RMAGEML 2.18.0
Steffen Durinck
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/RMAGEML | | Last Changed Rev: 39013 / Revision: 42512 | | Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (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 |
| pelham | Mac OS X Leopard (10.5.8) / i386 | N O T S U P P O R T E D |
* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.4-bioc/meat/RMAGEML.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RMAGEML/DESCRIPTION' ... OK
* this is package 'RMAGEML' version '2.18.0'
* 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
.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'
addDerivedData: no visible binding for global variable '..rmagemlJVM'
addNormToMAGEML: no visible binding for global variable '..rmagemlJVM'
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 files against version 2 parser ... 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
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* Installing *source* package 'RMAGEML' ...
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-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 'updateMAGEML':
rmageml.c:599: warning: cast from pointer to integer of different size
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-2.4-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
Loading required package: limma
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
** help
*** installing help indices
>>> 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)