Question: BiocCheck path escape issue
0
gravatar for Michael Steinbaugh
2.6 years ago by
Constellation Pharmaceuticals
Michael Steinbaugh40 wrote:

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​
bug bioccheck • 502 views
ADD COMMENTlink modified 2.5 years ago • written 2.6 years ago by Michael Steinbaugh40
Answer: BiocCheck path escape issue
1
gravatar for Martin Morgan
2.5 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

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).

ADD COMMENTlink written 2.5 years ago by Martin Morgan ♦♦ 24k
Answer: BiocCheck path escape issue
0
gravatar for Michael Steinbaugh
2.5 years ago by
Constellation Pharmaceuticals
Michael Steinbaugh40 wrote:

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

ADD COMMENTlink written 2.5 years ago by Michael Steinbaugh40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 300 users visited in the last hour