* 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
** arch - i386
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c CharBuffer.c -o CharBuffer.o
/var/tmp//cc5QCyMc.s:2232:indirect jmp without `*'
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gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c IntBuffer.c -o IntBuffer.o
/var/tmp//ccePXBfY.s:554:indirect jmp without `*'
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/var/tmp//ccePXBfY.s:689:indirect jmp without `*'
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/var/tmp//ccePXBfY.s:723:indirect jmp without `*'
/var/tmp//ccePXBfY.s:738:indirect jmp without `*'
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c R_init_Biostrings.c -o R_init_Biostrings.o
/var/tmp//ccMlv0Fy.s:272:indirect jmp without `*'
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c char_frequency.c -o char_frequency.o
/var/tmp//ccqrlS47.s:116:indirect jmp without `*'
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gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c reverseComplement.c -o reverseComplement.o
/var/tmp//ccuRUagV.s:403:indirect jmp without `*'
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gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c shiftor.c -o shiftor.o
/var/tmp//ccS5htA4.s:1073:indirect jmp without `*'
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/var/tmp//ccS5htA4.s:1287:indirect jmp without `*'
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gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c utils.c -o utils.o
/var/tmp//ccRGC7FL.s:1553:indirect jmp without `*'
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gcc-4.0 -arch i386 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Biostrings.so CharBuffer.o IntBuffer.o R_init_Biostrings.o char_frequency.o reverseComplement.o shiftor.o utils.o -F/Library/Frameworks/R.framework/.. -framework R
** arch - ppc
gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c CharBuffer.c -o CharBuffer.o
gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c IntBuffer.c -o IntBuffer.o
gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c char_frequency.c -o char_frequency.o
gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c reverseComplement.c -o reverseComplement.o
gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c shiftor.c -o shiftor.o
gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c utils.c -o utils.o
gcc-4.0 -arch ppc -std=gnu99 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Biostrings.so CharBuffer.o IntBuffer.o R_init_Biostrings.o char_frequency.o reverseComplement.o shiftor.o utils.o -F/Library/Frameworks/R.framework/.. -framework R
** 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.complex" 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
AAString-class text html latex example
AMINO_ACID_CODE text html latex example
BString-class text html latex example
BStringViews-class text html latex
BStringViews-constructors text html latex example
Biostrings-internals text html latex
DNAString-class text html latex example
GENETIC_CODE text html latex example
IUPAC_CODE_MAP text html latex example
RNAString-class text html latex example
alphabetFrequency text html latex example
as.complex 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
Loading required package: matchprobes
Loading required package: Biobase
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.
Loading required package: affy
Loading required package: affyio
Read 450 items
Loading required package: BSgenome
Warning message:
Ambiguous method selection for "==", target "BStringViews#BStringViews" (the first of the signatures shown will be used)
BStringViews#ANY
ANY#BStringViews
in: .findInheritedMethods(classes, fdef, mtable)
Warning message:
cannot open compressed file ''
Error: chunk 1 (label=a1)
Error in readChar(con, 5) : cannot open the connection
Error in buildVignettes(dir = ".") : Error: chunk 1 (label=a1)
Error in readChar(con, 5) : cannot open the connection
Execution halted