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Package 12/234 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
affyPLM1.13.0Ben BolstadLast Changed Date: 2007-04-24 11:31:42 -0700 Last Changed Rev: 24217 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | OK | |
wellington | Linux (SUSE 9.2) | i686 | [ OK ] | OK | ||
churchill | Solaris 2.9 | sparc | OK | OK | ||
lemming | Windows Server 2003 (32-bit) | x64 | OK | OK | OK |
Package: affyPLM |
Version: 1.13.0 |
Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD build affyPLM |
RetCode: 0 |
Time: 552.4 seconds |
Status: OK |
PackageFile: affyPLM_1.13.0.tar.gz |
* checking for file 'affyPLM/DESCRIPTION' ... OK * preparing 'affyPLM': * checking DESCRIPTION meta-information ... OK * cleaning src * checking whether 'INDEX' is up-to-date ... NO * use '--force' to overwrite the existing 'INDEX' * installing the package to re-build vignettes * Installing *source* package 'affyPLM' ... ** libs gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c avg_log.c -o avg_log.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c biweight.c -o biweight.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c chipbackground.c -o chipbackground.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c common_types.c -o common_types.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c do_PLMrlm.c -o do_PLMrlm.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c do_PLMrma.c -o do_PLMrma.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c idealmismatch.c -o idealmismatch.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c LESN.c -o LESN.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c lm.c -o lm.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c lm_threestep.c -o lm_threestep.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c log_avg.c -o log_avg.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c median_logPM.c -o median_logPM.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c medianPM.c -o medianPM.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c medianpolish.c -o medianpolish.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c nthLargestPM.c -o nthLargestPM.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c preprocess.c -o preprocess.o preprocess.c: In function `pp_bothstages': preprocess.c:667: warning: unused variable `exprs' gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c psi_fns.c -o psi_fns.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c qnorm.c -o qnorm.o qnorm.c: In function `qnorm_c_determine_target': qnorm.c:1489: warning: unused variable `ind' qnorm.c:1490: warning: unused variable `dimat' qnorm.c:1494: warning: unused variable `ranks' qnorm.c: In function `R_qnorm_using_target': qnorm.c:1572: warning: unused variable `dim2' qnorm.c: In function `qnorm_c_determine_target': qnorm.c:1564: warning: control reaches end of non-void function qnorm.c: At top level: qnorm.c:118: warning: `min' defined but not used qnorm.c:357: warning: `qnorm_c_old' defined but not used qnorm.c:431: warning: `qnorm_robust_c_old' defined but not used gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c qnorm_probeset.c -o qnorm_probeset.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c read_rmaexpress.c -o read_rmaexpress.o read_rmaexpress.c: In function `read_rmaexpress_header': read_rmaexpress.c:249: warning: unused variable `dimnames' read_rmaexpress.c: In function `gz_read_rmaexpress_header': read_rmaexpress.c:431: warning: unused variable `dimnames' gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c rlm_anova.c -o rlm_anova.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c rlm.c -o rlm.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c rlm_PLM.c -o rlm_PLM.o rlm_PLM.c:99: warning: `rlmPLM_alloc_space' defined but not used gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c rlm_se.c -o rlm_se.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c rlm_threestep.c -o rlm_threestep.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c rma_background2.c -o rma_background2.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c rma_common.c -o rma_common.o rma_common.c: In function `median': rma_common.c:60: warning: unused variable `i' rma_common.c: In function `median_nocopy': rma_common.c:103: warning: unused variable `i' gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c rma_PLM.c -o rma_PLM.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c R_rlm_interfaces.c -o R_rlm_interfaces.o R_rlm_interfaces.c: In function `R_wrlm_rma_default_model': R_rlm_interfaces.c:197: warning: implicit declaration of function `rlm_wfit_anova' gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c SCAB.c -o SCAB.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c scaling.c -o scaling.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c threestep.c -o threestep.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c threestep_common.c -o threestep_common.o threestep_common.c: In function `median_low': threestep_common.c:45: warning: unused variable `i' gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c threestep_PLM.c -o threestep_PLM.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c threestep_summary.c -o threestep_summary.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c threestep_summary_methods.c -o threestep_summary_methods.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c transfns.c -o transfns.o gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c weightedkerneldensity.c -o weightedkerneldensity.o gcc -std=gnu99 -shared -L/usr/local/lib -o affyPLM.so avg_log.o biweight.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o LESN.o lm.o lm_threestep.o log_avg.o matrix_functions.o median_logPM.o medianPM.o medianpolish.o nthLargestPM.o PLM_modelmatrix.o preprocess.o psi_fns.o qnorm.o qnorm_probeset.o read_rmaexpress.o rlm_anova.o rlm.o rlm_PLM.o rlm_se.o rlm_threestep.o rma_background2.o rma_common.o rma_PLM.o rmaPLM_pseudo.o R_rlm_interfaces.o SCAB.o scaling.o threestep.o threestep_common.o threestep_PLM.o threestep_summary.o threestep_summary_methods.o transfns.o weightedkerneldensity.o -lg2c -lm -L/loc/biocbuild/bbs-2.1-bioc/R/lib -lRlapack -L/loc/biocbuild/bbs-2.1-bioc/R/lib -lRblas -L/loc/biocbuild/bbs-2.1-bioc/R/lib -lR ** 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()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: affyio Loading required package: affydata Loading required package: gcrma Loading required package: matchprobes Loading required package: splines [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" [1] "phenoData" [1] "phenoData<-" [1] "pData" [1] "pData<-" [1] "description" [1] "annotation" ** 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 preprocess 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) * creating vignettes ... OK * cleaning src * removing junk files * checking for LF line-endings in source files * checking for empty or unneeded directories * building 'affyPLM_1.13.0.tar.gz'