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 <a...@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
> ______________________________________________________________________
>
> 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
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
