Hi,
Veterinarian learning microbiome analysis in R. Please be patient! :-) Windows computer, using R v3.2.2, R studio.
I was happily working with DESeq2 when R got stuck at:
>idx<-identify(res$baseMean, res$log2FoldChange) #to identify the genes in plotMA...
So I quit R (I actually had to go to the task manager to do it). Start R again. Try the original installation code:
>install.packages("DESeq2") >library(DESeq2)
Doesn't work. So I try:
>source("https://bioconductor.org/biocLite.R") #aiming to continue with: >biocLite("DESeq2") and >library("DESeq2")
But I stop here when I get: "Bioconductor version 3.1 (BiocInstaller 1.18.5), ?biocLite for help A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help"
So I obey and upgrade bioconductor:
>biocLite("BiocUpgrade")
Upgrade all packages to Bioconductor version 3.2? [y/n]:
y
>biocLite("DESeq2")
Update all/some/none? [a/s/n]:
a
Then I get this funny message with library (first words in Danish - I haven't figured out how to install R error messages in full English being Windows Danish...... but that is another story):
>library("DESeq2")
Indlæser krævet pakke: SummarizedExperiment
Error: package ‘GenomicRanges’ 1.20.8 is loaded, but >= 1.22.1 is required by ‘SummarizedExperiment’
Part of the reason that this is funny is because it is just one of the versions of all the different error messages I got trying again and again. Before I had other messages such as:
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
der er ingen pakke med navn ‘stringi’
Error: indlæsning af pakke eller navnerum fejlede for ‘DESeq2’
(Which translates like there is not such package called stringi / loading the package or namespace failed for 'DESeq2)
I also got the message about the RcppArmadillo (which has disappeared now) that is when I unsuccessfully tried what is discussed here: DESeq2 installation error although the armadillo message is gone now.
I am stuck, I would appreciate suggestions :-)
THANK YOU!
Also note messages at the end of my sessioninfo:
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=Danish_Denmark.1252 LC_CTYPE=Danish_Denmark.1252
[3] LC_MONETARY=Danish_Denmark.1252 LC_NUMERIC=C
[5] LC_TIME=Danish_Denmark.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils
[7] datasets methods base
other attached packages:
[1] BiocInstaller_1.20.1 RcppArmadillo_0.6.100.0.0
[3] Rcpp_0.12.1 GenomicRanges_1.20.8
[5] GenomeInfoDb_1.4.3 IRanges_2.2.9
[7] S4Vectors_0.6.6 BiocGenerics_0.14.0
loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning messages:
1: In FUN(X[[i]], ...) :
DESCRIPTION file of package 'XVector' is missing or broken
2: In FUN(X[[i]], ...) :
DESCRIPTION file of package 'Biobase' is missing or broken
Thank you James! I tried to fix it below :-)