Help installing depmap on R 3.6.3
1
1
Entering edit mode
@gene_bioconductor-22210
Last seen 11 months ago

I'm trying to install the depmap package on an R 3.6.3 system. When I do it through Bioconductor, I get: package ‘depmap’ is not available (for R version 3.6.3). So I tried installing from source and I get this error: error: ‘rnai_19Q2’ not found in ExperimentHub.

Here is the full output from the installation attempt:

> sudo R --vanilla  CMD INSTALL depmap_1.3.1.tar.gz
* installing to library ‘/usr/local/lib/R/site-library’
* installing *source* package ‘depmap’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Using temporary cache /tmp/RtmpgYP52U/BiocFileCache
Warning: `select_()` is deprecated as of dplyr 0.7.0.
Please use `select()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: `filter_()` is deprecated as of dplyr 0.7.0.
Please use `filter()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
snapshotDate(): 2019-04-29
Using temporary cache /tmp/RtmpgYP52U/BiocFileCache
Using temporary cache /tmp/RtmpgYP52U/BiocFileCache
Using temporary cache /tmp/RtmpgYP52U/BiocFileCache
snapshotDate(): 2019-04-29
Using temporary cache /tmp/RtmpgYP52U/BiocFileCache
Using temporary cache /tmp/RtmpgYP52U/BiocFileCache
Error: package or namespace load failed for ‘depmap’:
 .onLoad failed in loadNamespace() for 'depmap', details:
  call: FUN(X[[i]], ...)
  error: ‘rnai_19Q2’ not found in ExperimentHub
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/depmap’

So do I need to take the plunge and upgrade to R 4.0 to get depmap to install?

depmap • 221 views
ADD COMMENT
0
Entering edit mode
@martin-morgan-1513
Last seen 16 days ago
United States

When BiocManager::install("depmap") reports that the package is not available for your version of R, it's telling the truth. Trying to work around this results in an error. Apparently, it relies on resources present in ExperimentHub that were added when the package was added to Bioconductor.

If you'd like to use depmap, then I suggest updating your R to the current version (4.0.2).

ADD COMMENT

Login before adding your answer.

Traffic: 462 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6