Package: RMAGEML

Version: 2.8.0

Command: /home/biocbuild/bbs-1.9/R/bin/R CMD build RMAGEML

RetCode: 1

Time: 9.5 seconds

Status: ERROR

PackageFile: None

* 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 -std=gnu99 -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include -I/usr/lib64/jvm/java/include -I/usr/lib64/jvm/java/include/linux  -I/usr/local/include    -fpic  -g -O2 -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: In function 'destroyOM':
rmageml.c:91: warning: control reaches end of non-void function
rmageml.c: At top level:
rmageml.c:17: warning: 'JavaMethod_type_tag' defined but not used
gcc -std=gnu99 -shared -L/usr/local/lib64 -o RMAGEML.so rmageml.o -L/usr/lib64/jvm/java/jre/lib/amd64 -L/usr/lib64/jvm/java/jre/lib/i386 -ljava -L/usr/lib64/jvm/java/jre/lib/amd64/server -L/usr/lib64/jvm/java/jre/lib/i386/client -ljvm  
** R
** inst
** preparing package for lazy loading
Loading required package: marray
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 ... ERROR
Loading required package: marray
Loading required package: limma
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.


Error:  chunk 1 
Error in library(RMAGEML) : .First.lib failed for 'RMAGEML'
Error in buildVignettes(dir = ".") : Error:  chunk 1 
Error in library(RMAGEML) : .First.lib failed for 'RMAGEML'
Execution halted