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

[Jason Serviss]

I can confirm that I am experiencing similar problems on OSX with several other packages at the moment (openssl and git2r), I know that Xcode just updated and am not sure if this is causing some of the problems (potentially some update with their command line tools?)...

install.packages('openssl', type=‘source’)
...
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/openssl/libs/openssl.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/openssl/libs/openssl.so, 6): Symbol not found: _ERR_free_strings
  Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/openssl/libs/openssl.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/3.4/Resources/library/openssl/libs/openssl.so
Error: loading failed
Execution halted

install.packages(‘git2r', type=‘source’)
…
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/git2r/libs/git2r.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/git2r/libs/git2r.so, 6): Symbol not found: _SSL_library_init
  Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/git2r/libs/git2r.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/3.4/Resources/library/git2r/libs/git2r.so
Error: loading failed
Execution halted

sessionInfo()
R Under development (unstable) (2016-05-23 r70660)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.5 (El Capitan)

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] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] tools_3.4.0

Kind Regards,
Jason Serviss




> On 24 May 2016, at 17:06, Aaron Lun <alun at wehi.edu.au> wrote:
> 
> 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
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> 
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