Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:58:55 -0400 (Wed, 16 Oct 2019).
Package 1175/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
PathoStat 1.10.0 Solaiappan Manimaran
| 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: PathoStat |
Version: 1.10.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PathoStat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PathoStat_1.10.0.tar.gz |
StartedAt: 2019-10-16 05:22:58 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 05:30:35 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 456.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PathoStat.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PathoStat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PathoStat_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/PathoStat.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 ‘PathoStat/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PathoStat’ version ‘1.10.0’ * package encoding: UTF-8 * 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 ‘PathoStat’ 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 Namespaces in Imports field not imported from: ‘ComplexHeatmap’ ‘RColorBrewer’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 Examples with CPU or elapsed time > 5s user system elapsed Bootstrap_LOOCV_LR_AUC 20.632 0.226 20.891 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.9-bioc/meat/PathoStat.Rcheck/00check.log’ for details.
PathoStat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PathoStat ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘PathoStat’ ... ** 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 (PathoStat)
PathoStat.Rcheck/tests/testthat.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. > library(testthat) > library(PathoStat) > > test_check("PathoStat") ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ] > > proc.time() user system elapsed 17.484 1.511 18.946
PathoStat.Rcheck/PathoStat-Ex.timings
name | user | system | elapsed | |
Bootstrap_LOOCV_LR_AUC | 20.632 | 0.226 | 20.891 | |
Chisq_Test_Pam | 0.004 | 0.001 | 0.004 | |
Fisher_Test_Pam | 0.005 | 0.000 | 0.005 | |
GET_PAM | 0.003 | 0.000 | 0.003 | |
LOOAUC_simple_multiple_noplot_one_df | 4.505 | 0.018 | 4.522 | |
LOOAUC_simple_multiple_one_df | 4.767 | 0.037 | 4.804 | |
PathoStat-class | 0.071 | 0.001 | 0.071 | |
TranslateIdToTaxLevel | 0.003 | 0.001 | 0.003 | |
Wilcox_Test_df | 0.012 | 0.002 | 0.015 | |
findRAfromCount | 0.221 | 0.003 | 0.224 | |
findTaxonMat | 0.172 | 0.010 | 0.182 | |
findTaxonomy | 0.176 | 0.008 | 0.184 | |
findTaxonomy300 | 0.139 | 0.004 | 0.142 | |
getShinyInput | 0.000 | 0.000 | 0.001 | |
getShinyInputCombat | 0 | 0 | 0 | |
getShinyInputOrig | 0.000 | 0.000 | 0.001 | |
getSignatureFromMultipleGlmnet | 1.717 | 0.056 | 1.774 | |
grepTid | 0.001 | 0.000 | 0.001 | |
loadPathoscopeReports | 0.002 | 0.000 | 0.003 | |
loadPstat | 0.003 | 0.001 | 0.003 | |
log2CPM | 0.001 | 0.000 | 0.002 | |
percent | 0.001 | 0.000 | 0.001 | |
phyloseq_to_edgeR | 0.097 | 0.014 | 0.111 | |
plotPCAPlotly | 0.348 | 0.067 | 0.416 | |
plotPCoAPlotly | 0.274 | 0.045 | 0.321 | |
readPathoscopeData | 0.057 | 0.003 | 0.060 | |
runPathoStat | 0.096 | 0.001 | 0.098 | |
savePstat | 0.006 | 0.001 | 0.008 | |
setShinyInput | 0.000 | 0.001 | 0.001 | |
setShinyInputCombat | 0.000 | 0.000 | 0.001 | |
setShinyInputOrig | 0.001 | 0.000 | 0.001 | |
summarizeTable | 0.004 | 0.001 | 0.005 | |