Arthur Li
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/ArrayTools |
| Branch: RELEASE_3_7 |
| Last Commit: db52b4a |
| Last Changed Date: 2018-04-30 10:35:10 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:22:31 -0400 (Wed, 17 Oct 2018).
| Package 70/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ArrayTools 1.40.0 Arthur Li
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ArrayTools |
| Version: 1.40.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ArrayTools.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ArrayTools_1.40.0.tar.gz |
| StartedAt: 2018-10-15 22:31:19 -0400 (Mon, 15 Oct 2018) |
| EndedAt: 2018-10-15 22:32:13 -0400 (Mon, 15 Oct 2018) |
| EllapsedTime: 54.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ArrayTools.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ArrayTools.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ArrayTools_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/ArrayTools.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ArrayTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ArrayTools’ version ‘1.40.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ArrayTools’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘affy’ ‘Biobase’ ‘methods’ A package should be listed in only one of these fields. * checking top-level files ... OK * checking for left-over 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 package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘R2HTML’ ‘affyPLM’ ‘annaffy’ ‘gcrma’ ‘simpleaffy’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE createIndex: no visible global function definition for ‘HTMLStart’ createIndex: no visible global function definition for ‘as.title’ createIndex: no visible global function definition for ‘HTML’ createIndex: no visible global function definition for ‘HTMLStop’ geneFilter: no visible global function definition for ‘getText’ geneFilter: no visible global function definition for ‘aafSymbol’ geneFilter: no visible global function definition for ‘aafDescription’ geneFilter: no visible global function definition for ‘aafChromosome’ geneFilter: no visible global function definition for ‘aafGenBank’ geneFilter: no visible global function definition for ‘aafCytoband’ geneFilter: no visible global function definition for ‘aafUniGene’ geneFilter: no visible global function definition for ‘aafPubMed’ geneFilter: no visible global function definition for ‘aafLocusLink’ output.ing: no visible global function definition for ‘getText’ output.ing: no visible global function definition for ‘aafSymbol’ output.ing: no visible global function definition for ‘aafDescription’ output.ing: no visible global function definition for ‘aafChromosome’ output.ing: no visible global function definition for ‘aafGenBank’ output.ing: no visible global function definition for ‘aafCytoband’ output.ing: no visible global function definition for ‘aafUniGene’ output.ing: no visible global function definition for ‘aafPubMed’ output.ing: no visible global function definition for ‘aafLocusLink’ preProcess3prime: no visible global function definition for ‘gcrma’ preProcess3prime: no visible global function definition for ‘getText’ preProcess3prime: no visible global function definition for ‘aafSymbol’ preProcess3prime: no visible global function definition for ‘aafDescription’ preProcess3prime: no visible global function definition for ‘aafChromosome’ preProcess3prime: no visible global function definition for ‘aafGenBank’ preProcess3prime: no visible global function definition for ‘aafCytoband’ preProcess3prime: no visible global function definition for ‘aafUniGene’ preProcess3prime: no visible global function definition for ‘aafPubMed’ preProcess3prime: no visible global function definition for ‘aafLocusLink’ preProcessGeneST: no visible binding for global variable ‘hugene10stCONTROL’ preProcessGeneST: no visible binding for global variable ‘mogene10stCONTROL’ preProcessGeneST: no visible global function definition for ‘getText’ preProcessGeneST: no visible global function definition for ‘aafSymbol’ preProcessGeneST: no visible global function definition for ‘aafDescription’ preProcessGeneST: no visible global function definition for ‘aafChromosome’ preProcessGeneST: no visible global function definition for ‘aafGenBank’ preProcessGeneST: no visible global function definition for ‘aafCytoband’ preProcessGeneST: no visible global function definition for ‘aafUniGene’ preProcessGeneST: no visible global function definition for ‘aafPubMed’ preProcessGeneST: no visible global function definition for ‘aafLocusLink’ qa3prime: no visible global function definition for ‘setQCEnvironment’ qa3prime: no visible global function definition for ‘qc.get.alpha1’ qa3prime: no visible global function definition for ‘HTMLStart’ qa3prime: no visible global function definition for ‘as.title’ qa3prime: no visible global function definition for ‘HTML’ qa3prime: no visible global function definition for ‘HTMLInsertGraph’ qa3prime: no visible global function definition for ‘call.exprs’ qa3prime: no visible global function definition for ‘avbg’ qa3prime: no visible global function definition for ‘percent.present’ qa3prime: no visible global function definition for ‘sfs’ qa3prime: no visible global function definition for ‘spikeInProbes’ qa3prime: no visible global function definition for ‘ratios’ qa3prime: no visible global function definition for ‘fitPLM’ qa3prime: no visible global function definition for ‘HTMLStop’ qaGeneST: no visible global function definition for ‘HTMLStart’ qaGeneST: no visible global function definition for ‘as.title’ qaGeneST: no visible global function definition for ‘HTML’ qaGeneST: no visible global function definition for ‘HTMLInsertGraph’ qaGeneST: no visible global function definition for ‘HTMLStop’ regress: no visible global function definition for ‘permute.1’ regress: no visible binding for global variable ‘design’ Output2HTML,interactionResult: no visible global function definition for ‘aaf.handler’ Output2HTML,interactionResult: no visible global function definition for ‘aafTableAnn’ Output2HTML,interactionResult: no visible global function definition for ‘aafTable’ Output2HTML,interactionResult: no visible global function definition for ‘saveHTML’ Output2HTML,regressResult: no visible global function definition for ‘aaf.handler’ Output2HTML,regressResult: no visible global function definition for ‘aafTableAnn’ Output2HTML,regressResult: no visible global function definition for ‘aafTable’ Output2HTML,regressResult: no visible global function definition for ‘saveHTML’ Undefined global functions or variables: HTML HTMLInsertGraph HTMLStart HTMLStop aaf.handler aafChromosome aafCytoband aafDescription aafGenBank aafLocusLink aafPubMed aafSymbol aafTable aafTableAnn aafUniGene as.title avbg call.exprs design fitPLM gcrma getText hugene10stCONTROL mogene10stCONTROL percent.present permute.1 qc.get.alpha1 ratios saveHTML setQCEnvironment sfs spikeInProbes * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.7-bioc/meat/ArrayTools.Rcheck/00check.log’ for details.
ArrayTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL ArrayTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘ArrayTools’ ... ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (ArrayTools)
ArrayTools.Rcheck/ArrayTools-Ex.timings
| name | user | system | elapsed | |
| Output2HTML | 0.116 | 0.000 | 0.113 | |
| QC | 0.004 | 0.000 | 0.001 | |
| Sort | 0.072 | 0.000 | 0.072 | |
| contrastMatrix-class | 0.012 | 0.004 | 0.017 | |
| createExpressionSet | 0.048 | 0.000 | 0.045 | |
| createGSEAFiles | 0.004 | 0.000 | 0.003 | |
| createIndex | 0.120 | 0.000 | 0.121 | |
| createIngenuityFile | 0.032 | 0.000 | 0.029 | |
| designMatrix-class | 0.008 | 0.000 | 0.009 | |
| eSetExample | 0.004 | 0.000 | 0.002 | |
| exprsExample | 0.004 | 0.000 | 0.002 | |
| geneFilter | 2.860 | 0.088 | 2.954 | |
| interactionResult-class | 0.096 | 0.012 | 0.109 | |
| pDataExample | 0.000 | 0.000 | 0.002 | |
| postInteraction | 0.080 | 0.000 | 0.082 | |
| preProcess3prime | 2.580 | 0.048 | 2.635 | |
| preProcessGeneST | 0.020 | 0.000 | 0.018 | |
| qa3prime | 0 | 0 | 0 | |
| qaGeneST | 0.008 | 0.008 | 0.016 | |
| regress | 0.036 | 0.000 | 0.034 | |
| regressResult-class | 0.052 | 0.000 | 0.051 | |
| selectSigGene | 0.032 | 0.000 | 0.033 | |
| selectSigGeneInt | 0.092 | 0.000 | 0.094 | |