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| IMPORTANT NOTE: R was configured with --enable-strict-barrier on lamb1 |
| Package 17/247 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
AnnBuilder1.15.7J. ZhangLast Changed Date: 2007-08-20 15:26:04 -0700 Last Changed Rev: 26532 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | [ OK ] | |
| wellington | Linux (SUSE 9.2) | i686 | OK | OK | ||
| liverpool | Windows Server 2003 R2 (32-bit) | x64 | OK | OK | OK | |
| pitt | Mac OS X (10.4.10) | i386 | OK | OK | OK |
| Package: AnnBuilder |
| Version: 1.15.7 |
| Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check AnnBuilder_1.15.7.tar.gz |
| RetCode: 0 |
| Time: 61.5 seconds |
| Status: OK |
| CheckDir: AnnBuilder.Rcheck |
| Warnings: 0 |
* checking for working latex ... OK * using log directory '/home/biocbuild/bbs-2.1-bioc/meat/AnnBuilder.Rcheck' * using R version 2.6.0 Under development (unstable) (2007-08-06 r42439) * checking for file 'AnnBuilder/DESCRIPTION' ... OK * this is package 'AnnBuilder' version '1.15.7' * checking package name space information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'AnnBuilder' 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 findChrLength: possible error in getGPData(paste(srcUrl, "refGene.txt.gz", sep = ""), ncol = 10, keep = c(2, 4)): unused argument(s) (ncol = 10, keep = c(2, 4)) getChroLocation: possible error in read.table(file.path(srcUrl, srcUrl["gene"]), sep = sep, header = FALSE, what = "character", strip.white = TRUE, stringsAsFactors = FALSE, as.is = TRUE): unused argument(s) (what = "character") getHomoData: possible error in homoData(as.character(tolower(getShortSciName(mapOrgs(entries[3])))), as.logical(entries[4]), as.numeric(entries[5]), as.numeric(entries[6]), as.numeric(entries[7]), as.numeric(entries[8]), as.numeric(entries[9]), as.numeric(entries[10]), as.numeric(entries[11])): unused argument(s) (as.numeric(entries[10]), as.numeric(entries[11])) getPBased: no visible binding for global variable 'AnnInfo' .keepAround: no visible global function definition for 'saveColSepData' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgPath' .keepAround: no visible binding for global variable 'author' map2LL: no visible binding for global variable 'putmed' nameGOByCat: no visible binding for global variable 'GOWithEnv' .newHomoData : <anonymous>: no visible global function definition for 'homoBest' .newHomoData : <anonymous>: no visible global function definition for 'homoNucChange' .newHomoData : <anonymous>: no visible global function definition for 'homoNucChangeJc' .newHomoData : <anonymous>: no visible global function definition for 'homoProtChange' .newHomoData : <anonymous>: no visible global function definition for 'homoKA' .newHomoData : <anonymous>: no visible global function definition for 'homoKS' .newHomoData : <anonymous>: no visible global function definition for 'homoKNR' .newHomoData : <anonymous>: no visible global function definition for 'homoKNC' procYeastGeno: no visible global function definition for 'yeastGeno' procYeastGeno: no visible binding for global variable 'baseUrl' procYeastGeno: no visible binding for global variable 'fileNames' SPPkgBuilder: no visible binding for global variable 'AnnInfo' writeAccessory: no visible binding for global variable 'AnnInfo' writeDescription: no visible binding for global variable 'descriptionInfo' writeManPage: no visible binding for global variable 'AnnInfo' writeXMLHeader: no visible binding for global variable 'AnnInfo' * 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 data for non-ASCII characters ... OK * creating AnnBuilder-Ex.R ... OK * checking examples ... OK * checking package vignettes in 'inst/doc' ... OK * creating AnnBuilder-manual.tex ... OK * checking AnnBuilder-manual.tex ... OK
AnnBuilder.Rcheck/00install.out:
* Installing *source* package 'AnnBuilder' ...
** R
** data
** 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: XML
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
** help
>>> Building/Updating help pages for package 'AnnBuilder'
Formats: text html latex example
ABPkgBuilder text html latex example
EG-class text html latex
GEO-class text html latex example
GO-class text html latex
GOPkgBuilder text html latex example
GOXMLParser text html latex
GP-class text html latex example
HG-class text html latex
IPI-class text html latex example
KEGG-class text html latex example
KEGGPkgBuilder text html latex
LL-class text html latex example
MeSHParser text html latex
PFAM-class text html latex example
SPPkgBuilder text html latex
UG-class text html latex example
YEAST-class text html latex example
YG-class text html latex example
addNamespace text html latex example
athPkgBuilder text html latex example
cMapPathBuilder text html latex example
chrLocPkgBuilder text html latex example
cleanSrcObjs text html latex
cols2Env text html latex example
descriptionInfo text html latex example
downloadSourceData text html latex
fileMuncher text html latex example
fileToXML text html latex example
getChroLocation text html latex example
getDPStats text html latex example
getKEGGIDNName text html latex example
getPubDataGo text html latex
getSrcBuilt text html latex example
getSrcUrl text html latex
getUGShortName text html latex example
getYeastData text html latex example
homoPkgBuilder text html latex
loadFromUrl text html latex example
makeLLDB text html latex
makeSrcInfo text html latex example
map2LL text html latex example
pfamBuilder text html latex example
print.ABQCList text html latex example
pubDataURLs text html latex example
pubRepo-class text html latex example
queryGEO text html latex example
readSourceUrlConfig text html latex
resolveMaps text html latex example
sourceURLs text html latex example
unifyMappings text html latex example
wget text html latex
writeChrLength text html latex example
writeHomoXMLData text html latex
writeManPage text html latex example
writeSourceUrlConfig text html latex
writeXMLHeader text html latex example
yeastAnn text html latex example
yeastPkgBuilder text html latex example
** building package indices ...
* DONE (AnnBuilder)