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

Hi,
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.
Yannick

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)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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 2.8 years ago by Johannes Rainer1.0k • written 2.8 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("http://bioconductor.org/biocLite.R")
> BiocInstaller::biocLite("Biobase")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.1.2.
Installing package(s) 'Biobase'
trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/Biobase_2.26.0.tar.gz'
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 Biobase.so 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 2.8 years ago • written 2.8 years ago by Martin Morgan ♦♦ 20k
1
gravatar for Johannes Rainer
2.8 years ago by
Johannes Rainer1.0k
Italy
Johannes Rainer1.0k 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 2.8 years ago by Johannes Rainer1.0k

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!

Yannick

ADD REPLYlink written 2.8 years ago by yannick.lippi0
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