Package: oligo

Version: 0.99.11

Command: /loc/biocbuild/1.9d/R/bin/R CMD check oligo_0.99.11.tar.gz

RetCode: 0

Time: 54.8 seconds

Status: WARNINGS

CheckDir: oligo.Rcheck

Warnings: 2

* checking for working latex ... OK
* using log directory '/loc/biocbuild/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 for sufficient/correct file permissions ... 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
  /loc/biocbuild/1.9d/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
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c basecontent.c -o basecontent.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c baseProfile.c -o baseProfile.o
baseProfile.c: In function `gcrma_getSeq2':
baseProfile.c:14: warning: unused variable `nx'
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -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 -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c rma2.c -o rma2.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c rma_background2.c -o rma_background2.o
gcc -I/loc/biocbuild/1.9d/R/include -I/loc/biocbuild/1.9d/R/include -DHAVE_ZLIB=1  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c rma_common.c -o rma_common.o
gcc -shared -L/usr/local/lib64 -o oligo.so basecontent.o baseProfile.o qnorm.o rma2.o rma_background2.o rma_common.o -lz   
** R
** 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"
** 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
  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
  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
** building package indices ...
* DONE (oligo)