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Error Installing CMTK #4
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Hi @tpisano, Thanks for your bug report. It seems that the problem comes from a bug in jython that is present in the rather out of date jython 2.5.3 distributed with Fiji http://bugs.jython.org/issue1885 There are a few options
Sorry for the inconvenience! Best, Greg. Editing generated scripts #!/bin/sh
# 2012-08-29_11.06.04
cd "/GD/projects/PN2/warpbench"
"/Applications/Fiji.app/bin/cmtk/munger" -b "/Applications/Fiji.app/bin/cmtk" -a -w -r 010203 -X 26 -C 8 -G 80 -R 4 -A '--accuracy 0.4' -W '--accuracy 0.4' -T 4 -s "images/TKC1RLH_raw01.nrrd" images
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PS Just to add that I have tested option 1. above (enabling the IMCF Uni Basel update site) and I recommend it as the easiest solution for the time being. Full details of how to do this here: http://fiji.sc/How_to_follow_a_3rd_party_update_site. Best wishes, Greg. |
for reference Jython 2.5.3 is current production version even if it appears to contain "many bugs which have been fixed in 2.5.4rc1" |
Hi @tpisano, I have now commited a fix for this issue (in commit 97986f2). I would be grateful if you could try updating the CMTK gui code (either from within Fiji or reinstalling as per the README) and see if it works for you. Note that this does not require either of the workarounds described above (i.e. it works with the stock jython distributed with Fiji). Thanks, Greg Jefferis. |
Hi Greg, On Thu, Apr 16, 2015 at 11:20 AM, Gregory Jefferis <notifications@github.com
Tom Pisano |
Hi @tpisano,
Glad to hear that worked for you. If you look on the front page, you'll see there is now a new update mechanism, which should in theory simplify installation/updates. If you have the chance I would be grateful for feedback/testing. |
Hi @jefferis, Traceback (most recent call last): cmtkgui.download_and_untar_url(download_url,cmtkgui.install_dir(),untar_binaries,download_file) On Mon, Apr 20, 2015 at 7:55 PM, Gregory Jefferis notifications@github.com
Tom Pisano |
Hi Tristan, I have no experience on Windows, although if you have a cygwin environment it should definitely be possible to get it to work. On 6 May 2015, at 15:22, tpisano notifications@github.com wrote:
Thanks for any debugging you can do. Looks like there is a problem removing the temporary file (which should only happen at the end of the install process). Do you think the files have actually been installed? is the temp file still there? Gregory Jefferis, PhD http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis |
Hi @jefferis , I tried to install CMTK on my FIJI following the instruction on: https://github.com/jefferis/fiji-cmtk-gui. |
Hi Gregory, I have installed CMTK in Fiji and run it on an iMac 15,1 with OS 10.11.6. I then get a file named "munger_2016-10-25_14.50.29.command". When I open this file I get the following message in "Terminal": dhcp229:~ Jakob$ /Volumes/RAID\ 24\ GB/CMTK/commands/munger_2016-10-25_14.50.29.command ; exit; [Prozess beendet] Appararently, there appears to be a problem with "Can't locate IO/Compress/Gzip.pm in @inc". What should I do? Can you help? Thanks a lot! Jakob |
It seems a perl module is missing on your system. This is the module http://search.cpan.org/~pmqs/IO-Compress-2.069/lib/IO/Compress/Gzip.pm I think you need to run the cpan command line tool (see e.g. http://www.livejournal.com/doc/server/lj.install.perl_setup.modules.html) install IO::Compress More generally I think it might be that there is a more modern alternative to that module which would be installed on macosx 10.11 |
Thank you so much for your prompt response Gregory! I will try to install the missing module. Cheers, |
Followed the installation process as described on http://www.livejournal.com/doc/server/lj.install.perl_setup.modules.html using cpan. cpan[3]> reload cpan cpan shell -- CPAN exploration and modules installation (v2.14) cpan[4]> install IO::Compress
to find objects with matching identifiers. cpan[5]> install Compress::Zlib cpan[6]>Unfortunately, however, "install IO::Compress " failed (see above). And still same error when running "munger_2016-10-25_13.53.39.command" Last login: Tue Oct 25 17:13:37 on ttys000 [Prozess beendet]Not sure, how to proceed? Cheers, |
Sorry, overlooked this, used i /IO::Compress/cpan[6]> i /IO::Compress/ 27 items foundStill, does not work |
I think
should be what is required but I had trouble getting it to behave on my system. |
cpan[35]> install IO::Compress::Gzip cpan[36]> whereis gzip |
cpan[37]> install PMQS/IO-Compress-2.069.tar.gz |
OK. So now will munger run?! |
No. Have no idea why not? |
Always the sameCan't locate IO/Compress/Gzip.pm in @inc (@inc contains: /opt/local/lib/perl5/5.8.9/darwin-2level /opt/local/lib/perl5/5.8.9 /opt/local/lib/perl5/site_perl/5.8.9/darwin-2level /opt/local/lib/perl5/site_perl/5.8.9 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl/5.8.9/darwin-2level /opt/local/lib/perl5/vendor_perl/5.8.9 /opt/local/lib/perl5/vendor_perl .) at /Applications/Fiji.app/bin/cmtk/munger line 47. BEGIN failed--compilation aborted at /Applications/Fiji.app/bin/cmtk/munger line 47. |
Also several times re-run: Be aware that after freshly installing make / gcc, your perl installation will not necessarily detect it. This means module installation will still fail during the 'make' stage. You may need to invoke the CPAN shell and run the setup routine again, to point to the location of make: perl -MCPAN -e shell CPANcpan> o conf make /usr/bin/make cpan> o conf commit |
cpan[38]> whereis gzip cpan[39]> exit cpan shell -- CPAN exploration and modules installation (v2.14) cpan[1]> o conf make /usr/bin/make cpan[2]> o conf commit cpan[3]> |
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1. Closed Terminal. Double clicked on "munger_2016-10-25_15.12.28.command". Terminal opens in the split of a second with the followingLast login: Tue Oct 25 18:00:41 on ttys000 [Prozess beendet]
PS: Also downloaded and installed "IO-Compress-2.069.tar.gz" - dont't know if this causes problems |
! |
You have mail.
Munge a BioRad PIC or nrrd file or (recursively) parse a directory of PIC/nrrd [Prozess beendet] |
/Volumes/RAID\ 24\ GB/CMTK/commands/munger_2016-10-25_15.12.28.command ; exit; Ran 0 initial affine registrations of which 0 failed [Prozess beendet] |
Changed "#!/usr/bin/env perl" in munger (in Fiji) in "#!/usr/bin/perl" like you suggested |
So, I'm pretty sure my final diagnosis is correct – you have one or more conflicting perl installations. You should be fine to run like this for the time being. Best, Greg. |
Great diagnosis, Greg!!! Alright, so just changing the first line in the "munger" to another directory is sufficient for me to run it. I guess this is easier than to get rid of one of the two Perl versions, right? |
If you need to do some other perl stuff then you may need to figure out what's up with these different perls. But to run munger/cmtk you should be good to go as is. |
You have mail. |
Apparently, running now .. Thank you so much for your help, Greg, and regards to Cambridge (may be I have installed that other conflicting Perl version back there, I am not sure). Great! |
Hi,
I am quite a novice when it comes to scripting, so this could be a simple fix. However, after following the instructions (twice) on the README, I get the same errors from the FIJI log on the "Install CMTK" Step. See log below.
Thanks!
'''
/Applications/Fiji.app/bin/cmtk
Downloading CMTK-3.2.3-MacOSX-10.6-x86_64.tar.gz from url http://www.nitrc.org/frs/download.php/7365/CMTK-3.2.3-MacOSX-10.6-x86_64.tar.gz/?i_agree=1&download_now=1 to /Applications/Fiji.app/bin/cmtk
Downloading http://www.nitrc.org/frs/download.php/7365/CMTK-3.2.3-MacOSX-10.6-x86_64.tar.gz/?i_agree=1&download_now=1 to /var/folders/_m/5v483npn77j5_dwflsbylfk80000gp/T/tmppvyhQxCMTK-3.2.3-MacOSX-10.6-x86_64.tar.gz
Download size should be 60027277
Downloaded file has size 60027277
Extracting tar file
Installing binaries to /Applications/Fiji.app/bin/cmtk
Traceback (most recent call last):
File "/Applications/Fiji.app/plugins/CMTK_Registration/Install_CMTK.py", line 76, in
cmtkgui.download_and_untar_url(download_url,cmtkgui.install_dir(),untar_binaries,download_file)
File "pyclasspath/cmtkgui$py.class", line 317, in download_and_untar_url
File "/Applications/Fiji.app/plugins/CMTK_Registration/Install_CMTK.py", line 50, in untar_binaries
shutil.move(frompath,target_dir)
File "/Applications/Fiji.app/jars/jython-shaded-2.5.3.jar/Lib/shutil.py", line 205, in move
File "/Applications/Fiji.app/jars/jython-shaded-2.5.3.jar/Lib/shutil.py", line 97, in copy2
File "/Applications/Fiji.app/jars/jython-shaded-2.5.3.jar/Lib/shutil.py", line 74, in copystat
OSError: [Errno 20000] Unknown error: 20000: u'/Applications/Fiji.app/bin/cmtk/cmtk'
'''
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