* checking for file 'msbase/DESCRIPTION' ... OK
* preparing 'msbase':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking whether 'INDEX' is up-to-date ... NO
* use '--force' to overwrite the existing 'INDEX'
* installing the package to re-build vignettes
* Installing *source* package 'msbase' ...
** libs
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -ansi -g -fPIC -g -O2 -std=gnu99 -c llogic.c -o llogic.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -ansi -g -fPIC -g -O2 -std=gnu99 -c mscalibD.c -o mscalibD.o
gcc -G -L/usr/local/lib -o msbase.so llogic.o mscalibD.o
** R
** data
** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Loading required package: MASS
Loading required package: XML
Creating a new generic function for 'subset' in 'msbase'
Creating a new generic function for 'image' in 'msbase'
Creating a new generic function for 'summary' in 'msbase'
Creating a new generic function for 'plot' in 'msbase'
Creating a new generic function for 'points' in 'msbase'
[1] "test1"
Creating a new generic function for 'unlist' in 'msbase'
Creating a new generic function for 'hist' in 'msbase'
** help
>>> Building/Updating help pages for package 'msbase'
Formats: text html latex example
List text html latex example
Massvector-class text html latex example
Massvectorlist-class text html latex example
Mlist-class text html latex example
ROCDATA text html latex example
cals-methods text html latex example
calssim text html latex example
fbinary-methods text html latex example
fcor-methods text html latex example
fdist-methods text html latex example
finterS-methods text html latex example
fintersect-methods text html latex example
fis.element-methods text html latex example
fmatch-methods text html latex example
fmatchall-methods text html latex example
fsetdiff-methods text html latex example
fsetequal-methods text html latex example
funion-methods text html latex example
gamasses-methods text html latex example
listdist-methods text html latex
nrmatch-methods text html latex example
numeric-class text html latex example
pldata text html latex example
undocument-internal text html latex
** building package indices ...
* DONE (msbase)
* creating vignettes ... ERROR
Creating a new generic function for 'lapply' in '.GlobalEnv'
Error: chunk 18 (label=MEM)
Error in object.size(ca) : unimplemented type 'S4' in 'object.size'
Error in buildVignettes(dir = ".") : Error: chunk 18 (label=MEM)
Error in object.size(ca) : unimplemented type 'S4' in 'object.size'
Execution halted