Question: Problem to update the core packages
1
gravatar for ajaz240792
12 weeks ago by
ajaz24079210
ajaz24079210 wrote:

I tried to update the core packages using the suggested commands in Bioconductor

> BiocManager::install()

But I get the following error

The downloaded source packages are in
    ‘/tmp/Rtmp6l1eeP/downloaded_packages’
installation path not writeable, unable to update packages: abind, acepack,
  askpass, assertthat, backports, base64enc, BH, bitops, broom, caTools,
  cellranger, cli, clipr, colorspace, crayon, crosstalk, curl, data.table,
  DBI, estimability, fansi, forcats, foreach,.......... rpart, spatial, survival

I tried the way suggested by https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html#managing-multiple-versions using the method

> BiocManager::valid()

but the answer was the same

I suppose that the problem is: installation path not writeable,

software error • 118 views
ADD COMMENTlink modified 12 weeks ago by Martin Morgan ♦♦ 23k • written 12 weeks ago by ajaz24079210
Answer: Problem to update the core packages
0
gravatar for Martin Morgan
12 weeks ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

Yes, the path where the files abind, ... are not writeable by you. Probably these packages were installed by some other account, e.g., the administrator, and can't be updated by you. Mostly I would suggest ignoring these messages. Alternatively, investigate ?.libPaths and arrange that only directories you have control of are listed there. You might need to re-install a number of packages, so if you have a deadline tomorrow...

ADD COMMENTlink written 12 weeks ago by Martin Morgan ♦♦ 23k

Hello

Thanks for the advice

I figured out the problem

I only had to update the packages using the terminal of the system instead of RStudio

The exact commands inside the terminal were:

$ sudo R $ BiocManager::install() $ a

Thanks

ADD REPLYlink written 11 weeks ago by ajaz24079210
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