* checking for file 'Biostrings/DESCRIPTION' ... OK
* preparing 'Biostrings':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'Biostrings' ...
** libs
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -Wall -c alphabetFrequency.c -o alphabetFrequency.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -Wall -c bbuf.c -o bbuf.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -Wall -c ibuf.c -o ibuf.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -Wall -c reverseComplement.c -o reverseComplement.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -Wall -c shiftor.c -o shiftor.o
shiftor.c: In function `shiftor':
shiftor.c:224: warning: 'index' might be used uninitialized in this function
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -Wall -c utils.c -o utils.o
utils.c: In function `Biostrings_translate_charcpy_from_subset':
utils.c:261: warning: unused variable `b'
utils.c: In function `Biostrings_translate_charcpy_to_subset':
utils.c:344: warning: unused variable `b'
gcc -G -L/usr/local/lib -o Biostrings.so R_init_Biostrings.o alphabetFrequency.o bbuf.o ibuf.o reverseComplement.o shiftor.o utils.o
** R
** data
** inst
** save image
Creating a new generic function for 'as.integer' in 'Biostrings'
Creating a new generic function for 'toString' in 'Biostrings'
Creating a new generic function for 'nchar' in 'Biostrings'
Creating a new generic function for 'as.matrix' in 'Biostrings'
Creating a new generic function for 'as.list' in 'Biostrings'
Warning message:
in the method signature for function 'BStringViews' no definition for class: "file" in: matchSignature(signature, fdef, where)
** help
>>> Building/Updating help pages for package 'Biostrings'
Formats: text html latex example
BString-class text html latex example
BStringViews-class text html latex example
Biostrings-internals text html latex
alphabetFrequency text html latex example
blosum50 text html latex example
matchPattern text html latex example
needwunsQS text html latex example
readFASTA text html latex example
reverseComplement text html latex example
yeastSEQCHR1 text html latex example
** building package indices ...
* DONE (Biostrings)
* creating vignettes ... ERROR
Read 450 items
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Error: chunk 3 (label=c1)
Error: package 'affy' could not be loaded
Error in buildVignettes(dir = ".") : Error: chunk 3 (label=c1)
Error: package 'affy' could not be loaded
Execution halted