Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 11:57:21 -0400 (Wed, 16 Oct 2019).
Package 579/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
flowStats 3.42.0 Greg Finak
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | ![]() | ||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | ![]() |
Package: flowStats |
Version: 3.42.0 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:flowStats.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings flowStats_3.42.0.tar.gz |
StartedAt: 2019-10-16 01:41:56 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 01:44:42 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 165.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: flowStats.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:flowStats.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings flowStats_3.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/flowStats.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘flowStats/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘flowStats’ version ‘3.42.0’ * 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 ‘flowStats’ 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 Missing object imported by a ':::' call: ‘flowWorkspace:::.isBooleanGate.graphNEL’ Unexported objects imported by ':::' calls: ‘flowCore:::checkClass’ ‘flowCore:::copyFlowSet’ ‘flowCore:::findTimeChannel’ ‘flowCore:::inPolygon’ ‘flowViz:::evalError’ ‘flowViz:::plotType’ ‘flowWorkspace:::.isBoolGate’ 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 .plotGPAprocess: no visible binding for global variable ‘whichS’ .plotGPAprocess: no visible binding for global variable ‘cluster’ .plotWorkFlow: no visible binding for global variable ‘cluster’ .plotWorkFlow: no visible binding for global variable ‘bogus’ .usingSVD: no visible binding for global variable ‘params’ density1d_simple: no visible binding for global variable ‘y’ normQA: no visible binding for global variable ‘group’ normQA: no visible binding for global variable ‘hasPeak’ Undefined global functions or variables: bogus cluster group hasPeak params whichS y * 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 warpSet 16.344 0.012 16.362 gaussNorm 5.971 0.024 5.994 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.9-bioc/meat/flowStats.Rcheck/00check.log’ for details.
flowStats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL flowStats ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘flowStats’ ... ** using staged installation ** 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 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 (flowStats)
flowStats.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-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(flowStats) Loading required package: flowCore Loading required package: cluster Loading required package: flowWorkspace Loading required package: ncdfFlow Loading required package: RcppArmadillo Loading required package: BH > > test_check("flowStats") ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 6 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ] > > proc.time() user system elapsed 7.158 0.260 7.409
flowStats.Rcheck/flowStats-Ex.timings
name | user | system | elapsed | |
autoGate | 2.353 | 0.052 | 2.405 | |
binByRef | 0.831 | 0.020 | 0.851 | |
calcPBChiSquare | 0.586 | 0.020 | 0.606 | |
calcPearsonChi | 1.080 | 0.024 | 1.104 | |
curv1Filter-class | 0.207 | 0.000 | 0.207 | |
curv2Filter-class | 0.952 | 0.028 | 0.979 | |
curvPeaks | 0.507 | 0.020 | 0.527 | |
density1d | 2.74 | 0.06 | 2.80 | |
gate_singlet | 0.000 | 0.000 | 0.001 | |
gaussNorm | 5.971 | 0.024 | 5.994 | |
gpaSet | 4.377 | 0.008 | 4.385 | |
iProcrustes | 0.166 | 0.000 | 0.166 | |
idFeaturesByBackgating | 1.313 | 0.004 | 1.317 | |
landmarkMatrix | 0.851 | 0.028 | 0.880 | |
lymphGate | 3.648 | 0.036 | 3.683 | |
normalize | 0 | 0 | 0 | |
overton_like | 0.006 | 0.000 | 0.006 | |
plotBins | 0.767 | 0.016 | 0.783 | |
proBin | 0.518 | 0.008 | 0.527 | |
quadrantGate | 0 | 0 | 0 | |
rangeGate | 2.910 | 0.012 | 2.923 | |
warpSet | 16.344 | 0.012 | 16.362 | |