I'm a relatively novice R user - mainly using it to analyze RNAseq data. I recently updated my R version via an uninstall/re-install and now can no longer get DESeq2 to install or run properly. When trying to install with
> source("https://bioconductor.org/biocLite.R")
> biocLite("DESeq2")
I get the following errors:
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06).
Installing package(s) ‘DESeq2’
Warning: unable to access index for repository https://watson.nci.nih.gov/cran_mirror/src/contrib:
cannot download all files
Warning: dependencies ‘locfit’, ‘ggplot2’, ‘Hmisc’, ‘RcppArmadillo’ are not available
Warning: unable to access index for repository https://watson.nci.nih.gov/cran_mirror/bin/macosx/mavericks/contrib/3.3:
cannot download all files
trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/mavericks/contrib/3.3/DESeq2_1.14.1.tgz'
Content type 'application/x-gzip' length 1781581 bytes (1.7 MB)
==================================================
downloaded 1.7 MB
The downloaded binary packages are in
/var/folders/qy/ds05bqg15sq55qlgnx53k8zr0000gp/T//Rtmp8nDwEc/downloaded_packages
Warning: unable to access index for repository https://watson.nci.nih.gov/cran_mirror/src/contrib:
cannot download all files
Per an earlier post on a related subject (https://support.bioconductor.org/p/91529/), I've also tried:
> BiocInstaller::biocLite("DESeq2") and
> options(BioC_mirror="https://bioconductor.org")
These generated the same errors. I've also completely uninstalled R in terminal and tried to install the older version (which was previously working) but this didn't fix the issue either.
Thanks for any suggestions!!
Additional session info:
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Yosemite 10.10.5
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] IRanges_2.8.2 S4Vectors_0.12.2 BiocGenerics_0.20.0 BiocInstaller_1.24.0
loaded via a namespace (and not attached):
[1] tools_3.3.3
> BiocInstaller::biocValid()
Warning: unable to access index for repository https://watson.nci.nih.gov/cran_mirror/src/contrib:
cannot download all files
[1] TRUE
> traceback()
5: stop(gettextf("package %s could not be loaded", sQuote(pkg)),
call. = FALSE, domain = NA)
4: .getRequiredPackages2(pkgInfo, quietly = quietly)
3: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,
quietly = quietly)
2: .getRequiredPackages2(pkgInfo, quietly = quietly)
1: library(DESeq2)
Martin, Thanks very much the chooseCRANmirror() option allowed me to install. I was given the option to install from sources that required compilation, which I declined, and the option to update certain packages which I did. It seemed to complete fine but when I went to load DESeq2 with
I got the following error:
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Error 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
I thought maybe it would still be fine to run but it can't find basic DESeq functions.
Any suggestions to get me over this final hurdle would be very welcome!
Thanks!
Probably you could try to install RCurl
biocLite("RCurl")On Linux, you'd have to install the system dependency libcurl-dev, but it seems like you're on a Mac.
I just attempted:
BiocInstaller::biocLite("GenomicRanges")BiocInstaller::biocLite("GenomicInfoDb")But got the following error. I'm confused because I recently installed DESeq2 on another Mac in R version 3.3.3 so seems odd.
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06).
Installing package(s) ‘GenomicInfoDb’
Old packages: 'data.table'
Update all/some/none? [a/s/n]:
a
There is a binary version available but the source version is later:
binary source needs_compilation
data.table 1.10.0 1.10.4 TRUE
Do you want to install from sources the package which needs compilation?
y/n: n
trying URL 'https://cloud.r-project.org/bin/macosx/mavericks/contrib/3.3/data.table_1.10.0.tgz'
Content type 'application/x-gzip' length 1335637 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
The downloaded binary packages are in
/var/folders/qy/ds05bqg15sq55qlgnx53k8zr0000gp/T//Rtmp8nDwEc/downloaded_packages
Warning message:
package ‘GenomicInfoDb’ is not available (for R version 3.3.3)
The package is GenomeInfoDb.