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BioC 3.0: CHECK report for flowcatchR on moscato1

This page was generated on 2015-04-10 09:51:25 -0700 (Fri, 10 Apr 2015).

Package 300/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowcatchR 1.0.3
Federico Marini
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/flowcatchR
Last Changed Rev: 99005 / Revision: 102249
Last Changed Date: 2015-02-03 09:39:48 -0800 (Tue, 03 Feb 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: flowcatchR
Version: 1.0.3
Command: rm -rf flowcatchR.buildbin-libdir flowcatchR.Rcheck && mkdir flowcatchR.buildbin-libdir flowcatchR.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowcatchR.buildbin-libdir flowcatchR_1.0.3.tar.gz >flowcatchR.Rcheck\00install.out 2>&1 && cp flowcatchR.Rcheck\00install.out flowcatchR-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=flowcatchR.buildbin-libdir --install="check:flowcatchR-install.out" --force-multiarch --no-vignettes --timings flowcatchR_1.0.3.tar.gz
StartedAt: 2015-04-10 01:04:01 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:06:24 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 142.6 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-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowcatchR.buildbin-libdir flowcatchR_1.0.3.tar.gz >flowcatchR.Rcheck\00install.out 2>&1 && cp flowcatchR.Rcheck\00install.out flowcatchR-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=flowcatchR.buildbin-libdir --install="check:flowcatchR-install.out" --force-multiarch --no-vignettes --timings flowcatchR_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/flowcatchR.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-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 '1.0.3'
* 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 whether package 'flowcatchR' can be installed ... 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
* 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 '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 ...
** running examples for arch 'i386' ... [23s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
normalizeFrames 3.93   1.31    5.24
** running examples for arch 'x64' ... [28s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
normalizeFrames 5.28   2.14    7.41
* 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
  'D:/biocbld/bbs-3.0-bioc/meat/flowcatchR.Rcheck/00check.log'
for details.

flowcatchR.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'flowcatchR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowcatchR' as flowcatchR_1.0.3.zip
* DONE (flowcatchR)

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

nameusersystemelapsed
Frames0.780.050.83
add.contours0.160.010.17
channel.Frames0.420.100.52
crop.Frames0.630.070.70
export.Frames0.150.020.17
export.particles0.030.000.03
inspect.Frames0.210.020.22
kinematics0.670.010.69
length.Frames0.170.000.17
link.particles0.280.000.28
matchTrajToParticles0.550.020.56
normalizeFrames3.931.315.24
particles0.170.010.19
penaltyFunctionGenerator000
plot.TrajectorySet0.560.020.58
plot2D.TrajectorySet0.640.010.65
preprocess.Frames1.450.181.63
read.Frames000
read.particles000
rotate.Frames1.470.321.79
select.Frames1.871.173.04
select.particles0.090.000.10
shinyFlow000
show-Frames-method0.280.020.29
show-KinematicsFeatures-method0.640.000.64
show-KinematicsFeaturesSet-method0.470.010.48
show-LinkedParticleSet-method0.360.000.36
show-ParticleSet-method0.030.000.03
show-TrajectorySet-method0.420.000.43
snap000
trajectories0.490.000.48

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

nameusersystemelapsed
Frames1.170.181.36
add.contours0.190.020.20
channel.Frames0.500.050.55
crop.Frames0.840.090.94
export.Frames0.230.010.25
export.particles0.020.020.03
inspect.Frames0.230.020.25
kinematics0.640.031.12
length.Frames0.170.000.17
link.particles0.300.010.31
matchTrajToParticles0.590.020.61
normalizeFrames5.282.147.41
particles0.230.010.25
penaltyFunctionGenerator000
plot.TrajectorySet0.770.030.79
plot2D.TrajectorySet0.780.020.80
preprocess.Frames1.480.281.82
read.Frames000
read.particles000
rotate.Frames1.560.191.75
select.Frames2.001.173.17
select.particles0.060.000.06
shinyFlow000
show-Frames-method0.160.040.20
show-KinematicsFeatures-method0.510.000.52
show-KinematicsFeaturesSet-method0.780.000.78
show-LinkedParticleSet-method0.670.000.67
show-ParticleSet-method0.030.000.03
show-TrajectorySet-method0.520.000.51
snap000
trajectories0.540.000.55