When install DESeq2 to iMac 10.11.6 (R 3.3.1) using the commands
> source("https://bioconductor.org/biocLite.R")
> biocLite("DESeq2")
I receive the following message
Warning: unable to access index for repository https://watson.nci.nih.gov/cran_mirror/src/contrib:
cannot download all files
Warning: dependencies ‘locfit’, ‘Hmisc’, ‘RcppArmadillo’, ‘futile.logger’, ‘snow’, ‘XML’, ‘bitops’ are not available
also installing the dependencies ‘zlibbioc’, ‘RCurl’, ‘GenomeInfoDb’, ‘XVector’, ‘annotate’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘BiocParallel’, ‘genefilter’, ‘geneplotter’
Warning: unable to access index for repository https://watson.nci.nih.gov/cran_mirror/bin/macosx/mavericks/contrib/3.3:
cannot download all files
Package which is only available in
source form, and may need
compilation of C/C++/Fortran:
‘RCurl’
and messages such as
Do you want to attempt to install these from sources?
y/n:
trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/mavericks/contrib/3.3/zlibbioc_1.20.0.tgz'
Content type 'application/x-gzip' length 124132 bytes (121 KB)
==================================================
downloaded 121 KB
trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/mavericks/contrib/3.3/GenomeInfoDb_1.10.2.tgz'
Content type 'application/x-gzip' length 14728293 bytes (14.0 MB)
==================================================
downloaded 14.0 MB
When loading the package by
> library(DESeq2)
here are the error messages
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘Hmisc’
In addition: Warning messages:
1: package ‘DESeq2’ was built under R version 3.3.2
2: package ‘S4Vectors’ was built under R version 3.3.2
3: package ‘GenomicRanges’ was built under R version 3.3.2
4: package ‘GenomeInfoDb’ was built under R version 3.3.2
Error: package or namespace load failed for ‘DESeq2’
Shall different commands be needed for the installation to Mac?
Thank you Martin. I tried to install using
> BiocInstaller::biocLite("DESeq2")It produces similar error message
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R
3.3.2 (2016-10-31).
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’, ‘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
I work with NIH. It seems that it goes automatically to the mirror https://watson.nci.nih.gov/cran_mirror/src/contrib
This does not happen when installing under Windows though. For installation under Mac, would it help downloading the package DESeq2_1.14.1.tgz and then install from there.
You're right that the problem is the repository. It's probably set somewhere in a .Rprofile file, maybe in your home directory or in a site-wide installation. You can try starting R from the command line along the lines of R --vanilla. Or by over-riding the option with
options(BioC_mirror="https://bioconductor.org")before trying to install packages. You're looking for the output ofto point to bioconductor.org. You could install DESeq2 from the tgz
install.packages("DESeq2_1.14.1.tgz", repos=NULL), but that would require you to have all the dependencies already installed, and that would get tedious quickly. It would also open the door for mixing packages from different releases, which will lead to more headaches. So the best solution is to figure out where the repository is being set, and correcting that.