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Package 158/233HostnameOS / ArchBUILDCHECKBUILD BIN
pdInfoBuilder 1.2.0
Vince Carey
Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/pdInfoBuilder
Last Changed Rev: 27709 / Revision: 30966
Last Changed Date: 2007-10-02 17:41:09 -0700 (Tue, 02 Oct 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  OK 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  OK 
wellington Linux (openSUSE 10.3) / i686  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
lemming Windows Server 2003 (32-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
Package: pdInfoBuilder
Version: 1.2.0
Command: D:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check pdInfoBuilder_1.2.0.tar.gz
StartedAt: 2008-04-09 21:07:41 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 21:10:42 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 180.3 seconds
RetCode: 0
Status: OK
CheckDir: pdInfoBuilder.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/pdInfoBuilder.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'pdInfoBuilder/DESCRIPTION' ... OK
* this is package 'pdInfoBuilder' version '1.2.0'
* 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 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 ... 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 ... OK

pdInfoBuilder.Rcheck/00install.out:

installing R.css in D:/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-sjlj  -std=gnu99  -Id:/biocbld/bbs-2.1-bioc/R/include     -O3 -Wall  -c pdInfoBuilder.c -o pdInfoBuilder.o
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I d:/biocbld/bbs-2.1-bioc/R/include  -i pdInfoBuilder_res.rc -o pdInfoBuilder_res.o
gcc-sjlj  -std=gnu99  -shared -s  -o pdInfoBuilder.dll pdInfoBuilder.def pdInfoBuilder.o pdInfoBuilder_res.o  -Ld:/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: splines
Loading required package: preprocessCore
Loading required package: AnnotationDbi
Loading required package: oligoClasses
This is the oligo package

Attaching package: 'oligo'


	The following object(s) are masked from package:oligoClasses :

	 calls,
	 calls<-,
	 callsConfidence,
	 callsConfidence<-,
	 cnConfidence,
	 cnConfidence<-,
	 copyNumber,
	 copyNumber<- 

  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'pdInfoBuilder'
     Formats: text html latex example chm 
  AffySNPCNVPDInfoPkgSeed-class     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
HHC5012: Error: Cannot create a temporary file in your TEMP path.
HHC4016: Warning: Cannot open "gram Files\Intel\DMIX;c:\Program Files\Windows Resource Kits\Tools\;c:\Program Files\Affymetrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Fi".
Microsoft HTML Help Compiler 4.74.8702

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

HHC4016: Warning: Cannot open "gram Files\Intel\DMIX;c:\Program Files\Windows Resource Kits\Tools\;c:\Program Files\Affymetrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Fi".


The following files were not compiled:
  adding MD5 sums

* DONE (pdInfoBuilder)