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BioC 3.2: CHECK report for flowcatchR on oaxaca

This page was generated on 2016-04-23 10:28:24 -0700 (Sat, 23 Apr 2016).

Package 349/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowcatchR 1.4.0
Federico Marini
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/flowcatchR
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 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
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: flowcatchR
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowcatchR_1.4.0.tar.gz
StartedAt: 2016-04-23 00:05:51 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 00:06:56 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 65.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flowcatchR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowcatchR_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/flowcatchR.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.4.0’
* 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/5s] WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.2-bioc/meat/flowcatchR.Rcheck/00install.out’ for details.
* 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [16s/16s] 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/flowcatchR.Rcheck/00check.log’
for details.


flowcatchR.Rcheck/00install.out:

* installing *source* package ‘flowcatchR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (flowcatchR)

flowcatchR.Rcheck/flowcatchR-Ex.timings:

nameusersystemelapsed
Frames0.6230.1250.750
add.contours0.0020.0000.002
channel.Frames0.2190.0860.305
crop.Frames0.3000.0750.375
export.Frames0.0020.0000.002
export.particles0.0020.0010.003
inspect.Frames0.0010.0010.002
kinematics0.3510.0240.376
length.Frames0.0640.0110.074
link.particles0.1500.0110.161
matchTrajToParticles0.3050.0050.310
normalizeFrames2.7821.8594.648
particles0.0010.0000.002
penaltyFunctionGenerator0.0010.0000.000
plot.TrajectorySet0.2270.0160.243
plot2D.TrajectorySet0.3500.0040.355
preprocess.Frames0.7990.3081.108
read.Frames0.0000.0000.001
read.particles0.0000.0000.001
rotate.Frames0.8560.3351.192
select.Frames1.5251.6703.198
select.particles0.0400.0020.041
shinyFlow0.0010.0000.001
show-Frames-method0.0880.0500.138
show-KinematicsFeatures-method0.2410.0440.286
show-KinematicsFeaturesSet-method0.3220.0070.330
show-LinkedParticleSet-method0.1950.0020.197
show-ParticleSet-method0.0080.0010.008
show-TrajectorySet-method0.2380.0100.248
snap0.0010.0000.001
trajectories0.2530.0030.257