Bug#1042775: r-cran-stringi: fails being loaded in R
Dne 02. 08. 23 v 8:50 Andreas Tille napsal(a): Control: tags -1 unreproducible Am Mon, Jul 31, 2023 at 08:16:25PM +0200 schrieb Martin Weiser: Error: package or namespace load failed for ‘stringi’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib/R/site-library/stringi/libs/stringi.so': ^ are you sure you are loading the Debian packaged stringi? Kind regards Andreas. Dear Andreas, I am really sorry for wasting your time. With sincere apologies, Martin -- Please expect long response time (3d+) - this is because of family reasons
Bug#1042775: r-cran-stringi: fails being loaded in R
Package: r-cran-stringi
Version: 1.7.12-1
Severity: important
X-Debbugs-Cc: martin.wei...@natur.cuni.cz
Dear Maintainer,
I cannot load package "r-cran-stringi" from my R session.
Within an R session, issue:
library("stringi")
The R responds:
Error: package or namespace load failed for ‘stringi’ in dyn.load(file, DLLpath
= DLLpath, ...):
unable to load shared object
'/usr/local/lib/R/site-library/stringi/libs/stringi.so':
libicui18n.so.67: cannot open shared object file: No such file or directory
My R session info:
> sessionInfo()
R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 12 (bookworm)
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.2.2 tools_4.2.2
My .libPaths():
[1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"
[3] "/usr/lib/R/library"
With Bookworm, I have:
apt-file search libicui18n.so:
libicu-dev: /usr/lib/x86_64-linux-gnu/libicui18n.so
libicu72: /usr/lib/x86_64-linux-gnu/libicui18n.so.72
libicu72: /usr/lib/x86_64-linux-gnu/libicui18n.so.72.1
I installed all packages (both R and system) using apt.
Although I would be happy to help, I have not solved
the problem (loading the "stringi" package) myself yet...
Thank you for your consideration.
With regards,
Martin Weiser
-- System Information:
Debian Release: 12.1
APT prefers stable-updates
APT policy: (500, 'stable-updates'), (500, 'stable-security'), (500, 'stable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 6.1.0-10-amd64 (SMP w/16 CPU threads; PREEMPT)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8),
LANGUAGE=en_US:en
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages r-cran-stringi depends on:
ii libc62.36-9+deb12u1
ii libgcc-s112.2.0-14
ii libicu72 72.1-3
ii libstdc++6 12.2.0-14
ii r-base-core [r-api-4.0] 4.2.2.20221110-2
r-cran-stringi recommends no packages.
r-cran-stringi suggests no packages.
-- no debconf information
Bug#721758: gedit: Preferences menu option missing. Old preferences still applied.
Package: gedit Version: 3.14.0-3 Followup-For: Bug #721758 Dear Maintainer, I have encountered similar scenario: after todays apt-get dist upgrade, items in gedit gui - preferences stopped to respond and previous values are conserved. Although I have gedit-plugins and gedit-r-plugin installed, this bug disables their usage. I am using LXDE, so it is not just GNOME issue, probably. Thank you for your patience and possible help. -- Package-specific info: Active plugins: - 'docinfo' - 'drawspaces' - 'spell' - 'sort' - 'filebrowser' - 'bookmarks' - 'taglist' - 'wordcompletion' No plugin installed in $HOME. Module versions: - glib - gtk+ - gtksourceview - pygobject - enchant - iso-codes 3.57 -- System Information: Debian Release: 8.0 APT prefers proposed-updates APT policy: (500, 'proposed-updates'), (500, 'stable') Architecture: i386 (i686) Kernel: Linux 3.2.0-4-686-pae (SMP w/2 CPU cores) Locale: LANG=cs_CZ.UTF-8, LC_CTYPE=cs_CZ.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: unable to detect Versions of packages gedit depends on: ii gedit-common 3.14.0-3 ii gir1.2-peas-1.01.12.1-2 ii gnome-icon-theme-symbolic 3.12.0-1 ii gsettings-desktop-schemas 3.14.1-1 ii iso-codes 3.57-1 ii libatk1.0-02.14.0-1 ii libc6 2.19-18 ii libcairo-gobject2 1.14.0-2.1 ii libcairo2 1.14.0-2.1 ii libenchant1c2a 1.6.0-10.1 ii libgdk-pixbuf2.0-0 2.31.1-2+b1 ii libgirepository-1.0-1 1.42.0-2.2 ii libglib2.0-0 2.42.1-1 ii libgtk-3-0 3.14.5-1 ii libgtksourceview-3.0-1 3.14.1-1 ii libpango-1.0-0 1.36.8-3 ii libpangocairo-1.0-01.36.8-3 ii libpeas-1.0-0 1.12.1-2 ii libx11-6 2:1.6.2-3 ii libxml22.9.1+dfsg1-5 ii python3-gi 3.14.0-1 ii python3-gi-cairo 3.14.0-1 pn python3:anynone Versions of packages gedit recommends: ii yelp3.14.1-1 ii zenity 3.14.0-1 Versions of packages gedit suggests: ii gedit-plugins 3.14.0-2 -- no debconf information -- -- Pokud je tento e-mail součástí obchodního jednání, Přírodovědecká fakulta Univerzity Karlovy v Praze: a) si vyhrazuje právo jednání kdykoliv ukončit a to i bez uvedení důvodu, b) stanovuje, že smlouva musí mít písemnou formu, c) vylučuje přijetí nabídky s dodatkem či odchylkou, d) stanovuje, že smlouva je uzavřena teprve výslovným dosažením shody na všech náležitostech smlouvy. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#732296: octave: English locale,new attempt, same behaviour
Package: octave Version: 3.6.2-5+deb7u1 Followup-For: Bug #732296 Dear Maintainer, apt-get install octave fails, even when I (AFAIK) purged all traces of HDF5 from my system. Here I enclose new version of my bugreport (with English locale): root@zouzel:/home/louskacek# apt-get install octave Reading package lists... Done Building dependency tree Reading state information... Done The following packages were automatically installed and are no longer required: [...some packages' names here...] Use 'apt-get autoremove' to remove them. The following extra packages will be installed: libhdf5-7 liboctave1 libqrupdate1 octave-common Suggested packages: octave-info octave-doc octave-htmldoc The following NEW packages will be installed: libhdf5-7 liboctave1 libqrupdate1 octave octave-common 0 upgraded, 5 newly installed, 0 to remove and 2 not upgraded. Need to get 1331 kB/12.7 MB of archives. After this operation, 42.9 MB of additional disk space will be used. Do you want to continue [Y/n]? Y Get:1 http://ftp.cz.debian.org/debian/ wheezy/main libhdf5-7 i386 1.8.8-9 [1331 kB] Fetched 1331 kB in 0s (5520 kB/s) Can't set locale; make sure $LC_* and $LANG are correct! perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LANG = en_GB.UTF-8 are supported and installed on your system. perl: warning: Falling back to the standard locale (C). locale: Cannot set LC_CTYPE to default locale: No such file or directory locale: Cannot set LC_MESSAGES to default locale: No such file or directory locale: Cannot set LC_ALL to default locale: No such file or directory Selecting previously unselected package libhdf5-7. (Reading database ... 216009 files and directories currently installed.) Unpacking libhdf5-7 (from .../libhdf5-7_1.8.8-9_i386.deb) ... Selecting previously unselected package libqrupdate1. Unpacking libqrupdate1 (from .../libqrupdate1_1.1.1-1_i386.deb) ... Selecting previously unselected package liboctave1:i386. Unpacking liboctave1:i386 (from .../liboctave1_3.6.2-5+deb7u1_i386.deb) ... Selecting previously unselected package octave-common. Unpacking octave-common (from .../octave-common_3.6.2-5+deb7u1_all.deb) ... Selecting previously unselected package octave. Unpacking octave (from .../octave_3.6.2-5+deb7u1_i386.deb) ... Processing triggers for man-db ... locale: Cannot set LC_CTYPE to default locale: No such file or directory locale: Cannot set LC_MESSAGES to default locale: No such file or directory locale: Cannot set LC_ALL to default locale: No such file or directory Processing triggers for menu ... Processing triggers for gnome-menus ... Processing triggers for desktop-file-utils ... Setting up libhdf5-7 (1.8.8-9) ... Setting up libqrupdate1 (1.1.1-1) ... Setting up liboctave1:i386 (3.6.2-5+deb7u1) ... Setting up octave-common (3.6.2-5+deb7u1) ... Setting up octave (3.6.2-5+deb7u1) ... octave: error while loading shared libraries: libhdf5.so.6: cannot open shared object file: No such file or directory dpkg: error processing octave (--configure): subprocess installed post-installation script returned error exit status 127 Processing triggers for menu ... Errors were encountered while processing: octave E: Sub-process /usr/bin/dpkg returned an error code (1) Any idea or advice will is welcome. With the best regards, Martin Weiser -- System Information: Debian Release: 7.3 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'proposed-updates'), (500, 'oldstable-proposed-updates'), (500, 'stable') Architecture: i386 (i686) Kernel: Linux 3.2.0-4-686-pae (SMP w/2 CPU cores) Locale: LANG=cs_CZ.UTF-8, LC_CTYPE=cs_CZ.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Versions of packages octave depends on: ii libamd2.2.0 1:3.4.0-3 ii libarpack2 3.1.1-2.1 ii libatlas3-base [liblapack.so.3] 3.8.4-9+deb7u1 ii libblas3 [libblas.so.3] 1.2.20110419-5 ii libc62.13-38 ii libcamd2.2.0 1:3.4.0-3 ii libccolamd2.7.1 1:3.4.0-3 ii libcholmod1.7.1 1:3.4.0-3 ii libcolamd2.7.1 1:3.4.0-3 ii libcurl3-gnutls 7.26.0-1+wheezy6 ii libcxsparse2.2.3 1:3.4.0-3 ii libfftw3-3 3.3.2-3.1 ii libfltk1.1 1.1.10-14 ii libfreetype6 2.4.9-1.1 ii libgcc1 1:4.7.2-5 ii libgl1-mesa-glx [libgl1] 8.0.5-4+deb7u2 ii libglpk0 4.45-1 ii libgomp1 4.7.2-5 ii libgraphicsmagick++3 1.3.16-1.1 ii libgraphicsmagick3 1.3.16-1.1 ii liblapack3 [liblapack.so.3] 3.4.1+dfsg-1+deb70u1 ii liboctave1 3.6.2-5+deb7u1 ii libpcre3 1:8.30-5 ii libqhull52009.1-3 ii
Bug#732222: Bug#732222: imagej: does not see present JAVA
Andreas Tille píše v Po 16. 12. 2013 v 09:39 +0100: Hi Olivier, On Mon, Dec 16, 2013 at 09:14:06AM +0100, Olivier Sallou wrote: here is the result: java-gcj-4.7 /usr/lib/jvm/java-gcj-4.7 java-1.6.0-openjdk-i386 1061 /usr/lib/jvm/java-1.6.0-openjdk-i386 java-1.7.0-openjdk-i386 1051 /usr/lib/jvm/java-1.7.0-openjdk-i386 I submitted a patch to SVN that picks always the latest openjdk version. In the meanwhile, setting: #export JAVA_HOME=/usr/lib/jvm/java-1.7.0-openjdk-i386 #imagej should work My patch should have the same effect. Some testing / sanity check of the wrapper script would be helpful. Generally spoken I'd be happy if somebody could revise the script since Paolo who did invent the script seems to be not active any more on imagej packaging. Kind regards Andreas. Dear friends, maybe there is something else involved (should I open another bug?), as Olivier's workaround helps only partially: me@here:~$ export JAVA_HOME=/usr/lib/jvm/java-1.7.0-openjdk-i386 me@here:~$ echo $JAVA_HOME /usr/lib/jvm/java-1.7.0-openjdk-i386 me@here:~$ imagej Open other images in this ImageJ panel as follows: imagej -p 1 image1 [image2 ... imageN] Exception in thread main java.awt.HeadlessException at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:207) at java.awt.Window.init(Window.java:535) at java.awt.Frame.init(Frame.java:420) at ij.ImageJ.init(ImageJ.java:129) at ij.ImageJ.main(ImageJ.java:597) Any advice? Once again: thank you for your patience. With the best regards, Martin. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#732222: Bug#732222: imagej: does not see present JAVA
Andreas Tille píše v Po 16. 12. 2013 v 13:33 +0100: Hi Martin, On Mon, Dec 16, 2013 at 12:55:33PM +0100, Martin Weiser wrote: Dear friends, maybe there is something else involved (should I open another bug?), as Olivier's workaround helps only partially: me@here:~$ export JAVA_HOME=/usr/lib/jvm/java-1.7.0-openjdk-i386 me@here:~$ echo $JAVA_HOME /usr/lib/jvm/java-1.7.0-openjdk-i386 me@here:~$ imagej Open other images in this ImageJ panel as follows: imagej -p 1 image1 [image2 ... imageN] Exception in thread main java.awt.HeadlessException at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:207) at java.awt.Window.init(Window.java:535) at java.awt.Frame.init(Frame.java:420) at ij.ImageJ.init(ImageJ.java:129) at ij.ImageJ.main(ImageJ.java:597) Any advice? Once again: thank you for your patience. Please try the script: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/imagej/trunk/debian/imagej.sh?view=markup which is the usual wrapper around imagej with a patch that should properly select the JAVA_HOME. It would be nice to know whether this would help or not. Kind regards Andreas. Hi Andreas, unfortunately, the same behaviour occurs: louskacek@zouzel:~$ chmod 777 imagej.sh louskacek@zouzel:~$ ./imagej.sh Open other images in this ImageJ panel as follows: imagej -p 1 image1 [image2 ... imageN] Exception in thread main java.awt.HeadlessException at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:207) at java.awt.Window.init(Window.java:535) at java.awt.Frame.init(Frame.java:420) at ij.ImageJ.init(ImageJ.java:129) at ij.ImageJ.main(ImageJ.java:597) Any advice? Best, Martin. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#732296: octave: fails to get installed
Package: octave Version: 3.6.2-5+deb7u1 Severity: important Dear Maintainer, I failed to install octave both using Synaptic and apt-get. (I use Czech locale, but I hope it is still intelligible): #: apt-get install octave Následující extra balíky budou instalovány: liboctave1 libqrupdate1 octave-common Navrhované balíky: octave-info octave-doc octave-htmldoc Následující NOVÉ balíky budou nainstalovány: liboctave1 libqrupdate1 octave octave-common 0 aktualizováno, 4 nově instalováno, 0 k odstranění a 2 neaktualizováno. Potřebuji stáhnout 9 555 kB/11,4 MB archivů. Po této operaci bude na disku použito dalších 39,1 MB. Chcete pokračovat [Y/n]? Y Mám:1 http://ftp.cz.debian.org/debian/ wheezy/main libqrupdate1 i386 1.1.1-1 [70,4 kB] Mám:2 http://ftp.cz.debian.org/debian/ wheezy/main liboctave1 i386 3.6.2-5+deb7u1 [8 391 kB] Mám:3 http://ftp.cz.debian.org/debian/ wheezy/main octave-common all 3.6.2-5+deb7u1 [1 094 kB] Staženo 9 555 kB za 0s (9 942 kB/s) Vybírám dosud nevybraný balík libqrupdate1. (Čtu databázi … nyní je nainstalováno 222469 souborů a adresářů.) Rozbaluji libqrupdate1 (z …/libqrupdate1_1.1.1-1_i386.deb) … Vybírám dosud nevybraný balík liboctave1:i386. Rozbaluji liboctave1:i386 (z …/liboctave1_3.6.2-5+deb7u1_i386.deb) … Vybírám dosud nevybraný balík octave-common. Rozbaluji octave-common (z …/octave-common_3.6.2-5+deb7u1_all.deb) … Vybírám dosud nevybraný balík octave. Rozbaluji octave (z …/octave_3.6.2-5+deb7u1_i386.deb) … Zpracování spouštěčů pro balík man-db … Zpracování spouštěčů pro balík menu … Zpracování spouštěčů pro balík gnome-menus … Zpracování spouštěčů pro balík desktop-file-utils … Nastavuji balík libqrupdate1 (1.1.1-1) … Nastavuji balík liboctave1:i386 (3.6.2-5+deb7u1) … Nastavuji balík octave-common (3.6.2-5+deb7u1) … Nastavuji balík octave (3.6.2-5+deb7u1) … octave: error while loading shared libraries: libhdf5.so.6: cannot open shared object file: No such file or directory dpkg: chyba při zpracovávání octave (--configure): podproces instalovaný post-installation skript vrátil chybový status 127 Zpracování spouštěčů pro balík menu … Při zpracování nastaly chyby: octave E: Sub-process /usr/bin/dpkg returned an error code (1) Any suggestions? Thank you. Kind regards, Martin -- System Information: Debian Release: 7.3 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'proposed-updates'), (500, 'oldstable-proposed-updates'), (500, 'stable') Architecture: i386 (i686) Kernel: Linux 3.2.0-4-686-pae (SMP w/2 CPU cores) Locale: LANG=cs_CZ.UTF-8, LC_CTYPE=cs_CZ.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Versions of packages octave depends on: ii libamd2.2.0 1:3.4.0-3 ii libarpack2 3.1.1-2.1 ii libatlas3-base [liblapack.so.3] 3.8.4-9+deb7u1 ii libblas3 [libblas.so.3] 1.2.20110419-5 ii libc62.13-38 ii libcamd2.2.0 1:3.4.0-3 ii libccolamd2.7.1 1:3.4.0-3 ii libcholmod1.7.1 1:3.4.0-3 ii libcolamd2.7.1 1:3.4.0-3 ii libcurl3-gnutls 7.26.0-1+wheezy6 ii libcxsparse2.2.3 1:3.4.0-3 ii libfftw3-3 3.3.2-3.1 ii libfltk1.1 1.1.10-14 ii libfreetype6 2.4.9-1.1 ii libgcc1 1:4.7.2-5 ii libgl1-mesa-glx [libgl1] 8.0.5-4+deb7u2 ii libglpk0 4.45-1 ii libgomp1 4.7.2-5 ii libgraphicsmagick++3 1.3.16-1.1 ii libgraphicsmagick3 1.3.16-1.1 ii liblapack3 [liblapack.so.3] 3.4.1+dfsg-1+deb70u1 ii liboctave1 3.6.2-5+deb7u1 ii libpcre3 1:8.30-5 ii libqhull52009.1-3 ii libqrupdate1 1.1.1-1 ii libstdc++6 4.7.2-5 ii libumfpack5.4.0 1:3.4.0-3 ii octave-common3.6.2-5+deb7u1 ii texinfo 4.13a.dfsg.1-10 ii zlib1g 1:1.2.7.dfsg-13 Versions of packages octave recommends: ii gnuplot-x11 4.6.0-8 ii libatlas3-base 3.8.4-9+deb7u1 Versions of packages octave suggests: pn octave-doc none pn octave-htmldoc none pn octave-info none -- no debconf information -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#732222: fiji acted - was:Re: Bug#732222: imagej: does not see present JAVA
Andreas Tille píše v Po 16. 12. 2013 v 15:07 +0100:
Hi Martin,
On Mon, Dec 16, 2013 at 02:04:34PM +0100, Martin Weiser wrote:
Sorry. I hope I get it know:
louskacek@zouzel:~$ ./imagej.sh
+ ./imagej.sh
+ set +u
+ shopt -s extglob
+ '[' -z /usr/lib/jvm/java-1.7.0-openjdk-i386 ']'
+ ij_path=/usr/share/java
+ ij_user_path=/home/louskacek/.imagej
+ ijadmin=debian-med-packag...@lists.alioth.debian.org
+ doc_url=http://imagej.nih.gov/ij/
+ ij_tmp=/home/louskacek/.imagej/tmp
+ newwindow=true
+ separator=:
+ declare -i mem
+ declare -i default_mem=500
+ declare -i min_mem=16
+ declare -i max_mem
+ declare -i free_mem
++ pwd
+ dir=/home/louskacek
++ whoami
+ user=louskacek
++ hostname
+ host=zouzel
+ [[ -z :0 ]]
+ display=:0
+ declare -i port=0
+ declare -i verbosity=0
+ images=
+ macrocmd=
+ macroargs=
++ uname
+ [[ Linux == \S\u\n\O\S ]]
++ uname
+ [[ Linux == \L\i\n\u\x ]]
++ uname -m
+ [[ i686 == \x\8\6\_\6\4 ]]
+ arch=-d32
+ java_path=/usr/share/java/jre/bin/java
++ free
++ awk 'NR == 2 {fmem=int($2 / 1024); if (fmem 1800) {print fmem} else
{print 1800}}'
+ max_mem=1800
++ free
++ awk 'NR == 3 {fmem=int($4 / 1024); if (fmem 1800) {print fmem} else
{print 1800}}'
+ free_mem=1800
+ mem='1800/3*2'
+ (( 1200 500 || 1200 16 ))
+ mem=500
+ mkdir -p /home/louskacek/.imagej/plugins
+ mkdir -p /home/louskacek/.imagej/macros
+ mkdir -p /home/louskacek/.imagej/luts
+ [[ ! -d /home/louskacek/.imagej/tmp ]]
+ ls /usr/share/imagej/plugins
+ read p
+ '[' '!' -e /home/louskacek/.imagej/plugins/JavaScriptEvaluator.class
']'
+ read p
+ '[' '!' -e /home/louskacek/.imagej/plugins/MacAdapter.class ']'
+ read p
+ '[' '!' -e /home/louskacek/.imagej/plugins/MacClipboard.class ']'
+ read p
+ read p
+ ls /usr/share/imagej/macros
+ '[' '!' -e /home/louskacek/.imagej/macros/AddParticles.txt ']'
+ read p
+ '[' '!' -e /home/louskacek/.imagej/macros/ConvertStackToBinary.txt ']'
+ read p
+ '[' '!' -e /home/louskacek/.imagej/macros/EnlargeSelection.txt ']'
+ read p
+ '[' '!' -e /home/louskacek/.imagej/macros/HyperStackMaker.txt ']'
+ read p
+ '[' '!' -e /home/louskacek/.imagej/macros/MoveSelection.txt ']'
+ read p
+ '[' '!' -e /home/louskacek/.imagej/macros/RotateSelection.txt ']'
+ read p
+ '[' '!' -e /home/louskacek/.imagej/macros/Search.txt ']'
+ read p
+ '[' '!' -e '/home/louskacek/.imagej/macros/Stack Tools.txt' ']'
+ read p
+ '[' '!' -e /home/louskacek/.imagej/macros/StartupMacros.txt ']'
+ read p
+ '[' '!' -e /home/louskacek/.imagej/macros/TimeStamp.ijm ']'
+ read p
+ ls /usr/share/imagej/luts
+ read p
+ '[' '!' -e /home/louskacek/.imagej/luts/HiLo.lut.enc ']'
+ read p
+ '[' '!' -e /home/louskacek/.imagej/luts/RedHot.lut.enc ']'
+ read p
+ modules='-cp /usr/share/java/ij.jar'
+ tools=/usr/lib/jvm/java-1.7.0-openjdk-i386/lib/tools.jar
+ getopts b:ce:hi:m:op:r:vx: options
+ declare -i i=1
+ (( i 1 ))
+ [[ -n '' ]]
+ (( 0 0 ))
+ pushd /home/louskacek/.imagej/tmp
+ declare -i count=1
+ portopen=false
+ lockFileCreated=false
+ locklist=(`ls | grep '[0-9][0-9]-.*'`)
++ grep '[0-9][0-9]-.*'
++ ls
+ declare -a locklist
+ (( 0 0 ))
+ (( 0 0 ))
+ [[ true == \f\a\l\s\e ]]
+ [[ false == \f\a\l\s\e ]]
+ (( 0 == 0 ))
+ (( 0 == 0 ))
+ count=1
++ printf %02u 1
+ prefix=01
+ lockname=01-louskacek-zouzel-:0
+ (( 0 0 ))
+ touch 01-louskacek-zouzel-:0
+ trap '\rm -f ${ij_tmp}/$lockname /dev/null ; exit 1' EXIT TERM
+ (( 0 0 ))
+ lockFileCreated=true
+ echo 'Open other images in this ImageJ panel as follows:'
Open other images in this ImageJ panel as follows:
+ echo ' imagej -p 1 image1 [image2 ... imageN]'
imagej -p 1 image1 [image2 ... imageN]
+ (( 0 0 ))
+ echo
+ popd
+ '[' -d /usr/share/imagej/jni/ ']'
+ '[' /usr/lib/jvm/java-1.7.0-openjdk-i386 ']'
+ (( 0 0 ))
+ eval /usr/lib/jvm/java-1.7.0-openjdk-i386/bin/java -d32 -mx500m
-cp /usr/share/java/ij.jar ij.ImageJ -ijpath /home/louskacek/.imagej
-port1
++ /usr/lib/jvm/java-1.7.0-openjdk-i386/bin/java -d32 -mx500m
-cp /usr/share/java/ij.jar ij.ImageJ -ijpath /home/louskacek/.imagej
-port1
Exception in thread main java.awt.HeadlessException
at
java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:207)
at java.awt.Window.init(Window.java:535)
at java.awt.Frame.init(Frame.java:420)
at ij.ImageJ.init(ImageJ.java:129)
at ij.ImageJ.main(ImageJ.java:597)
+ exit 0
+ rm -f /home/louskacek/.imagej/tmp/01-louskacek-zouzel-:0
+ exit 1
louskacek@zouzel:~$
Is this OK?
This is what we wanted to know and it seems you are running this on a i386
system. I tested the resulting call on my amd64 system by
/usr/lib/jvm/java-1.7.0-openjdk-amd64/bin/java -d64 -mx500m -cp
/usr/share/java/ij.jar ij.ImageJ -ijpath /home/tillea/.imagej -port1
Bug#732222: imagej: does not see present JAVA
Package: imagej Version: 1.46a-1 Severity: important Dear Maintainer, when I try to start ImageJ, I get info about non-packaged JAVA, what is not right: louskacek@zouzel:~$ imagej Open other images in this ImageJ panel as follows: imagej -p 1 image1 [image2 ... imageN] No JVM found to run ImageJ Please apt-get install a JVM to run ImageJ or set JAVA_HOME if it's not a JVM from a Debian Package. I have installed JAVA through packaging system. (Besides, I do not know yet where to look for JAVA_HOME setting, but I guess it should be easy - I will google that) Thank you for your patience -- System Information: Debian Release: 7.3 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'proposed-updates'), (500, 'oldstable-proposed-updates'), (500, 'stable') Architecture: i386 (i686) Kernel: Linux 3.2.0-4-686-pae (SMP w/2 CPU cores) Locale: LANG=cs_CZ.UTF-8, LC_CTYPE=cs_CZ.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Versions of packages imagej depends on: ii openjdk-6-jre 6b27-1.12.6-1~deb7u1 imagej recommends no packages. Versions of packages imagej suggests: ii gcj-jre-headless [java-virtual-machine] 4:4.7.2-1 -- no debconf information -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#732222: imagej: does not see present JAVA
Andreas Tille píše v Ne 15. 12. 2013 v 21:46 +0100: Hi, thanks for your bug report. On Sun, Dec 15, 2013 at 08:49:12PM +0100, Martin Weiser wrote: Package: imagej Version: 1.46a-1 Severity: important Dear Maintainer, when I try to start ImageJ, I get info about non-packaged JAVA, what is not right: louskacek@zouzel:~$ imagej Open other images in this ImageJ panel as follows: imagej -p 1 image1 [image2 ... imageN] No JVM found to run ImageJ Could you please try /usr/sbin/update-java-alternatives -l and post the result in this bug report? Kind regards Andreas. Hi Andreas, here is the result: java-gcj-4.7 /usr/lib/jvm/java-gcj-4.7 java-1.6.0-openjdk-i386 1061 /usr/lib/jvm/java-1.6.0-openjdk-i386 java-1.7.0-openjdk-i386 1051 /usr/lib/jvm/java-1.7.0-openjdk-i386 Thank you. Best, Martin -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#622345: imagej: still the same with Squeeze...
Hi Andreas,
thank You for your patience.
ImageJ now works OK. I do not know the reason (lame answer, I know) -
therefore I did not send a message, as I do not know what the cure was.
What may be the cause: after one of the updates, the machine died
after restart (no reaction on keyboard input or mouse input), so I
decided to not to waste time with bug fixing (well, maybe it could
gave me invaluable lessons in linux administration, but...) and
reinstalled the system.
Here is the output of Michael's suggested commands (I have got CZ locales):
/usr/sbin/update-java-alternatives --list :
java-6-openjdk 1061 /usr/lib/jvm/java-6-openjdk
/usr/sbin/update-alternatives --display java
java - automatický režim
odkaz momentálně ukazuje na /usr/lib/jvm/java-6-openjdk/jre/bin/java
/usr/bin/gij-4.4 - priorita 1044
/usr/lib/jvm/java-6-openjdk/jre/bin/java - priorita 1061
závislost java.1.gz: /usr/lib/jvm/java-6-openjdk/jre/man/man1/java.1.gz
Momentální „nejlepší“ verze je „/usr/lib/jvm/java-6-openjdk/jre/bin/java“.
My attempt to translate it:
java - automatic mode
link currently points to /usr/lib/jvm/java-6-openjdk/jre/bin/java
/usr/bin/gij-4.4 - priority 1044
/usr/lib/jvm/java-6-openjdk/jre/bin/java - priority 1061
dependency java.1.gz: /usr/lib/jvm/java-6-openjdk/jre/man/man1/java.1.gz
Current best version is „/usr/lib/jvm/java-6-openjdk/jre/bin/java“
Again, thanks for Your help and patience.
Best,
Martin
Cituji Andreas Tille ti...@debian.org:
Hi Matrtin,
do you continuosely observe this problem? If yes, could you please
follow the instructions given by Michael below? If it is not possible
to reproduce the problem I'm tempted to lower the severity of this
problem.
Kind regards
Andreas.
On Fri, Jul 22, 2011 at 03:53:54PM +0200, Michael Schutte wrote:
Hi Martin!
On Sat, Apr 16, 2011 at 02:25:11AM +0200, Martin Weiser wrote:
Here is the sample session:
louskacek@zouzel:~$ imagej
Open other images in this ImageJ panel as follows:
imagej -p 1 image1 [image2 ... imageN]
#guess what happens here :-)
#yes, you are right, the main panel appears and disappears
#with this version it is faster than before :-)
Exception in thread main java.lang.NullPointerException
at java.awt.Component.setDropTarget(libgcj.so.10)
at ij.plugin.DragAndDrop.run(DragAndDrop.java:28)
at ij.IJ.runPlugIn(IJ.java:156)
at ij.IJ.runPlugIn(IJ.java:139)
at ij.ImageJ.init(ImageJ.java:196)
at ij.ImageJ.main(ImageJ.java:588)
louskacek@zouzel:~$
Are you still experiencing this issue? If so, it would be useful to see
the output for the commands
/usr/sbin/update-java-alternatives --list
and
/usr/sbin/update-alternatives --display java
because I suspect the problem is due to gij somehow being the default
JRE implementation on your system. I can indeed reproduce the bug by
running “gij-4.6 -jar /usr/share/java/ij.jar”.
All the best,
--
Michael Schutte | michi@{uiae.at,debian.org}
Innsbruck, Austria| happily accepting encrypted mail
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Bug#646566: PDF-Form: some non-Latin1 characters disappear when form field looses focus
Package: evince Version: 2.30.3-2 Severity: normal Hello, when I try to complete a pdf-form (eg. this one: http://www.irs.gov/pub/irs- pdf/f1000.pdf - but it holds for all that I have tried) with non-ASCII characters, those characters can be filled in but disappear instantly when the field of the form looses focus (eg. when filling another field is started). When the field gets focus again, characters appear. They are visible only when the field has focus. Some affected characters: ě,č,ř,ů,ť,ď,ľ,ĺ,ň Any advice? Thank you. -- System Information: Debian Release: 6.0.3 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'proposed-updates'), (500, 'stable') Architecture: i386 (i686) Kernel: Linux 2.6.32-5-686 (SMP w/2 CPU cores) Locale: LANG=cs_CZ.utf8, LC_CTYPE=cs_CZ.utf8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Versions of packages evince depends on: ii evince-common 2.30.3-2 Document (PostScript, PDF) viewer ii gconf2 2.28.1-6 GNOME configuration database syste ii gnome-icon-theme 2.30.3-2 GNOME Desktop icon theme ii libatk1.0-01.30.0-1 The ATK accessibility toolkit ii libc6 2.11.2-10 Embedded GNU C Library: Shared lib ii libcairo2 1.8.10-6 The Cairo 2D vector graphics libra ii libdbus-1-31.2.24-4+squeeze1 simple interprocess messaging syst ii libdbus-glib-1-2 0.88-2.1 simple interprocess messaging syst ii libevince2 2.30.3-2 Document (PostScript, PDF) renderi ii libfontconfig1 2.8.0-2.1 generic font configuration library ii libfreetype6 2.4.2-2.1+squeeze1FreeType 2 font engine, shared lib ii libgconf2-42.28.1-6 GNOME configuration database syste ii libglib2.0-0 2.24.2-1 The GLib library of C routines ii libgnome-keyring0 2.30.1-1 GNOME keyring services library ii libgtk2.0-02.20.1-2 The GTK+ graphical user interface ii libice62:1.0.6-2 X11 Inter-Client Exchange library ii libnautilus-extens 2.30.1-2squeeze1 libraries for nautilus components ii libpango1.0-0 1.28.3-1+squeeze2 Layout and rendering of internatio ii libsm6 2:1.1.1-1 X11 Session Management library ii libx11-6 2:1.3.3-4 X11 client-side library ii libxml22.7.8.dfsg-2+squeeze1 GNOME XML library ii shared-mime-info 0.71-4FreeDesktop.org shared MIME databa ii zlib1g 1:1.2.3.4.dfsg-3 compression library - runtime Versions of packages evince recommends: ii dbus-x11 1.2.24-4+squeeze1 simple interprocess messaging syst ii gvfs 1.6.4-3 userspace virtual filesystem - ser Versions of packages evince suggests: ii nautilus2.30.1-2squeeze1 file manager and graphical shell f pn poppler-datanone (no description available) pn unrar none (no description available) -- no debconf information -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#622345: imagej: still the same with Squeeze...
Package: imagej Version: 1.45e-1 Severity: normal Hi, I upgraded to Squeeze (with ImageJ from Sid, ver. 1.45e-1), but it did not make things better (neither did Squeeze's original version). Any other idea how to solve this? Around me there are some Windows machines and ImageJ seems to run smoothly :-) I have not anything else with Debian, but I may try it on other machines with Ubuntu Maverick Meerkat or SuseLinuxEnterpriseDesktop 11 if that could help find the solution of the problem. Shall I do it? Best, Martin W. Here is the sample session: louskacek@zouzel:~$ imagej Open other images in this ImageJ panel as follows: imagej -p 1 image1 [image2 ... imageN] #guess what happens here :-) #yes, you are right, the main panel appears and disappears #with this version it is faster than before :-) Exception in thread main java.lang.NullPointerException at java.awt.Component.setDropTarget(libgcj.so.10) at ij.plugin.DragAndDrop.run(DragAndDrop.java:28) at ij.IJ.runPlugIn(IJ.java:156) at ij.IJ.runPlugIn(IJ.java:139) at ij.ImageJ.init(ImageJ.java:196) at ij.ImageJ.main(ImageJ.java:588) louskacek@zouzel:~$ -- System Information: Debian Release: 6.0.1 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable') Architecture: amd64 (x86_64) Kernel: Linux 2.6.26-2-amd64 (SMP w/2 CPU cores) Locale: LANG=cs_CZ.UTF-8, LC_CTYPE=cs_CZ.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Versions of packages imagej depends on: ii openjdk-6-jre 6b18-1.8.3-2 OpenJDK Java runtime, using Hotspo imagej recommends no packages. Versions of packages imagej suggests: pn java-virtual-machine none (no description available) -- no debconf information -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#622345: imagej: 1.45e - well, still nothing
Package: imagej Version: 1.45e-1 Followup-For: Bug #622345 Hi, I installed the 1.45e-1 version of ImageJ as Andreas suggested, and its behaviour is still the same: short blink of some panel (looks like main menu) and failure. Of course, it could be my fault, but I cannot see it. Thank You for your support. Best, Martin W. Here is the session: louskacek@zouzel:~$ imagej Open other images in this ImageJ panel as follows: imagej -p 1 image1 [image2 ... imageN] #here the panel appeared and swiftly disappeared Exception in thread main java.lang.NullPointerException at java.awt.Component.setDropTarget(libgcj.so.90) at ij.plugin.DragAndDrop.run(DragAndDrop.java:28) at ij.IJ.runPlugIn(IJ.java:156) at ij.IJ.runPlugIn(IJ.java:139) at ij.ImageJ.init(ImageJ.java:196) at ij.ImageJ.main(ImageJ.java:588) louskacek@zouzel:~$ -- System Information: Debian Release: 5.0.8 APT prefers oldstable-proposed-updates APT policy: (500, 'oldstable-proposed-updates'), (500, 'oldstable') Architecture: amd64 (x86_64) Kernel: Linux 2.6.26-2-amd64 (SMP w/2 CPU cores) Locale: LANG=cs_CZ.UTF-8, LC_CTYPE=cs_CZ.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/bash Versions of packages imagej depends on: ii openjdk-6-jre6b18-1.8.3-2~lenny1 OpenJDK Java runtime, using Hotspo imagej recommends no packages. Versions of packages imagej suggests: ii gij [java-virtual-ma 4:4.3.2-2 The GNU Java bytecode interpreter ii gij-4.3 [java-virtua 4.3.2-2 The GNU Java bytecode interpreter ii java-gcj-compat [jav 1.0.78-2Java runtime environment using GIJ ii java-gcj-compat-head 1.0.78-2Java runtime environment using GIJ ii openjdk-6-jre-headle 6b18-1.8.3-2~lenny1 OpenJDK Java runtime, using Hotspo -- no debconf information -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#622345: imagej: I have got openjdk-6-jre
Package: imagej Version: 1.45e-1 Followup-For: Bug #622345 Hi, as can be seen from the report below, I have got openjdk-6-jre, in the oldstable (Lenny) version 6b18-1.8.3-2~lenny1. Shall I upgrade it? If yes, is stable (Squeeze) version OK, or do I have to take it from Wheezy or Sid? Best, Martin W. -- System Information: Debian Release: 5.0.8 APT prefers oldstable-proposed-updates APT policy: (500, 'oldstable-proposed-updates'), (500, 'oldstable'), (500, 'testing') Architecture: amd64 (x86_64) Kernel: Linux 2.6.26-2-amd64 (SMP w/2 CPU cores) Locale: LANG=cs_CZ.UTF-8, LC_CTYPE=cs_CZ.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/bash Versions of packages imagej depends on: ii openjdk-6-jre6b18-1.8.3-2~lenny1 OpenJDK Java runtime, using Hotspo imagej recommends no packages. Versions of packages imagej suggests: ii gij [java-virtual-ma 4:4.3.2-2 The GNU Java bytecode interpreter ii gij-4.3 [java-virtua 4.3.2-2 The GNU Java bytecode interpreter ii java-gcj-compat [jav 1.0.78-2Java runtime environment using GIJ ii java-gcj-compat-head 1.0.78-2Java runtime environment using GIJ ii openjdk-6-jre-headle 6b18-1.8.3-2~lenny1 OpenJDK Java runtime, using Hotspo -- no debconf information -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#622345: imagej: 1.44c - same behaviour
Package: imagej Version: 1.44c-3 Followup-For: Bug #622345 Hi, upgrade of ImageJ to 1.44c did not help - I see the same behaviour. Shall I check the 1.44n version? Thank you for your interest. Martin Weiser -- System Information: Debian Release: 5.0.8 APT prefers oldstable-proposed-updates APT policy: (500, 'oldstable-proposed-updates'), (500, 'oldstable') Architecture: amd64 (x86_64) Kernel: Linux 2.6.26-2-amd64 (SMP w/2 CPU cores) Locale: LANG=cs_CZ.UTF-8, LC_CTYPE=cs_CZ.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/bash Versions of packages imagej depends on: ii openjdk-6-jre6b18-1.8.3-2~lenny1 OpenJDK Java runtime, using Hotspo imagej recommends no packages. Versions of packages imagej suggests: ii gij [java-virtual-ma 4:4.3.2-2 The GNU Java bytecode interpreter ii gij-4.3 [java-virtua 4.3.2-2 The GNU Java bytecode interpreter ii java-gcj-compat [jav 1.0.78-2Java runtime environment using GIJ ii java-gcj-compat-head 1.0.78-2Java runtime environment using GIJ ii openjdk-6-jre-headle 6b18-1.8.3-2~lenny1 OpenJDK Java runtime, using Hotspo -- no debconf information -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#622345: imagej: Version 1.44n-1 - still the same
Package: imagej Version: 1.44n-1 Followup-For: Bug #622345 Dear maintainers, I updated ImageJ to 1.44n-1 and the behaviour is still the same - short blink of menu and failure. Any advice? Thank you. Martin Weiser -- System Information: Debian Release: 5.0.8 APT prefers oldstable-proposed-updates APT policy: (500, 'oldstable-proposed-updates'), (500, 'oldstable') Architecture: amd64 (x86_64) Kernel: Linux 2.6.26-2-amd64 (SMP w/2 CPU cores) Locale: LANG=cs_CZ.UTF-8, LC_CTYPE=cs_CZ.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/bash Versions of packages imagej depends on: ii openjdk-6-jre6b18-1.8.3-2~lenny1 OpenJDK Java runtime, using Hotspo imagej recommends no packages. Versions of packages imagej suggests: ii gij [java-virtual-ma 4:4.3.2-2 The GNU Java bytecode interpreter ii gij-4.3 [java-virtua 4.3.2-2 The GNU Java bytecode interpreter ii java-gcj-compat [jav 1.0.78-2Java runtime environment using GIJ ii java-gcj-compat-head 1.0.78-2Java runtime environment using GIJ ii openjdk-6-jre-headle 6b18-1.8.3-2~lenny1 OpenJDK Java runtime, using Hotspo -- no debconf information -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#622345: imagej: fails just after the invocation
Package: imagej Version: 1.40a-1 Severity: important Hello, when I invoke ImageJ from the command line, it fails after several (approx. 3) seconds. After printing the first two lines of the response, some graphic element appears and swiftly disappears. I have no idea about the cause, sorry. Thank you for your patience. Martin Weiser Here is an example of the session: louskacek@zouzel:~$ imagej Open other images in this ImageJ panel as follows: imagej -p 1 image1 [image2 ... imageN] # here something appears and disappears instantly, it looks like some # kind of menu Exception in thread main java.lang.NullPointerException at java.awt.Component.setDropTarget(libgcj.so.90) at ij.plugin.DragAndDrop.run(DragAndDrop.java:24) at ij.IJ.runPlugIn(IJ.java:131) at ij.IJ.runPlugIn(IJ.java:113) at ij.ImageJ.init(ImageJ.java:182) at ij.ImageJ.main(ImageJ.java:506) louskacek@zouzel:~$ -- System Information: Debian Release: 5.0.8 APT prefers oldstable-proposed-updates APT policy: (500, 'oldstable-proposed-updates'), (500, 'oldstable') Architecture: amd64 (x86_64) Kernel: Linux 2.6.26-2-amd64 (SMP w/2 CPU cores) Locale: LANG=cs_CZ.UTF-8, LC_CTYPE=cs_CZ.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/bash Versions of packages imagej depends on: ii gij 4:4.3.2-2 The GNU Java bytecode interpreter ii java-gcj-compat [java2-runtim 1.0.78-2 Java runtime environment using GIJ imagej recommends no packages. Versions of packages imagej suggests: pn java2-compilernone (no description available) -- no debconf information -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
