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Package 205/294HostnameOS / ArchBUILDCHECKBUILD BIN
pdInfoBuilder 1.6.0
Benilton Carvalho
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/pdInfoBuilder
Last Changed Rev: 34811 / Revision: 38965
Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.6) / i386  OK [ OK ] OK 
Package: pdInfoBuilder
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/2.8/Resources/bin/R CMD check --no-vignettes pdInfoBuilder_1.6.0.tar.gz
StartedAt: 2009-04-18 18:04:20 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 18:05:30 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 69.7 seconds
RetCode: 0
Status: OK
CheckDir: pdInfoBuilder.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/pdInfoBuilder.Rcheck'
* using R version 2.8.1 Patched (2009-03-18 r48200)
* using session charset: ASCII
* checking for file 'pdInfoBuilder/DESCRIPTION' ... OK
* this is package 'pdInfoBuilder' version '1.6.0'
* 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'
loadUnits.affyTiling: no visible binding for global variable 'ispm'
* checking Rd files ... 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
* creating pdInfoBuilder-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating pdInfoBuilder-manual.tex ... OK
* checking pdInfoBuilder-manual.tex using pdflatex ... OK

pdInfoBuilder.Rcheck/00install.out:

* Installing *source* package 'pdInfoBuilder' ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -c pdInfoBuilder.c -o pdInfoBuilder.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pdInfoBuilder.so pdInfoBuilder.o   -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c pdInfoBuilder.c -o pdInfoBuilder.o
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pdInfoBuilder.so pdInfoBuilder.o   -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc64
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c pdInfoBuilder.c -o pdInfoBuilder.o
gcc-4.2 -arch ppc64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pdInfoBuilder.so pdInfoBuilder.o   -L/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64 -lR -dylib_file libRblas.dylib:/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64/libRblas.dylib -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c pdInfoBuilder.c -o pdInfoBuilder.o
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pdInfoBuilder.so pdInfoBuilder.o   -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** 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: splines
Loading required package: preprocessCore
Loading required package: AnnotationDbi
Loading required package: oligoClasses
oligo Package - Series 1.5.x
** help
 >>> Building/Updating help pages for package 'pdInfoBuilder'
     Formats: text html latex example 
  AffyExpressionPDInfoPkgSeed-class text    html    latex   example
  AffyGeneSTPDInfoPkgSeed-class     text    html    latex   example
  AffySNPCNVPDInfoPkgSeed-class     text    html    latex   example
  AffySNPPDInfoPkgSeed-class        text    html    latex   example
  AffyTilingPDInfoPkgSeed-class     text    html    latex   example
  NgsExpressionPDInfoPkgSeed-class  text    html    latex   example
  NgsPDInfoPkgSeed-class            text    html    latex   example
  NgsTilingPDInfoPkgSeed-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)