[Bioc-devel] problems linking to Rhtslib on Mac OSX

[Dan Tenenbaum]

----- Original Message -----
> From: "Aaron Lun" <alun at wehi.EDU.AU>
> To: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Tuesday, May 24, 2016 8:06:13 AM
> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX

> Dear Martin and List,
> 
> I have a problem with linking to Rhtslib on Mac OSX when my R installation
> directory differs from the package installation directory. Trying to load csaw
> (Bioc release version) gives me:
> 
>> require(csaw)
> # ... whole lot of dependencies...
> Loading required package: csaw
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared object
>  '/Users/lun01/Library/R/3.3/library/csaw/libs/csaw.so':
>  dlopen(/Users/lun01/Library/R/3.3/library/csaw/libs/csaw.so, 6): Library not
>  loaded:
>  /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/lib/libhts.0.dylib
>  Referenced from: /Users/lun01/Library/R/3.3/library/csaw/libs/csaw.so
>  Reason: image not found
> 
> ... which is because my Rhtslib shared library is sitting instead at
> /Users/lun01/Library/R/3.3/library/Rhtslib/lib/libhts.0.dylib (along with all
> my other non-recommended, non-base packages). I presume this linking failure
> occurs because the Makevars file (which would normally indicate where the
> shared library is living) doesn't get run when installing a prebuilt binary?
> The same issue occurs with deepSNV, which is the other package that links to
> Rhtslib.


I can't reproduce this issue after installing the binaries of csaw and Rhtslib. I believe that htslib is statically linked inside of Rhtslib so you don't need your own installation of htslib on your machine in order to use it.If you look at the Mac tarball (https://bioconductor.org/packages/release/bioc/bin/macosx/mavericks/contrib/3.3/Rhtslib_1.4.2.tgz) untar it and go to the Rhtslib/lib directory you see the following files:

libhts.0.dylib
libhts.a
libhts.dylib

...in addition to Rhtslib.so which is in Rhtslib/libs.

Dan



> 
> Any thoughts? I don't usually use Macs, so I don't know exactly what goes on
> during package installation, or whether my setup (i.e., with different
> package/R locations) is atypical or not.
> 
> Aaron
> 
>> sessionInfo()
> R version 3.3.0 (2016-05-03)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X 10.10.5 (Yosemite)
> 
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
> 
> attached base packages:
> [1] stats4    parallel  stats     graphics  grDevices utils     datasets
> [8] methods   base
> 
> other attached packages:
> [1] SummarizedExperiment_1.2.2 Biobase_2.32.0
> [3] GenomicRanges_1.24.0       GenomeInfoDb_1.8.1
> [5] IRanges_2.6.0              S4Vectors_0.10.1
> [7] BiocGenerics_0.18.0        BiocInstaller_1.22.2
> 
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.34.3    XVector_0.12.0          edgeR_3.14.0
> [4] GenomicAlignments_1.8.0 zlibbioc_1.18.0         BiocParallel_1.6.2
> [7] tools_3.3.0             DBI_0.4-1               Rhtslib_1.4.2
> [10] rtracklayer_1.32.0      bitops_1.0-6            RCurl_1.95-4.8
> [13] biomaRt_2.28.0          RSQLite_1.0.0           limma_3.28.5
> [16] GenomicFeatures_1.24.2  Biostrings_2.40.1       Rsamtools_1.24.0
> [19] XML_3.98-1.4
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