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.
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
______________________________________________________________________
The information in this email is confidential and intend...{{dropped:4}}
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
