RnBeads install problem caused by FDb.InfiniumMethylation.hg19 package

[Sandra Laurentino]

Hi!

I've been having problems with installing RnBeads and was wondering if anyone has a solution or could point me in the right direction. I have contacted the support email more than once but never got an answer so I'm starting to think nobody actually checks it.

My problem seems to change but I'm only going to show you the most recent. I have tried installing RnBeads using source("http://rnbeads.mpi-inf.mpg.de/install.R") and also by manual installing. I used RStudio, thought it might be a bug there and tried R directly but the problems remain. My problem seems to change but I'm only going to show you the most recent. When try loading RnBeads I get

Error: package ‘FDb.InfiniumMethylation.hg19’ required by ‘methylumi’ could not be found

I tried installing this package but get:

Warning messages:
1: running command '"//ukmuenster.de/dir1$/Users2/laurents/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "\\ukmuenster.de\dir1$\Users2\laurents\R\R-3.3.1\library" C:\Users\Laurents\AppData\Local\Temp\RtmpGqh6wK/downloaded_packages/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ had non-zero exit status
3: running command '"//ukmuenster.de/dir1$/Users2/laurents/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "\\ukmuenster.de\dir1$\Users2\laurents\R\R-3.3.1\library" C:\Users\Laurents\AppData\Local\Temp\RtmpGqh6wK/downloaded_packages/org.Hs.eg.db_3.4.0.tar.gz' had status 1 
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘org.Hs.eg.db’ had non-zero exit status
5: running command '"//ukmuenster.de/dir1$/Users2/laurents/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "\\ukmuenster.de\dir1$\Users2\laurents\R\R-3.3.1\library" C:\Users\Laurents\AppData\Local\Temp\RtmpGqh6wK/downloaded_packages/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz' had status 1 
6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘FDb.InfiniumMethylation.hg19’ had non-zero exit status

If I try loading the package

Error in library(FDb.InfiniumMethylation.hg19) : 
  there is no package called ‘FDb.InfiniumMethylation.hg19’

And also, if I try loading RnBeads or Methylumi I get again the error 

Error: package ‘FDb.InfiniumMethylation.hg19’ required by ‘methylumi’ could not be found

I have tried different computers, re-installing R and R-studio, re-installing all the packages and I still get the same result. Does anyone have a suggestion?

[Fabian]

Hi,
is a Bioconductor package, that methylumi (one of the dependencies of RnBeads) depends on. It can be installed like any other Bioconductor package:

source("https://bioconductor.org/biocLite.R")
biocLite("FDb.InfiniumMethylation.hg19")

Were those the commands that resulted in the warnings? If so, could it be that you don't have permissions to install R packages on your system?

Best,
Fabian

[hanna_e...@yahoo.se]

Hi Sandra,

I get the exact same error message when trying to install "FDb.InfiniumMethylation.hg19" as you explain above. Were you able to solve it? If yes, how did you do it?

Thanks in advance!

[Tim Triche, Jr.]

it looks like an issue with the upstream org.Hs.eg.db and/or TxDb.Hsapiens.UCSC.hg19.knownGene packages

Try installing the Homo.sapiens organism package like so:

library(BiocInstaller)

biocLite("Homo.sapiens")

if that suceeds and FDb.Infinium...hg19 fails, then I need to update the latter package.

Conversely, if Homo.sapiens fails, then the problem is upstream and Bioc-core needs to fix it.

Best,

--t