Open thawn opened 1 year ago
p.s. the conda bug is hilarious to read
I guess this is the reason that the TUD HPC team discourages the use of conda and recommends virtualenv instead.
Hi Till @thawn ,
I just uploaded clijx-assistant version 0.6.2.0 to the ImageJ update site. What's new: It asks where to save the notebook. This should allow mac-users to open the notebook themselves in their Jupyter lab. Would you mind trying out if it works on your Mac?
Thanks!
Best, Robert
Hi @haesleinhuepf,
thanks a lot for the quick fix. Saving a notebook works now. There are two (more cosmetic) issues remaining:
null.ipynb
which sounds like a variable is not set/Users/korten/Applications/Fiji.app/ conda activate dbnapari-arm64 cd /Users/korten/Applications/Fiji.app jupyter nbconvert --execute --to notebook /Users/korten/Desktop/null.ipynb jupyter notebook /Users/korten/Desktop/null.nbconvert.ipynb Attempt 1 java.lang.RuntimeException: java.io.IOException: Cannot run program "/Users/korten/Applications/Fiji.app/temp.bat" (in directory "/Users/korten/Applications/Fiji.app"): error=13, Permission denied at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:135) at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:69) at net.haesleinhuepf.clijx.assistant.utilities.AssistantUtilities$6.run(AssistantUtilities.java:1404) at java.lang.Thread.run(Thread.java:750) Caused by: java.io.IOException: Cannot run program "/Users/korten/Applications/Fiji.app/temp.bat" (in directory "/Users/korten/Applications/Fiji.app"): error=13, Permission denied at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at java.lang.Runtime.exec(Runtime.java:622) at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:96) ... 3 more Caused by: java.io.IOException: error=13, Permission denied at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 5 more Attempt 2 java.lang.RuntimeException: java.io.IOException: Cannot run program "/Users/korten/Applications/Fiji.app/temp.bat" (in directory "/Users/korten/Applications/Fiji.app"): error=13, Permission denied at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:135) at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:69) at net.haesleinhuepf.clijx.assistant.utilities.AssistantUtilities$6.run(AssistantUtilities.java:1422) at java.lang.Thread.run(Thread.java:750) Caused by: java.io.IOException: Cannot run program "/Users/korten/Applications/Fiji.app/temp.bat" (in directory "/Users/korten/Applications/Fiji.app"): error=13, Permission denied at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at java.lang.Runtime.exec(Runtime.java:622) at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:96) ... 3 more Caused by: java.io.IOException: error=13, Permission denied at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess. (UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 5 more
When I generate a notebook on my M1 mac with clij in fiji, jupyter lab does not open and I get the following error on the console.
error message
cd /Users/korten/Applications/Fiji.app jupyter nbconvert --execute --to notebook /var/folders/8s/7jr95f1d28vflnwm1cfqv7t40000gr/T/temp1685006993158/new1.ipynb jupyter notebook /var/folders/8s/7jr95f1d28vflnwm1cfqv7t40000gr/T/temp1685006993158/new1.nbconvert.ipynb Attempt 1 java.lang.RuntimeException: java.io.IOException: Cannot run program "/Users/korten/Applications/Fiji.app/temp.bat" (in directory "/Users/korten/Applications/Fiji.app"): error=13, Permission denied at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:135) at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:69) at net.haesleinhuepf.clijx.assistant.utilities.AssistantUtilities$6.run(AssistantUtilities.java:1404) at java.lang.Thread.run(Thread.java:750) Caused by: java.io.IOException: Cannot run program "/Users/korten/Applications/Fiji.app/temp.bat" (in directory "/Users/korten/Applications/Fiji.app"): error=13, Permission denied at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at java.lang.Runtime.exec(Runtime.java:622) at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:96) ... 3 more Caused by: java.io.IOException: error=13, Permission denied at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.Fix
chmod a+x temp.bat
I would have loved to submit a pull request, but the code that creates temp.bat appears at two positions and I was not sure where to fix it.