Back to the "Multiple platform build/check report"
| Package 133/208 | OS | Arch | BUILD | CHECK | BUILD BIN |
oligo0.99.29Benilton 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: E:\biocbld\2.0d\R\bin\R.exe CMD check oligo_0.99.29.tar.gz |
| RetCode: 1 |
| Time: 467.3 seconds |
| Status: ERROR |
| CheckDir: oligo.Rcheck |
| Warnings: NA |
* checking for working latex ... OK
* using log directory 'E:/biocbld/2.0d/Rpacks/oligo.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-12-05 r40126)
* 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 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:
addPriorRegions addRegions alleleAB antisenseThetaA antisenseThetaB
calls calls<- callsConfidence callsConfidence<- center chromosome
cnConfidence cnConfidence<- copyNumber copyNumber<-
CorrectSequenceLength 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:
oligoSnpSet SnpCallSet SnpCallSetPlus SnpCopyNumberSet SnpQSet
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 ... ERROR
LaTeX errors when creating DVI version.
This typically indicates Rd problems.
oligo.Rcheck/00install.out:
installing R.css in E:/biocbld/2.0d/Rpacks/oligo.Rcheck
---------- Making package oligo ------------
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
making baseProfile.d from baseProfile.c
making basecontent.d from basecontent.c
making qnorm.d from qnorm.c
making rma2.d from rma2.c
making rma_background2.d from rma_background2.c
making rma_common.d from rma_common.c
gcc -Ie:/biocbld/2.0d/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c baseProfile.c -o baseProfile.o
baseProfile.c: In function `gcrma_getSeq2':
baseProfile.c:14: warning: unused variable `nx'
gcc -Ie:/biocbld/2.0d/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c basecontent.c -o basecontent.o
gcc -Ie:/biocbld/2.0d/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c qnorm.c -o qnorm.o
qnorm.c: In function `qnorm_c_determine_target':
qnorm.c:1518: warning: unused variable `ind'
qnorm.c:1519: warning: unused variable `dimat'
qnorm.c:1523: warning: unused variable `ranks'
qnorm.c: In function `R_qnorm_using_target':
qnorm.c:1599: warning: unused variable `dim2'
qnorm.c: In function `qnorm_c_determine_target':
qnorm.c:1591: warning: control reaches end of non-void function
qnorm.c: At top level:
qnorm.c:114: warning: 'min' defined but not used
qnorm.c:387: warning: 'qnorm_c_old' defined but not used
qnorm.c:461: warning: 'qnorm_robust_c_old' defined but not used
gcc -Ie:/biocbld/2.0d/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c rma2.c -o rma2.o
gcc -Ie:/biocbld/2.0d/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c rma_background2.c -o rma_background2.o
gcc -Ie:/biocbld/2.0d/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c rma_common.c -o rma_common.o
windres --include-dir e:/biocbld/2.0d/R/include -i oligo_res.rc -o oligo_res.o
gcc -shared -s -o oligo.dll oligo.def baseProfile.o basecontent.o qnorm.o rma2.o rma_background2.o rma_common.o oligo_res.o -Le:/biocbld/2.0d/R/bin -lR
... DLL made
installing DLL
installing R files
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"
installing man source files
installing indices
installing help
>>> Building/Updating help pages for package 'oligo'
Formats: text html latex example chm
FeatureSet-class text html latex chm
FeatureSet-methods text html latex chm
SubClasses text html latex example chm
accessors text html latex example chm
allele text html latex example chm
as.data.frame.platformDesign text html latex example chm
basecontent text html latex example chm
bg.correct text html latex chm
characterOrNULL-class text html latex chm
cleanPlatformName text html latex example chm
crlmm text html latex example chm
dimensions text html latex example chm
featureIndex text html latex chm
featureInfo text html latex chm
fileManip text html latex chm
getPlatformDesign text html latex example chm
indexFeatureSetName text html latex chm
indexTools text html latex chm
initialize-methods text html latex chm
justsnprma text html latex example chm
methods-Sequences text html latex example chm
nProbes text html latex chm
names text html latex example chm
normalize.quantiles text html latex chm
parsers text html latex example chm
platformDesign-class text html latex chm
platformDesignName text html latex chm
plotDensity text html latex example chm
probeMatch-methods text html latex example chm
probeNames-methods text html latex chm
probeNames text html latex chm
read.celfiles text html latex example chm
rma text html latex example chm
snprma text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\2.0d\Rpacks\oligo.Rcheck\00_pkg_src\oligo\chm\oligo.chm
Compile time: 0 minutes, 0 seconds
35 Topics
153 Local links
2 Internet links
1 Graphic
Created e:\biocbld\2.0d\Rpacks\oligo.Rcheck\00_pkg_src\oligo\chm\oligo.chm, 44,694 bytes
Compression decreased file by 62,790 bytes.
adding MD5 sums
* DONE (oligo)