Package: pdInfoBuilder

Version: 1.1.9

Command: E:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check pdInfoBuilder_1.1.9.tar.gz

RetCode: 0

Time: 69.8 seconds

Status: WARNINGS

CheckDir: pdInfoBuilder.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory 'E:/biocbld/bbs-2.1-bioc/meat/pdInfoBuilder.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* 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 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
  E:/biocbld/bbs-2.1-bioc/meat/pdInfoBuilder.Rcheck/00check.log
for details

installing R.css in E:/biocbld/bbs-2.1-bioc/meat/pdInfoBuilder.Rcheck


---------- Making package pdInfoBuilder ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making pdInfoBuilder.d from pdInfoBuilder.c
gcc   -Ie:/biocbld/bbs-2.1-bioc/R/include  -Wall -O3 -std=gnu99   -c pdInfoBuilder.c -o pdInfoBuilder.o
windres -I e:/biocbld/bbs-2.1-bioc/R/include  -i pdInfoBuilder_res.rc -o pdInfoBuilder_res.o
gcc  -shared -s  -o pdInfoBuilder.dll pdInfoBuilder.def pdInfoBuilder.o pdInfoBuilder_res.o  -Le:/biocbld/bbs-2.1-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  preparing package pdInfoBuilder 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
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'pdInfoBuilder'
     Formats: text html latex example chm 
  AffySNPPDInfoPkgSeed-class        text    html    latex   example chm
  PDInfoPkgSeed-class               text    html    latex   example chm
  PkgSeed-class                     text    html    latex   example chm
  chipName                          text    html    latex           chm
  makePdInfoPackage                 text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.1-bioc\meat\pdInfoBuilder.Rcheck\00_pkg_src\pdInfoBuilder\chm\pdInfoBuilder.chm


Compile time: 0 minutes, 0 seconds
6	Topics
16	Local links
0	Internet links
1	Graphic


Created e:\biocbld\bbs-2.1-bioc\meat\pdInfoBuilder.Rcheck\00_pkg_src\pdInfoBuilder\chm\pdInfoBuilder.chm, 21,728 bytes
Compression increased file by 437 bytes.
  adding MD5 sums

* DONE (pdInfoBuilder)