RMAGEML 2.27.0
Steffen Durinck
| Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RMAGEML | | Last Changed Rev: 54810 / Revision: 55359 | | Last Changed Date: 2011-04-13 18:14:51 -0700 (Wed, 13 Apr 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | N O T S U P P O R T E D |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | 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 |
* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/RMAGEML.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RMAGEML/DESCRIPTION’ ... OK
* this is package ‘RMAGEML’ version ‘2.27.0’
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘RMAGEML’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 14.2Mb
sub-directories of 1Mb or more:
jaxp 7.5Mb
MAGEMLdata 3.0Mb
classes 2.7Mb
* 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 whether the package can be unloaded cleanly ... 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 metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... 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-2.9-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:599:23: warning: cast from pointer to integer of different size
rmageml.c: At top level:
rmageml.c:17:13: warning: ‘JavaMethod_type_tag’ defined but not used
rmageml.c: In function ‘destroyOM’:
rmageml.c:95:1: warning: control reaches end of non-void function
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-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/RMAGEML.Rcheck/RMAGEML/libs
** R
** inst
** preparing package for lazy loading
Loading required package: limma
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation("pkgname")'.
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
‘RMAGEML.Rnw’
** testing if installed package can be loaded
* DONE (RMAGEML)