Package: pdInfoBuilder

Version: 1.15.2

Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings pdInfoBuilder_1.15.2.tar.gz

StartedAt: 2011-02-24 19:16:40 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 19:18:21 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 100.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: pdInfoBuilder.Rcheck

Warnings: 1

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/pdInfoBuilder.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pdInfoBuilder/DESCRIPTION' ... OK
* this is package 'pdInfoBuilder' version '1.15.2'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'pdInfoBuilder' 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 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 ... NOTE
combinePgfClfProbesetsMps: no visible binding for global variable
  'ptype'
parseNgsTrio: no visible binding for global variable 'mismatch'
parseProbeSequenceFile: no visible binding for global variable 'count'
makePdInfoPackage,NgsExpressionPDInfoPkgSeed: no visible binding for
  global variable 'ngsExprMmFeatureSchema'
makePdInfoPackage,NgsTilingPDInfoPkgSeed: no visible binding for global
  variable 'tiledRegionMmFeatureSchema'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'AffySNPPDInfoPkgSeed2-class':
Slots for class 'AffySNPPDInfoPkgSeed2'
  Code: author axiom biocViews cdfFile chipName csvAnnoFile csvSeqFile
        email genomebuild license manufacturer organism species url
        version
  Inherited: version license author email biocViews chipName
        manufacturer url genomebuild organism species
  Docs: author biocViews cdfFile chipName csvAnnoFile csvSeqFile email
        genomebuild license manufacturer organism species url version

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'E:/biocbld/bbs-2.8-bioc/meat/pdInfoBuilder.Rcheck/00check.log'
for details

* installing *source* package 'pdInfoBuilder' ...
** libs
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c pdInfoBuilder.c -o pdInfoBuilder.o
gcc -shared -s -static-libgcc -o pdInfoBuilder.dll tmp.def pdInfoBuilder.o -LE:/biocbld/BBS-2˜1.8-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.8-bioc/meat/pdInfoBuilder.Rcheck/pdInfoBuilder/libs/i386
** R
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: DBI
Loading required package: oligoClasses
================================================================================
Welcome to oligoClasses version 1.13.9
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
================================================================================
Welcome to oligo version 1.15.4
================================================================================
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (pdInfoBuilder)

name	user	system	elapsed
AffyExpressionPDInfoPkgSeed-class	0	0	0
AffySNPCNVPDInfoPkgSeed-class	0	0	0
AffySNPCNVPDInfoPkgSeed2-class	0	0	0
AffySNPPDInfoPkgSeed-class	0.50	0.02	0.51
AffySNPPDInfoPkgSeed2-class	0	0	0
AffySTPDInfoPkgSeed-class	0	0	0
AffyTilingPDInfoPkgSeed-class	0	0	0
NgsExpressionPDInfoPkgSeed-class	0	0	0
NgsTilingPDInfoPkgSeed-class	0	0	0
NimbleGenPDInfoPkgSeed-class	0	0	0
makePdInfoPackage	0	0	0