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CHECK report for flowFit on tokay1

This page was generated on 2019-04-13 11:22:53 -0400 (Sat, 13 Apr 2019).

Package 534/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowFit 1.20.1
Davide Rambaldi
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/flowFit
Branch: RELEASE_3_8
Last Commit: dfa5ee7
Last Changed Date: 2019-01-04 13:14:36 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowFit
Version: 1.20.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowFit.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings flowFit_1.20.1.tar.gz
StartedAt: 2019-04-13 02:16:57 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:19:37 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 160.1 seconds
RetCode: 0
Status:  OK  
CheckDir: flowFit.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowFit.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings flowFit_1.20.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/flowFit.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowFit/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowFit' version '1.20.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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
  which will be used as from R 3.4.0
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
flowFit-package      10.22   0.05   10.28
proliferationFitting  9.18   0.02    9.22
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
flowFit-package      9.00   0.01    9.02
proliferationFitting 7.91   0.05    7.95
* 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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/flowFit.Rcheck/00check.log'
for details.



Installation output

flowFit.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/flowFit_1.20.1.tar.gz && rm -rf flowFit.buildbin-libdir && mkdir flowFit.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowFit.buildbin-libdir flowFit_1.20.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL flowFit_1.20.1.zip && rm flowFit_1.20.1.tar.gz flowFit_1.20.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 46926  100 46926    0     0  1039k      0 --:--:-- --:--:-- --:--:-- 1145k

install for i386

* installing *source* package 'flowFit' ...
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowFit'
    finding HTML links ... done
    flowFit-package                         html  
    finding level-2 HTML links ... done

    generationsDistance                     html  
    getGenerations                          html  
    logTicks                                html  
    parentFitting                           html  
    parentFittingData-class                 html  
    plot-methods                            html  
    proliferationFitting                    html  
    proliferationFittingData-class          html  
    proliferationGrid                       html  
    proliferationIndex                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'flowFit' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowFit' as flowFit_1.20.1.zip
* DONE (flowFit)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'flowFit' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

flowFit.Rcheck/examples_i386/flowFit-Ex.timings

nameusersystemelapsed
flowFit-package10.22 0.0510.28
generationsDistance000
getGenerations0.660.000.66
logTicks0.050.000.04
parentFitting0.540.000.55
parentFittingData-class0.070.000.06
proliferationFitting9.180.029.22
proliferationFittingData-class0.520.000.52
proliferationGrid000
proliferationIndex0.420.030.45

flowFit.Rcheck/examples_x64/flowFit-Ex.timings

nameusersystemelapsed
flowFit-package9.000.019.02
generationsDistance000
getGenerations0.560.000.56
logTicks0.040.000.03
parentFitting0.430.000.44
parentFittingData-class0.050.020.06
proliferationFitting7.910.057.95
proliferationFittingData-class0.500.010.52
proliferationGrid000
proliferationIndex0.420.020.44