Entering edit mode
vivekr
•
0
@vivekr-14904
Last seen 5.3 years ago
Hi,
Everytime, when I execute any of the script (NGS pipeline most of the time) in which bioconductor is called, then I got the following message every time :
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help BioC_mirror: https://bioconductor.org Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30). installation path not writeable, unable to update packages: RMySQL, cluster, Matrix Old packages: 'lme4', 'network' Update all/some/none? [a/s/n]:
This will not succeed until I press `n`. I tried some other ways to update packages by working in R as a sudo user and then call bioconductor and then press `a` so that there is no issue related to permission. But in case of few packages, it is still not working. I need suggestions. Thanks.
As the posting guide instructs, you should show the code that is causing the problem. We aren't psychic. I presume you're calling
biocLite()
in your script (unnecessarily, it would seem); what are the arguments? What is the context?