Problem loading minfi on macOS
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Entering edit mode
@holbrookjoanna-10650
Last seen 5.2 years ago

 

Please help!

I can not install minfi but not load it.  It says it can't find rgl.so

I have tried updating all packages from source: biocLite(pkgs, type="source") and I get a load of warnings including 

14: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘minfi’ had non-zero exit status

I'm running R version 3.2.3 under El Capitan but I note the installation URL has mavericks in the address.  Is this the problem?

> biocLite("minfi")

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.2), R 3.2.3 (2015-12-10).
Installing package(s) ‘minfi’
trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/macosx/mavericks/contrib/3.2/minfi_1.16.1.tgz'
Content type 'application/x-gzip' length 667635 bytes (651 KB)
==================================================
downloaded 651 KB


The downloaded binary packages are in
    /var/folders/q1/vlhwkhq96jn7n99rgv556cgr0000gn/T//RtmpXlMIp0/downloaded_packages
> require(minfi)
Loading required package: minfi
Error : .onLoad failed in loadNamespace() for 'rgl', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rgl/libs/rgl.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rgl/libs/rgl.so, 6): Library not loaded: /opt/X11/lib/libGLU.1.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rgl/libs/rgl.so
  Reason: image not found

 

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.4 (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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] bumphunter_1.10.0          locfit_1.5-9.1             iterators_1.0.8            foreach_1.4.3             
 [5] Biostrings_2.38.4          XVector_0.10.0             SummarizedExperiment_1.0.2 GenomicRanges_1.22.4      
 [9] GenomeInfoDb_1.6.3         IRanges_2.4.8              S4Vectors_0.8.11           lattice_0.20-33           
[13] Biobase_2.30.0             BiocGenerics_0.16.1        BiocInstaller_1.20.2      

loaded via a namespace (and not attached):
 [1] mclust_5.2              base64_1.1              Rcpp_0.12.4             Rsamtools_1.22.0        digest_0.6.9           
 [6] plyr_1.8.3              futile.options_1.0.0    RSQLite_1.0.0           zlibbioc_1.16.0         GenomicFeatures_1.22.13
[11] annotate_1.48.0         Matrix_1.2-6            preprocessCore_1.32.0   splines_3.2.3           BiocParallel_1.4.3     
[16] stringr_1.0.0           igraph_1.0.1            RCurl_1.95-4.8          biomaRt_2.26.1          rtracklayer_1.30.4     
[21] multtest_2.26.0         pkgmaker_0.22           GEOquery_2.36.0         quadprog_1.5-5          codetools_0.2-14       
[26] matrixStats_0.50.2      XML_3.98-1.4            reshape_0.8.5           GenomicAlignments_1.6.3 MASS_7.3-45            
[31] bitops_1.0-6            grid_3.2.3              nlme_3.1-127            xtable_1.8-2            registry_0.3           
[36] DBI_0.4                 magrittr_1.5            stringi_1.0-1           genefilter_1.52.1       doRNG_1.6              
[41] limma_3.26.9            futile.logger_1.4.1     nor1mix_1.2-1           lambda.r_1.1.7          RColorBrewer_1.1-2     
[46] siggenes_1.44.0         tools_3.2.3             illuminaio_0.12.0       rngtools_1.2.4          survival_2.39-3        
[51] AnnotationDbi_1.32.3    beanplot_1.2       
minfi minfidata rgl. mac os x el capitan • 795 views
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Entering edit mode
@kasper-daniel-hansen-2979
Last seen 26 days ago
United States
I think you have problems with the rgl package, which sometimes causes problems. The easiest fix is to upgrade R to version 3.3 and re-install Bioconductor (which was released a few days ago). In the new version of minfi in Bioconductor 3.3 we no longer indirectly depend on the rgl package so it should be smooth. Best, Kasper
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