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CHECK report for alsace on malbec1

This page was generated on 2018-04-12 13:11:56 -0400 (Thu, 12 Apr 2018).

Package 37/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alsace 1.14.0
Ron Wehrens
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/alsace
Branch: RELEASE_3_6
Last Commit: aebb13b
Last Changed Date: 2017-10-30 12:40:12 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: alsace
Version: 1.14.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings alsace_1.14.0.tar.gz
StartedAt: 2018-04-11 21:22:58 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 21:23:46 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 47.9 seconds
RetCode: 0
Status:  OK 
CheckDir: alsace.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings alsace_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/alsace.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alsace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘alsace’ version ‘1.14.0’
* 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 ‘alsace’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘lattice’ 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 ... NOTE
correctPeaks : <anonymous> : <anonymous>: no visible global function
  definition for ‘predict’
doALS: no visible global function definition for ‘capture.output’
findpeaks: no visible global function definition for ‘embed’
fitpeaks : fitpk: no visible global function definition for ‘dnorm’
getAllPeaks: no visible global function definition for ‘median’
getPeakTable: no visible global function definition for ‘par’
getPeakTable: no visible global function definition for
  ‘colorRampPalette’
getPeakTable : clusterPeaks: no visible global function definition for
  ‘hclust’
getPeakTable : clusterPeaks: no visible global function definition for
  ‘dist’
getPeakTable : clusterPeaks: no visible global function definition for
  ‘cutree’
getPeakTable : clusterPeaks: no visible global function definition for
  ‘aggregate’
getPeakTable : clusterPeaks: no visible global function definition for
  ‘stripplot’
getPeakTable : clusterPeaks : <anonymous>: no visible global function
  definition for ‘panel.stripplot’
getPeakTable : clusterPeaks : <anonymous>: no visible global function
  definition for ‘panel.abline’
matchCprofiles : <anonymous>: no visible global function definition for
  ‘cor’
matchCprofiles: no visible global function definition for ‘median’
matchCprofiles: no visible global function definition for ‘cutree’
matchCprofiles: no visible global function definition for ‘hclust’
matchCprofiles: no visible global function definition for ‘as.dist’
mergeTimeWindows : <anonymous>: no visible global function definition
  for ‘cor’
mergeTimeWindows: no visible global function definition for ‘cor’
mergeTimeWindows: no visible global function definition for ‘cutree’
mergeTimeWindows: no visible global function definition for ‘hclust’
mergeTimeWindows: no visible global function definition for ‘as.dist’
mergeTimeWindows: no visible global function definition for ‘aggregate’
plot.ALS: no visible global function definition for ‘matplot’
plot.ALS: no visible global function definition for ‘abline’
preprocess : <anonymous>: no visible global function definition for
  ‘approx’
preprocess : <anonymous>: no visible global function definition for
  ‘smooth.spline’
showALSresult: no visible global function definition for
  ‘terrain.colors’
showALSresult: no visible global function definition for ‘par’
showALSresult: no visible global function definition for ‘layout’
showALSresult: no visible global function definition for ‘matplot’
showALSresult: no visible global function definition for ‘title’
showALSresult: no visible global function definition for ‘image’
showALSresult: no visible global function definition for ‘box’
showALSresult: no visible global function definition for ‘contour’
showALSresult: no visible global function definition for ‘plot’
showALSresult: no visible global function definition for ‘text’
showALSresult: no visible global function definition for ‘rect’
showALSresult: no visible global function definition for ‘axTicks’
suggestCompCombis : cC.aux: no visible global function definition for
  ‘cor’
suggestCompCombis: no visible global function definition for ‘as.dist’
suggestCompCombis: no visible global function definition for ‘hclust’
suggestCompCombis: no visible global function definition for ‘cutree’
Undefined global functions or variables:
  abline aggregate approx as.dist axTicks box capture.output
  colorRampPalette contour cor cutree dist dnorm embed hclust image
  layout matplot median panel.abline panel.stripplot par plot predict
  rect smooth.spline stripplot terrain.colors text title
Consider adding
  importFrom("grDevices", "colorRampPalette", "terrain.colors")
  importFrom("graphics", "abline", "axTicks", "box", "contour", "image",
             "layout", "matplot", "par", "plot", "rect", "text", "title")
  importFrom("stats", "aggregate", "approx", "as.dist", "cor", "cutree",
             "dist", "dnorm", "embed", "hclust", "median", "predict",
             "smooth.spline")
  importFrom("utils", "capture.output")
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 ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
components   8.256  0.028   8.291
correctPeaks 5.452  0.008   5.468
* 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-3.6-bioc/meat/alsace.Rcheck/00check.log’
for details.



Installation output

alsace.Rcheck/00install.out

* installing *source* package ‘alsace’ ...
** 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 (alsace)

Tests output


Example timings

alsace.Rcheck/alsace-Ex.timings

nameusersystemelapsed
components8.2560.0288.291
correctPeaks5.4520.0085.468
correctRT2.5080.0002.508
doALS2.7760.0042.779
filterPeaks0.0520.0000.054
fitpeaks2.9080.0002.911
getAllPeaks0.0320.0000.031
getPeakTable2.7040.0042.712
opa1.0880.0121.098
preprocess0.1520.0000.152
showALSresult0.0800.0040.084
tea0.1000.0040.102
teaMerged3.9000.0123.913
windows0.2240.0080.231