Open peteratfunction opened 6 months ago
Hi @peteratfunction, looking at it now
Just checking up on this and to ask if there is any testing I can do to help identify the source of the problem?
To follow up on this I'm having the same issue, is there any update?
Having the same issue running the command from the dockerfile.
@jcjimbo @peteratfunction We had fixed a couple of things in crisprScore
to support code that was written in Python 2.7.
The latest version (1.9.1) should work
Many thanks for the reply and addressing the issue.
I managed to get it running initally with an error:
Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'query': failed to connect reason: lazy-load database '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/yaml/R/yaml.rdb' is corrupt Consider rerunning with 'localHub=TRUE'
Upon an R session refesh the error is now:
snapshotDate(): 2024-07-16 see ?crisprScoreData and browseVignettes('crisprScoreData') for documentation loading from cache Traceback (most recent call last): File "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/crisprScore/python/crisprai/getWeissmanScores.py", line 105, in <module> scores = predictWeissmanScore(tssTable, p1p2Table, sgrnaTable, libraryTable, pickleFile, fastaFile, chromatinFiles, modality, verbose) File "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/crisprScore/python/crisprai/getWeissmanScores.py", line 26, in predictWeissmanScore paramTable = getParamTable(tssTable, p1p2Table, sgrnaTable, libraryTable, fastaFile, chromatinFiles, verbose) File "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/crisprScore/python/crisprai/getWeissmanScores.py", line 61, in getParamTable raise Exception('Error generating parameter table.') Exception: Error generating parameter table. Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file '/var/folders/vm/gdslj1hs0w1dj_wdlp589w700000gn/T//RtmpRJYKQ8/scores.txt': No such file or directory
So I am unsure how to get it running from now, do you have any suggestions?
I am trying to run getCrispraiScores using the vignette example, but run into the following error.
Docker install:
R:
R output:
sessionInfo