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| Package: RMAGEML |
| Version: 2.6.0 |
| Command: /home/biocbuild/R-2.3.0/bin/R CMD build RMAGEML |
| RetCode: 0 |
| Time: 16.3 seconds |
| Status: OK |
| PackageFile: RMAGEML_2.6.0.tar.gz |
* checking for file 'RMAGEML/DESCRIPTION' ... OK
* preparing 'RMAGEML':
* 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 'RMAGEML' ...
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/home/biocbuild/R-2.3.0/include -I/home/biocbuild/R-2.3.0/include -I/usr/lib64/jvm/jre/include -I/usr/lib64/jvm/jre/include/linux -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c rmageml.c -o rmageml.o
rmageml.c: In function 'arji_createJVM':
rmageml.c:61: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'destroyOM':
rmageml.c:88: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'newRMAGESTK':
rmageml.c:105: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'importFeatures':
rmageml.c:130: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getGridDimensions':
rmageml.c:165: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'selectQTypesDeriv':
rmageml.c:207: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getSizeDED':
rmageml.c:241: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'selectQTypes':
rmageml.c:291: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getExternalData':
rmageml.c:345: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getQuantitationTypes':
rmageml.c:390: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getQTypeDescription':
rmageml.c:428: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'createNewQTDim':
rmageml.c:460: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'addQuantitationTypeInfo':
rmageml.c:486: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'createNewMBASet':
rmageml.c:521: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'setMBA':
rmageml.c:545: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'updateMAGEML':
rmageml.c:578: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c:595: warning: cast from pointer to integer of different size
rmageml.c: In function 'writeMAGEML':
rmageml.c:625: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getVoidArrayInt':
rmageml.c:655: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getVoidArrayStr':
rmageml.c:690: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getVoidStr':
rmageml.c:724: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getVoidVoid':
rmageml.c:747: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: At top level:
rmageml.c:17: warning: 'JavaMethod_type_tag' defined but not used
rmageml.c: In function 'destroyOM':
rmageml.c:91: warning: control reaches end of non-void function
gcc -shared -L/usr/local/lib64 -o RMAGEML.so rmageml.o -L/usr/lib64/jvm/jre/jre/lib/amd64 -L/usr/lib64/jvm/jre/jre/lib/i386 -ljava -L/usr/lib64/jvm/jre/jre/lib/amd64/server -L/usr/lib64/jvm/jre/jre/lib/i386/client -ljvm
** R
** inst
** preparing package for lazy loading
Loading required package: marray
Loading required package: limma
Loading required package: limma
Loading required package: Biobase
Loading required package: tools
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.
** help
>>> Building/Updating help pages for package 'RMAGEML'
Formats: text html latex example
JavaVMRef-class text html latex
MEXP14 text html latex
addDerivedData text html latex example
addNormToMAGEML text html latex example
getArrayID text html latex example
getArrayLayout text html latex example
getArrayLayoutLimma text html latex example
getGnames text html latex example
getNumberOfFeatures text html latex example
getOrganization text html latex example
getQTDimensions text html latex example
getQTypeDescription text html latex example
getQuantitationTypes text html latex example
getSubmitterAddress text html latex example
importMAGEML text html latex example
importMAGEOM text html latex example
makeEset text html latex example
makeMarrayRaw text html latex example
makeRG text html latex example
reset text html latex example
writeMAGEML text html latex example
** building package indices ...
* DONE (RMAGEML)
* creating vignettes ...sh: line 1: 32211 Segmentation fault '/home/biocbuild/R-2.3.0/bin/R' --vanilla --no-save --quiet /tmp/Rout3071207059 2>&1
OK
* cleaning src
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building 'RMAGEML_2.6.0.tar.gz'