CHECK report for oligo on derby

* checking for working latex ... OK * using log directory '/Users/biocbuild/2.0d/Rpacks/oligo.Rcheck' * using R version 2.5.0 Under development (unstable) (2006-10-21 r39702) * checking for file 'oligo/DESCRIPTION' ... OK * this is package 'oligo' version '0.99.29' * checking package dependencies ... WARNING 'library' or 'require' calls not declared from: limma ellipse cluster methods 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 'oligo' 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 ... WARNING Subdirectory 'data' contains no data sets. * 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 whether the name space can be loaded with stated dependencies ... OK * checking S3 generic/method consistency ... WARNING as.data.frame: function(x, row.names, optional, ...) as.data.frame.platformDesign: function(x, row.names, optional) See section 'Generic functions and methods' of the 'Writing R Extensions' manual. * 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 ... WARNING Undocumented code objects: CorrectSequenceLength addPriorRegions addRegions alleleAB antisenseThetaA antisenseThetaB calls calls<- callsConfidence callsConfidence<- center chromosome cnConfidence cnConfidence<- copyNumber copyNumber<- f0 fitAffySnpMixture fitRma genomeBuild getA getAffySnpCalls getAffySnpConfidence getAffySnpDistance getAffySnpGenotypeRegionParams getAffySnpPriors getChrXIndex getGenotypeRegionParams getInitialAffySnpCalls getM getRmaPars getScale getSnpFragmentLength imageAffy imageNGS logRatioAntisense logRatioSense normalizeToSample plotRegions plotSnpConfidenceSilhouette pmAlleleAB pmChr pmPosition pmSnpBasePair position preProcess replaceAffySnpParams rowEntropy rowEntropy.old rowIndepChiSqTest senseThetaA senseThetaB snpBasePair snpGenderCall snpMedianSilhouette snpSilhouette summSnp updateAffySnpParams updateSnpQSet Undocumented S4 classes: SnpCallSet SnpCallSetPlus SnpCopyNumberSet SnpQSet oligoSnpSet Undocumented S4 methods: generic 'alleleAB' and siglist 'SnpFeatureSet' generic 'antisenseThetaA' and siglist 'SnpQSet' generic 'antisenseThetaB' and siglist 'SnpQSet' generic 'calls' and siglist 'SnpCallSet' generic 'calls<-' and siglist 'SnpCallSet,matrix' generic 'callsConfidence' and siglist 'SnpCallSet' generic 'callsConfidence<-' and siglist 'SnpCallSet,matrix' generic 'chromosome' and siglist 'TilingFeatureSet' generic 'cnConfidence' and siglist 'SnpCopyNumberSet' generic 'cnConfidence<-' and siglist 'SnpCopyNumberSet,matrix' generic 'copyNumber' and siglist 'SnpCopyNumberSet' generic 'copyNumber<-' and siglist 'SnpCopyNumberSet,matrix' generic 'genomeBuild' and siglist 'TilingFeatureSet' generic 'getA' and siglist 'SnpQSet' generic 'getM' and siglist 'SnpQSet' generic 'initialize' and siglist 'SnpCallSet' generic 'initialize' and siglist 'SnpCopyNumberSet' generic 'initialize' and siglist 'SnpQSet' generic 'initialize' and siglist 'SnpCallSetPlus' generic 'logRatioAntisense' and siglist 'SnpCallSetPlus' generic 'logRatioSense' and siglist 'SnpCallSetPlus' generic 'mm<-' and siglist 'FeatureSet,matrix' generic 'pm<-' and siglist 'FeatureSet,matrix' generic 'pmAlleleAB' and siglist 'SnpFeatureSet' generic 'pmChr' and siglist 'TilingFeatureSet' generic 'pmPosition' and siglist 'TilingFeatureSet' generic 'pmSnpBasePair' and siglist 'SnpFeatureSet' generic 'position' and siglist 'TilingFeatureSet' generic 'senseThetaA' and siglist 'SnpQSet' generic 'senseThetaB' and siglist 'SnpQSet' generic 'snpBasePair' and siglist 'SnpFeatureSet' generic 'snpMedianSilhouette' and siglist 'SnpCallSetPlus' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See the chapter 'Writing R documentation files' in manual 'Writing R Extensions'. * checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'crlmm': crlmm Code: function(object, correction = NULL, recalibrate = TRUE, minLLRforCalls = c(50, 40, 50), returnCorrectedM = TRUE, returnParams = FALSE, verbose = TRUE) Docs: function(object, correction = NULL, recalibrate = TRUE, minLLRforCalls = c(50, 40, 50), returnCorrectedM = FALSE, returnParams = FALSE, verbose = TRUE) Mismatches in argument default values: Name: returnCorrectedM Code: TRUE Docs: FALSE Codoc mismatches from documentation object 'justsnprma': justsnprma Code: function(files, phenoData = NULL) Docs: function(files) Argument names in code not in docs: phenoData Codoc mismatches from documentation object 'File Parsers': read.celfiles Code: function(filenames, pdenv = TRUE, arrayType = NULL, pkgname = NULL, sd = FALSE, npixels = FALSE, phenoData = new("AnnotatedDataFrame"), featureData = NULL, description = NULL, notes = "", verbose = FALSE, compress = FALSE, rm.mask = FALSE, rm.outliers = FALSE, rm.extra = FALSE) Docs: function(filenames, pdenv = TRUE, arrayType = NULL, pkgname = NULL, sd = FALSE, npixels = FALSE, phenoData = new("AnnotatedDataFrame"), description = NULL, notes = "", verbose = FALSE, compress = FALSE, rm.mask = FALSE, rm.outliers = FALSE, rm.extra = FALSE) Argument names in code not in docs: featureData Mismatches in argument names (first 3): Position: 8 Code: featureData Docs: description Position: 9 Code: description Docs: notes Position: 10 Code: notes Docs: verbose * 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 oligo-Ex.R ... OK * checking examples ... OK * creating oligo-manual.tex ... OK * checking oligo-manual.tex ... OK WARNING: There were 5 warnings, see /Users/biocbuild/2.0d/Rpacks/oligo.Rcheck/00check.log for details

* Installing *source* package 'oligo' ... 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 ** arch - i386 gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c baseProfile.c -o baseProfile.o /var/tmp//ccIDFVNW.s:192:indirect jmp without `*' /var/tmp//ccIDFVNW.s:207:indirect jmp without `*' /var/tmp//ccIDFVNW.s:222:indirect jmp without `*' /var/tmp//ccIDFVNW.s:237:indirect jmp without `*' /var/tmp//ccIDFVNW.s:252:indirect jmp without `*' /var/tmp//ccIDFVNW.s:267:indirect jmp without `*' gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c basecontent.c -o basecontent.o /var/tmp//ccrPtReq.s:401:indirect jmp without `*' /var/tmp//ccrPtReq.s:416:indirect jmp without `*' /var/tmp//ccrPtReq.s:431:indirect jmp without `*' /var/tmp//ccrPtReq.s:446:indirect jmp without `*' /var/tmp//ccrPtReq.s:465:indirect jmp without `*' /var/tmp//ccrPtReq.s:480:indirect jmp without `*' /var/tmp//ccrPtReq.s:495:indirect jmp without `*' /var/tmp//ccrPtReq.s:510:indirect jmp without `*' /var/tmp//ccrPtReq.s:529:indirect jmp without `*' /var/tmp//ccrPtReq.s:548:indirect jmp without `*' /var/tmp//ccrPtReq.s:563:indirect jmp without `*' /var/tmp//ccrPtReq.s:578:indirect jmp without `*' /var/tmp//ccrPtReq.s:593:indirect jmp without `*' gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c qnorm.c -o qnorm.o /var/tmp//ccFgZqQS.s:5478:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5497:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5512:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5527:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5542:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5557:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5572:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5587:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5602:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5617:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5632:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5647:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5662:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5677:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5692:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5707:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5722:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5737:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5752:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5767:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5782:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5801:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5816:indirect jmp without `*' /var/tmp//ccFgZqQS.s:5831:indirect jmp without `*' gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c rma2.c -o rma2.o /var/tmp//ccXMYzFg.s:1637:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1652:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1667:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1682:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1697:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1712:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1727:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1742:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1757:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1772:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1787:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1802:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1817:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1832:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1851:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1866:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1881:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1896:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1911:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1926:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1945:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1960:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1975:indirect jmp without `*' /var/tmp//ccXMYzFg.s:1990:indirect jmp without `*' /var/tmp//ccXMYzFg.s:2005:indirect jmp without `*' gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c rma_background2.c -o rma_background2.o /var/tmp//ccBr2wyH.s:1296:indirect jmp without `*' /var/tmp//ccBr2wyH.s:1311:indirect jmp without `*' /var/tmp//ccBr2wyH.s:1326:indirect jmp without `*' /var/tmp//ccBr2wyH.s:1341:indirect jmp without `*' /var/tmp//ccBr2wyH.s:1356:indirect jmp without `*' /var/tmp//ccBr2wyH.s:1371:indirect jmp without `*' /var/tmp//ccBr2wyH.s:1386:indirect jmp without `*' /var/tmp//ccBr2wyH.s:1401:indirect jmp without `*' /var/tmp//ccBr2wyH.s:1416:indirect jmp without `*' /var/tmp//ccBr2wyH.s:1431:indirect jmp without `*' /var/tmp//ccBr2wyH.s:1446:indirect jmp without `*' /var/tmp//ccBr2wyH.s:1461:indirect jmp without `*' /var/tmp//ccBr2wyH.s:1476:indirect jmp without `*' /var/tmp//ccBr2wyH.s:1491:indirect jmp without `*' /var/tmp//ccBr2wyH.s:1506:indirect jmp without `*' /var/tmp//ccBr2wyH.s:1521:indirect jmp without `*' /var/tmp//ccBr2wyH.s:1536:indirect jmp without `*' /var/tmp//ccBr2wyH.s:1555:indirect jmp without `*' /var/tmp//ccBr2wyH.s:1570:indirect jmp without `*' /var/tmp//ccBr2wyH.s:1585:indirect jmp without `*' gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c rma_common.c -o rma_common.o gcc-4.0 -arch i386 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o oligo.so baseProfile.o basecontent.o qnorm.o rma2.o rma_background2.o rma_common.o -lz -F/Library/Frameworks/R.framework/.. -framework R ** R ** data chmod: /Users/biocbuild/2.0d/Rpacks/oligo.Rcheck/oligo/data/*: No such file or directory ** save image 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: splines Creating a new generic function for "hist" in "oligo" Creating a new generic function for "boxplot" in "oligo" Creating a new generic function for "image" in "oligo" Creating a new generic function for "sd" in "oligo" ** help >>> Building/Updating help pages for package 'oligo' Formats: text html latex example FeatureSet-class text html latex FeatureSet-methods text html latex SubClasses text html latex example accessors text html latex example allele text html latex example as.data.frame.platformDesign text html latex example basecontent text html latex example bg.correct text html latex characterOrNULL-class text html latex cleanPlatformName text html latex example crlmm text html latex example dimensions text html latex example featureIndex text html latex featureInfo text html latex fileManip text html latex getPlatformDesign text html latex example indexFeatureSetName text html latex indexTools text html latex initialize-methods text html latex justsnprma text html latex example methods-Sequences text html latex example nProbes text html latex names text html latex example normalize.quantiles text html latex parsers text html latex example platformDesign-class text html latex platformDesignName text html latex plotDensity text html latex example probeMatch-methods text html latex example probeNames-methods text html latex probeNames text html latex read.celfiles text html latex example rma text html latex example snprma text html latex example ** building package indices ... * DONE (oligo)

Package 133/208	OS	Arch	BUILD	CHECK	BUILD BIN
oligo 0.99.29 Benilton Carvalho	Linux (SUSE 9.2)	x86_64	OK	WARNINGS
	Linux (SUSE 10.1)	x86_64	OK	WARNINGS
	Linux (SUSE 9.2)	i686	OK	WARNINGS
	Solaris 2.9	sparc	OK	WARNINGS
	Windows Server 2003	x86_64	OK	WARNINGS	OK
	Windows Server 2003	NA	OK	ERROR	OK
	Mac OS X (10.4.6)	i686	OK	[ WARNINGS ]

oligo

0.99.29

Command output