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BioC 3.5: CHECK report for flowcatchR on veracruz2

This page was generated on 2017-10-18 14:32:33 -0400 (Wed, 18 Oct 2017).

Package 448/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowcatchR 1.10.0
Federico Marini
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/flowcatchR
Branch: RELEASE_3_5
Last Commit: f6b4725
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: flowcatchR
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowcatchR_1.10.0.tar.gz
StartedAt: 2017-10-18 03:31:38 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 03:32:40 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 61.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flowcatchR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowcatchR_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/flowcatchR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowcatchR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowcatchR’ version ‘1.10.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowcatchR’ can be installed ... WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.5-bioc/meat/flowcatchR.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    3.0Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘EBImage’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
computeMSD: no visible global function definition for ‘na.omit’
export.particles: no visible global function definition for
  ‘write.table’
extractKinematics.traj: no visible global function definition for ‘acf’
link.particles: no visible global function definition for
  ‘txtProgressBar’
link.particles: no visible global function definition for
  ‘setTxtProgressBar’
normalizeFrames: no visible global function definition for ‘median’
plot2D.TrajectorySet: no visible global function definition for ‘plot’
plot2D.TrajectorySet: no visible global function definition for ‘text’
plot2D.TrajectorySet: no visible global function definition for ‘lines’
plot2D.TrajectorySet: no visible global function definition for ‘grid’
read.particles: no visible global function definition for ‘read.table’
snap: no visible global function definition for ‘locator’
snap: no visible global function definition for ‘text’
Undefined global functions or variables:
  acf grid lines locator median na.omit plot read.table
  setTxtProgressBar text txtProgressBar write.table
Consider adding
  importFrom("graphics", "grid", "lines", "locator", "plot", "text")
  importFrom("stats", "acf", "median", "na.omit")
  importFrom("utils", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
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 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: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/flowcatchR.Rcheck/00check.log’
for details.


flowcatchR.Rcheck/00install.out:

* installing *source* package ‘flowcatchR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (flowcatchR)

flowcatchR.Rcheck/flowcatchR-Ex.timings:

nameusersystemelapsed
Frames0.6770.1110.806
add.contours0.0020.0010.002
channel.Frames0.4320.0960.546
crop.Frames0.2860.0750.371
export.Frames0.0010.0010.002
export.particles0.0020.0010.002
inspect.Frames0.0010.0000.002
kinematics0.4040.0200.438
length.Frames0.0590.0060.065
link.particles0.3180.0110.347
matchTrajToParticles0.3300.0050.343
normalizeFrames2.7521.5054.416
particles0.0010.0000.002
penaltyFunctionGenerator0.0010.0000.001
plot.TrajectorySet0.2100.0080.226
plot2D.TrajectorySet0.3000.0090.314
preprocess.Frames0.6240.2360.887
read.Frames0.0010.0000.000
read.particles0.0010.0000.001
rotate.Frames0.3210.0970.433
select.Frames1.2711.1002.447
select.particles0.0320.0020.034
shinyFlow000
show-Frames-method0.1470.0610.222
show-KinematicsFeatures-method0.1850.0110.199
show-KinematicsFeaturesSet-method0.2610.0030.278
show-LinkedParticleSet-method0.1690.0030.179
show-ParticleSet-method0.0060.0010.008
show-TrajectorySet-method0.2090.0050.223
snap0.0010.0000.001
trajectories0.2070.0020.216