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Package 16/234 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
AnnBuilder1.15.4J. ZhangLast Changed Date: 2007-05-11 21:56:41 -0700 Last Changed Rev: 24616 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | [ WARNINGS ] | |
wellington | Linux (SUSE 9.2) | i686 | OK | OK | ||
churchill | Solaris 2.9 | sparc | ERROR | skipped | ||
lemming | Windows Server 2003 (32-bit) | x64 | OK | OK | OK |
Package: AnnBuilder |
Version: 1.15.4 |
Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check AnnBuilder_1.15.4.tar.gz |
RetCode: 0 |
Time: 49.6 seconds |
Status: WARNINGS |
CheckDir: AnnBuilder.Rcheck |
Warnings: 1 |
* 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) (2007-05-03 r41426) * checking for file 'AnnBuilder/DESCRIPTION' ... OK * this is package 'AnnBuilder' version '1.15.4' * 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 ... WARNING Found the following significant warnings: Warning: unmatched brace ('}') in 'EG-class.Rd' on or after line 15 Warning: unmatched brace ('}') in 'EG-class.Rd' on or after line 15 Warning: unmatched brace ('}') in 'EG-class.Rd' on or after line 15 Warning: unmatched brace ('}') in 'EG-class.Rd' on or after line 15 Warning: unmatched brace ('}') in 'GO-class.Rd' on or after line 14 Warning: unmatched brace ('}') in 'GO-class.Rd' on or after line 14 Warning: unmatched brace ('}') in 'GO-class.Rd' on or after line 14 Warning: unmatched brace ('}') in 'GO-class.Rd' on or after line 14 Warning: unmatched brace ('}') in 'HG-class.Rd' on or after line 41 Warning: unmatched brace ('}') in 'HG-class.Rd' on or after line 41 Warning: unmatched brace ('}') in 'HG-class.Rd' on or after line 41 Warning: unmatched brace ('}') in 'HG-class.Rd' on or after line 41 Warning: unmatched brace ('}') in 'resolveMaps.Rd' on or after line 61 Warning: unmatched brace ('}') in 'resolveMaps.Rd' on or after line 61 Warning: unmatched brace ('}') in 'resolveMaps.Rd' on or after line 61 Warning: unmatched brace ('}') in 'resolveMaps.Rd' on or after line 61 See '/home/biocbuild/bbs-2.1-bioc/meat/AnnBuilder.Rcheck/00install.out' for details. * 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 ABPkgBuilder: no visible binding for global variable 'GOTERM' athPkgBuilder: no visible binding for global variable 'GOTERM' createGo2AllProbesEnv: no visible binding for global variable 'GOCCOFFSPRING' createGo2AllProbesEnv: no visible binding for global variable 'GOMFOFFSPRING' createGo2AllProbesEnv: no visible binding for global variable 'GOBPOFFSPRING' findChrLength : estimateLength: no visible global function definition for 'as.numberic' 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") getChroLocation: no visible binding for global variable 'locatFile' getFileExt: no visible global function definition for 'getCurlHandle' getFileExt: no visible global function definition for 'getURL' getFileExt: no visible global function definition for 'getURL' getFileExt: no visible global function definition for 'getURL' getFileExt: no visible global function definition for 'getURL' getFileExt: no visible global function definition for 'getURL' 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 'pkgPath' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgPath' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgName' .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 'pkgPath' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgPath' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgName' .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 'pkgPath' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgPath' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgName' .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 'pkgPath' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgPath' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgName' .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 'pkgPath' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgPath' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgName' .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 'pkgPath' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgPath' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgPath' .keepAround: no visible binding for global variable 'author' .keepAround: no visible binding for global variable 'pkgPath' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgPath' .keepAround: no visible binding for global variable 'pkgPath' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgPath' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgPath' .keepAround: no visible binding for global variable 'pkgPath' .keepAround: no visible binding for global variable 'pkgName' .keepAround: no visible binding for global variable 'pkgName' 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 'homoBest' .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 'homoNucChange' .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 'homoNucChangeJc' .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 'homoProtChange' .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 'homoKA' .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 'homoKS' .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 'homoKNR' .newHomoData : <anonymous>: no visible global function definition for 'homoKNR' .newHomoData : <anonymous>: no visible global function definition for 'homoKNC' .newHomoData : <anonymous>: no visible global function definition for 'homoKNC' .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' procYeastGeno: no visible binding for global variable 'fileNames' SPPkgBuilder: no visible binding for global variable 'AnnInfo' SPPkgBuilder: no visible binding for global variable 'AnnInfo' unzipFile: no visible global function definition for 'zip.unpack' writeAccessory: no visible binding for global variable 'AnnInfo' writeDescription: no visible binding for global variable 'descriptionInfo' writeDescription: no visible binding for global variable 'descriptionInfo' writeManPage: no visible binding for global variable 'AnnInfo' writeXMLHeader: no visible binding for global variable 'AnnInfo' writeXMLHeader: no visible binding for global variable 'AnnInfo' yeastPkgBuilder: no visible binding for global variable 'GOTERM' * 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 WARNING: There was 1 warning, see /home/biocbuild/bbs-2.1-bioc/meat/AnnBuilder.Rcheck/00check.log for details
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 Warning: unmatched brace ('}') in 'EG-class.Rd' on or after line 15 Warning: unmatched brace ('}') in 'EG-class.Rd' on or after line 15 Warning: unmatched brace ('}') in 'EG-class.Rd' on or after line 15 Warning: unmatched brace ('}') in 'EG-class.Rd' on or after line 15 Warning: unmatched brace ('}') in 'GO-class.Rd' on or after line 14 Warning: unmatched brace ('}') in 'GO-class.Rd' on or after line 14 Warning: unmatched brace ('}') in 'GO-class.Rd' on or after line 14 Warning: unmatched brace ('}') in 'GO-class.Rd' on or after line 14 Warning: unmatched brace ('}') in 'HG-class.Rd' on or after line 41 Warning: unmatched brace ('}') in 'HG-class.Rd' on or after line 41 Warning: unmatched brace ('}') in 'HG-class.Rd' on or after line 41 Warning: unmatched brace ('}') in 'HG-class.Rd' on or after line 41 Warning: unmatched brace ('}') in 'resolveMaps.Rd' on or after line 61 Warning: unmatched brace ('}') in 'resolveMaps.Rd' on or after line 61 Warning: unmatched brace ('}') in 'resolveMaps.Rd' on or after line 61 Warning: unmatched brace ('}') in 'resolveMaps.Rd' on or after line 61 >>> 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)