----- 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. 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
