CHECK report for affyPLM on churchill

* checking for working latex ... OK * using log directory '/loc/biocbuild/1.9d/Rpacks/affyPLM.Rcheck' * using R version 2.4.0 Under development (unstable) (2006-07-18 r38641) * checking for file 'affyPLM/DESCRIPTION' ... OK * this is package 'affyPLM' version '1.9.15' * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'affyPLM' 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 S3 generic/method consistency ...Killed WARNING ld.so.1: R: fatal: relocation error: file /loc/biocbuild/1.9d/Rpacks/affyPLM.Rcheck/affyPLM/libs/affyPLM.so: symbol R_moduleCdynload: referenced symbol not found See section 'Generic functions and methods' of the 'Writing R Extensions' manual. * checking replacement functions ...Killed WARNING ld.so.1: R: fatal: relocation error: file /loc/biocbuild/1.9d/Rpacks/affyPLM.Rcheck/affyPLM/libs/affyPLM.so: symbol R_moduleCdynload: referenced symbol not found In R, the argument of a replacement function which corresponds to the right hand side must be named 'value'. * checking foreign function calls ...Killed WARNING ld.so.1: R: fatal: relocation error: file /loc/biocbuild/1.9d/Rpacks/affyPLM.Rcheck/affyPLM/libs/affyPLM.so: symbol R_moduleCdynload: referenced symbol not found See section 'System and foreign language interfaces' of the 'Writing R Extensions' manual. * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ...Killed WARNING ld.so.1: R: fatal: relocation error: file /loc/biocbuild/1.9d/Rpacks/affyPLM.Rcheck/affyPLM/libs/affyPLM.so: symbol R_moduleCdynload: referenced symbol not found All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in manual 'Writing R Extensions'. * checking for code/documentation mismatches ...Killed WARNING ld.so.1: R: fatal: relocation error: file /loc/biocbuild/1.9d/Rpacks/affyPLM.Rcheck/affyPLM/libs/affyPLM.so: symbol R_moduleCdynload: referenced symbol not found Killed ld.so.1: R: fatal: relocation error: file /loc/biocbuild/1.9d/Rpacks/affyPLM.Rcheck/affyPLM/libs/affyPLM.so: symbol R_moduleCdynload: referenced symbol not found Killed ld.so.1: R: fatal: relocation error: file /loc/biocbuild/1.9d/Rpacks/affyPLM.Rcheck/affyPLM/libs/affyPLM.so: symbol R_moduleCdynload: referenced symbol not found * 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 * creating affyPLM-Ex.R ... OK * checking examples ...Killed ERROR Running examples in affyPLM-Ex.R failed.

* Installing *source* package 'affyPLM' ... ** libs gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c LESN.c -o LESN.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c PLM_modelmatrix.c -o PLM_modelmatrix.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c R_rlm_interfaces.c -o R_rlm_interfaces.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c SCAB.c -o SCAB.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c avg_log.c -o avg_log.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c biweight.c -o biweight.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c chipbackground.c -o chipbackground.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c common_types.c -o common_types.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c do_PLMrlm.c -o do_PLMrlm.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c do_PLMrma.c -o do_PLMrma.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c do_PLMthreestep.c -o do_PLMthreestep.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c idealmismatch.c -o idealmismatch.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c lm.c -o lm.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c lm_threestep.c -o lm_threestep.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c log_avg.c -o log_avg.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c matrix_functions.c -o matrix_functions.o matrix_functions.c: In function 'Lapack_Init': matrix_functions.c:62: warning: implicit declaration of function 'R_moduleCdynload' gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c medianPM.c -o medianPM.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c median_logPM.c -o median_logPM.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c medianpolish.c -o medianpolish.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c nthLargestPM.c -o nthLargestPM.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c preprocess.c -o preprocess.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c psi_fns.c -o psi_fns.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c qnorm.c -o qnorm.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c qnorm_probeset.c -o qnorm_probeset.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c read_rmaexpress.c -o read_rmaexpress.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c rlm.c -o rlm.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c rlm_PLM.c -o rlm_PLM.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c rlm_anova.c -o rlm_anova.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c rlm_se.c -o rlm_se.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c rlm_threestep.c -o rlm_threestep.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c rma_PLM.c -o rma_PLM.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c rma_background2.c -o rma_background2.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c rma_common.c -o rma_common.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c scaling.c -o scaling.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c threestep.c -o threestep.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c threestep_PLM.c -o threestep_PLM.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c threestep_common.c -o threestep_common.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c threestep_summary.c -o threestep_summary.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c threestep_summary_methods.c -o threestep_summary_methods.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c transfns.c -o transfns.o gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -I/usr/local/include -fPIC -g -O2 -std=gnu99 -c weightedkerneldensity.c -o weightedkerneldensity.o gcc -G -L/usr/local/lib -o affyPLM.so LESN.o PLM_modelmatrix.o R_rlm_interfaces.o SCAB.o avg_log.o biweight.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm.o lm_threestep.o log_avg.o matrix_functions.o medianPM.o median_logPM.o medianpolish.o nthLargestPM.o preprocess.o psi_fns.o qnorm.o qnorm_probeset.o read_rmaexpress.o rlm.o rlm_PLM.o rlm_anova.o rlm_se.o rlm_threestep.o rmaPLM_pseudo.o rma_PLM.o rma_background2.o rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o weightedkerneldensity.o -L/loc/biocbuild/1.9d/R/lib -lRlapack ** R ** inst ** save image Loading required package: affy 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. Loading required package: affyio Loading required package: affydata Loading required package: Biobase Loading required package: gcrma Loading required package: matchprobes [1] "PLMset" [1] "cdfName" Creating a new generic function for 'weights' in 'affyPLM' [1] "weights" [1] "weights<-" [1] "weights<-" [1] "coefs" [1] "coefs" [1] "coefs<-" [1] "coefs<-" [1] "coefs.probe" [1] "coefs.probe" [1] "se" [1] "se" [1] "se.probe" [1] "se.probe" [1] "se<-" [1] "se<-" [1] "indexProbes" [1] "indexProbesProcessed" [1] "indexProbesProcessed" [1] "image" [1] "boxplot" [1] "show" [1] "coefs.const" [1] "coefs.const" [1] "se.const" [1] "se.const" Creating a new generic function for 'summary' in 'affyPLM' [1] "summary" [1] "Mbox" [1] "resid<-" [1] "resid<-" Creating a new generic function for 'resid' in 'affyPLM' [1] "resid" [1] "residuals<-" [1] "residuals<-" Creating a new generic function for 'residuals' in 'affyPLM' [1] "residuals" [1] "normvec" [1] "normvec" [1] "varcov" [1] "varcov" [1] "residSE" [1] "residSE" [1] "sampleNames" [1] "sampleNames<-" [1] "model.description" [1] "model.description" [1] "MAplot" [1] "nuse" [1] "nuse" [1] "NUSE" [1] "NUSE" [1] "RLE" [1] "RLE" ** help >>> Building/Updating help pages for package 'affyPLM' Formats: text html latex example MAplot text html latex PLMset-class text html latex example PLMset2exprSet text html latex example ReadRMAExpress text html latex affyPLM-internal text html latex bg.correct.LESN text html latex example fitPLM text html latex example normalize.exprSet text html latex example normalize.quantiles.in.blocks text html latex example normalize.quantiles.probeset text html latex normalize.quantiles.target text html latex normalize.scaling text html latex example pseudo text html latex example rmaPLM text html latex example threestep text html latex example threestepPLM text html latex example ** building package indices ... * DONE (affyPLM)

Package 12/205	OS	Arch	BUILD	CHECK	BUILD BIN
affyPLM 1.9.15 Ben Bolstad	Linux (SUSE 9.2)	x86_64	OK	WARNINGS
	Linux (SUSE 9.2)	i686	OK	WARNINGS
	Solaris 2.9	sparc	OK	[ ERROR ]
	Linux (SUSE 10.0)	x86_64	OK	WARNINGS
	Windows Server 2003	x86_64	ERROR	skipped	skipped
	Windows XP	i686	ERROR	skipped	skipped
	Mac OS X (10.4.6)	i686	OK	WARNINGS

affyPLM

1.9.15

Command output