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

Aaron Lun alun at wehi.EDU.AU
Tue May 24 17:06:13 CEST 2016

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.

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.


> 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)

[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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