Question

FactoMineR failed after installing Bioconductor

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dany_wm44 • 0

@dany_wm44-7762

Last seen 9.5 years ago

Mexico

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!

software error factomineR bioclite • 4.5k views

ADD COMMENT • link updated 9.5 years ago by Martin Morgan 25k • written 9.5 years ago by dany_wm44 • 0

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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 REPLY • link 9.5 years ago dany_wm44 • 0

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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 REPLY • link 9.5 years ago Martin Morgan 25k

score 0 · Answer 1 · 2015-05-18

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Martin Morgan 25k

@martin-morgan-1513

Last seen 4 months ago

United States

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 COMMENT • link 9.5 years ago Martin Morgan 25k

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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 REPLY • link 9.5 years ago dany_wm44 • 0

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

ADD REPLY • link 9.5 years ago Martin Morgan 25k