CHECK report for RMAGEML on gladstone

* checking for working latex ... OK * using log directory '/home/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: 28936 Segmentation fault '/home/biocbuild/1.9d/R/bin/R' --vanilla --quiet /tmp/Rout2766219271 2>&1 OK * creating RMAGEML-manual.tex ... OK * checking RMAGEML-manual.tex ... OK WARNING: There was 1 warning, see /home/biocbuild/1.9d/Rpacks/RMAGEML.Rcheck/00check.log for details

* Installing *source* package 'RMAGEML' ... configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -I/home/biocbuild/1.9d/R/include -I/home/biocbuild/1.9d/R/include -I/usr/lib64/jvm/jre/include -I/usr/lib64/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: At top level: rmageml.c:17: warning: 'JavaMethod_type_tag' defined but not used rmageml.c: In function 'destroyOM': rmageml.c:91: warning: control reaches end of non-void function gcc -shared -L/usr/local/lib64 -o RMAGEML.so rmageml.o -L/usr/lib64/jvm/jre/jre/lib/amd64 -L/usr/lib64/jvm/jre/jre/lib/i386 -ljava -L/usr/lib64/jvm/jre/jre/lib/amd64/server -L/usr/lib64/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)

Package 152/188	OS	Arch	BUILD	CHECK	BUILD BIN
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
	Linux (SUSE 10.0)	x86_64	OK	[ WARNINGS ]
	Windows Server 2003	x86_64	ERROR	skipped	skipped

RMAGEML

2.8.0

Command output