Question

csaw intallation issue: cannot find "lib" in Rhtslib installation

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favorov • 0

@favorov-14274

Last seen 3.1 years ago

JHMI; VIGG RAS

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

diffhic csaw Rhtslib • 1.5k views

ADD COMMENT • link updated 7.0 years ago by Martin Morgan 25k • written 7.0 years ago by favorov • 0

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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 REPLY • link 7.0 years ago Aaron Lun ★ 28k

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Thank you! I've added the tag.

ADD REPLY • link 7.0 years ago favorov • 0

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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 REPLY • link 7.0 years ago Martin Morgan 25k