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gtDMMB / RNAStructViz

Visualization, comparison, and analysis of RNA secondary structures via a cross-platform GUI
https://github.com/gtDMMB/RNAStructViz/wiki
GNU General Public License v3.0
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permissions on sample files? #43

Closed ceheitsch closed 5 years ago

ceheitsch commented 5 years ago

$ /usr/local/opt/rnastructviz/share/RNAStructViz/ERROR: Opening file "/usr/local/opt/rnastructviz/share/RNAStructViz/sample_structures/C.elegans_GTfold_16S.dot" : Permission denied [1]+ Segmentation fault: 11 /usr/local/opt/rnastructviz/bin/RNAStructViz

Note that the ct files (like C.elegans_GTfold_16S.ct) opened fine, so it's a file problem not a directory problem.

ceheitsch commented 5 years ago

Noting that file content is visible in RNAStructViz viewer (right frame of file loader window).

ceheitsch commented 5 years ago

Appears to be the same problem: $ /usr/local/opt/rnastructviz/bin/RNAStructViz ERROR: Opening file "/usr/local/opt/rnastructviz/share/RNAStructViz/sample_structures/helix_format_sample.helix" : Permission denied Segmentation fault: 11

maxieds commented 5 years ago

@ceheitsch I was not able to reproduce your error on the remote Mac OSX box, nor on Linux. The first run instructions suggest that you copy the sample structure files into your home directory. I did also change the Makefile on the most recent version of RNAStructViz (v1.6.5-testing) to chmod those files to permissions of 555, which might make a difference on your system. Please reinstall StructViz and try again to see if the problem persists.

maxieds commented 5 years ago

@ceheitsch Can you please respond to the previous message? So we can get this issue handled and on the closed list?

ceheitsch commented 5 years ago

@maxieds Same problem with C.elegans_GTfold_16S.dot file even when sample_structures is copied to home directory. The file can be edited in vi, so unclear why RNAStructViz won't load it.

ceheitsch commented 5 years ago

@maxieds Confirming that RNAStructViz (v1.6.5-testing) was reinstalled prior to testing. There are no differences in the permissions of the files on the command line. The *.dot file preview correctly appears in the small window. It is only when actually loading the file that the error message (documented above) appears.

maxieds commented 5 years ago

@ceheitsch Please test out the new permissions on the installed files with version v1.6.6-testing. The updated brew package for this version is now posted. You will need to reinstall to test the changes. I for some reason cannot get the VNC client to work over the slow house wifi connection, so I am not able to test it myself at the moment.

ceheitsch commented 5 years ago

Followed reinstall instructions on wiki. Resulted in:

Error: Directory not empty @ dir_s_rmdir - /usr/local/Cellar/rnastructviz/v1.6.6-testing_1 Installed version is still v1.6.5-testing and it's unlikely that I will have time to circle back to this until next week.

maxieds commented 5 years ago

This is fixed in the latest release. The sample structures directory files are now copied with the brew script installer, which leads to correct (and tested) permissions.