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 <dtene...@fredhutch.org> wrote: > > [renamed the thread] > > ----- Original Message ----- >> From: "Jason Serviss" <jason.serv...@ki.se> >> To: "Dan Tenenbaum" <dtene...@fredhutch.org> >> Cc: "Aaron Lun" <a...@wehi.edu.au>, "bioc-devel" <bioc-devel@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 >> <dtene...@fredhutch.org<mailto:dtene...@fredhutch.org>> wrote: >> >> >> >> ----- Original Message ----- >> From: "Jason Serviss" <jason.serv...@ki.se<mailto:jason.serv...@ki.se>> >> To: "Aaron Lun" <a...@wehi.edu.au<mailto:a...@wehi.edu.au>> >> Cc: "bioc-devel" <bioc-devel@r-project.org<mailto:bioc-devel@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 >> <a...@wehi.edu.au<mailto: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<mailto:Bioc-devel@r-project.org> mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> _______________________________________________ >> Bioc-devel@r-project.org<mailto: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