Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P [Q] R  S  T  U  V  W  X  Y  Z 

BioC 3.4: CHECK report for quantro on malbec1

This page was generated on 2017-04-15 16:12:19 -0400 (Sat, 15 Apr 2017).

Package 981/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
quantro 1.8.0
Stephanie Hicks
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/quantro
Last Changed Rev: 123129 / Revision: 128728
Last Changed Date: 2016-10-27 18:03:18 -0400 (Thu, 27 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: quantro
Version: 1.8.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings quantro_1.8.0.tar.gz
StartedAt: 2017-04-15 00:39:22 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:42:52 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 210.4 seconds
RetCode: 0
Status:  OK 
CheckDir: quantro.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings quantro_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/quantro.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘quantro/DESCRIPTION’ ... OK
* this is package ‘quantro’ version ‘1.8.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘quantro’ 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
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
matboxplot: no visible global function definition for ‘palette’
matboxplot: no visible global function definition for ‘boxplot’
matdensity : getdensity : <anonymous>: no visible global function
  definition for ‘density’
matdensity: no visible global function definition for ‘palette’
matdensity: no visible global function definition for ‘matplot’
quantro: no visible binding for global variable ‘median’
quantro: no visible global function definition for ‘lm’
quantro: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  boxplot density lm matplot median palette quantile
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "boxplot", "matplot")
  importFrom("stats", "density", "lm", "median", "quantile")
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’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/quantro.Rcheck/00check.log’
for details.


quantro.Rcheck/00install.out:

* installing *source* package ‘quantro’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (quantro)

quantro.Rcheck/quantro-Ex.timings:

nameusersystemelapsed
MSbetween2.4360.0202.455
MSwithin1.1240.0161.139
anova1.1360.0081.145
matboxplot1.0200.0121.031
matdensity0.6400.0120.653
quantro1.6000.0041.602
quantroPlot000
quantroPvalPerm1.6040.0041.608
quantroStat1.1680.0041.175
quantroStatPerm1.2360.0041.241
summary1.5960.0081.605