Question: Error installing Biobase on R 3.1.2
gravatar for yannick.lippi
3.9 years ago by
European Union
yannick.lippi0 wrote:

I am upgrading packages since R have been upgraded on our linux server.
But an error occurs when installing Biobase 2.26.
I tried installing the currently installed version (just to see) but I have the same error, so depending on the R version.
Thanks for your help.

Code and info below:
> biocLite(Biobase)
installing to /save/ylippi/LIB/Rlib/Biobase/libs
** R
** data
** inst
** preparing package for lazy loading
Warning in superClassDepth(ClassDef, simpleOnly = simpleOnly) :
  class “list” extends an undefined class, “AssayData”
Error in extends(classDef2, cliDef) :
  'class2' must be the name of a class or a class definition
Error in setClass("Versions", contains = "list") :
  error in contained classes ("list") for class “Versions”; class definition removed from ‘Biobase’
Error : unable to load R code in package ‘Biobase’
ERROR: lazy loading failed for package ‘Biobase’
* removing ‘/path2libloc/Biobase’
* restoring previous ‘/path2libloc/Biobase’

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C

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

other attached packages:
[1] Biobase_2.20.1     BiocGenerics_0.6.0 gplots_2.11.3      MASS_7.3-35
[5] KernSmooth_2.23-13 caTools_1.14       gdata_2.13.3       gtools_3.4.1

loaded via a namespace (and not attached):
[1] bitops_1.0-6

ADD COMMENTlink modified 3.9 years ago by Johannes Rainer1.3k • written 3.9 years ago by yannick.lippi0

The code chunk you've listed doesn't seem accurate. Normally you'd biocLite("Biobase") (quoted string) and R would respond by downloading the package. Make sure you are not using an old biocLite script that you might have installed on your computer --


> source("")
> BiocInstaller::biocLite("Biobase")
Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.1.2.
Installing package(s) 'Biobase'
trying URL ''
Content type 'application/x-gzip' length 1674714 bytes (1.6 MB)
opened URL
downloaded 1.6 MB

Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help
* installing *source* package 'Biobase' ...
** libs
clang -I/home/mtmorgan/bin/R-3-1-branch/include -DNDEBUG  -I/usr/local/include    -fpic  -ggdb -O0 -Wall -pedantic -c Rinit.c -o Rinit.o
clang -I/home/mtmorgan/bin/R-3-1-branch/include -DNDEBUG  -I/usr/local/include    -fpic  -ggdb -O0 -Wall -pedantic -c anyMissing.c -o anyMissing.o
clang -I/home/mtmorgan/bin/R-3-1-branch/include -DNDEBUG  -I/usr/local/include    -fpic  -ggdb -O0 -Wall -pedantic -c envir.c -o envir.o
clang -I/home/mtmorgan/bin/R-3-1-branch/include -DNDEBUG  -I/usr/local/include    -fpic  -ggdb -O0 -Wall -pedantic -c matchpt.c -o matchpt.o
clang -I/home/mtmorgan/bin/R-3-1-branch/include -DNDEBUG  -I/usr/local/include    -fpic  -ggdb -O0 -Wall -pedantic -c rowMedians.c -o rowMedians.o
clang -I/home/mtmorgan/bin/R-3-1-branch/include -DNDEBUG  -I/usr/local/include    -fpic  -ggdb -O0 -Wall -pedantic -c sublist_extract.c -o sublist_extract.o
clang -shared -L/usr/local/lib64 -o Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o
installing to /home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.1/Biobase/libs
** R

Please update your post with the actual commands and output used. Also, if you have a 'custom' repository set, try using the standard repositories instead -- optoins(repos=BiocInstaller::biocinstallRepos())

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by Martin Morgan ♦♦ 22k
gravatar for Johannes Rainer
3.9 years ago by
Johannes Rainer1.3k
Johannes Rainer1.3k wrote:

hi Yannick,

from the error messages it is hard to tell what happened, so I can only guess.

Could it be that the you have an R_HOME or R_LIBS environment variable pointing to some old versions of installed packages that are loaded by the new R?

Also, I am really skeptical whether updating R and any packages really is advisable; I'm usually compiling R from source on the server and installing it to it's own directory (e.g. /usr/local/R/R-3.1.2) and making a symlink to the R binary. This ensures that I have a working R with all the correct R-package versions (including Bioconductor). So, in case I have to repeat an old analysis for a paper I can always go back to exactly that version that I used at that time of the first analysis.

best, jo

ADD COMMENTlink written 3.9 years ago by Johannes Rainer1.3k

Hi Jo,

Thanks for your reply!

The problem came from a conflict between the 2 lib.loc where the packages are installed...

One installed by the system admin

The other one is mine when i install new packages (because no privilege on the admin files).

I just deleted the package from my personal lib.loc and the problem is solved..

many thanks!


ADD REPLYlink written 3.9 years ago by yannick.lippi0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 188 users visited in the last hour