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Package 6/214 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
affy1.14.0Rafael A. IrizarryLast Changed Date: 2007-04-24 11:21:48 -0700 Last Changed Rev: 24214 | 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 | |
liverpool | Windows Server 2003 R2 (32-bit) | x64 | OK | OK | OK | |
derby | Mac OS X (10.4.9) | i686 | OK | OK |
Package: affy |
Version: 1.14.0 |
Command: /home/biocbuild/bbs-2.0-bioc/R/bin/R CMD build affy |
RetCode: 0 |
Time: 21.6 seconds |
Status: OK |
PackageFile: affy_1.14.0.tar.gz |
* checking for file 'affy/DESCRIPTION' ... OK * preparing 'affy': * checking DESCRIPTION meta-information ... OK * cleaning src * running cleanup * installing the package to re-build vignettes * Installing *source* package 'affy' ... creating cache ./config.cache checking how to run the C preprocessor... cc -E checking for main in -lz... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc -std=gnu99 -I/home/biocbuild/bbs-2.0-bioc/R/include -I/home/biocbuild/bbs-2.0-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -fpic -g -O2 -Wall -c chipbackground.c -o chipbackground.o gcc -std=gnu99 -I/home/biocbuild/bbs-2.0-bioc/R/include -I/home/biocbuild/bbs-2.0-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -fpic -g -O2 -Wall -c getall_locations.c -o getall_locations.o gcc -std=gnu99 -I/home/biocbuild/bbs-2.0-bioc/R/include -I/home/biocbuild/bbs-2.0-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -fpic -g -O2 -Wall -c mas5calls.c -o mas5calls.o gcc -std=gnu99 -I/home/biocbuild/bbs-2.0-bioc/R/include -I/home/biocbuild/bbs-2.0-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -fpic -g -O2 -Wall -c qnorm.c -o qnorm.o qnorm.c: In function 'qnorm_c_determine_target': qnorm.c:1494: warning: unused variable 'ranks' qnorm.c:1490: warning: unused variable 'dimat' qnorm.c:1489: warning: unused variable 'ind' 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/home/biocbuild/bbs-2.0-bioc/R/include -I/home/biocbuild/bbs-2.0-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -fpic -g -O2 -Wall -c rma2.c -o rma2.o rma2.c: In function 'get_col_median': rma2.c:183: warning: unused variable 'i' gcc -std=gnu99 -I/home/biocbuild/bbs-2.0-bioc/R/include -I/home/biocbuild/bbs-2.0-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -fpic -g -O2 -Wall -c rma_background2.c -o rma_background2.o gcc -std=gnu99 -I/home/biocbuild/bbs-2.0-bioc/R/include -I/home/biocbuild/bbs-2.0-bioc/R/include -DHAVE_ZLIB=1 -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 -shared -L/usr/local/lib64 -o affy.so chipbackground.o getall_locations.o mas5calls.o qnorm.o rma2.o rma_background2.o rma_common.o -lz -L/home/biocbuild/bbs-2.0-bioc/R/lib -lR ** R ** data ** demo ** inst ** save image 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 [1] "ProgressBarText" [1] "initialize" Creating a new generic function for "open" in "affy" [1] "open" Creating a new generic function for "update" in "affy" [1] "update" Creating a new generic function for "close" in "affy" [1] "close" [1] "AffyBatch" [1] "initialize" [1] "updateObject" [1] "exprs" [1] "exprs<-" [1] "se.exprs" [1] "se.exprs<-" [1] "cdfName" [1] "cdfName" [1] "intensity" [1] "intensity" [1] "intensity<-" [1] "intensity<-" [1] "length" [1] "dim" [1] "geneNames" [1] "geneNames<-" [1] "show" [1] "indexProbes" [1] "indexProbes" [1] "indexProbes" [1] "pmindex" [1] "pmindex" [1] "mmindex" [1] "mmindex" [1] "probeNames" [1] "probeNames" [1] "probes" [1] "probes" [1] "pm" [1] "pm" [1] "pm<-" [1] "pm<-" [1] "mm" [1] "mm" [1] "mm<-" [1] "mm<-" [1] "probeset" [1] "probeset" [1] "[" [1] "[<-" [1] "bg.correct" [1] "bg.correct" [1] "normalize.methods" [1] "normalize.methods" [1] "normalize" [1] "normalize" [1] "computeExprSet" [1] "computeExprSet" [1] "image" [1] "image" [1] "boxplot" [1] "boxplot" [1] "hist" [1] "hist" [1] "mas5calls" [1] "mas5calls" [1] "Mbox" [1] "Mbox" [1] "MAplot" [1] "MAplot" [1] "ProbeSet" [1] "show" [1] "colnames" [1] "sampleNames" [1] "colnames" [1] "pm" [1] "pm<-" [1] "mm" [1] "mm<-" [1] "express.summary.stat" [1] "express.summary.stat" [1] "barplot" [1] "barplot" [1] "mas5calls" ** help >>> Building/Updating help pages for package 'affy' Formats: text html latex example AffyBatch-class text html latex example AffyRNAdeg text html latex example MAplot text html latex example ProbeSet-class text html latex example ProgressBarText-class text html latex example SpikeIn text html latex affy-options text html latex example affy.scalevalue.exprSet text html latex affybatch.example text html latex barplot.ProbeSet text html latex example bg.adjust text html latex bgc text html latex example cdfFromBioC text html latex example cdfenv.example text html latex cleancdfname text html latex example debug.affy123 text html latex expresso text html latex example expressoWidget text html latex example fit.li.wong text html latex example generateExprSet-methods text html latex example generateExprVal-methods text html latex example generateExprVal.method.avgdiff text html latex example generateExprVal.method.playerout text html latex hlog text html latex justrma text html latex example list.celfiles text html latex example loess.normalize text html latex maffy.normalise text html latex example maffy.subset text html latex example mas5 text html latex example mas5calls text html latex example merge.AffyBatch text html latex example multiloess text html latex mva.pairs text html latex example normalize-methods text html latex example normalize text html latex normalize.constant text html latex normalize.contrast text html latex example normalize.invariantset text html latex normalize.loess text html latex example normalize.qspline text html latex normalize.quantiles text html latex normalize.quantiles.robust text html latex pairs.AffyBatch text html latex example plot.ProbeSet text html latex example plot.density text html latex example plotLocation text html latex example pmcorrect text html latex example ppsetApply text html latex example probeMatch-methods text html latex probeNames-methods text html latex read.affybatch text html latex example read.probematrix text html latex example rma text html latex example setAffyOptions text html latex example simplemultiLoess text html latex summary text html latex tukey.biweight text html latex whatcdf text html latex xy2indices text html latex example ** building package indices ... * DONE (affy) * creating vignettes ... OK * cleaning src * running cleanup * removing junk files * checking for LF line-endings in source files * checking for empty or unneeded directories * building 'affy_1.14.0.tar.gz'