryton = 2.4 2.5? I assume that would generate conflicts once 2.6 is made available, but GNU Health still depends on an earlier version... I admit a quick search has not uncovered the answer how to express this Tryton = 2.4 2.5 relation correctly. So I ask on debian-mentors list for help. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121126071837.ga11...@an3as.eu
Bug#694632: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
Hi Erik, it seems I missed your ITP - otherwise I would have most probably pinged you whether you intent to do the packaging inside the Debian Med team. We try to inject medical and microbiological software into Debian and your ITP seems to fit perfectly into our biology task[1]. So I would suggest you join the Debian Med team (I checked whether you just have an account on alioth.debian.org but failed in searching for your name - otherwise I would have added you to the team right now). All steps are described in our team policy[2]. Meanwhile I might check your packaging you provided at mentors however, I would strongly recommend (you might need require) that you choose at your preference either our SVN or Git repository (see [2]) for your packaging work to enable effective team maintenance. For instance I would turn your citation of the scientific paper into a debian/upstream reference which is way more flexible than simply putting it into the long description (which is deprecated). I hope you like this idea and we would be very happy to welcome you in our team. Kind regards Andreas. [1] http://debian-med.alioth.debian.org/tasks/bio [2] http://debian-med.alioth.debian.org/docs/policy.html Package: wnpp Severity: wishlist Owner: Erik Sjölund erik.sjol...@gmail.com * Package name : prime-phylo Version : 1.0.3 Upstream Author : Lars Arvestada...@csc.kth.se, Bengt Sennbladbengt.sennb...@ki.se and others * URL : http://prime.sbc.su.se * License : GPL-3 Programming Lang: C++ Description: Bayesian estimation of gene trees taking the species tree into account PrIME (Probabilistic Integrated Models of Evolution) is a package supporting inference of evolutionary parameters in a Bayesian framework using MCMC. A distinguishing feature of PrIME is that the species tree is taken into account when analyzing gene trees. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121129083145.gd4...@an3as.eu
Bug#694632: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
Hi Erik, could you please confirm that you are interested in finding a sponsor for your work? As I said the Debian Med team is really interested. In case you have some time constraints or whatever I'd volunteer to commit your work to our Vcs (please specify whether you prefer Git or SVN) and will check whether it is ready for upload. Kind regards and thanks so far for your work Andreas. On Thu, Nov 29, 2012 at 09:31:45AM +0100, Andreas Tille wrote: Hi Erik, it seems I missed your ITP - otherwise I would have most probably pinged you whether you intent to do the packaging inside the Debian Med team. We try to inject medical and microbiological software into Debian and your ITP seems to fit perfectly into our biology task[1]. So I would suggest you join the Debian Med team (I checked whether you just have an account on alioth.debian.org but failed in searching for your name - otherwise I would have added you to the team right now). All steps are described in our team policy[2]. Meanwhile I might check your packaging you provided at mentors however, I would strongly recommend (you might need require) that you choose at your preference either our SVN or Git repository (see [2]) for your packaging work to enable effective team maintenance. For instance I would turn your citation of the scientific paper into a debian/upstream reference which is way more flexible than simply putting it into the long description (which is deprecated). I hope you like this idea and we would be very happy to welcome you in our team. Kind regards Andreas. [1] http://debian-med.alioth.debian.org/tasks/bio [2] http://debian-med.alioth.debian.org/docs/policy.html Package: wnpp Severity: wishlist Owner: Erik Sjölund erik.sjol...@gmail.com * Package name : prime-phylo Version : 1.0.3 Upstream Author : Lars Arvestada...@csc.kth.se, Bengt Sennbladbengt.sennb...@ki.se and others * URL : http://prime.sbc.su.se * License : GPL-3 Programming Lang: C++ Description: Bayesian estimation of gene trees taking the species tree into account PrIME (Probabilistic Integrated Models of Evolution) is a package supporting inference of evolutionary parameters in a Bayesian framework using MCMC. A distinguishing feature of PrIME is that the species tree is taken into account when analyzing gene trees. -- 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/20121129083145.gd4...@an3as.eu -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121206151629.ga31...@an3as.eu
Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
Hi Erik, On Tue, Dec 11, 2012 at 03:37:28PM +0100, Erik Sjölund wrote: Hi Andreas, I've now created the account eriksjolund-guest at alioth.debian.org Fine I've just added you to the Debian Med team. I would prefer to use git for the repository. OK. If I understand you correctly, the next step will be that you now upload the debian packaging sub directory from prime-phylo into the Vcs? If you have any suggestions regarding the packaging you are most welcome to perform changes in the packaging code. I'd prefer if you would try to follow http://debian-med.alioth.debian.org/docs/policy.html to create the Git repository yourself and once you did so I would have a look. For sure I could do this as well but I'd regard this as a reasonable exercise for you to become comfortable with the Debian Med team work. For sure you will get all our support if something might not work as smooth as expected. For the very beginning to test you ssh login make sure you read the ssh tips paragraph specifically the link to the Debian wiki in the end of the paragraph. Just let us know in case of any trouble. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121211220816.ga20...@an3as.eu
Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
Hi Erik, thanks for your work on prime-phylo. On Mon, Dec 17, 2012 at 11:06:28AM +0100, Erik Sjölund wrote: I have now created: http://anonscm.debian.org/gitweb/?p=debian-med/prime-phylo.git Looks good so far with one exception I've found: Please check the copyright by using $ cme fix dpkg-copyright Fixing from Dpkg::Copyright... Configuration item 'Files:src/cxx/libraries/prime/beep2blas.hh License short_name' has a wrong value: value 'Software License for MTL' does not match grammar: ... The syntax is not really DEP5 conformant. I would have changed this simply to License: MTL but when I checked the License paragraph I detected some additional copyright statements which is somehow confusing. Does this mean the license is also copyrighted and has some authors? Could you please clarify this a bit? Besides this I'd regard the package ready for upload and I'd go for this once debian/copyright is passing cme. In the debian sub directory I also created the file upstream where I provided information about the scientific paper Simultaneous Bayesian gene tree reconstruction and reconciliation analysis I used utf-8 encoding to be able to write the name Åkerborg, Ö. Maybe utf-8 is not allowed for debian/upstream? debian/upstream file should be UTF-8 - so all is fine here. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121217110106.gb3...@an3as.eu
Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
Hi Erik, On Mon, Dec 17, 2012 at 02:37:30PM +0100, Erik Sjölund wrote: I followed your suggestion and changed the license short name to MTL. OK. Regarding the file src/cxx/libraries/prime/beep2blas.hh when I started packaging Prime I tried to investigate where the file content came from. In the file the following text could be read: /* Basic Linear Algebra Subprograms for C/C++ Version 1.0 Matthew E. Gaston May 6, 1998 --*/ I searched google for that text and saw that the file had its origin from the file $ wget --quiet http://osl.iu.edu/download/research/mtl/mtl-2.1.2-22.tar.gz $ tar tvfz mtl-2.1.2-22.tar.gz | grep mtl/blas_interface.h -rw-r--r-- pgottsch/research 3534 2005-07-05 17:11 mtl-2.1.2-22/mtl/blas_interface.h I added the license text from the file $ tar tvfz mtl-2.1.2-22.tar.gz | grep -i license -rw-r--r-- pgottsch/research 3096 2005-06-02 19:01 mtl-2.1.2-22/license.mtl.txt to the files debian/copyright src/cxx/libraries/prime/beep2blas.hh Maybe I shouldn't have copied the license text? Copying the license text is correct. However, your debian/copyright says: Files: src/cxx/libraries/prime/beep2blas.hh Copyright: 2002 - 2007 The Maxtrix Template Library authors 2007 - 2012 Bengt Sennbladbengt.sennb...@ki.se License: MTL ... License: MTL Copyright (c) 2001-2005 The Trustees of Indiana University. All rights reserved. Copyright (c) 1998-2001 University of Notre Dame. All rights reserved. Authors: Andrew Lumsdaine, Jeremy G. Siek, Lie-Quan Lee . This file is part of the Matrix Template Library . According to DEP5 the Copyright field should be attached to the Files and here you give some additional and even conflicting information as free text in the license paragraph. The relation between The Maxtrix Template Library authors and Bengt Sennbladbengt.sennb...@ki.se and The Trustees of Indiana Universityand University of Notre Dame as well as Andrew Lumsdaine, Jeremy G. Siek, Lie-Quan Lee remains unclear. My reading of the copyright would be: Files: src/cxx/libraries/prime/beep2blas.hh Copyright: 2001-2005 The Trustees of Indiana University. All rights reserved. 1998-2001 University of Notre Dame. All rights reserved Andrew Lumsdaine, Jeremy G. Siek, Lie-Quan Lee 2007-2012 Bengt Sennblad bengt.sennb...@ki.se License: MTL which specifies former authors and the later changes done by Bengt Sennblad. The specification of the License: MTL paragraph should come without the extra Copyright information in the beginning - all else is fine. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121217140154.gd3...@an3as.eu
Bug#694632: Bug#684039: Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
On Mon, Dec 17, 2012 at 05:24:00PM +0100, Erik Sjölund wrote: I made a new upstream release http://prime.sbc.su.se/download/prime-phylo-1.0.11.tar.gz where I added the extra copyright statement // Copyright: Modifications to the original file by Bengt Sennblad bengt.sennb...@ki.se 2007-2012 to the file src/cxx/libraries/prime/beep2blas.hh I also modified the debian git http://anonscm.debian.org/gitweb/?p=debian-med/prime-phylo.git;a=commitdiff;h=9785baea0e5efe3f80f1970183e3ec109bb40e51 as you suggested. OK. How do I upload the new source code release into git.debian.org? Maybe I will figure it out by myself ... http://debian-med.alioth.debian.org/docs/policy.html Seek for pristine-tar. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121217162608.gf3...@an3as.eu
Bug#694632: Bug#684039: Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
Hi Erik, On Tue, Dec 18, 2012 at 10:06:15AM +0100, Erik Sjölund wrote: I think the documentation http://debian-med.alioth.debian.org/docs/policy.html was not so clear about how to handle a new upstream release. Anyway when I also found http://wiki.debian.org/Games/VCS/git#Adding_a_new_upstream_release I came to the conclusion that I needed to run git import-orig --pristine-tar again. Yes, in dead. We would be happy about any patch to the Debian Med policy that might5 make this more clear. Sometimes it is hard to describe things which are clear to the people who are comfortable with the procedure to describe it for newcomers - so any hint is welcome. ... erik@linux:~/prime-phylo$ git push --tags Enter passphrase for key '/home/erik/.ssh/id_rsa': Counting objects: 1, done. Writing objects: 100% (1/1), 184 bytes, done. Total 1 (delta 0), reused 0 (delta 0) This worked for me. So the package is in principle ready for uploading with the one minor exception that the ITP bug is closed in some previous version and not the latest to be uploaded one. If you ask me I would simply strip the changelog to prime-phylo (1.0.11-1) unstable; urgency=low * Initial release (Closes: #684039) -- Erik Sjolund erik.sjol...@gmail.com Mon, 17 Dec 2012 14:11:13 +0100 by simply droping the detailed pre-Debian upload history which is not relevant for the *debian/*changelog. Usually ftpmasters are a bit disturbed about longish and for them uninteresting history and finally we do have the data inside Git repository anyway. In case you insist in keeping the longish changelog (which would be fine for me if you might have your personal preference) I would move the Closes statement just up to the latest changelog entry. However, in this case we should change the target distribution from unstable to UNRELEASED to make pretty clear that these versions never have hit the Debian mirrors. Please either change it in the way of your choice or tell me what you prefer and I'll do the change and upload. Thanks for preparing the package Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121218133053.ga19...@an3as.eu
Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
Hi Erik On Tue, Dec 18, 2012 at 04:18:26PM +0100, Erik Sjölund wrote: On Tue, Dec 18, 2012 at 2:30 PM, Andreas Tille andr...@an3as.eu wrote: Sometimes it is hard to describe things which are clear to the people who are comfortable with the procedure to describe it for newcomers - so any hint is welcome. I understand. I'll think about it... This would be great. prime-phylo (1.0.11-1) unstable; urgency=low * Initial release (Closes: #684039) -- Erik Sjolund erik.sjol...@gmail.com Mon, 17 Dec 2012 14:11:13 +0100 I followed your suggestion (i.e. stripping the changelog). Thanks and uploaded. BTW, in the Debian Med team we did not formalised the sponsering process via filing RFS bugs (for no specific reason - it just worked without this.) I'm just not comfortable with the procedure and do not know where and when to close this RFS bug. If it should have been done in the changelog as well I just missed this. If its done by the sponsee please do so - if the sponsor is expected to close it just tell me to do so. Kind regards and thanks for your work on the package Andreas. PS: Please let us know whether you are subscribed to the list - I would stop CCing you in this case (and you can definitely remove me from CCs and rather use list-reply.) -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121218155314.ge19...@an3as.eu
Re: Status of SIGAR (Was: InVesalius packaging)
On Mon, Mar 29, 2010 at 10:11:09AM -0300, Tatiana Al-Chueyr wrote: Until now, we haven't had advances on SIGAR packaging [1]. How should we proceed? I had a (quick) look at Thiagos packaging[2] and while the package builds somehow there are several lintian warnings. If you try lintian -i *.dsc *.deb you get explanations and several of these are relatively easy to fix. An absolute no go is the missing copyright information which definitely needs fixing. Please try to work down the list of lintian problems and feel free to ask for any help if something remains unclear. BTW, it might make sense to join a packaging team on alioth (python-modules-team ??) and use their SVN for the packaging stuff. This enables potential helpers for packaging to commit changes easily. Hope this helps for the moment Andreas. [1] http://lists.debian.org/debian-mentors/2010/03/msg00324.html [2] http://dl.dropbox.com/u/817671/packages/sigar_1.7.0%7Esvn5287-1.dsc -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100329134010.ga2...@an3as.eu
Re: Status of SIGAR (Was: InVesalius packaging)
On Mon, Mar 29, 2010 at 03:46:20PM -0300, Thiago Franco Moraes wrote: I fixed some of lintian problems. One of the problems that remains is: W: libsigar: package-installs-python-pyc usr/lib/python2.6/dist-packages/sigar.pyc N: N:Compiled python source files should not be included in the package. N:These files should be removed from the package and created at package N:installation time in the postinst. N: N:Severity: normal, Certainty: certain How can I only compile in installation time? I'm using this command in rule file to install the files: cd $(CURDIR)/bindings/python python setup.py install --install-layout=deb --root=$(CURDIR)/debian/$(PACKAGE) I have limited experience with python packages but the principle is that the *.pyc files will be created at package install time in the postinst script. This is done by python-support and is described in the Debian Python Policy[1]. Perhaps you might have a look into this document and if something remains unclear, it is a good idea to ask on debian-mentors. Kind regards Andreas. [1] http://www.debian.org/doc/packaging-manuals/python-policy/ -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100329193611.gb16...@an3as.eu
Help with autoconf / libtool
Hi, I would like to seek some help with libtool / autoconf for a small package I would like to put into Debian Med. Upstream has written a small library to interact with the German Gesundheitskarte and I tried to provide the libtool stuff to enable architecture independent building of static and dynamic library. Obviosely my knowledge in this field is limited as well because after an ABI change I tried to increase the soversion but failed - it just stays at 0.0.0 whatever I try. I have uploaded my try to http://people.debian.org/~tille/packages/ctapi-mkt/ and perhaps some kind soul might have a look at this package. I guess neither upstream nor me would care if libtool is replaced by some other build system - it just should work. Feel free to ask me for any further information which helps tracking down the problem. The task is to fix the (not yet released) upstream tarball to get an increased soversion on the resulting dynamic library. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100707165539.ga21...@an3as.eu
Re: Help with autoconf / libtool
On Thu, Jul 08, 2010 at 10:16:35AM +0200, Sebastian Harl wrote: and @GENERIC_LIBRARY_VERSION@ is not a standard name, but rather something the other projects that use it have defined in their configure.ac (and I'd hardcode it in the Makefile.am). Yep. In this case, that's already defined in configure.ac, though. I can confirm that the solution works and upstream is happy. Thanks for your help Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100709073813.gh2...@an3as.eu
Help for watch file
Hi, I wonder how I might get a watch file for code.google.com working. For FreeDiams I tried version=3 http://code.google.com/p/freemedforms/downloads/list \ http://freemedforms.googlecode.com/files/freediams_([.\d]+).*\.tar\.gz but uscan does not find any matching entry - probably because all this JavaScript which is now injected in this page. Some time ago the watch file worked this way. Any idea? Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100709075820.ga5...@an3as.eu
Re: Help for watch file
On Fri, Jul 09, 2010 at 06:10:16PM +1000, Aníbal Monsalve Salazar wrote: I just did it for irqbalance. cat debian/watch version=3 http://code.google.com/p/irqbalance/downloads/list \ .*irqbalance-([\d\.]+).tbz2.* According to this example this works ersion=3 http://code.google.com/p/freemedforms/downloads/list \ .*freediams_([.\d]+).*\.tar\.gz.* for *detecting* that there is actually a new version, but it does not download from the server. Is this possibly connected to the problem that upstream names his tarball just orig.tar.gz (I told him not to do this - but this might take just some more releases ;-))? Newest version on remote site is 0.4.2., local version is 0.4.0 = detail already in package directory -- Scan finished Thanks for your help anyway Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100709083644.ga6...@an3as.eu
Re: Help for watch file
On Fri, Jul 09, 2010 at 04:13:55PM +0800, Paul Wise wrote: You'll need a downloadurlmangle too: version=3 opts=downloadurlmangle=s_^.*name=([^]*).*_http://freemedforms.googlecode.com/files/$1_ \ http://code.google.com/p/freemedforms/downloads/list \ .*name=freediams_([\d\.]+)\.orig\.tar\.gz.* $ uscan --verbose --verbose -- Scanning for watchfiles in . -- Found watchfile in ./debian -- In debian/watch, processing watchfile line: opts=downloadurlmangle=s_^.*name=([^]*).*_http://freemedforms.googlecode.com/files/$1_ http://code.google.com/p/freemedforms/downloads/list .*name=freediams_([\d\.]+)\.orig\.tar\.gz.* -- Found the following matching hrefs: detail?name=freediams_0.4.2.orig.tar.gzamp;can=2amp;q= detail?name=freediams_0.4.2.orig.tar.gzamp;can=2amp;q= detail?name=freediams_0.4.2.orig.tar.gzamp;can=2amp;q= detail?name=freediams_0.4.2.orig.tar.gzamp;can=2amp;q= detail?name=freediams_0.4.2.orig.tar.gzamp;can=2amp;q= detail?name=freediams_0.3.0.orig.tar.gzamp;can=2amp;q= detail?name=freediams_0.3.0.orig.tar.gzamp;can=2amp;q= detail?name=freediams_0.3.0.orig.tar.gzamp;can=2amp;q= detail?name=freediams_0.3.0.orig.tar.gzamp;can=2amp;q= detail?name=freediams_0.3.0.orig.tar.gzamp;can=2amp;q= detail?name=freediams_0.1.4.orig.tar.gzamp;can=2amp;q= detail?name=freediams_0.1.4.orig.tar.gzamp;can=2amp;q= detail?name=freediams_0.1.4.orig.tar.gzamp;can=2amp;q= detail?name=freediams_0.1.4.orig.tar.gzamp;can=2amp;q= detail?name=freediams_0.1.4.orig.tar.gzamp;can=2amp;q= detail?name=freediams_0.1.2.orig.tar.gzamp;can=2amp;q= detail?name=freediams_0.1.2.orig.tar.gzamp;can=2amp;q= detail?name=freediams_0.1.2.orig.tar.gzamp;can=2amp;q= detail?name=freediams_0.1.2.orig.tar.gzamp;can=2amp;q= detail?name=freediams_0.1.2.orig.tar.gzamp;can=2amp;q= Newest version on remote site is 0.4.2, local version is 0.4.0 = detail already in package directory -- Scan finished Unfortunately no downloads are happening (but see my last mail because of the orig.tar.gz naming issue). Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100709084037.gb6...@an3as.eu
Re: Help for watch file
On Fri, Jul 09, 2010 at 05:28:57PM +0200, Christian Kastner wrote: version=3 opts=\ downloadurlmangle=s|.*[?]name=(.*?).*|http://freemedforms.googlecode.com/files/$1|,\ filenamemangle=s|[^/]+[?]name=(.*?).*|$1| \ http://code.google.com/p/freemedforms/downloads/detail[?]name=freediams_([0-9.]+).orig.tar.gz.* Works. Thanks ANdreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100710161550.ge8...@an3as.eu
Re: Help for watch file
On Wed, Jul 14, 2010 at 09:53:20AM +0800, Paul Wise wrote: 16 packages use it, there should be none. May I ask why ? It should be pretty obvious: less work for Debian and others: less work for ... ... But more work for package maintainers because these redirectors are quite useful to keep your watch file simple (and thus less error prone). For me the reasoning to not have a googlecode redirector while having sf and githup redirector does not sound logical except if your include all redirectors in general into this. Probably the best way to deal with that is to add code to uscan to do add the right opts rather than creating redirect sites. It looks like even sf.net could now be automatically scanned with the right downloadurlmangle and filenamemangle options. This would be cool because it would make my more work for package maintainers argument moot by solving your arguments as well. Kind regards and thanks for the clarification Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100714065338.ga4...@an3as.eu
Re: Help for watch file
On Wed, Jul 14, 2010 at 09:31:26AM +0200, David Paleino wrote: If Google changes again, I find it better to change code in one place than in tons of debian/watch files. Well, 16 (+1 in NEW queue now ;-)) are not really tons. IMHO the main advantage of redirectors in general (or equivalently a better uscan) is that you can fix a change at the target site without any new package upload. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100714074336.ga7...@an3as.eu
Re: Help me find a project to join!
Hi Henrik, thanks for your interest in Debian and your attempt to help. In addition to the other responses I might have some hint for you. Your introduction sounded like you are interested in sciences and so the Debian Science Blend might be an interesting home for you. You might like to lurk on the Debian Science mailing list[1] and perhaps you might like to have a look into the packages which are maintained in Debian Science which are listed at the so called tasks pages[2]. Once you know what packages belong to what task and to find a target to work on there are also bugs pages which are listing all the bugs that are reported against packages maintained by Debian Science. Feel free to keep on asking on the list if something remains unclear. Kind regards Andreas. [1] http://lists.debian.org/debian-science [2] http://blends.alioth.debian.org/science/tasks [3] http://blends.alioth.debian.org/science/bugs -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100721073501.gb22...@an3as.eu
Re: RFS: bambam
On Tue, Aug 03, 2010 at 12:13:55PM -0400, Paul Wise wrote: On Tue, Aug 3, 2010 at 11:50 AM, Taylor LeMasurier-Wren I am looking for a sponsor for my package bambam. ... Section : games You might want to join the Debian Games Team, we would appreciate more members, especially if they want to work on multiple existing games as well as introducing new games. You might also be interested in the Debian Junior project[1] which is unfortunately dead / orphaned, but perhaps somebody will care for it. I'd love to support it from the BLends techniques site (which is actually not that much of a deal). Kind regards Andreas. [1] http://blends.alioth.debian.org/junior/tasks/index -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100803214611.ga2...@an3as.eu
What is the role of system user bin?
Hi, the Debian Med team tries to support the pacakging of a hostpital management system which is based on the Mumps implementation GT.M. The actual maintainer wants to use the system user bin as owner of the installed files[1]. I personally have no idea for what purpose this system user was invented but I doubt that using it as file owner of random application files is the purpose. To make sure I can give correct advise I would like to know what the purpose of this system user ID finally is. Kind regards Andreas. [1] http://lists.debian.org/debian-med/2010/08/msg00077.html -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100830065034.ga26...@an3as.eu
Re: RFS: rss2email (updated package)
On Mon, Dec 06, 2010 at 06:30:50PM +0100, Etienne Millon wrote: Have you contacted the MIA team[1]? No, I didn't, as I pinged him only four days ago. I don't know if it's enough ? There is no real limit for enough but the fact that Vcs vanished does IMHO give a sign that you probably can wait longer for the response. instead of simply deleting the dead links. This enables more transparency in packaging and useful group maintenance (in case the original maintainer might come back somehow). I actually used git to prepare this package. It's available on github : https://github.com/emillon/rss2email but I can push it on alioth and set Vcs-git to that if it helps. I don't know if it helps but IMHO alioth is a reasonable place (I do not mind whether Git or SVN is used). BTW, I tried rss2email and just get links in the content of the mails? Is this a configuration issue or just a (mis)feature of the RS feeding site? Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20101206203436.gb14...@an3as.eu
Re: RFS: gummi - GTK+ based LaTeX editor with auto refreshing preview pane
On Thu, Dec 09, 2010 at 09:24:35AM +0100, Daniel Stender wrote: Sure, it's: http://mentors.debian.net/debian/pool/main/g/gummi/ Missing Build-Depends: intltool Two lintian warnings which should be fixed. Thanks for your work on this Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20101209123231.gb28...@an3as.eu
