BioC 3.1: CHECK report for flowcatchR on petty

Package: flowcatchR

Version: 1.2.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowcatchR_1.2.2.tar.gz

StartedAt: 2015-10-08 22:57:42 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:59:20 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 98.5 seconds

RetCode: 0

Status:  OK

CheckDir: flowcatchR.Rcheck

Warnings: 0

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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_1.2.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/flowcatchR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.2.2’
* 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 ... [8s/8s] OK
* 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 ... OK
* 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 ... [25s/25s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
normalizeFrames 4.182  3.215     7.4
* 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-3.1-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 in fun(libname, pkgname) : Error in 'rgl_init'
** 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 in fun(libname, pkgname) : Error in 'rgl_init'
* DONE (flowcatchR)

name	user	system	elapsed
Frames	0.947	0.223	1.169
add.contours	0.002	0.001	0.003
channel.Frames	0.444	0.139	0.583
crop.Frames	0.418	0.124	0.541
export.Frames	0.001	0.000	0.002
export.particles	0.001	0.000	0.002
inspect.Frames	0.001	0.000	0.002
kinematics	0.381	0.040	0.421
length.Frames	0.100	0.007	0.107
link.particles	0.211	0.016	0.228
matchTrajToParticles	0.459	0.004	0.464
normalizeFrames	4.182	3.215	7.400
particles	0.002	0.000	0.003
penaltyFunctionGenerator	0.001	0.000	0.001
plot.TrajectorySet	0.395	0.033	0.429
plot2D.TrajectorySet	0.586	0.005	0.592
preprocess.Frames	1.296	0.531	1.827
read.Frames	0.000	0.000	0.001
read.particles	0.001	0.001	0.001
rotate.Frames	1.415	0.607	2.024
select.Frames	2.467	2.513	4.983
select.particles	0.044	0.002	0.046
shinyFlow	0.001	0.000	0.001
show-Frames-method	0.159	0.079	0.239
show-KinematicsFeatures-method	0.306	0.016	0.321
show-KinematicsFeaturesSet-method	0.320	0.002	0.323
show-LinkedParticleSet-method	0.263	0.001	0.265
show-ParticleSet-method	0.012	0.001	0.013
show-TrajectorySet-method	0.321	0.009	0.330
snap	0.001	0.001	0.001
trajectories	0.307	0.002	0.310