BiocCheck path escape issue
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@mjsteinbaugh
Last seen 9 months ago
28-7 Therapeutics

I sync my local R package library over Dropbox for easy switching between machines. Our group recently upgraded to Dropbox Business, which consequently changed the path to my library from ~/Dropbox/R/library to ~/"Dropbox (Personal)/R/library".  I noticed that BiocCheck doesn't appear to escape the file path to the package library in some of the commands performed. Here's a copy of the output:

This is BiocCheck version 1.11.7. BiocCheck is a work in progress. Output and
severity of issues may change. Installing package...
sh: -c: line 0: syntax error near unexpected token `('
sh: -c: line 0: `R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Users/mike/Dropbox (Personal)/R/library/BiocCheck/script/checkBadDeps.R --args "/var/folders/j1/hw6j14mj3wq381x7mynwfbp00000gn/T//Rtmp8RbPbf/lib/basejump" 2>/dev/null'
Warning: running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Users/mike/Dropbox (Personal)/R/library/BiocCheck/script/checkBadDeps.R --args "/var/folders/j1/hw6j14mj3wq381x7mynwfbp00000gn/T//Rtmp8RbPbf/lib/basejump" 2>/dev/null' had status 2​
bioccheck bug • 703 views
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@martin-morgan-1513
Last seen 50 minutes ago
United States

Thanks, that should be fixed in the 'devel' version 1.13.1, available in svn now. (Probably this developer-related question belongs on the bioc-devel mailing list).

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@mjsteinbaugh
Last seen 9 months ago
28-7 Therapeutics

Thanks I'll be sure to post anything like this to bioc-devel in the future.

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