[Bioc-devel] building packages that depend on openssl (was Re: problems linking to Rhtslib on Mac OSX)
Jason Serviss
jason.serviss at ki.se
Tue May 24 20:54:55 CEST 2016
Dan,
Alright, I guess for the time being the most practical solution is to work in the R-release version and, potentially, deal with this problem at a later date. Thanks again!
Jason
> On 24 May 2016, at 20:46, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
>
> [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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