Sara Aibar
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/geNetClassifier |
| Branch: RELEASE_3_9 |
| Last Commit: 84e9c14 |
| Last Changed Date: 2019-05-02 11:53:42 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:51:19 -0400 (Wed, 16 Oct 2019).
| Package 642/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| geNetClassifier 1.24.0 Sara Aibar
| 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: geNetClassifier |
| Version: 1.24.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:geNetClassifier.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings geNetClassifier_1.24.0.tar.gz |
| StartedAt: 2019-10-16 03:06:31 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:08:17 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 105.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: geNetClassifier.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:geNetClassifier.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings geNetClassifier_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/geNetClassifier.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 ‘geNetClassifier/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘geNetClassifier’ version ‘1.24.0’ * 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 ‘geNetClassifier’ 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: ‘RColorBrewer’ ‘igraph’ ‘infotheo’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: plot.GeNetClassifierReturn plot.GenesNetwork plot.GenesRanking See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE calculateGenesRanking: no visible global function definition for ‘brewer.pal’ calculateGenesRanking: no visible global function definition for ‘rainbow’ calculateGenesRanking: no visible global function definition for ‘lines’ calculateGenesRanking: no visible global function definition for ‘title’ calculateGenesRanking: no visible global function definition for ‘abline’ calculateGenesRanking: no visible global function definition for ‘text’ calculateGenesRanking: no visible global function definition for ‘legend’ configurePlotOutput: no visible global function definition for ‘pdf’ configurePlotOutput: no visible global function definition for ‘par’ correlation.net: no visible global function definition for ‘cor’ geNetClassifier: no visible global function definition for ‘flush.console’ geNetClassifier :: no visible global function definition for ‘sd’ geNetClassifier : : no visible global function definition for ‘na.omit’ geNetClassifier: no visible global function definition for ‘sd’ geNetClassifier: no visible global function definition for ‘pdf’ geNetClassifier: no visible global function definition for ‘dev.off’ iqr.filter: no visible global function definition for ‘quantile’ plotAssignments: no visible global function definition for ‘rect’ plotAssignments: no visible global function definition for ‘abline’ plotAssignments: no visible global function definition for ‘axis’ plotAssignments: no visible global function definition for ‘text’ plotAssignments: no visible global function definition for ‘legend’ plotAssignments: no visible global function definition for ‘strwidth’ plotAssignments: no visible global function definition for ‘points’ plotAssignments: no visible global function definition for ‘dev.cur’ plotAssignments: no visible binding for global variable ‘coordinates’ plotDiscriminantPower: no visible global function definition for ‘colorRampPalette’ plotDiscriminantPower: no visible global function definition for ‘barplot’ plotDiscriminantPower: no visible global function definition for ‘abline’ plotDiscriminantPower: no visible global function definition for ‘text’ plotDiscriminantPower: no visible global function definition for ‘par’ plotDiscriminantPower: no visible global function definition for ‘dev.off’ plotDiscriminantPower: no visible global function definition for ‘flush.console’ plotErrorNumGenes: no visible global function definition for ‘pdf’ plotErrorNumGenes: no visible global function definition for ‘brewer.pal’ plotErrorNumGenes: no visible global function definition for ‘rainbow’ plotErrorNumGenes: no visible global function definition for ‘plot.new’ plotErrorNumGenes: no visible global function definition for ‘plot.window’ plotErrorNumGenes: no visible global function definition for ‘title’ plotErrorNumGenes: no visible global function definition for ‘axis’ plotErrorNumGenes: no visible global function definition for ‘lines’ plotErrorNumGenes: no visible global function definition for ‘points’ plotErrorNumGenes: no visible global function definition for ‘text’ plotErrorNumGenes: no visible global function definition for ‘barplot’ plotErrorNumGenes: no visible global function definition for ‘dev.off’ plotExpressionProfiles: no visible global function definition for ‘hcl’ plotExpressionProfiles: no visible global function definition for ‘setNames’ plotExpressionProfiles: no visible global function definition for ‘title’ plotExpressionProfiles: no visible global function definition for ‘text’ plotExpressionProfiles: no visible global function definition for ‘abline’ plotExpressionProfiles: no visible global function definition for ‘lines’ plotExpressionProfiles: no visible global function definition for ‘boxplot’ plotExpressionProfiles: no visible global function definition for ‘par’ plotExpressionProfiles: no visible global function definition for ‘dev.off’ plotExpressionProfiles: no visible global function definition for ‘flush.console’ plotExpressionProfiles: no visible global function definition for ‘dev.cur’ plotGeNetClassifierReturn: no visible global function definition for ‘pdf’ plotGeNetClassifierReturn: no visible global function definition for ‘dev.off’ plotGeNetClassifierReturn: no visible global function definition for ‘installed.packages’ plotGeNetClassifierReturn: no visible global function definition for ‘x11’ plotGeNetClassifierReturn: no visible global function definition for ‘flush.console’ plotNetwork: no visible global function definition for ‘installed.packages’ plotNetwork: no visible global function definition for ‘pdf’ plotNetwork: no visible global function definition for ‘par’ plotNetwork: no visible global function definition for ‘graph.data.frame’ plotNetwork: no visible global function definition for ‘vcount’ plotNetwork: no visible global function definition for ‘layout.fruchterman.reingold’ plotNetwork: no visible global function definition for ‘get.vertex.attribute’ plotNetwork: no visible global function definition for ‘colorRampPalette’ plotNetwork: no visible global function definition for ‘get.edge.attribute’ plotNetwork: no visible global function definition for ‘ecount’ plotNetwork: no visible global function definition for ‘tkplot’ plotNetwork: no visible global function definition for ‘plot.new’ plotNetwork: no visible global function definition for ‘title’ plotNetwork: no visible global function definition for ‘text’ plotNetwork: no visible global function definition for ‘points’ plotNetwork: no visible global function definition for ‘lines’ plotNetwork: no visible global function definition for ‘dev.off’ plotNetwork: no visible global function definition for ‘flush.console’ queryGeNetClassifier: no visible global function definition for ‘flush.console’ queryGeNetClassifier: no visible global function definition for ‘predict’ querySummary: no visible global function definition for ‘sd’ querySummary: no visible global function definition for ‘flush.console’ extractGenes,GenesRanking: no visible global function definition for ‘na.omit’ extractGenes,GenesRanking : : no visible global function definition for ‘na.omit’ network2txt,GenesNetwork: no visible global function definition for ‘write.table’ Undefined global functions or variables: abline axis barplot boxplot brewer.pal colorRampPalette coordinates cor dev.cur dev.off ecount flush.console get.edge.attribute get.vertex.attribute graph.data.frame hcl installed.packages layout.fruchterman.reingold legend lines na.omit par pdf plot.new plot.window points predict quantile rainbow rect sd setNames strwidth text title tkplot vcount write.table x11 Consider adding importFrom("grDevices", "colorRampPalette", "dev.cur", "dev.off", "hcl", "pdf", "rainbow", "x11") importFrom("graphics", "abline", "axis", "barplot", "boxplot", "legend", "lines", "par", "plot.new", "plot.window", "points", "rect", "strwidth", "text", "title") importFrom("stats", "cor", "na.omit", "predict", "quantile", "sd", "setNames") importFrom("utils", "flush.console", "installed.packages", "write.table") 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 plot.GeNetClassifierReturn 4.632 0.809 5.553 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ 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 ‘/Users/biocbuild/bbs-3.9-bioc/meat/geNetClassifier.Rcheck/00check.log’ for details.
geNetClassifier.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL geNetClassifier ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘geNetClassifier’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** 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 (geNetClassifier)
geNetClassifier.Rcheck/tests/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("geNetClassifier")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
03:08:08 - Filtering data and calculating the genes ranking...
Warning in plotExpressionProfiles(eset = myEset, genes = rownames(myEset), :
The argument 'sampleLabels' had to be converted into a factor.
Warning in plotExpressionProfiles(eset = myEset, genes = rownames(myEset), :
The data labels vector is not named, it will be assumed the labels are in order: the first label applies to the first sample...
RUNIT TEST PROTOCOL -- Wed Oct 16 03:08:09 2019
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
geNetClassifier RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3
Number of errors: 0
Number of failures: 0
Warning messages:
1: In geNetClassifier(matrix(sample(50000, 5 * 2), 5, 2), c(rep("one", :
The argument 'classification sampleLabels' had to be converted into a factor.
2: In geNetClassifier(matrix(sample(50000, 5 * 3), 5, 3), c(rep("one", :
The argument 'classification sampleLabels' had to be converted into a factor.
3: In geNetClassifier(matrix(sample(50000, 5 * 3), 5, 3), c(rep("one", :
The data labels vector is not named, it is assumed the labels are in order: the first label applies to the first sample...
4: In geNetClassifier(matrix(sample(50000, 5 * 3), 5, 3), c(rep("one", :
It is recommended to have the *same* number of samples in each class in order to obtain balanced external validation stats.
>
> proc.time()
user system elapsed
1.693 0.289 1.930
geNetClassifier.Rcheck/geNetClassifier-Ex.timings
| name | user | system | elapsed | |
| GeNetClassifierReturn-class | 0.968 | 0.143 | 1.114 | |
| GeneralizationError-class | 0.544 | 0.064 | 0.608 | |
| GenesNetwork-class | 2.826 | 0.539 | 3.385 | |
| GenesRanking-class | 0.907 | 0.126 | 1.032 | |
| calculateGenesRanking | 0.515 | 0.077 | 0.591 | |
| externalValidation.probMatrix | 1.120 | 0.105 | 1.223 | |
| externalValidation.stats | 1.136 | 0.065 | 1.200 | |
| gClasses-methods | 0.313 | 0.019 | 0.332 | |
| geNetClassifier | 0.173 | 0.016 | 0.188 | |
| geneSymbols | 0.118 | 0.006 | 0.123 | |
| genesDetails-methods | 0.550 | 0.054 | 0.602 | |
| getEdges-methods | 0.410 | 0.028 | 0.438 | |
| getNodes-methods | 0.385 | 0.021 | 0.406 | |
| getNumEdges-methods | 0.388 | 0.022 | 0.410 | |
| getNumNodes-methods | 0.398 | 0.022 | 0.419 | |
| getRanking-methods | 0.394 | 0.029 | 0.423 | |
| getSubNetwork-methods | 0.451 | 0.032 | 0.483 | |
| getTopRanking-methods | 0.350 | 0.025 | 0.375 | |
| leukemiasClassifier | 0.377 | 0.039 | 0.414 | |
| network2txt | 0.454 | 0.049 | 0.502 | |
| numGenes-methods | 0.360 | 0.018 | 0.378 | |
| numSignificantGenes-methods | 0.389 | 0.025 | 0.414 | |
| overview-methods | 0.399 | 0.042 | 0.440 | |
| plot.GeNetClassifierReturn | 4.632 | 0.809 | 5.553 | |
| plot.GenesRanking | 0.412 | 0.032 | 0.445 | |
| plotAssignments | 0.991 | 0.092 | 1.082 | |
| plotDiscriminantPower | 0.853 | 0.183 | 1.037 | |
| plotExpressionProfiles | 1.417 | 0.197 | 1.604 | |
| plotNetwork | 3.132 | 0.455 | 3.583 | |
| queryGeNetClassifier | 1.420 | 0.126 | 1.537 | |
| querySummary | 0.936 | 0.078 | 1.014 | |