Package: pdInfoBuilder

Version: 1.1.9

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check pdInfoBuilder_1.1.9.tar.gz

RetCode: 0

Time: 73.6 seconds

Status: WARNINGS

CheckDir: pdInfoBuilder.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/Users/biocbuild/bbs-2.1-bioc/meat/pdInfoBuilder.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-10 r42465)
* checking for file 'pdInfoBuilder/DESCRIPTION' ... OK
* this is package 'pdInfoBuilder' version '1.1.9'
* 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 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 ... NOTE
dbImportLine.AFFYHUEX_DB.Transcript: possible error in
  dbInsert_multipart_data(conn, "protein_domains", protein_domains,
  acc2id, new_accessions, transcript_cluster_ID): unused argument(s)
  (new_accessions, transcript_cluster_ID)
dbImportLine.AFFYHUEX_DB.Transcript: no visible binding for global
  variable 'acc2id'
dbImportLine.AFFYHUEX_DB.Transcript: no visible binding for global
  variable 'new_accessions'
dbImportLine.AFFYHUEX_DB.Transcript: possible error in
  dbInsert_multipart_data(conn, "protein_families", protein_families,
  acc2id, new_accessions, transcript_cluster_ID): unused argument(s)
  (new_accessions, transcript_cluster_ID)
dbInitTableIds.AFFYHUEX_DB: no visible binding for global variable
  'id0'
importTrDicts: no visible binding for global variable
  'transcript_cluster_table'
importTrDicts: no visible binding for global variable 'acc2id_dict'
importTrDicts: no visible binding for global variable 'TR2mrna_dict'
importTrDicts : <anonymous>: no visible binding for global variable
  'TR2mrna_dict'
importTrDicts: no visible binding for global variable
  'TR2mrna_details_dict'
importTrDicts: no visible binding for global variable 'gene_dict'
importTrDicts: no visible binding for global variable 'acc2genes_dict'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  AffySNPCNVPDInfoPkgSeed
Undocumented S4 methods:
  generic 'chipName' and siglist 'AffySNPCNVPDInfoPkgSeed'
  generic 'initialize' and siglist 'AffySNPCNVPDInfoPkgSeed'
  generic 'makePdInfoPackage' and siglist 'AffySNPCNVPDInfoPkgSeed'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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
* creating pdInfoBuilder-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating pdInfoBuilder-manual.tex ... OK
* checking pdInfoBuilder-manual.tex ... OK

WARNING: There was 1 warning, see
  /Users/biocbuild/bbs-2.1-bioc/meat/pdInfoBuilder.Rcheck/00check.log
for details

* Installing *source* package 'pdInfoBuilder' ...
** libs
** arch - i386
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -Wall -std=gnu99 -march=nocona -c pdInfoBuilder.c -o pdInfoBuilder.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pdInfoBuilder.so pdInfoBuilder.o   -F/Library/Frameworks/R.framework/.. -framework R
** arch - ppc
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c pdInfoBuilder.c -o pdInfoBuilder.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pdInfoBuilder.so pdInfoBuilder.o   -F/Library/Frameworks/R.framework/.. -framework R
** R
** inst
** preparing package for lazy loading
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: RSQLite
Loading required package: DBI
Loading required package: affxparser
Loading required package: oligo
Loading required package: affyio
Loading required package: splines
Loading required package: BufferedMatrix
Loading required package: BufferedMatrixMethods
Loading required package: preprocessCore
Loading required package: AnnotationDbi
This is the oligo package
** help
 >>> Building/Updating help pages for package 'pdInfoBuilder'
     Formats: text html latex example 
  AffySNPPDInfoPkgSeed-class        text    html    latex   example
  PDInfoPkgSeed-class               text    html    latex   example
  PkgSeed-class                     text    html    latex   example
  chipName                          text    html    latex
  makePdInfoPackage                 text    html    latex   example
** building package indices ...
* DONE (pdInfoBuilder)