Hi,
I am following a ChIP-seq data analysis practical guide that requires me to use the packages ChIPQC, GenomicAlignments, and GenomicRanges. I am not having any trouble with the last two packages, however I cannot install the ChIPQC package. I have tried to install the package using library(biocInstaller)
, and then biocLite("ChIPQC")
, but I get an error from R stating the package had a "non-zero exit status." I don't know what the error means or how to fix it. Does anyone know what this means exactly or what I can do to try to resolve the issue? Is it possible that the package is dependent on other packages which may be incompatible with my version of R (3.5.0)? Or is there a chance that there is a "bug" in my code/R/other that I'm unaware of which may be interfering with my ability to install and load the package?
(The code below is just part of the error that I got)
Any suggestions would be greatly appreciated, thanks!
biocLite("ChIPQC")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).
Installing package(s) ‘ChIPQC’
also installing the dependencies ‘TxDb.Hsapiens.UCSC.hg18.knownGene’, ‘TxDb.Mmusculus.UCSC.mm10.knownGene’, ‘TxDb.Mmusculus.UCSC.mm9.knownGene’, ‘TxDb.Rnorvegicus.UCSC.rn4.ensGene’, ‘TxDb.Celegans.UCSC.ce6.ensGene’, ‘TxDb.Dmelanogaster.UCSC.dm3.ensGene’
trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/ChIPQC_1.16.0.zip'
Content type 'application/zip' length 2017947 bytes (1.9 MB)
downloaded 1.9 MB
package ‘ChIPQC’ successfully unpacked and MD5 sums checked
Content type 'application/x-gzip' length 4588884 bytes (4.4 MB)
downloaded 4.4 MB
* installing *source* package 'TxDb.Hsapiens.UCSC.hg18.knownGene' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for 'GenomeInfoDb' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called 'RCurl'
Error : package 'GenomeInfoDb' could not be loaded
ERROR: lazy loading failed for package 'TxDb.Hsapiens.UCSC.hg18.knownGene'
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘TxDb.Hsapiens.UCSC.hg18.knownGene’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘TxDb.Mmusculus.UCSC.mm10.knownGene’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘TxDb.Mmusculus.UCSC.mm9.knownGene’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘TxDb.Rnorvegicus.UCSC.rn4.ensGene’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘TxDb.Celegans.UCSC.ce6.ensGene’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘TxDb.Dmelanogaster.UCSC.dm3.ensGene’ had non-zero exit status
Could you post your session information so we can see which versions of libraries you currently have installed?
best,
tom