Bug#815174: staden: Missing links in /usr/bin
Package: staden Version: 2.0.0+b10-1.1 Severity: grave Justification: renders package unusable Dear Maintainer, I tried to convert *.ab1 files to *.exp files with pregap4, which failed with an error message that eba could not be found. I copied an eba from the sourceforge download bay into /usr/bin and retried conversion of the ABI chromatograms. The error message concerning eba was gone, instead conversion failed because of a missing init_exp command. Thereafter I had a closer look into /usr/bin and realized that the staden parts were links to /usr/lib/staden/bin, but of the multiple files in the sourceforge package, only pregap, gap4, gap5, trev and spin had such a link. I thus, created the missing links by hand and conversion worked out. The files could be opened and assembled with gap4. Working furtheron with the files, however, is still hampered by another problem, which I suspect to be of a different kind, thus will be subject to a separate bug report. Kerstin -- System Information: Debian Release: 8.3 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable') Architecture: i386 (i686) Kernel: Linux 3.2.0-4-686-pae (SMP w/2 CPU cores) Locale: LANG=de_DE.utf8, LC_CTYPE=de_DE.utf8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages staden depends on: ii libc62.19-18+deb8u3 ii libcurl3 7.38.0-4+deb8u3 ii libfontconfig1 2.11.0-6.3 ii libfreetype6 2.5.2-3+deb8u1 ii libgcc1 1:4.9.2-10 ii liblzma5 5.1.1alpha+20120614-2+b3 ii libpng12-0 1.2.50-2+deb8u2 ii libstaden-read1 1.13.7-1 ii libstdc++6 4.9.2-10 ii libtcl8.68.6.2+dfsg-2 ii libtk8.6 8.6.2-1 ii libx11-6 2:1.6.2-3 ii libxext6 2:1.3.3-1 ii libxft2 2.3.2-1 ii libxss1 1:1.2.2-1 ii staden-common2.0.0+b10-1.1 ii staden-io-lib-utils 1.13.7-1 ii tklib0.6-1 ii zlib1g 1:1.2.8.dfsg-2+b1 staden recommends no packages. Versions of packages staden suggests: pn staden-doc -- no debconf information
Bug#815176: staden: Gap4 contig editor does not show sequences
Package: staden Version: 2.0.0+b10-1.1 Severity: grave Justification: renders package unusable Dear Maintainer, I loaded pregap-converted *.exp sequences into gap4 to do an assembly. The assembly worked out, but I cannot open the contig editor for proofreading. More correctly described: It actually opens, but only the upper window bar is visible, neither sequences nor trace files are displayed. Since no information on this problem shows up in the log files of gap4, I have got no idea concerning the nature of the problem. Perhaps something connected to the graphical surface? Before upgrading to jessie, I had staden from the sourceforge site installed and it worked, but under jessie I have got the problem with both, the debian and with the sourceforge package. Kerstin -- System Information: Debian Release: 8.3 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable') Architecture: i386 (i686) Kernel: Linux 3.2.0-4-686-pae (SMP w/2 CPU cores) Locale: LANG=de_DE.utf8, LC_CTYPE=de_DE.utf8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages staden depends on: ii libc62.19-18+deb8u3 ii libcurl3 7.38.0-4+deb8u3 ii libfontconfig1 2.11.0-6.3 ii libfreetype6 2.5.2-3+deb8u1 ii libgcc1 1:4.9.2-10 ii liblzma5 5.1.1alpha+20120614-2+b3 ii libpng12-0 1.2.50-2+deb8u2 ii libstaden-read1 1.13.7-1 ii libstdc++6 4.9.2-10 ii libtcl8.68.6.2+dfsg-2 ii libtk8.6 8.6.2-1 ii libx11-6 2:1.6.2-3 ii libxext6 2:1.3.3-1 ii libxft2 2.3.2-1 ii libxss1 1:1.2.2-1 ii staden-common2.0.0+b10-1.1 ii staden-io-lib-utils 1.13.7-1 ii tklib0.6-1 ii zlib1g 1:1.2.8.dfsg-2+b1 staden recommends no packages. Versions of packages staden suggests: pn staden-doc -- no debconf information
Bug#815176: staden: Gap4 contig editor does not show sequences
Hi Andreas, Am 20.02.2016 um 08:33 schrieb Andreas Tille: > Hi Kerstin, > > thanks agein for your bug report. I agree that this problem might be a > bit more tricky than the other bug. I have a slight suspicion that this > user oriented issue might be connected to a later Tcl/Tk version than > you might have used before. I checked it on my computer at home, which is a 64-bit machine: same problem. Best wishes, Kerstin > > On Fri, Feb 19, 2016 at 06:56:36PM +0100, Kerstin Hoef-Emden wrote: >> Package: staden >> Version: 2.0.0+b10-1.1 >> Severity: grave >> Justification: renders package unusable >> >> Dear Maintainer, >> >> >> I loaded pregap-converted *.exp sequences into gap4 to do an assembly. The >> assembly worked out, but I cannot open the contig editor for proofreading. >> More correctly described: It actually opens, but only the upper window bar >> is visible, neither sequences nor trace files are displayed. Since no >> information on this problem shows up in the log files of gap4, I have got no >> idea concerning the nature of the problem. Perhaps something connected to >> the graphical surface? >> >> Before upgrading to jessie, I had staden from the sourceforge site installed >> and it worked, but under jessie I have got the problem with both, the debian >> and with the sourceforge package. >> >> Kerstin >> >> >> >> -- System Information: >> Debian Release: 8.3 >> APT prefers stable-updates >> APT policy: (500, 'stable-updates'), (500, 'stable') >> Architecture: i386 (i686) >> >> Kernel: Linux 3.2.0-4-686-pae (SMP w/2 CPU cores) >> Locale: LANG=de_DE.utf8, LC_CTYPE=de_DE.utf8 (charmap=UTF-8) >> Shell: /bin/sh linked to /bin/dash >> Init: systemd (via /run/systemd/system) >> >> Versions of packages staden depends on: >> ii libc62.19-18+deb8u3 >> ii libcurl3 7.38.0-4+deb8u3 >> ii libfontconfig1 2.11.0-6.3 >> ii libfreetype6 2.5.2-3+deb8u1 >> ii libgcc1 1:4.9.2-10 >> ii liblzma5 5.1.1alpha+20120614-2+b3 >> ii libpng12-0 1.2.50-2+deb8u2 >> ii libstaden-read1 1.13.7-1 >> ii libstdc++6 4.9.2-10 >> ii libtcl8.68.6.2+dfsg-2 >> ii libtk8.6 8.6.2-1 >> ii libx11-6 2:1.6.2-3 >> ii libxext6 2:1.3.3-1 >> ii libxft2 2.3.2-1 >> ii libxss1 1:1.2.2-1 >> ii staden-common2.0.0+b10-1.1 >> ii staden-io-lib-utils 1.13.7-1 >> ii tklib0.6-1 >> ii zlib1g 1:1.2.8.dfsg-2+b1 >> >> staden recommends no packages. >> >> Versions of packages staden suggests: >> pn staden-doc >> >> -- no debconf information >> >> ___ >> Debian-med-packaging mailing list >> debian-med-packag...@lists.alioth.debian.org >> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging >> > signature.asc Description: OpenPGP digital signature
Bug#815176: staden: Gap4 contig editor does not show sequences
Hi to all, at what time intervals syncing takes place? I just tried pregap for the fix of the missing links and it did not yet work. I tested uncommenting the line in the tcl-script of the contig editor with a version downloaded from sourceforge and installed with stow and the fix worked (I use xfce4). Best wishes, Kerstin On Mon, 22 Feb 2016, Andreas Tille wrote: Hi James, thanks a lot for the quick help. On Mon, Feb 22, 2016 at 09:56:12AM +, James Bonfield wrote: Please try commenting out (#) the "wm resizable $w 1 0" line of the contig_editor procedure (approx line 111) in /usr/share/staden/tcl/gap/contig_editor.tcl. I've applied the suggested patch (which can be found in the packaging repository[1]). (It may not be /usr/share - Andreas, where does Debian by default install Gap4?) The patch will be applied to the source and later installed in the location you named above. This disables the attempt to inform the window manager that the X dimension is under user control and Y dimension under the program control. I don't know if this is sufficient as testing this requires checking every window manager out there and see which options they honour, but it cures the problem for me with xfwm4. Since I also can't really test we simply rely on Kerstin to check whether it solves her problem. Kerstin, you might like to wait for the next mirror sync until staden 2.0.0+b10-3 will be available. Please confirm whether both problems you reported are solved. Thanks for testing. James, if you are interested there are some more patches[2] in the packaging reporitory. Some of them might be of interest - at least the spelling.patch with some spelling fixes. Thanks again for your prompt help Andreas. [1] https://anonscm.debian.org/viewvc/debian-med/trunk/packages/staden/trunk/debian/patches/cope_with_modern_windowmanager.patch?revision=21446&view=markup [2] https://anonscm.debian.org/viewvc/debian-med/trunk/packages/staden/trunk/debian/patches/ -- PD Dr. Kerstin Hoef-Emden Zülpicher Str. 47b Universität zu Köln 50674 Köln Biozentrum Köln (Cologne Biocenter) Germany Botanisches Institut http://www.uni-koeln.de/~aeb25/
Bug#815176: staden: Gap4 contig editor does not show sequences
Hi to all, On Mon, 22 Feb 2016, Andreas Tille wrote: Hmmm, lets hunt down this as well. Could you please write the output of apt-get policy staden You probably mean apt-cache policy staden? khe@euler:~$ apt-cache policy staden staden: Installiert: 2.0.0+b10-1.1 Installationskandidat: 2.0.0+b10-1.1 Versionstabelle: *** 2.0.0+b10-1.1 0 500 http://ftp.de.debian.org/debian/ jessie/main amd64 Packages 100 /var/lib/dpkg/status Actually I tried update and upgrade first, which did not include staden, then I deinstalled staden and reinstalled it. cat `which pregap4` Do you really want to see the whole script? Perhaps you try cp `which pregap4` ~/pregap4 edit ~/pregap4 and add set -x Did not work. as the second line in this script. For me this looks pretty sensible. Alternatively you could try explicitly calling /usr/lib/staden/bin/pregap4 What happens if you do this? Did not work (I am surprised - this is the path containing all modules). Best wishes, Kerstin -- PD Dr. Kerstin Hoef-Emden Zülpicher Str. 47b Universität zu Köln 50674 Köln Biozentrum Köln (Cologne Biocenter) Germany Botanisches Institut http://www.uni-koeln.de/~aeb25/
Bug#815176: staden: Gap4 contig editor does not show sequences
Hi to all,
On Tue, 23 Feb 2016, Andreas Tille wrote:
Kerstin, you can either download the staden packages from unstable from
here:
https://packages.debian.org/source/unstable/staden
and install manually on your Jessie system
I had a look at the requirements in the README.build file. Manual
install is not straightforward. Itcl, itk and iwidgets are not available
for jessie. Also configure complains about a missing io_lib. I search
the packages and found staden-io-lib-utils, but could not find a
staden-io_lib.so or something to which I could point with a path.
Libstaden is something different is it? All other dependencies seem to
be sufficient.
or you add unstable to your
/etc/apt/sources.list. ATTENTION: You need to adapt
/etc/apt/preferences to make sure you will not bump your whole system
to unstable!
The most "dangerous" and possibly destabilizing actions I did, were
installations of backports. I usually don't dare to touch sid. Probably
the install will also result in the missing itcl etc. being installed?
Will it work, if I restrict it as such?
Package: staden
Pin: release n=sid
Pin-Priority: 900
Best wishes,
Kerstin
On Mon, Feb 22, 2016 at 05:42:38PM +, James Bonfield wrote:
On Mon, Feb 22, 2016 at 04:34:13PM +0100, Andreas Tille wrote:
if I understand you correctly you are suggesting a further change. Could
you please confirm that this patch
https://anonscm.debian.org/viewvc/debian-med/trunk/packages/staden/trunk/debian/patches/cope_with_modern_windowmanager.patch?view=markup
Yes that's it.
The other change was an improvement to resizing.
This is long and tedious so feel free to ignore, but if you're curious
then here are the details. Typically window managers treat windows as
one of two flavours:
1) The program set the size, so it's permitted to change it again
itself.
2) The user resized the window, so the application request to resize
it will be ignored.
Tk wm geometry command allows you to programatically change the size
of window or with the blank size (wm geometry . {} {}) it'll reset the
window to case 1 - governed by the program rather than the user.
This is all very ICKY and it gets worse. Gap4's contig editor is
"courageously" setting the Y dimension itself based on how many rows
of sequences it wants to display. The X dimension can be controlled
by the user, but as the user increases the size in X, more sequences
can become visible causing the Y dimension to be resized. In the past
this caused massive fights between various parts of tcl/tk and window
managers, sometimes triggering event loops with oscillating window
dimensions. The workaround for this was to have a 1 second delay
between resizing the window and asking the program to recompute the
size.
That in turn though broke all modern window managers. Basically if
you resized quickly and let go it'd just snap back - you had to
resize, hold and wait for 1 sec, and then release. Bizantine... Try
hard as I may I couldn't recreate the strange oscillations so this
change basically pushes it back to how it used to be with instant
recomputation. It seems to work much better in general, but still
isn't perfect.
Perfection isn't possible when you start with the premise of X being
user controlled and Y being program controlled! With Gap5 fortunately
we had an attack of sanity and chose a more traditional strategy.
James
PS. Kerstin if you're still reading this, if set -x doesn't work then
just editing the first #! line to be "#!/bin/sh -x" (without the
quotes) should do the same thing, or simpler still typing in
sh -x `which pregap4`
--
James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi.
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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--
PD Dr. Kerstin Hoef-Emden Zülpicher Str. 47b
Universität zu Köln 50674 Köln
Biozentrum Köln (Cologne Biocenter) Germany
Botanisches Institut
http://www.uni-koeln.de/~aeb25/
Bug#815176: staden: Gap4 contig editor does not show sequences
Hi to all, On Tue, 23 Feb 2016, Andreas Tille wrote: We are talking about different things when talking about "manual install". You can download the packages manually via wget http://ftp.de.debian.org/debian/pool/main/s/staden/staden_2.0.0+b10-3_amd64.deb http://ftp.de.debian.org/debian/pool/main/s/staden/staden-common_2.0.0+b10-3_all.deb Ok, that's much easier. any *may* *be* you might also need http://ftp.de.debian.org/debian/pool/main/s/staden-io-lib/libstaden-read11_1.14.7-1_amd64.deb Actually, also staden-common from unstable was required, but then install went through. All operations worked: Converting the files with pregap and opening of contig editor and of the trace files in gap4! Thanks a lot! You may install the backport ... Best wishes, Kerstin -- PD Dr. Kerstin Hoef-Emden Zülpicher Str. 47b Universität zu Köln 50674 Köln Biozentrum Köln (Cologne Biocenter) Germany Botanisches Institut http://www.uni-koeln.de/~aeb25/
