BioC 3.1: CHECK report for flowcatchR on moscato2

Package: flowcatchR

Version: 1.2.2

Command: rm -rf flowcatchR.buildbin-libdir flowcatchR.Rcheck && mkdir flowcatchR.buildbin-libdir flowcatchR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowcatchR.buildbin-libdir flowcatchR_1.2.2.tar.gz >flowcatchR.Rcheck\00install.out 2>&1 && cp flowcatchR.Rcheck\00install.out flowcatchR-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=flowcatchR.buildbin-libdir --install="check:flowcatchR-install.out" --force-multiarch --no-vignettes --timings flowcatchR_1.2.2.tar.gz

StartedAt: 2015-10-09 01:43:11 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:44:52 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 100.3 seconds

RetCode: 0

Status:  OK

CheckDir: flowcatchR.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf flowcatchR.buildbin-libdir flowcatchR.Rcheck && mkdir flowcatchR.buildbin-libdir flowcatchR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowcatchR.buildbin-libdir flowcatchR_1.2.2.tar.gz >flowcatchR.Rcheck\00install.out 2>&1 && cp flowcatchR.Rcheck\00install.out flowcatchR-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=flowcatchR.buildbin-libdir --install="check:flowcatchR-install.out" --force-multiarch --no-vignettes --timings flowcatchR_1.2.2.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/flowcatchR.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'flowcatchR' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [15s] OK
** running examples for arch 'x64' ... [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

Status: 3 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/flowcatchR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'flowcatchR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'flowcatchR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowcatchR' as flowcatchR_1.2.2.zip
* DONE (flowcatchR)

name	user	system	elapsed
Frames	0.57	0.06	0.62
add.contours	0	0	0
channel.Frames	0.29	0.14	0.44
crop.Frames	0.36	0.10	0.45
export.Frames	0	0	0
export.particles	0.00	0.01	0.02
inspect.Frames	0	0	0
kinematics	0.28	0.02	0.30
length.Frames	0.11	0.00	0.10
link.particles	0.16	0.01	0.18
matchTrajToParticles	0.26	0.00	0.26
normalizeFrames	2.28	1.52	3.79
particles	0	0	0
penaltyFunctionGenerator	0	0	0
plot.TrajectorySet	0.2	0.0	0.2
plot2D.TrajectorySet	0.41	0.00	0.41
preprocess.Frames	1.14	0.16	1.32
read.Frames	0	0	0
read.particles	0	0	0
rotate.Frames	1.23	0.25	1.48
select.Frames	1.51	1.03	2.54
select.particles	0.03	0.00	0.03
shinyFlow	0	0	0
show-Frames-method	0.09	0.03	0.13
show-KinematicsFeatures-method	0.22	0.01	0.23
show-KinematicsFeaturesSet-method	0.24	0.00	0.24
show-LinkedParticleSet-method	0.20	0.02	0.22
show-ParticleSet-method	0	0	0
show-TrajectorySet-method	0.22	0.00	0.22
snap	0	0	0
trajectories	0.33	0.00	0.33

name	user	system	elapsed
Frames	0.77	0.05	0.81
add.contours	0.00	0.01	0.02
channel.Frames	0.32	0.13	0.45
crop.Frames	0.46	0.06	0.51
export.Frames	0	0	0
export.particles	0	0	0
inspect.Frames	0	0	0
kinematics	0.34	0.03	0.38
length.Frames	0.12	0.00	0.12
link.particles	0.22	0.00	0.22
matchTrajToParticles	0.41	0.00	0.41
normalizeFrames	3.26	1.40	4.66
particles	0.00	0.02	0.02
penaltyFunctionGenerator	0	0	0
plot.TrajectorySet	0.25	0.00	0.25
plot2D.TrajectorySet	0.34	0.03	0.37
preprocess.Frames	0.92	0.22	1.45
read.Frames	0.00	0.01	0.02
read.particles	0	0	0
rotate.Frames	0.95	0.24	1.18
select.Frames	1.81	0.87	2.70
select.particles	0.05	0.00	0.05
shinyFlow	0	0	0
show-Frames-method	0.15	0.03	0.18
show-KinematicsFeatures-method	0.37	0.02	0.39
show-KinematicsFeaturesSet-method	0.45	0.00	0.45
show-LinkedParticleSet-method	0.28	0.00	0.28
show-ParticleSet-method	0.02	0.00	0.01
show-TrajectorySet-method	0.33	0.00	0.33
snap	0	0	0
trajectories	0.29	0.00	0.30