Package: pdInfoBuilder

Version: 1.11.2

Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes pdInfoBuilder_1.11.2.tar.gz

StartedAt: 2009-12-07 18:21:22 -0800 (Mon, 07 Dec 2009)

EndedAt: 2009-12-07 18:23:34 -0800 (Mon, 07 Dec 2009)

EllapsedTime: 132.5 seconds

RetCode: 0

Status: OK

CheckDir: pdInfoBuilder.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/pdInfoBuilder.Rcheck'
* using R version 2.11.0 Under development (unstable) (2009-11-10 r50388)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pdInfoBuilder/DESCRIPTION' ... OK
* this is package 'pdInfoBuilder' version '1.11.2'
* 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 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 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
  'pstype'
combinePgfClfProbesetsMps: no visible binding for global variable
  'ptype'
parseCdfCelProbe: no visible binding for global variable 'fsetid'
parseCdfCelProbe: no visible binding for global variable 'isPm'
parseNgsTrio: no visible binding for global variable 'mismatch'
makePdInfoPackage,AffySTPDInfoPkgSeed: no visible binding for global
  variable 'exonTranscriptionMmFeatureSchema'
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 ... OK
* checking Rd \usage sections ... 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

* install options are ' --no-html'

* installing *source* package 'pdInfoBuilder' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c pdInfoBuilder.c -o pdInfoBuilder.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o pdInfoBuilder.so pdInfoBuilder.o -L/home/biocbuild/bbs-2.6-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading

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: DBI
Loading required package: oligoClasses
Welcome to oligoClasses version 1.9.14
Loading required package: preprocessCore
Welcome to oligo version 1.11.9
** help
*** installing help indices
** building package indices ...
* DONE (pdInfoBuilder)