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Question: csaw intallation issue: cannot find "lib" in Rhtslib installation
0
11 months 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
modified 11 months ago by Martin Morgan ♦♦ 22k • written 11 months 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.

Thank you! I've added the tag.

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?