BioC 3.2: CHECK report for flowcatchR on moscato1

Package: flowcatchR

Version: 1.3.2

Command: rm -rf flowcatchR.buildbin-libdir flowcatchR.Rcheck && mkdir flowcatchR.buildbin-libdir flowcatchR.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowcatchR.buildbin-libdir flowcatchR_1.3.2.tar.gz >flowcatchR.Rcheck\00install.out 2>&1 && cp flowcatchR.Rcheck\00install.out flowcatchR-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=flowcatchR.buildbin-libdir --install="check:flowcatchR-install.out" --force-multiarch --no-vignettes --timings flowcatchR_1.3.2.tar.gz

StartedAt: 2015-08-14 04:50:36 -0700 (Fri, 14 Aug 2015)

EndedAt: 2015-08-14 04:52:43 -0700 (Fri, 14 Aug 2015)

EllapsedTime: 127.2 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 && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowcatchR.buildbin-libdir flowcatchR_1.3.2.tar.gz >flowcatchR.Rcheck\00install.out 2>&1 && cp flowcatchR.Rcheck\00install.out flowcatchR-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=flowcatchR.buildbin-libdir --install="check:flowcatchR-install.out" --force-multiarch --no-vignettes --timings flowcatchR_1.3.2.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/flowcatchR.Rcheck'
* using R version 3.2.2 beta (2015-08-04 r68843)
* 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 '1.3.2'
* 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' ... [18s] OK
** running examples for arch 'x64' ... [22s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
normalizeFrames 4.18   1.79    5.97
* 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
  'D:/biocbld/bbs-3.2-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_1.3.2.zip
* DONE (flowcatchR)

name	user	system	elapsed
Frames	0.70	0.14	0.85
add.contours	0	0	0
channel.Frames	0.30	0.22	0.52
crop.Frames	0.46	0.09	0.56
export.Frames	0.00	0.02	0.01
export.particles	0	0	0
inspect.Frames	0	0	0
kinematics	0.41	0.00	0.41
length.Frames	0.14	0.02	0.16
link.particles	0.17	0.00	0.17
matchTrajToParticles	0.41	0.00	0.40
normalizeFrames	3.41	1.56	4.98
particles	0	0	0
penaltyFunctionGenerator	0	0	0
plot.TrajectorySet	0.22	0.00	0.22
plot2D.TrajectorySet	0.33	0.01	0.34
preprocess.Frames	1.09	0.14	1.26
read.Frames	0	0	0
read.particles	0	0	0
rotate.Frames	1.67	0.25	1.92
select.Frames	1.95	0.97	2.92
select.particles	0.03	0.01	0.04
shinyFlow	0	0	0
show-Frames-method	0.23	0.02	0.25
show-KinematicsFeatures-method	0.39	0.00	0.39
show-KinematicsFeaturesSet-method	0.45	0.00	0.45
show-LinkedParticleSet-method	0.27	0.02	0.29
show-ParticleSet-method	0	0	0
show-TrajectorySet-method	0.30	0.01	0.31
snap	0	0	0
trajectories	0.2	0.0	0.2

name	user	system	elapsed
Frames	0.83	0.16	0.98
add.contours	0	0	0
channel.Frames	0.36	0.15	0.51
crop.Frames	0.41	0.10	0.50
export.Frames	0	0	0
export.particles	0.00	0.01	0.02
inspect.Frames	0	0	0
kinematics	0.48	0.03	0.51
length.Frames	0.12	0.02	0.14
link.particles	0.22	0.00	0.22
matchTrajToParticles	0.47	0.00	0.47
normalizeFrames	4.18	1.79	5.97
particles	0.02	0.00	0.02
penaltyFunctionGenerator	0	0	0
plot.TrajectorySet	0.39	0.00	0.39
plot2D.TrajectorySet	0.53	0.02	0.54
preprocess.Frames	1.17	0.25	1.64
read.Frames	0	0	0
read.particles	0	0	0
rotate.Frames	1.23	0.22	1.45
select.Frames	2.09	1.31	3.40
select.particles	0.05	0.00	0.05
shinyFlow	0	0	0
show-Frames-method	0.12	0.01	0.14
show-KinematicsFeatures-method	0.30	0.02	0.31
show-KinematicsFeaturesSet-method	0.33	0.00	0.33
show-LinkedParticleSet-method	0.23	0.00	0.23
show-ParticleSet-method	0.01	0.00	0.02
show-TrajectorySet-method	0.33	0.00	0.33
snap	0	0	0
trajectories	0.30	0.00	0.29