BioC 3.0: CHECK report for flowcatchR on zin1

Package: flowcatchR

Version: 1.0.3

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings flowcatchR_1.0.3.tar.gz

StartedAt: 2015-04-09 23:49:25 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 23:50:41 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 75.8 seconds

RetCode: 0

Status:  OK

CheckDir: flowcatchR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings flowcatchR_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/flowcatchR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.0.3’
* 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 ... [5s/6s] OK
* checking installed package size ... OK
* 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 ‘shiny’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/17s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/flowcatchR.Rcheck/00check.log’
for details.

* installing *source* package ‘flowcatchR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowcatchR)

name	user	system	elapsed
Frames	0.812	0.044	0.858
add.contours	0.148	0.000	0.147
channel.Frames	0.436	0.044	0.483
crop.Frames	0.440	0.032	0.470
export.Frames	0.128	0.008	0.134
export.particles	0.020	0.000	0.021
inspect.Frames	0.120	0.012	0.134
kinematics	0.472	0.000	0.471
length.Frames	0.132	0.004	0.134
link.particles	0.256	0.000	0.258
matchTrajToParticles	0.408	0.004	0.416
normalizeFrames	3.116	0.156	3.350
particles	0.200	0.024	0.225
penaltyFunctionGenerator	0.000	0.000	0.001
plot.TrajectorySet	0.492	0.016	0.582
plot2D.TrajectorySet	0.528	0.016	0.550
preprocess.Frames	1.112	0.064	1.247
read.Frames	0	0	0
read.particles	0.000	0.000	0.001
rotate.Frames	1.156	0.200	1.377
select.Frames	1.468	0.228	1.703
select.particles	0.048	0.004	0.051
shinyFlow	0.004	0.000	0.001
show-Frames-method	0.132	0.000	0.135
show-KinematicsFeatures-method	0.396	0.000	0.399
show-KinematicsFeaturesSet-method	0.408	0.000	0.412
show-LinkedParticleSet-method	0.336	0.000	0.339
show-ParticleSet-method	0.024	0.000	0.023
show-TrajectorySet-method	0.372	0.004	0.379
snap	0.000	0.000	0.001
trajectories	0.360	0.004	0.362