Problem loading minfi on macOS
1
0
Entering edit mode
@holbrookjoanna-10650
Last seen 8.0 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 • 1.5k views
ADD COMMENT
0
Entering edit mode
@kasper-daniel-hansen-2979
Last seen 10 months 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
ADD COMMENT

Login before adding your answer.

Traffic: 608 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6