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.
Edit
I don't have a .Rprofile file.
Note about 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/local/lib/R/site-library" , "/usr/lib/R/site-library" and "/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()[1], lib=.libPaths()[1]) 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:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.28.0
loaded via a namespace (and not attached):
[1] compiler_3.4.3 tools_3.4.3
Thank you very much!
