Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-15 12:08:50 -0400 (Wed, 15 Apr 2020).
Package 588/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
flowDensity 1.20.0 Mehrnoush Malek
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: flowDensity |
Version: 1.20.0 |
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:flowDensity.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings flowDensity_1.20.0.tar.gz |
StartedAt: 2020-04-15 02:18:12 -0400 (Wed, 15 Apr 2020) |
EndedAt: 2020-04-15 02:19:52 -0400 (Wed, 15 Apr 2020) |
EllapsedTime: 99.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: flowDensity.Rcheck |
Warnings: 5 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:flowDensity.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings flowDensity_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/flowDensity.Rcheck’ * using R version 3.6.3 (2020-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘flowDensity/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘flowDensity’ version ‘1.20.0’ * 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 ‘flowDensity’ can be installed ... WARNING Found the following significant warnings: Warning: bad markup (extra space?) at plotDens.Rd:62:19 Warning: replacing previous import ‘flowCore::plot’ by ‘graphics::plot’ when loading ‘flowDensity’ See ‘/home/biocbuild/bbs-3.10-bioc/meat/flowDensity.Rcheck/00install.out’ for details. * 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 ... OK * 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 ... WARNING prepare_Rd: bad markup (extra space?) at plotDens.Rd:62:19 * checking Rd metadata ... WARNING Rd files with duplicated alias 'flowDensity': ‘flowDensity-methods.Rd’ ‘flowDensity.Rd’ * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic 'flowDensity' and siglist 'CellPopulation,ANY,logical,missing' generic 'flowDensity' and siglist 'GatingHierarchy,ANY,logical,ANY' generic 'flowDensity' and siglist 'flowFrame,ANY,logical,missing' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Objects in \usage without \alias in documentation object 'flowDensity-methods': ‘\S4method{flowDensity}{CellPopulation,ANY,logical,missing}’ ‘\S4method{flowDensity}{flowFrame,ANY,logical,missing}’ ‘\S4method{flowDensity}{GatingHierarchy,ANY,logical,ANY}’ Undocumented arguments in documentation object 'plotDens' ‘dens.col’ ‘cex’ ‘dens.type’ Documented arguments not in \usage in documentation object 'plotDens': ‘density.type’ ‘density.col’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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: 5 WARNINGs See ‘/home/biocbuild/bbs-3.10-bioc/meat/flowDensity.Rcheck/00check.log’ for details.
flowDensity.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL flowDensity ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘flowDensity’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘flowCore::plot’ by ‘graphics::plot’ when loading ‘flowDensity’ ** help Warning: bad markup (extra space?) at plotDens.Rd:62:19 *** installing help indices ** building package indices ** installing vignettes ‘flowDensity.Rmd’ ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘flowCore::plot’ by ‘graphics::plot’ when loading ‘flowDensity’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘flowCore::plot’ by ‘graphics::plot’ when loading ‘flowDensity’ ** testing if installed package keeps a record of temporary installation path * DONE (flowDensity)
flowDensity.Rcheck/flowDensity-Ex.timings
name | user | system | elapsed | |
CellPopulation-class | 0.000 | 0.000 | 0.001 | |
deGate | 0.212 | 0.024 | 0.299 | |
flowDensity | 0.076 | 0.000 | 0.079 | |
getPeaks | 0.032 | 0.000 | 0.033 | |
getflowFrame | 0.072 | 0.000 | 0.075 | |
nmRemove | 0.264 | 0.004 | 0.288 | |
notSubFrame | 0.116 | 0.000 | 0.117 | |
plotDens | 0.144 | 0.008 | 0.151 | |