Gabor Csardi
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/eisa |
| Branch: RELEASE_3_9 |
| Last Commit: 801a7d9 |
| Last Changed Date: 2019-05-02 11:53:13 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:47:50 -0400 (Wed, 16 Oct 2019).
| Package 492/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| eisa 1.36.0 Gabor Csardi
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: eisa |
| Version: 1.36.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:eisa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings eisa_1.36.0.tar.gz |
| StartedAt: 2019-10-16 02:31:55 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:38:04 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 368.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: eisa.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:eisa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings eisa_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/eisa.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘eisa/DESCRIPTION’ ... OK * this is package ‘eisa’ version ‘1.36.0’ * 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 ‘eisa’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * 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: ‘GO.db’ ‘KEGG.db’ ‘MASS’ ‘biclust’ ‘igraph’ ‘xtable’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Unexported objects imported by ':::' calls: ‘Category:::getDataEnv’ ‘Category:::getKeggToProbeMap’ ‘Category:::probeToEntrezMapHelper’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE ISA :: no visible global function definition for ‘IQR’ ISA: no visible binding for global variable ‘var’ ISA2heatmap: no visible global function definition for ‘heatmap’ ISACHR: no visible global function definition for ‘p.adjust’ ISAEnrichment: no visible global function definition for ‘p.adjust’ ISAGO: no visible global function definition for ‘p.adjust’ ISAHTMLModules: no visible global function definition for ‘GO_dbconn’ ISAHTMLModules : go.graph: no visible global function definition for ‘graph.data.frame’ ISAHTMLTable: no visible global function definition for ‘GO_dbconn’ ISAHTMLTable : f: no visible binding for global variable ‘KEGGPATHID2NAME’ ISAKEGG: no visible global function definition for ‘p.adjust’ ISASweepGraph: no visible global function definition for ‘V’ ISASweepGraph: no visible global function definition for ‘V<-’ ISASweepGraph: no visible global function definition for ‘remove.vertex.attribute’ ISASweepGraphPlot: no visible global function definition for ‘V’ ISASweepGraphPlot: no visible global function definition for ‘axis’ ISASweepGraphPlot: no visible global function definition for ‘par’ ISASweepGraphPlot: no visible global function definition for ‘abline’ ISASweepGraphPlot: no visible global function definition for ‘text’ ISAmiRNA: no visible global function definition for ‘p.adjust’ cnvrt.coords: no visible global function definition for ‘xy.coords’ cnvrt.coords: no visible global function definition for ‘par’ condPlot: no visible global function definition for ‘sd’ condPlot: no visible global function definition for ‘par’ condPlot: no visible global function definition for ‘barplot’ condPlot: no visible global function definition for ‘abline’ condPlot: no visible global function definition for ‘text’ condPlot: no visible global function definition for ‘points’ convert.miRNA: no visible global function definition for ‘read.delim’ expPlot: no visible global function definition for ‘layout’ expPlot: no visible global function definition for ‘par’ expPlot: no visible global function definition for ‘image’ expPlot: no visible global function definition for ‘title’ expPlot: no visible global function definition for ‘axis’ expPlot: no visible global function definition for ‘abline’ expPlot: no visible global function definition for ‘lines’ expPlot: no visible global function definition for ‘text’ expPlot: no visible global function definition for ‘segments’ expPlotColbar: no visible global function definition for ‘par’ expPlotColbar: no visible global function definition for ‘image’ expPlotColbar: no visible global function definition for ‘axis’ expPlotColbar: no visible global function definition for ‘abline’ expPlotCreate: no visible global function definition for ‘hcl’ gograph: no visible binding for global variable ‘GOTERM’ gograph: no visible global function definition for ‘GO_dbconn’ gograph: no visible global function definition for ‘graph.data.frame’ gograph: no visible global function definition for ‘V’ gograph: no visible global function definition for ‘vcount’ gograph: no visible global function definition for ‘neighborhood’ gograph: no visible global function definition for ‘induced_subgraph’ gograph: no visible global function definition for ‘hcl’ gograph: no visible global function definition for ‘V<-’ gograph: no visible global function definition for ‘topological.sort’ gograph: no visible global function definition for ‘unfold.tree’ gograph: no visible global function definition for ‘E’ gograph: no visible global function definition for ‘E<-’ gograph: no visible global function definition for ‘layout.reingold.tilford’ gograph: no visible global function definition for ‘as_ids’ gographPlot: no visible global function definition for ‘dev.cur’ gographPlot: no visible global function definition for ‘par’ gographPlot: no visible global function definition for ‘V’ gographPlot: no visible global function definition for ‘text’ html.df: no visible global function definition for ‘xtable’ isa.autogen.module : tabulate: no visible binding for global variable ‘KEGGPATHID2NAME’ isa.autogen.module: no visible global function definition for ‘png’ isa.autogen.module: no visible global function definition for ‘dev.off’ isa.autogen.module : gp: no visible global function definition for ‘graph.empty’ isa.autogen.module : gp: no visible global function definition for ‘png’ isa.autogen.module : gp: no visible global function definition for ‘dev.off’ isa.autogen.module : ann: no visible global function definition for ‘vcount’ isa.autogen.module : ann: no visible global function definition for ‘V’ mnplot: no visible global function definition for ‘abline’ overlap: no visible global function definition for ‘cor’ overlap: no visible global function definition for ‘isoMDS’ overlap: no visible global function definition for ‘graph.adjacency’ overlap: no visible global function definition for ‘V’ overlap: no visible global function definition for ‘V<-’ overlap: no visible global function definition for ‘graph.empty’ overlap: no visible global function definition for ‘E’ overlap: no visible global function definition for ‘E<-’ overlap: no visible global function definition for ‘layout.fruchterman.reingold’ overlap: no visible global function definition for ‘layout.drl’ overlap: no visible global function definition for ‘ecount’ overlapPlot: no visible global function definition for ‘V’ overlapPlot: no visible global function definition for ‘layout.norm’ overlapPlot: no visible global function definition for ‘par’ profilePlot: no visible global function definition for ‘gray’ profilePlot : pp: no visible global function definition for ‘par’ profilePlot : pp: no visible global function definition for ‘title’ profilePlot : pp: no visible global function definition for ‘axis’ profilePlot : pp: no visible global function definition for ‘lines’ profilePlot: no visible global function definition for ‘par’ getFeatureMatrix,ISAModules: no visible global function definition for ‘Matrix’ getSampleMatrix,ISAModules: no visible global function definition for ‘Matrix’ htmlReport,GOListHyperGResult: no visible binding for global variable ‘GOTERM’ htmlReport,KEGGListHyperGResult: no visible binding for global variable ‘KEGGPATHID2NAME’ Undefined global functions or variables: E E<- GOTERM GO_dbconn IQR KEGGPATHID2NAME Matrix V V<- abline as_ids axis barplot cor dev.cur dev.off ecount graph.adjacency graph.data.frame graph.empty gray hcl heatmap image induced_subgraph isoMDS layout layout.drl layout.fruchterman.reingold layout.norm layout.reingold.tilford lines neighborhood p.adjust par png points read.delim remove.vertex.attribute sd segments text title topological.sort unfold.tree var vcount xtable xy.coords Consider adding importFrom("grDevices", "dev.cur", "dev.off", "gray", "hcl", "png", "xy.coords") importFrom("graphics", "abline", "axis", "barplot", "image", "layout", "lines", "par", "points", "segments", "text", "title") importFrom("stats", "IQR", "cor", "heatmap", "p.adjust", "sd", "var") importFrom("utils", "read.delim") to your NAMESPACE file. * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed ISA 31.224 1.848 33.158 ISA.sweep 18.574 3.928 22.580 ISA.iterate 9.409 1.155 10.603 ISA.unique 9.152 1.151 10.330 ISA.GO 7.922 0.720 8.716 gograph 7.849 0.747 8.636 ListHyperGResult-class 7.093 0.656 7.888 eisa.biclust 5.244 1.980 7.405 ListHyperGParams-class 6.116 0.511 6.670 ISA.normalize 4.967 0.552 5.590 ISAExpressionSet 4.702 0.433 5.160 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.9-bioc/meat/eisa.Rcheck/00check.log’ for details.
eisa.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL eisa ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘eisa’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘coerce’ with signature ‘"Biclust","ISAModules"’: no definition for class “Biclust” in method for ‘coerce’ with signature ‘"ISAModules","Biclust"’: no definition for class “Biclust” ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (eisa)
eisa.Rcheck/eisa-Ex.timings
| name | user | system | elapsed | |
| ALLModules | 0.042 | 0.009 | 0.052 | |
| ISA.CHR | 1.702 | 0.122 | 1.833 | |
| ISA.GO | 7.922 | 0.720 | 8.716 | |
| ISA.KEGG | 3.173 | 0.121 | 3.297 | |
| ISA | 31.224 | 1.848 | 33.158 | |
| ISA.html | 0.001 | 0.001 | 0.001 | |
| ISA.iterate | 9.409 | 1.155 | 10.603 | |
| ISA.miRNA | 1.116 | 0.097 | 1.238 | |
| ISA.normalize | 4.967 | 0.552 | 5.590 | |
| ISA.sweep | 18.574 | 3.928 | 22.580 | |
| ISA.unique | 9.152 | 1.151 | 10.330 | |
| ISA2heatmap | 1.324 | 0.132 | 1.476 | |
| ISAExpressionSet | 4.702 | 0.433 | 5.160 | |
| ISAModules-class | 0.014 | 0.006 | 0.019 | |
| ListHyperGParams-class | 6.116 | 0.511 | 6.670 | |
| ListHyperGResult-class | 7.093 | 0.656 | 7.888 | |
| cond.plot | 1.872 | 0.234 | 2.152 | |
| eisa.biclust | 5.244 | 1.980 | 7.405 | |
| enrichment | 0.545 | 0.017 | 0.593 | |
| exp.plot | 1.866 | 0.237 | 2.125 | |
| gograph | 7.849 | 0.747 | 8.636 | |
| mnplot | 2.365 | 0.223 | 2.599 | |
| overlap | 0.106 | 0.067 | 0.177 | |
| profilePlot | 1.368 | 0.183 | 1.565 | |
| robustness | 2.498 | 0.211 | 2.719 | |