Question: FactoMineR failed after installing Bioconductor
0
gravatar for dany_wm44
4.5 years ago by
dany_wm440
Mexico
dany_wm440 wrote:

Hi everyone!!

I´ve recently installed Bioconductor and run it this way:

source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite("affydata")
library(affydata)

it was not for me, it was for a partner that wanted to show me something.

after this I tried to run my PCA scrip, using FactoMineR package, it return this:

> library (FactoMineR)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘pbkrtest’
Error: package or namespace load failed for ‘FactoMineR’

before installing bioconductor I used FactoMineR package, so the instalation of Bioconductor may be the cause.

 

Please Help!!!

Thanks!

ADD COMMENTlink modified 4.5 years ago by Martin Morgan ♦♦ 24k • written 4.5 years ago by dany_wm440

It also happend with ggplot2, 

> library(ggplot2)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘Rcpp’
Error: package or namespace load failed for ‘ggplot2’

ADD REPLYlink written 4.5 years ago by dany_wm440

biocLite / BiocInstaller do not change the paths where R looks for installed packages, so the problem is elsewhere. Start R with the --vanilla flag (from the command line, R --vanilla). Make sure you are looking in the right place for your packages via .libPaths(). Make sure sessionInfo() returns the version of R you're expecting. Verify that ggplot2 is installed via installed.packages().

ADD REPLYlink written 4.5 years ago by Martin Morgan ♦♦ 24k
Answer: FactoMineR failed after installing Bioconductor
0
gravatar for Martin Morgan
4.5 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

It is not likely that Bioconductor corrupted your installation. Try re-installing FactoMineR, e.g.,

source("http://bioconductor.org/biocLite.R")
biocLite("FactoMineR")

(biocLite will install non-Bioconductor packages, too).

ADD COMMENTlink written 4.5 years ago by Martin Morgan ♦♦ 24k

Thanks for answering so fast!! unfortunatly it didn´t work, when I run the code you tell me and try the PCA again, it return this again, it is also happening with ggplot2 package:

> library (FactoMineR)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘pbkrtest’
Error: package or namespace load failed for ‘FactoMineR’

ADD REPLYlink written 4.5 years ago by dany_wm440

And when you try to install the missing package, biocLite("pbkrtest") ? Please also provide the output of the command sessionInfo().

ADD REPLYlink written 4.5 years ago by Martin Morgan ♦♦ 24k
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