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BioC 3.5: CHECK report for alsace on malbec2

This page was generated on 2017-08-16 13:15:33 -0400 (Wed, 16 Aug 2017).

Package 37/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alsace 1.12.0
Ron Wehrens
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/alsace
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: alsace
Version: 1.12.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings alsace_1.12.0.tar.gz
StartedAt: 2017-08-15 21:04:53 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:05:41 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 47.9 seconds
RetCode: 0
Status:  OK 
CheckDir: alsace.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings alsace_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/alsace.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.12.0’
* 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   8.320  0.004   8.328
correctPeaks 5.428  0.008   5.440
* 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-3.5-bioc/meat/alsace.Rcheck/00check.log’
for details.


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)

alsace.Rcheck/alsace-Ex.timings:

nameusersystemelapsed
components8.3200.0048.328
correctPeaks5.4280.0085.440
correctRT2.5280.0002.529
doALS2.7440.0002.745
filterPeaks0.0480.0000.049
fitpeaks2.8920.0042.902
getAllPeaks0.0400.0000.043
getPeakTable2.5840.0002.588
opa1.1560.0001.160
preprocess0.1080.0040.111
showALSresult0.0880.0000.084
tea0.1040.0000.103
teaMerged3.5680.0083.579
windows0.2040.0000.204