Update package permission Everytime

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vivekr • 0

@vivekr-14904

Last seen 5.6 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.

software error R bioconductor rmysql • 996 views

ADD COMMENT • link 6.7 years ago vivekr • 0

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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?

ADD REPLY • link 6.7 years ago Aaron Lun ★ 28k

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