[Bioc-devel] building packages that depend on openssl (was Re: problems linking to Rhtslib on Mac OSX)

Dan Tenenbaum dtenenba at fredhutch.org
Tue May 24 20:46:54 CEST 2016 

[renamed the thread]

----- Original Message -----
> From: "Jason Serviss" <jason.serviss at ki.se>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: "Aaron Lun" <alun at wehi.edu.au>, "bioc-devel" <bioc-devel at r-project.org>
> Sent: Tuesday, May 24, 2016 11:32:17 AM
> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX

> Dan,
> 
> Thanks for the input. Yes, maybe it is a different problem altogether. If it is
> more convenient I can start another “thread” to keep the issues separated…
> 
> Due to the fact that I am running R-devel, as far as I am aware, all (?)
> packages need to be installed from source. I have carefully followed the
> instructions for installing openssl on my system and testing the installation
> with:
> 

Why are you using R-devel? Bioconductor (even its devel version) does not use R-devel.
So your question may not really be a Bioconductor question.

If you are intending to work with the devel version of Bioconductor (3.4) it runs on R.3.3.0.
CRAN binaries are available for that version of R. Bioconductor is not yet providing Mac binaries for Bioconductor 3.4 due to an ill-timed hardware crash, but we are working on getting them building agains oon.

So...first, decide whether you really need R-devel. If so, you could try installing the R-3.3.0 binaries of git2r and openssl. They may work.
If they don't (and I see now that you tried this already without luck) you might want to talk to the maintainer of openssl about this, which is incidentally not a Bioconductor package.

But if you don't need R-devel, then you don't have to do anything special, just:
biocLite(c("git2r","openssl"))

Dan


> 
> openssl version -a
> 
> gives:
> 
> OpenSSL 1.1.0-pre6-dev  xx XXX xxxx
> built on: reproducible build, date unspecified
> platform: darwin64-x86_64-cc
> compiler: cc -DDSO_DLFCN -DHAVE_DLFCN_H -DNDEBUG -DOPENSSL_THREADS
> -DOPENSSL_NO_STATIC_ENGINE -DOPENSSL_PIC -DOPENSSL_IA32_SSE2
> -DOPENSSL_BN_ASM_MONT -DOPENSSL_BN_ASM_MONT5 -DOPENSSL_BN_ASM_GF2m -DSHA1_ASM
> -DSHA256_ASM -DSHA512_ASM -DMD5_ASM -DAES_ASM -DVPAES_ASM -DBSAES_ASM
> -DGHASH_ASM -DECP_NISTZ256_ASM -DPOLY1305_ASM -DOPENSSLDIR="\"/usr/local/ssl\""
> -DENGINESDIR="\"/usr/local/lib/engines\""
> OPENSSLDIR: "/usr/local/ssl"
> ENGINESDIR: "/usr/local/lib/engines”
> 
> Since I am also experiencing the same problem with git2r, I don’t think that in
> my case the problem is isolated to openssl but I am struggling to identify what
> it is specifically. I can download the .zip file for either of the packages and
> install with R CMD INSTALL -no-test-load and see that the files (openssl.so and
> git2r.so) are present in the libs directory but then library(git2r) or
> library(openssl) generates the same warning. I also tried reinstalling the
> previous version of Xcode and command line tools, thinking as mentioned
> previously that the problem could lie there, but to no avail.
> 
> Jason
> 
> 
> On 24 May 2016, at 19:48, Dan Tenenbaum
> <dtenenba at fredhutch.org<mailto:dtenenba at fredhutch.org>> wrote:
> 
> 
> 
> ----- Original Message -----
> From: "Jason Serviss" <jason.serviss at ki.se<mailto:jason.serviss at ki.se>>
> To: "Aaron Lun" <alun at wehi.edu.au<mailto:alun at wehi.edu.au>>
> Cc: "bioc-devel" <bioc-devel at r-project.org<mailto: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<mailto: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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