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Question: csaw intallation issue: cannot find "lib" in Rhtslib installation
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gravatar for favorov
25 days ago by
favorov0
JHMI; VIGG RAS
favorov0 wrote:

I have got an issue with the csaw (and, thus, diffHiC) installation.

I install it with biocLite('csaw') (or, it is called if I ran biocLite('diffHic')) 

It asks the system for lib folder of Rhstlib: system.file("lib", package = "Rhtslib", mustWork = TRUE)

But, on my system, Rhtslib created 'lib64' folder instead:

> ls /home/sasha/R/x86_64-suse-linux-gnu-library/3.4/Rhtslib
DESCRIPTION  doc  help  html  include  INDEX  lib64  libs  Meta  NAMESPACE  R

I've cheated it with "ln -s lib64 lib" in the folder, but it does not look a proper way. 

R version 3.4.2 (2017-09-28)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE Leap 42.2


 Rhtslib_1.8.0; csaw_1.10.0; diffHic_1.8.1
ADD COMMENTlink modified 24 days ago by Martin Morgan ♦♦ 20k • written 25 days ago by favorov0

I would add a Rhtslib tag to this post. In particular, this seems to be a Rhtslib problem as the problematic call occurs in Rhtslib::pkgconfig. It's probably because RHTSLIB_LIBDIR specifies ${R_ARCH} but pkgconfig does not - this variable seems to be empty most of the time, which is why pkgconfig usually works, but in your case it fails.

ADD REPLYlink modified 25 days ago • written 25 days ago by Aaron Lun17k

Thank you! I've added the tag.

 

ADD REPLYlink written 24 days ago by favorov0

On windows, it seems like R_ARCH is defined as, e.g, '\x86' and the library is placed in ilb\x86\... Can you verify what, from the command line, R CMD env | grep R_ARCH reports on your system? Can you also indicate how you installed R and Rhtslib?

ADD REPLYlink written 24 days ago by Martin Morgan ♦♦ 20k
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