Question: Problem loading minfi on macOS
0
gravatar for holbrookjoanna
3.3 years ago by
holbrookjoanna0 wrote:

 

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       
ADD COMMENTlink modified 3.3 years ago by Kasper Daniel Hansen6.4k • written 3.3 years ago by holbrookjoanna0
Answer: Problem loading minfi on macOS
0
gravatar for Kasper Daniel Hansen
3.3 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
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
ADD COMMENTlink modified 3.3 years ago by Dan Tenenbaum8.2k • written 3.3 years ago by Kasper Daniel Hansen6.4k
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