RMAGEML 2.12.0
Steffen Durinck
| Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/RMAGEML | | Last Changed Rev: 28558 / Revision: 30966 | | Last Changed Date: 2007-11-07 23:08:50 -0800 (Wed, 07 Nov 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | [ OK ] | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | OK | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | N O T S U P P O R T E D |
| lemming | Windows Server 2003 (32-bit) / x64 | N O T S U P P O R T E D |
| pitt | Mac OS X Tiger (10.4.11) / i386 | N O T S U P P O R T E D |
* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.1-bioc/meat/RMAGEML.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'RMAGEML/DESCRIPTION' ... OK
* this is package 'RMAGEML' version '2.12.0'
* checking package dependencies ... OK
* 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 non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addDerivedData: no visible binding for global variable '..rmagemlJVM'
addNormToMAGEML: no visible binding for global variable '..rmagemlJVM'
.checkJVM: no visible binding for global variable '..JVMAlive'
.createJVM: no visible binding for global variable '..JVMAlive'
.destroyJVM: no visible binding for global variable '..rmagemlJVM'
.destroyJVM: no visible binding for global variable '..JVMAlive'
getArrayID: no visible binding for global variable '..rmagemlJVM'
getArrayLayout: no visible binding for global variable '..rmagemlJVM'
getArrayLayoutLimma: no visible binding for global variable
'..rmagemlJVM'
getGnames: no visible binding for global variable '..rmagemlJVM'
getNumberOfFeatures: no visible binding for global variable
'..rmagemlJVM'
getOrganization: no visible binding for global variable '..rmagemlJVM'
getQTDimensions: no visible binding for global variable '..rmagemlJVM'
getQTypeDescription: no visible binding for global variable
'..rmagemlJVM'
getQuantitationTypes: no visible binding for global variable
'..rmagemlJVM'
getSubmitterAddress: no visible binding for global variable
'..rmagemlJVM'
importMAGEML: no visible binding for global variable '..rmagemlJVM'
importMAGEOM: no visible binding for global variable '..rmagemlJVM'
makeEset: no visible binding for global variable '..rmagemlJVM'
makeMarrayRaw: no visible binding for global variable '..rmagemlJVM'
makeRG: no visible binding for global variable '..rmagemlJVM'
reset: no visible binding for global variable '..rmagemlJVM'
writeMAGEML: no visible binding for global variable '..rmagemlJVM'
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... 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' ... OK
* creating RMAGEML-manual.tex ... OK
* checking RMAGEML-manual.tex ... OK
* Installing *source* package 'RMAGEML' ...
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/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:65: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'destroyOM':
rmageml.c:92: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'newRMAGESTK':
rmageml.c:109: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'importFeatures':
rmageml.c:134: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getGridDimensions':
rmageml.c:169: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'selectQTypesDeriv':
rmageml.c:211: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getSizeDED':
rmageml.c:245: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'selectQTypes':
rmageml.c:295: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getExternalData':
rmageml.c:349: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getQuantitationTypes':
rmageml.c:394: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getQTypeDescription':
rmageml.c:432: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'createNewQTDim':
rmageml.c:464: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'addQuantitationTypeInfo':
rmageml.c:490: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'createNewMBASet':
rmageml.c:525: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'setMBA':
rmageml.c:549: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'updateMAGEML':
rmageml.c:582: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c:599: warning: cast from pointer to integer of different size
rmageml.c: In function 'writeMAGEML':
rmageml.c:629: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getVoidArrayInt':
rmageml.c:659: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getVoidArrayStr':
rmageml.c:694: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getVoidStr':
rmageml.c:728: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'getVoidVoid':
rmageml.c:751: warning: dereferencing type-punned pointer will break strict-aliasing rules
rmageml.c: In function 'destroyOM':
rmageml.c:95: 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 -L/home/biocbuild/bbs-2.1-bioc/R/lib -lR
** 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()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
** 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)