Entering edit mode
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
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 becauseRHTSLIB_LIBDIRspecifies${R_ARCH}butpkgconfigdoes not - this variable seems to be empty most of the time, which is whypkgconfigusually 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_ARCHreports on your system? Can you also indicate how you installed R and Rhtslib?