Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:27:23 -0400 (Wed, 17 Oct 2018).
Package 1195/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
rcellminer 2.2.0 Augustin Luna
| 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: rcellminer |
Version: 2.2.0 |
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:rcellminer.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings rcellminer_2.2.0.tar.gz |
StartedAt: 2018-10-16 03:05:29 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 03:12:46 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 437.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: rcellminer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:rcellminer.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings rcellminer_2.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/rcellminer.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 ‘rcellminer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rcellminer’ version ‘2.2.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘rcellminer’ 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 ... NOTE Warning: no function found corresponding to methods exports from ‘rcellminer’ for: ‘initialize’ A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking 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 getColumnQuantiles: no visible global function definition for ‘quantile’ getDrugActivityRange: no visible global function definition for ‘IQR’ getRsd: no visible binding for global variable ‘sd’ parCorPatternComparison: no visible global function definition for ‘residuals’ parCorPatternComparison: no visible global function definition for ‘lm’ parCorPatternComparison: no visible global function definition for ‘na.exclude’ plotCellMiner: no visible global function definition for ‘par’ plotCellMiner: no visible global function definition for ‘layout’ plotCellMiner: no visible global function definition for ‘lcm’ plotCellMiner: no visible global function definition for ‘axis’ plotCellMiner2D: no visible global function definition for ‘element_text’ plotCellMiner2D: no visible global function definition for ‘xlim’ plotCellMiner2D: no visible global function definition for ‘ylim’ plotDrugActivityRepeats: no visible global function definition for ‘pdf’ plotDrugActivityRepeats: no visible global function definition for ‘dev.off’ plotDrugSets: no visible binding for global variable ‘sd’ plotDrugSets: no visible global function definition for ‘pdf’ plotDrugSets: no visible global function definition for ‘par’ plotDrugSets: no visible global function definition for ‘axis’ plotDrugSets: no visible global function definition for ‘segments’ plotDrugSets: no visible global function definition for ‘dev.off’ plotStructures: no visible global function definition for ‘par’ rcdkplot: no visible global function definition for ‘par’ rcdkplot: no visible global function definition for ‘get.depictor’ rcdkplot: no visible global function definition for ‘plot’ rcdkplot: no visible global function definition for ‘rasterImage’ Undefined global functions or variables: IQR axis dev.off element_text get.depictor layout lcm lm na.exclude par pdf plot quantile rasterImage residuals sd segments xlim ylim Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "axis", "layout", "lcm", "par", "plot", "rasterImage", "segments") importFrom("stats", "IQR", "lm", "na.exclude", "quantile", "residuals", "sd") 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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 ‘/home/biocbuild/bbs-3.7-bioc/meat/rcellminer.Rcheck/00check.log’ for details.
rcellminer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL rcellminer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘rcellminer’ ... ** R ** data *** moving datasets to lazyload DB ** 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 * DONE (rcellminer)
rcellminer.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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. > library(testthat) > library(rcellminer) Loading required package: Biobase Loading required package: BiocGenerics Loading required package: parallel 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, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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")'. Loading required package: rcdk Loading required package: rcdklibs Loading required package: rJava Attaching package: 'rcdk' The following object is masked from 'package:testthat': matches Loading required package: fingerprint Loading required package: rcellminerData Consider citing this package: Luna A, et al. rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R. PMID: 26635141; citation("rcellminer") > > #test_package("rcellminer") > test_check("rcellminer") ══ testthat results ═══════════════════════════════════════════════════════════ OK: 239 SKIPPED: 1 FAILED: 0 > > proc.time() user system elapsed 376.860 1.232 374.417
rcellminer.Rcheck/rcellminer-Ex.timings
name | user | system | elapsed | |
compareFingerprints | 1.444 | 0.096 | 1.116 | |
crossCors | 0.000 | 0.004 | 0.007 | |
crossCorsSpearman | 0.000 | 0.000 | 0.001 | |
getActivityRangeStats | 0.024 | 0.008 | 0.032 | |
getColumnQuantiles | 0.000 | 0.000 | 0.003 | |
getDrugActivityData | 0.004 | 0.000 | 0.003 | |
getDrugActivityRange | 0.004 | 0.000 | 0.003 | |
getDrugActivityRepeatData | 0.004 | 0.000 | 0.002 | |
getDrugMoaList | 0.052 | 0.004 | 0.056 | |
getDrugName | 0.044 | 0.000 | 0.042 | |
getFeatureDataFromMatList | 2.648 | 0.244 | 2.958 | |
getFingerprintList | 0.092 | 0.000 | 0.030 | |
getMedSenLineActivity | 0.004 | 0.000 | 0.002 | |
getMinDrugActivityRepeatCor | 0.008 | 0.000 | 0.004 | |
getMoaStr | 0.092 | 0.000 | 0.093 | |
getMoaToCompounds | 0.032 | 0.000 | 0.030 | |
getMolDataMatrices | 0.436 | 0.060 | 0.497 | |
getNumDrugActivityRepeats | 0.000 | 0.000 | 0.002 | |
getNumMissingLines | 0.004 | 0.000 | 0.001 | |
getRsd | 0.008 | 0.000 | 0.009 | |
getSmiles | 0.052 | 0.000 | 0.051 | |
hasMoa | 0.036 | 0.000 | 0.033 | |
isPublic | 0.000 | 0.000 | 0.002 | |
loadCellminerPlotInfo | 0.000 | 0.000 | 0.001 | |
loadNciColorSet | 0.000 | 0.000 | 0.001 | |
parCorPatternComparison | 0.320 | 0.004 | 0.327 | |
passRuleOf5 | 0.120 | 0.004 | 0.098 | |
passRuleOf5FromNsc | 0.088 | 0.008 | 0.045 | |
patternComparison | 0.476 | 0.064 | 0.542 | |
plotCellMiner | 0.272 | 0.032 | 0.302 | |
plotCellMiner2D | 0.000 | 0.000 | 0.001 | |
plotDrugActivityRepeats | 0.500 | 0.116 | 0.616 | |
plotDrugSets | 0.064 | 0.008 | 0.073 | |
plotStructures | 1.860 | 0.076 | 1.056 | |
plotStructuresFromNscs | 0.476 | 0.016 | 0.250 | |
rcdkplot | 0.100 | 0.004 | 0.067 | |
removeMolDataType | 0.000 | 0.000 | 0.001 | |
rowCors | 0.000 | 0.000 | 0.001 | |
runShinyApp | 0.000 | 0.000 | 0.001 | |
runShinyComparePlots | 0 | 0 | 0 | |
runShinyCompareStructures | 0.000 | 0.000 | 0.001 | |
runShinyCompoundBrowser | 0.004 | 0.000 | 0.001 | |
searchForNscs | 0.008 | 0.004 | 0.013 | |
selectCorrelatedRows | 0.004 | 0.000 | 0.001 | |
selectCorrelatedRowsFromMatrices | 0.000 | 0.004 | 0.004 | |