BioC 3.5: CHECK report for flowcatchR on oaxaca

Package: flowcatchR

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowcatchR_1.9.0.tar.gz

StartedAt: 2017-03-04 02:48:39 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 02:49:44 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 65.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowcatchR.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowcatchR_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/flowcatchR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.9.0’
* 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.

* 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)

name	user	system	elapsed
Frames	0.586	0.110	0.697
add.contours	0.002	0.001	0.001
channel.Frames	0.405	0.077	0.483
crop.Frames	0.295	0.079	0.374
export.Frames	0.001	0.001	0.002
export.particles	0.001	0.000	0.002
inspect.Frames	0.002	0.000	0.002
kinematics	0.452	0.032	0.483
length.Frames	0.067	0.003	0.070
link.particles	0.329	0.013	0.342
matchTrajToParticles	0.282	0.004	0.286
normalizeFrames	2.342	1.343	3.687
particles	0.001	0.001	0.002
penaltyFunctionGenerator	0.001	0.000	0.000
plot.TrajectorySet	0.192	0.010	0.202
plot2D.TrajectorySet	0.302	0.010	0.312
preprocess.Frames	0.693	0.251	0.945
read.Frames	0.001	0.000	0.001
read.particles	0.001	0.000	0.001
rotate.Frames	0.675	0.237	0.912
select.Frames	0.991	1.032	2.022
select.particles	0.025	0.001	0.025
shinyFlow	0.000	0.000	0.001
show-Frames-method	0.060	0.031	0.091
show-KinematicsFeatures-method	0.207	0.026	0.233
show-KinematicsFeaturesSet-method	0.239	0.002	0.241
show-LinkedParticleSet-method	0.185	0.002	0.186
show-ParticleSet-method	0.007	0.001	0.008
show-TrajectorySet-method	0.233	0.008	0.240
snap	0	0	0
trajectories	0.194	0.001	0.194