Back to Multiple platform build/check report for BioC 3.11
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

CHECK report for flowFit on malbec2

This page was generated on 2019-11-27 11:58:24 -0500 (Wed, 27 Nov 2019).

Package 581/1805HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowFit 1.25.0
Davide Rambaldi
Snapshot Date: 2019-11-26 16:45:15 -0500 (Tue, 26 Nov 2019)
URL: https://git.bioconductor.org/packages/flowFit
Branch: master
Last Commit: a99b573
Last Changed Date: 2019-10-29 13:36:51 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowFit
Version: 1.25.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:flowFit.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings flowFit_1.25.0.tar.gz
StartedAt: 2019-11-27 02:02:06 -0500 (Wed, 27 Nov 2019)
EndedAt: 2019-11-27 02:03:15 -0500 (Wed, 27 Nov 2019)
EllapsedTime: 69.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flowFit.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:flowFit.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings flowFit_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/flowFit.Rcheck’
* using R Under development (unstable) (2019-10-24 r77329)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowFit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowFit’ version ‘1.25.0’
* 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 ‘flowFit’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
* 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 ... NOTE
.generationsPercent: no visible global function definition for
  ‘integrate’
parentFitting: no visible global function definition for ‘sd’
parentFitting: no visible global function definition for ‘hist’
proliferationFitting: no visible global function definition for ‘hist’
proliferationGrid: no visible global function definition for ‘rgb’
proliferationGrid: no visible global function definition for ‘dev.cur’
proliferationGrid: no visible global function definition for ‘abline’
plot,parentFittingData-ANY: no visible global function definition for
  ‘par’
plot,parentFittingData-ANY: no visible global function definition for
  ‘layout’
plot,parentFittingData-ANY: no visible global function definition for
  ‘lines’
plot,parentFittingData-ANY: no visible global function definition for
  ‘axis’
plot,parentFittingData-ANY: no visible global function definition for
  ‘plot.new’
plot,parentFittingData-ANY: no visible binding for global variable
  ‘black’
plot,proliferationFittingData-ANY: no visible global function
  definition for ‘dev.interactive’
plot,proliferationFittingData-ANY: no visible global function
  definition for ‘par’
plot,proliferationFittingData-ANY: no visible global function
  definition for ‘rainbow’
plot,proliferationFittingData-ANY: no visible global function
  definition for ‘layout’
plot,proliferationFittingData-ANY: no visible global function
  definition for ‘lines’
plot,proliferationFittingData-ANY: no visible global function
  definition for ‘axis’
plot,proliferationFittingData-ANY: no visible global function
  definition for ‘plot.new’
plot,proliferationFittingData-ANY: no visible global function
  definition for ‘polygon’
plot,proliferationFittingData-ANY: no visible global function
  definition for ‘text’
plot,proliferationFittingData-ANY: no visible binding for global
  variable ‘black’
summary,parentFittingData: no visible global function definition for
  ‘df.residual’
summary,proliferationFittingData: no visible global function definition
  for ‘df.residual’
Undefined global functions or variables:
  abline axis black dev.cur dev.interactive df.residual hist integrate
  layout lines par plot.new polygon rainbow rgb sd text
Consider adding
  importFrom("grDevices", "dev.cur", "dev.interactive", "rainbow", "rgb")
  importFrom("graphics", "abline", "axis", "hist", "layout", "lines",
             "par", "plot.new", "polygon", "text")
  importFrom("stats", "df.residual", "integrate", "sd")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'parentFittingData-class.Rd':
  ‘Data’

Missing link or links in documentation object 'proliferationFittingData-class.Rd':
  ‘Data’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
flowFit-package      11.304  0.100  11.713
proliferationFitting  5.182  0.011   5.194
* 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/flowFit.Rcheck/00check.log’
for details.



Installation output

flowFit.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL flowFit
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘flowFit’ ...
** using staged installation
** R
** demo
** 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 (flowFit)

Tests output


Example timings

flowFit.Rcheck/flowFit-Ex.timings

nameusersystemelapsed
flowFit-package11.304 0.10011.713
generationsDistance000
getGenerations0.5650.0080.573
logTicks0.0350.0000.035
parentFitting0.4340.0080.442
parentFittingData-class0.0410.0000.041
proliferationFitting5.1820.0115.194
proliferationFittingData-class0.3870.0000.387
proliferationGrid0.0030.0000.002
proliferationIndex0.2270.0000.227