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
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())