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BioC 3.4: CHECK report for flowcatchR on moscato1

This page was generated on 2016-09-21 03:46:24 -0700 (Wed, 21 Sep 2016).

Package 411/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowcatchR 1.7.2
Federico Marini
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowcatchR
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowcatchR
Version: 1.7.2
Command: rm -rf flowcatchR.buildbin-libdir flowcatchR.Rcheck && mkdir flowcatchR.buildbin-libdir flowcatchR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowcatchR.buildbin-libdir flowcatchR_1.7.2.tar.gz >flowcatchR.Rcheck\00install.out 2>&1 && cp flowcatchR.Rcheck\00install.out flowcatchR-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=flowcatchR.buildbin-libdir --install="check:flowcatchR-install.out" --force-multiarch --no-vignettes --timings flowcatchR_1.7.2.tar.gz
StartedAt: 2016-09-20 08:15:43 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 08:17:38 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 114.8 seconds
RetCode: 0
Status:  OK  
CheckDir: flowcatchR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf flowcatchR.buildbin-libdir flowcatchR.Rcheck && mkdir flowcatchR.buildbin-libdir flowcatchR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowcatchR.buildbin-libdir flowcatchR_1.7.2.tar.gz >flowcatchR.Rcheck\00install.out 2>&1 && cp flowcatchR.Rcheck\00install.out flowcatchR-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=flowcatchR.buildbin-libdir --install="check:flowcatchR-install.out" --force-multiarch --no-vignettes --timings flowcatchR_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/flowcatchR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.7.2'
* 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 4 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/flowcatchR.Rcheck/00check.log'
for details.


flowcatchR.Rcheck/00install.out:


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_1.7.2.zip
* DONE (flowcatchR)

flowcatchR.Rcheck/examples_i386/flowcatchR-Ex.timings:

nameusersystemelapsed
Frames0.620.040.68
add.contours000
channel.Frames0.390.070.45
crop.Frames0.310.110.42
export.Frames000
export.particles000
inspect.Frames000
kinematics0.280.010.30
length.Frames0.110.000.11
link.particles0.120.000.13
matchTrajToParticles0.250.000.24
normalizeFrames2.781.284.06
particles0.020.000.02
penaltyFunctionGenerator000
plot.TrajectorySet0.20.00.2
plot2D.TrajectorySet0.340.000.34
preprocess.Frames0.910.221.13
read.Frames0.010.000.01
read.particles000
rotate.Frames1.160.171.33
select.Frames1.561.162.71
select.particles0.030.000.03
shinyFlow000
show-Frames-method0.100.010.11
show-KinematicsFeatures-method0.220.020.23
show-KinematicsFeaturesSet-method0.230.000.24
show-LinkedParticleSet-method0.170.010.18
show-ParticleSet-method000
show-TrajectorySet-method0.200.000.21
snap0.020.000.01
trajectories0.20.00.2

flowcatchR.Rcheck/examples_x64/flowcatchR-Ex.timings:

nameusersystemelapsed
Frames0.640.110.75
add.contours000
channel.Frames0.370.060.43
crop.Frames0.360.020.38
export.Frames000
export.particles000
inspect.Frames0.000.020.01
kinematics0.310.010.33
length.Frames0.070.030.09
link.particles0.120.020.15
matchTrajToParticles0.250.000.24
normalizeFrames2.641.574.22
particles000
penaltyFunctionGenerator000
plot.TrajectorySet0.240.000.24
plot2D.TrajectorySet0.360.000.36
preprocess.Frames0.850.211.59
read.Frames000
read.particles000
rotate.Frames0.960.211.16
select.Frames1.450.982.43
select.particles0.010.010.03
shinyFlow000
show-Frames-method0.100.030.13
show-KinematicsFeatures-method0.240.000.25
show-KinematicsFeaturesSet-method0.270.000.26
show-LinkedParticleSet-method0.20.00.2
show-ParticleSet-method000
show-TrajectorySet-method0.240.000.24
snap0.010.000.01
trajectories0.240.000.27