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Question: Error message that there is no package called Biobase
0
gravatar for mdroog
17 months ago by
mdroog0
mdroog0 wrote:

I am trying to learn bioconductor (as a wetlabber). I think it's super interesting. But allready at the base it is tough. I keep getting the following error:

Error in library(Biobase) : there is no package called ‘Biobase’

 

Eventhough I did install Biobase. Can anybody tell me what is going wrong? Because of this I also cannot get DESeq2 to work:

> library(DESeq2)
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘Biobase’
Error: package or namespace load failed for ‘DESeq2’

Please help.

 

O, and the sessioninfo()

 

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Dutch_Netherlands.1252  LC_CTYPE=Dutch_Netherlands.1252    LC_MONETARY=Dutch_Netherlands.1252
[4] LC_NUMERIC=C                       LC_TIME=Dutch_Netherlands.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RcppArmadillo_0.6.700.3.0 Rcpp_0.12.4               GenomicRanges_1.18.4      GenomeInfoDb_1.2.5       
[5] IRanges_2.0.1             S4Vectors_0.4.0           BiocGenerics_0.12.1       edgeR_3.8.6              
[9] limma_3.22.7             

loaded via a namespace (and not attached):
[1] tools_3.1.2   XVector_0.6.0

ADD COMMENTlink modified 17 months ago • written 17 months ago by mdroog0
3
gravatar for Martin Morgan
17 months ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

Packages need to be installed onto your computer

source("https://bioconductor.org/biocLite.R")
biocLite("Biobase")

This needs to be done once per installation.

And then loaded into each R session

library("Biobase")

Usually, installing a package also installs its dependencies, so to use DESeq2 it would only be necessary to install it

source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")

Your particular installation seems to be messed up, with some dependencies not available, either because you installed packages in some non-standard way (e.g., by downloading the package and installing it 'by hand') or because you installed packages correctly but then did something to your R environment (e.g., removing a library path from .libPaths()).

ADD COMMENTlink modified 17 months ago by Sean Davis21k • written 17 months ago by Martin Morgan ♦♦ 22k
0
gravatar for mdroog
17 months ago by
mdroog0
mdroog0 wrote:

Thanks, your solution was indeed what I needed. 

ADD COMMENTlink written 17 months ago by mdroog0
1

Your R version (3.1.2) is badly out of date. You'll have more fun with a more recent version, e.g. the current version is 3.4.1, see https://cran.r-project.org/

Also, if you haven't, consider using R-Studio, it makes many things around using R much easier.

ADD REPLYlink modified 17 months ago • written 17 months ago by Wolfgang Huber13k
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