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RMAGEML

2.8.0

Steffen Durinck		Linux (SUSE 9.2) x86_64 OK [ WARNINGS ]
Linux (SUSE 9.2) i686 OK  WARNINGS 
Solaris 2.9 sparc ERROR skipped
Windows Server 2003 x86_64 ERROR skippedskipped
Package: RMAGEML
Version: 2.8.0
Command: /loc/biocbuild/1.9d/R/bin/R CMD check RMAGEML_2.8.0.tar.gz
RetCode: 0
Time: 67.8 seconds
Status: WARNINGS
CheckDir: RMAGEML.Rcheck
Warnings: 1

Command output

* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.9d/Rpacks/RMAGEML.Rcheck'
* using R version 2.4.0 (2006-10-03)
* checking for file 'RMAGEML/DESCRIPTION' ... OK
* this is package 'RMAGEML' version '2.8.0'
* checking package dependencies ... WARNING
package 'methods' is used but not declared
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking if this is a source package ... OK
* checking whether package 'RMAGEML' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for non-ASCII characters ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating RMAGEML-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ...sh: line 1:  1982 Segmentation fault      '/loc/biocbuild/1.9d/R/bin/R' --vanilla --quiet /tmp/Rout3264260235 2>&1
 OK
* creating RMAGEML-manual.tex ... OK
* checking RMAGEML-manual.tex ... OK

WARNING: There was 1 warning, see
  /loc/biocbuild/1.9d/Rpacks/RMAGEML.Rcheck/00check.log
for details

RMAGEML.Rcheck/00install.out:

* Installing *source* package 'RMAGEML' ...
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/lib/jvm/jre/include -I/usr/lib/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: 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 -shared -L/usr/local/lib64 -o RMAGEML.so rmageml.o -L/usr/lib/jvm/jre/jre/lib/amd64 -L/usr/lib/jvm/jre/jre/lib/i386 -ljava -L/usr/lib/jvm/jre/jre/lib/amd64/server -L/usr/lib/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: 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)