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Package 133/208OSArchBUILDCHECKBUILD 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 ]
Package: oligo
Version: 0.99.29
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check oligo_0.99.29.tar.gz
RetCode: 0
Time: 60.3 seconds
Status: WARNINGS
CheckDir: oligo.Rcheck
Warnings: 5

Command output

* 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

oligo.Rcheck/00install.out:

* 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
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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
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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
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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
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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
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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)