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NOTES: (1) a maintainance reboot of lemming prevented these builds to complete on this machine (2) these are the last builds with R 2.6.0 (2007-06-03 r41797) on lamb1 and lemming, next builds will be with R 2.6.0 (2007-06-10 r41908) configured with --enable-strict-barrier |
Package 12/238 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
affyPLM1.13.5Ben BolstadLast Changed Date: 2007-06-05 12:44:17 -0700 Last Changed Rev: 25196 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | WARNINGS | |
wellington | Linux (SUSE 9.2) | i686 | [ OK ] | WARNINGS | ||
churchill | Solaris 2.9 | sparc | OK | WARNINGS | ||
lemming | Windows Server 2003 (32-bit) | x64 | ERROR | skipped | skipped |
Package: affyPLM |
Version: 1.13.5 |
Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD build affyPLM |
RetCode: 0 |
Time: 571.2 seconds |
Status: OK |
PackageFile: affyPLM_1.13.5.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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c avg_log.c -o avg_log.o avg_log.c: In function `AverageLog_threestep': avg_log.c:64: warning: implicit declaration of function `AverageLog' avg_log.c: In function `AverageLog_PLM': avg_log.c:80: warning: implicit declaration of function `averagelog_no_copy' 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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c biweight.c -o biweight.o biweight.c: In function `TukeyBiweight_threestep': biweight.c:66: warning: implicit declaration of function `TukeyBiweight' 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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c preprocess.c -o preprocess.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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c qnorm_probeset.c -o qnorm_probeset.o qnorm_probeset.c: In function `qnorm_probeset_c': qnorm_probeset.c:154: warning: implicit declaration of function `AverageLog_noSE' 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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c read_rmaexpress.c -o read_rmaexpress.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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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' 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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include" -fpic -g -O2 -Wall -c threestep_common.c -o threestep_common.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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/loc/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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_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_probeset.o read_rmaexpress.o rlm_PLM.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 ** preparing package for lazy loading 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: preprocessCore Loading required package: affydata Loading required package: gcrma Loading required package: matchprobes Loading required package: splines Creating a new generic function for "weights" in "affyPLM" Creating a new generic function for "summary" in "affyPLM" Creating a new generic function for "resid" in "affyPLM" Creating a new generic function for "residuals" in "affyPLM" ** help Note: unmatched right brace in 'threestep' on or after line 33 >>> 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.probeset 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_1.13.5.tar.gz'