----- Original Message ----- > From: "Dan Tenenbaum" <dtene...@fredhutch.org> > To: "Aaron Lun" <a...@wehi.edu.au> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Tuesday, May 24, 2016 9:38:01 AM > Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
> ----- Original Message ----- >> From: "Dan Tenenbaum" <dtene...@fredhutch.org> >> To: "Aaron Lun" <a...@wehi.edu.au> >> Cc: "bioc-devel" <bioc-devel@r-project.org> >> Sent: Tuesday, May 24, 2016 8:51:30 AM >> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX > >> ----- Original Message ----- >>> From: "Aaron Lun" <a...@wehi.edu.au> >>> To: "bioc-devel" <bioc-devel@r-project.org> >>> Sent: Tuesday, May 24, 2016 8:06:13 AM >>> Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX >> >>> 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. >> >> >> I can't reproduce this issue after installing the binaries of csaw and >> Rhtslib. >> I believe that htslib is statically linked inside of Rhtslib so you don't >> need >> your own installation of htslib on your machine in order to use it.If you >> look >> at the Mac tarball >> (https://bioconductor.org/packages/release/bioc/bin/macosx/mavericks/contrib/3.3/Rhtslib_1.4.2.tgz) >> untar it and go to the Rhtslib/lib directory you see the following files: >> >> libhts.0.dylib >> libhts.a >> libhts.dylib >> >> ...in addition to Rhtslib.so which is in Rhtslib/libs. >> > > Actually I can induce issues if I install Rhtslib in a different library > directory, which is what you were saying. Will look into this a little. The following seems to fix it: cd ~/Library/R/3.3/csaw/libs # change dtenenba to your username in the below sudo install_name_tool -change "/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/lib/libhts.0.dylib" "/Users/dtenenba/Library/R/3.3/Rhtslib/lib/libhts.0.dylib" csaw.so (the sudo may not be necessary) Then I can require(csaw) and it works. I'm not sure if there is something that the bioc group should be doing about this....we'll discuss it when we meet soon. Dan > Dan > > >> Dan >> >> >> >>> >>> 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 inte...{{dropped:6}} >> >> _______________________________________________ >> 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
