Back to the "Multiple platform build/check report"
| Package 122/187 | OS | Arch | BUILD | CHECK | BUILD BIN |
oligo0.99.11Benilton Carvalho | Linux (SUSE 9.2) | x86_64 | OK | WARNINGS | |
| Linux (SUSE 9.2) | i686 | OK | WARNINGS | ||
| Solaris 2.9 | sparc | OK | ERROR | ||
| Linux (SUSE 10.0) | x86_64 | OK | WARNINGS | ||
| Windows Server 2003 | x86_64 | OK | [ WARNINGS ] | OK |
| Package: oligo |
| Version: 0.99.11 |
| Command: D:\biocbld\1.9d\R\bin\R.exe CMD check oligo_0.99.11.tar.gz |
| RetCode: 0 |
| Time: 54.5 seconds |
| Status: WARNINGS |
| CheckDir: oligo.Rcheck |
| Warnings: 2 |
* checking for working latex ... OK * using log directory 'D:/biocbld/1.9d/Rpacks/oligo.Rcheck' * using R version 2.4.0 Under development (unstable) (2006-06-04 r38279) * checking for file 'oligo/DESCRIPTION' ... OK * this is package 'oligo' version '0.99.11' * checking package dependencies ... OK * 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 ... OK * checking R files for syntax errors ... OK * checking R files for non-ASCII characters ... OK * checking R files for library.dynam ... 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 Rd files ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: chromosome GenomeBuild pmChr pmPosition position Undocumented S4 methods: generic chromosome and siglist TilingFeatureSet generic GenomeBuild and siglist TilingFeatureSet generic pmChr and siglist TilingFeatureSet generic pmPosition and siglist TilingFeatureSet generic position and siglist TilingFeatureSet All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter 'Writing R documentation files' in manual 'Writing R Extensions'. * checking for code/documentation mismatches ... OK * 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 * creating oligo-Ex.R ... OK * checking examples ... OK * creating oligo-manual.tex ... OK * checking oligo-manual.tex ... OK WARNING: There were 2 warnings, see D:/biocbld/1.9d/Rpacks/oligo.Rcheck/00check.log for details
oligo.Rcheck/00install.out:
installing R.css in D:/biocbld/1.9d/Rpacks/oligo.Rcheck
---------- Making package oligo ------------
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
adding build stamp to DESCRIPTION
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 -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -c baseProfile.c -o baseProfile.o
baseProfile.c: In function `gcrma_getSeq2':
baseProfile.c:14: warning: unused variable `nx'
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -c basecontent.c -o basecontent.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -c qnorm.c -o qnorm.o
qnorm.c: In function `qnorm_c_determine_target':
qnorm.c:1517: warning: unused variable `ind'
qnorm.c:1518: warning: unused variable `dimat'
qnorm.c:1522: warning: unused variable `ranks'
qnorm.c: In function `R_qnorm_using_target':
qnorm.c:1598: warning: unused variable `dim2'
qnorm.c: In function `qnorm_c_determine_target':
qnorm.c:1590: warning: control reaches end of non-void function
qnorm.c: At top level:
qnorm.c:113: warning: 'min' defined but not used
qnorm.c:386: warning: 'qnorm_c_old' defined but not used
qnorm.c:460: warning: 'qnorm_robust_c_old' defined but not used
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -c rma2.c -o rma2.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -c rma_background2.c -o rma_background2.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -c rma_common.c -o rma_common.o
windres --include-dir d:/biocbld/1.9d/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 -Ld:/biocbld/1.9d/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
[1] "platformDesign"
[1] "FeatureSet"
[1] "characterOrNULL"
[1] "ExpressionFeatureSet"
[1] "SnpFeatureSet"
[1] "TilingFeatureSet"
[1] "manufacturer"
[1] "manufacturer<-"
[1] "platform"
[1] "platform<-"
[1] "platformDesignName"
[1] "getPlatformDesign"
[1] "pmindex"
[1] "mmindex"
[1] "indexFeatureSetName"
[1] "nrow"
[1] "hist"
[1] "names"
[1] "nProbes"
[1] "pm"
[1] "pm<-"
[1] "mm"
[1] "mm<-"
[1] "image"
[1] "featureIndex"
[1] "boxplot"
[1] "npixels"
[1] "allele"
[1] "chromosome"
[1] "position"
[1] "GenomeBuild"
[1] "pmChr"
[1] "pmPosition"
[1] "names"
[1] "show"
[1] "nProbes"
[1] "pmindex"
[1] "mmindex"
[1] "initialize"
[1] "exprs"
[1] "platform"
[1] "platform<-"
[1] "manufacturer"
[1] "manufacturer<-"
[1] "length"
[1] "platformDesignName"
[1] "getPlatformDesign"
[1] "geneNames"
[1] "pmindex"
[1] "mmindex"
[1] "indexFeatureSetName"
[1] "ncol"
[1] "nrow"
[1] "hist"
[1] "pm"
[1] "pm<-"
[1] "mm"
[1] "mm<-"
[1] "featureIndex"
[1] "boxplot"
[1] "image"
Creating a new generic function for 'sd' in 'oligo'
[1] "sd"
[1] "npixels"
[1] "allele"
[1] "chromosome"
[1] "position"
[1] "GenomeBuild"
[1] "pmPosition"
[1] "pmChr"
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
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
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
Microsoft HTML Help Compiler 4.74.8702
Compiling d:\biocbld\1.9d\Rpacks\oligo.Rcheck\00_pkg_src\oligo\chm\oligo.chm
Compile time: 0 minutes, 0 seconds
32 Topics
143 Local links
2 Internet links
1 Graphic
Created d:\biocbld\1.9d\Rpacks\oligo.Rcheck\00_pkg_src\oligo\chm\oligo.chm, 41,483 bytes
Compression decreased file by 58,213 bytes.
adding MD5 sums
* DONE (oligo)