I am trying to install
RnBeads from bioconductor but the installation of its dependancy
TxDb.Hsapiens.UCSC.hg19.knownGene fails. The error is:
biocLite("RnBeads") BioC_mirror: https://bioconductor.org Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30). Installing package(s) ‘RnBeads’ also installing the dependencies ‘FDb.InfiniumMethylation.hg19’, ‘methylumi’ trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz' Content type 'application/x-gzip' length 38996322 bytes (37.2 MB) ================================================== downloaded 37.2 MB trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/methylumi_2.24.1.tar.gz' Content type 'application/x-gzip' length 6178909 bytes (5.9 MB) ================================================== downloaded 5.9 MB trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/RnBeads_1.10.2.tar.gz' Content type 'application/x-gzip' length 6437974 bytes (6.1 MB) ================================================== downloaded 6.1 MB * installing *source* package ‘FDb.InfiniumMethylation.hg19’ ... ** R ** data ** demo ** inst ** preparing package for lazy loading Error: package or namespace load failed for ‘TxDb.Hsapiens.UCSC.hg19.knownGene’: .onLoad failed in loadNamespace() for 'TxDb.Hsapiens.UCSC.hg19.knownGene', details: call: NULL error: evaluation nested too deeply: infinite recursion / options(expressions=)? Error : package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ could not be loaded ERROR: lazy loading failed for package ‘FDb.InfiniumMethylation.hg19’ The downloaded source packages are in ‘/tmp/RtmpY8Yf4l/downloaded_packages’ installation path not writeable, unable to update packages: doMC, doSNOW, foreach, iterators, snow, boot, class, cluster, codetools, foreign, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival
As suggested by the error message, I tried setting
options(expressions=500000), which unfortunately did not change the error message. An important note may be that I am under network mount and don't have administrative access rights.
I don't have a .Rprofile file.
installation path not writeable:
Typing .libPaths() reveals that my home R folder is at the first position (and it is writable). The other paths (
"/usr/lib/R/library") are not writable without sudo.
I also tried to delete my home R folder and to reinstall it. The reinstallation of all packages worked for all packages except for the three listed above (same error message). I also tried
biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene", lib.loc=.libPaths(), lib=.libPaths()) to specifically address my home R directory, but the same error is showing up (but without the
installation path not writeable part).
Here is my sessionInfo():
R version 3.4.3 (2017-11-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.4 LTS Matrix products: default BLAS: /usr/lib/openblas-base/libopenblas.so.0 LAPACK: /usr/lib/lapack/liblapack.so.3.0 locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  BiocInstaller_1.28.0 loaded via a namespace (and not attached):  compiler_3.4.3 tools_3.4.3
Thank you very much!