----- Original Message ----- > From: "Aaron Lun" <a...@wehi.edu.au> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Tuesday, May 24, 2016 11:04:59 AM > Subject: Re: [Bioc-devel] problems linking to Rhtslib on Mac OSX
> Yep, works on my machine as well. Seems like it would be a pain to have > to do it manually every time csaw (or deepSNV, or diffHic) gets > re-installed, though. > > I should stress that I didn't do anything special to my R installation > to get it to install packages in a different place. As far as I know, > that's just what R decided to do by itself. (I never run R with sudo > permissions, so it wouldn't be able to put packages in the central R > installation folder anyway.) > > So I think it's worth seriously thinking about whether this scenario > should be supported; a user (i.e., me) would reasonably expect that BioC > packages would work off the bat on this "standard" setting. Perhaps the > csaw.so library can be built with static linkage to the libhts.a? > > Or maybe I'm just spouting rubbish here. I don't know, I never do any > serious work on a Mac. > Martin just provided a fix that worked in my testing--Rhtslib now links statically against htslib. I have committed the fix and bumped the version of all packages that depend directly on Rhtslib, in release and devel. Thanks, Dan > Cheers, > > Aaron > > > On 24/05/16 18:42, Dan Tenenbaum wrote: >> >> >> ----- 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
