Package: oligo

Version: 1.0.2

Command: D:\biocbld\bbs-2.0-bioc\R\bin\R.exe CMD check oligo_1.0.2.tar.gz

RetCode: 0

Time: 89.4 seconds

Status: WARNINGS

CheckDir: oligo.Rcheck

Warnings: 2

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.0-bioc/meat/oligo.Rcheck'
* using R version 2.5.0 (2007-04-23)
* checking for file 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '1.0.2'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'oligo' can be installed ... WARNING
Found the following significant warnings:
       missing link(s):  eSet-class VersionedBiobase-class Versioned-class eSet-class VersionedBiobase-class Versioned-class
       missing link(s):  eSet-class VersionedBiobase-class Versioned-class eSet-class VersionedBiobase-class Versioned-class
       missing link(s):  eSet-class VersionedBiobase-class Versioned-class eSet-class VersionedBiobase-class Versioned-class
       missing link(s):  eSet-class VersionedBiobase-class Versioned-class eSet-class VersionedBiobase-class Versioned-class
See 'D:/biocbld/bbs-2.0-bioc/meat/oligo.Rcheck/00install.out' for details.
* 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 non-ASCII characters ... OK
* checking R files for syntax errors ... 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* 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 ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'crlmm':
crlmm
  Code: function(object, correction = NULL, recalibrate = TRUE,
                 minPforCalls = c(0.5, 0.1, 0.5), verbose = TRUE,
                 correctionFile = NULL)
  Docs: function(object, correction = NULL, recalibrate = TRUE,
                 minLLRforCalls = c(25, 5, 25), verbose = TRUE,
                 correctionFile = NULL)
  Argument names in code not in docs:
    minPforCalls
  Argument names in docs not in code:
    minLLRforCalls
  Mismatches in argument names:
    Position: 4 Code: minPforCalls Docs: minLLRforCalls

* 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 2 warnings, see
  D:/biocbld/bbs-2.0-bioc/meat/oligo.Rcheck/00check.log
for details

installing R.css in D:/biocbld/bbs-2.0-bioc/meat/oligo.Rcheck


---------- Making package oligo ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making M_estimator2.d from M_estimator2.c
making baseProfile.d from baseProfile.c
making basecontent.d from basecontent.c
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c M_estimator2.c -o M_estimator2.o
M_estimator2.c: In function `R_HuberMatrixRows2':
M_estimator2.c:129: warning: 'scale1' might be used uninitialized in this function
M_estimator2.c:129: warning: 'scale2' might be used uninitialized in this function
M_estimator2.c:129: warning: 'scale3' might be used uninitialized in this function
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c baseProfile.c -o baseProfile.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c basecontent.c -o basecontent.o
windres -I d:/biocbld/bbs-2.0-bioc/R/include  -i oligo_res.rc -o oligo_res.o
gcc  -shared -s  -o oligo.dll oligo.def M_estimator2.o baseProfile.o basecontent.o oligo_res.o  -Ld:/biocbld/bbs-2.0-bioc/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()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: affyio
Loading required package: splines
Loading required package: RSQLite
Loading required package: DBI
Loading required package: BufferedMatrix
Loading required package: BufferedMatrixMethods
  installing inst files
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'oligo'
     Formats: text html latex example chm 
  DBPDInfo-class                    text    html    latex   example chm
  FeatureSet-class                  text    html    latex   example chm
     missing link(s):  eSet-class VersionedBiobase-class Versioned-class eSet-class VersionedBiobase-class Versioned-class
  FeatureSetExtensions-class        text    html    latex   example chm
     missing link(s):  eSet-class VersionedBiobase-class Versioned-class eSet-class VersionedBiobase-class Versioned-class
  Index-methods                     text    html    latex   example chm
  IntensityMatrix-methods           text    html    latex   example chm
  PDInfo-class                      text    html    latex   example chm
  PDInfo-methods                    text    html    latex   example chm
  Sequences-methods                 text    html    latex   example chm
  SnpCallSet-methods                text    html    latex   example chm
  SnpCopyNumberSet-methods          text    html    latex   example chm
  SnpQSet-class                     text    html    latex   example chm
     missing link(s):  eSet-class VersionedBiobase-class Versioned-class eSet-class VersionedBiobase-class Versioned-class
  SnpQSet-methods                   text    html    latex   example chm
  SnpSetExtensions-class            text    html    latex   example chm
     missing link(s):  eSet-class VersionedBiobase-class Versioned-class eSet-class VersionedBiobase-class Versioned-class
  basecontent                       text    html    latex   example chm
  boxplot                           text    html    latex   example chm
  chromosome                        text    html    latex   example chm
  crlmm                             text    html    latex   example chm
  featureIndex                      text    html    latex   example chm
  genomeBuild                       text    html    latex   example chm
  getPlatformDesign                 text    html    latex   example chm
  hist                              text    html    latex   example chm
  image                             text    html    latex   example chm
  internals                         text    html    latex   example chm
  kind                              text    html    latex   example chm
  list.celfiles                     text    html    latex   example chm
  manufacturer                      text    html    latex   example chm
  nProbes                           text    html    latex   example chm
  ncol                              text    html    latex   example chm
  oligo-package                     text    html    latex   example chm
  platform                          text    html    latex   example chm
  platformDesign-class              text    html    latex   example chm
  plotDensity                       text    html    latex   example chm
  pmAllele                          text    html    latex   example chm
  pmPosition                        text    html    latex   example chm
  pmStrand                          text    html    latex   example chm
  probeNames                        text    html    latex   example chm
  read.celfiles                     text    html    latex   example chm
  read.xysfiles                     text    html    latex   example chm
  rma                               text    html    latex   example chm
  sequenceDesignMatrix              text    html    latex   example chm
  snprma                            text    html    latex   example chm
  snprmaSummaries                   text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\bbs-2.0-bioc\meat\oligo.Rcheck\00_pkg_src\oligo\chm\oligo.chm


Compile time: 0 minutes, 0 seconds
43	Topics
215	Local links
0	Internet links
1	Graphic


Created d:\biocbld\bbs-2.0-bioc\meat\oligo.Rcheck\00_pkg_src\oligo\chm\oligo.chm, 41,506 bytes
Compression decreased file by 89,518 bytes.
  adding MD5 sums

* DONE (oligo)