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

[Dan Tenenbaum]

----- Original Message -----
> From: "Jason Serviss" <jason.serviss at ki.se>
> To: "Aaron Lun" <alun at wehi.edu.au>
> Cc: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Tuesday, May 24, 2016 8:20:18 AM
> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX

> 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
> 


I think this is a different problem. You are building these packages from source and they require that you have the openssl libraries and headers. 
Either read the Mac section of https://github.com/jeroenooms/openssl#installation or just install the binary versions (omit type="source").
Dan


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