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holbrookjoanna
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@holbrookjoanna-10650
Last seen 8.5 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