pdInfoBuilder 1.2.0
Vince Carey
| Snapshot Date: 2008-04-02 12:12:36 -0700 (Wed, 02 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/pdInfoBuilder | | Last Changed Rev: 27709 / Revision: 30807 | | 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 |
* 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
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)