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Question: R says include dir is empty, but it's not.
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gravatar for ariel
5 weeks ago by
ariel0
ariel0 wrote:

I don't know if this is an R issue, RStudio issue, or Bioconductor issue.

When I try to install some packages, in this specific case DECIPHER, I get:

> biocLite('DECIPHER', suppressUpdates=T)
trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/DECIPHER_2.6.0.tar.gz'
Content type 'application/x-gzip' length 12633118 bytes (12.0 MB)
==================================================
downloaded 12.0 MB

* installing *source* package ‘DECIPHER’ ...
** libs
Warning: R include directory is empty -- perhaps need to install R-devel.rpm or similar
/home/balter/conda/lib/R/etc/Makeconf:10: /envs/dada2/lib/R/share/make/vars.mk: No such file or directory
make: /envs/dada2/lib/R/share/make/shlib.mk: No such file or directory
make: *** No rule to make target '/envs/dada2/lib/R/share/make/shlib.mk'.  Stop.
ERROR: compilation failed for package ‘DECIPHER’
* removing ‘/home/balter/conda/envs/dada2/lib/R/library/DECIPHER’

The downloaded source packages are in
    ‘/tmp/RtmpwH2lcr/downloaded_packages’

> Sys.getenv('R_INCLUDE_DIR')
[1] "/home/balter/conda/envs/dada2/lib/R/include/"
> list.files(Sys.getenv('R_INCLUDE_DIR'))
 [1] "R_ext"        "R.h"          "Rconfig.h"    "Rdefines.h"   "Rembedded.h"  "Rinterface.h" "Rinternals.h"
 [8] "Rmath.h"      "Rversion.h"   "S.h" 
ADD COMMENTlink modified 5 weeks ago by Martin Morgan ♦♦ 22k • written 5 weeks ago by ariel0
0
gravatar for Martin Morgan
5 weeks ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

Remember that you are using a conda installation, so that the correct way to install Bioconductor packages is to use conda install, NOT biocLite. This is a conda issue, and should be reported there (readers of this forum are not in a position to fix it).

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Martin Morgan ♦♦ 22k
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