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CHECK report for flowCHIC on merida1

This page was generated on 2019-04-16 11:58:05 -0400 (Tue, 16 Apr 2019).

Package 527/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowCHIC 1.16.1
Author: Joachim Schumann
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/flowCHIC
Branch: RELEASE_3_8
Last Commit: 824c93f
Last Changed Date: 2019-01-04 13:31:42 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  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: flowCHIC
Version: 1.16.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowCHIC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowCHIC_1.16.1.tar.gz
StartedAt: 2019-04-15 23:56:56 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:59:03 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 127.0 seconds
RetCode: 0
Status:  OK 
CheckDir: flowCHIC.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowCHIC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowCHIC_1.16.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/flowCHIC.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowCHIC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowCHIC’ version ‘1.16.1’
* 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 ‘flowCHIC’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
fcs_to_img,character: warning in hexbin(x, y, xbin = 128): partial
  argument match of 'xbin' to 'xbins'
img_sub,character: warning in hexbin(x, y, xbin = xbin): partial
  argument match of 'xbin' to 'xbins'
fcs_to_img,character: no visible global function definition for ‘png’
fcs_to_img,character: no visible binding for global variable ‘count’
fcs_to_img,character: no visible global function definition for
  ‘dev.off’
img_sub,character: no visible global function definition for ‘png’
img_sub,character: no visible binding for global variable ‘count’
img_sub,character: no visible global function definition for ‘dev.off’
plot_nmds,data.frame-data.frame: no visible global function definition
  for ‘as.dist’
plot_nmds,data.frame-data.frame: no visible global function definition
  for ‘par’
plot_nmds,data.frame-data.frame: no visible global function definition
  for ‘plot’
plot_nmds,data.frame-data.frame: no visible global function definition
  for ‘hclust’
plot_nmds,data.frame-data.frame: no visible global function definition
  for ‘points’
plot_nmds,data.frame-data.frame: no visible global function definition
  for ‘text’
plot_nmds,data.frame-data.frame: no visible global function definition
  for ‘legend’
Undefined global functions or variables:
  as.dist count dev.off hclust legend par plot png points text
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "par", "plot", "points", "text")
  importFrom("stats", "as.dist", "hclust")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
calculate_overlaps_xor 15.905  1.252  17.635
plot_nmds               8.430  0.599   9.153
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/flowCHIC.Rcheck/00check.log’
for details.



Installation output

flowCHIC.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowCHIC
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘flowCHIC’ ...
** 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
* DONE (flowCHIC)

Tests output


Example timings

flowCHIC.Rcheck/flowCHIC-Ex.timings

nameusersystemelapsed
calculate_overlaps_xor15.905 1.25217.635
fcs_to_img2.1730.1382.386
img_sub4.3340.1434.492
plot_nmds8.4300.5999.153