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BioC 3.5: CHECK report for DTA on oaxaca

This page was generated on 2017-03-04 16:41:50 -0500 (Sat, 04 Mar 2017).

Package 356/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DTA 2.21.0
Bjoern Schwalb
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DTA
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: DTA
Version: 2.21.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DTA_2.21.0.tar.gz
StartedAt: 2017-03-04 02:05:25 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 02:09:30 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 244.9 seconds
RetCode: 0
Status:  OK 
CheckDir: DTA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DTA_2.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/DTA.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DTA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DTA’ version ‘2.21.0’
* 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 ‘DTA’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
    doc    2.6Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DTA.dynamic.estimate : ellipse.coordinates: no visible global function
  definition for ‘qchisq’
DTA.dynamic.estimate : plotsfkt: no visible global function definition
  for ‘par’
DTA.dynamic.estimate: no visible global function definition for
  ‘quantile’
DTA.dynamic.estimate : plotsfkt: no visible global function definition
  for ‘plot’
DTA.dynamic.estimate : plotsfkt: no visible global function definition
  for ‘points’
DTA.dynamic.estimate : plotsfkt: no visible global function definition
  for ‘sd’
DTA.dynamic.estimate : plotsfkt: no visible global function definition
  for ‘legend’
DTA.dynamic.generate: no visible global function definition for ‘rf’
DTA.dynamic.generate: no visible global function definition for
  ‘median’
DTA.dynamic.generate : <anonymous>: no visible global function
  definition for ‘rnorm’
DTA.dynamic.generate: no visible binding for global variable ‘median’
DTA.dynamic.singlegenerate : plotsfkt: no visible global function
  definition for ‘par’
DTA.dynamic.singlegenerate : plotsfkt: no visible global function
  definition for ‘plot’
DTA.dynamic.singlegenerate : plotsfkt: no visible global function
  definition for ‘points’
DTA.dynamic.singlegenerate : plotsfkt: no visible global function
  definition for ‘abline’
DTA.dynamic.singlegenerate : plotsfkt: no visible global function
  definition for ‘legend’
DTA.generate: no visible global function definition for ‘rf’
DTA.generate: no visible global function definition for ‘rnorm’
DTA.map.it: no visible global function definition for ‘aggregate’
DTA.map.it : <anonymous>: no visible global function definition for
  ‘median’
DTA.plot.it: no visible global function definition for ‘jpeg’
DTA.plot.it: no visible global function definition for ‘png’
DTA.plot.it: no visible global function definition for ‘bmp’
DTA.plot.it: no visible global function definition for ‘tiff’
DTA.plot.it: no visible global function definition for ‘postscript’
DTA.plot.it: no visible global function definition for ‘pdf’
DTA.plot.it: no visible global function definition for ‘dev.off’
DTA.plot.it: no visible global function definition for ‘dev.new’
DTA.singleestimate: no visible global function definition for ‘median’
DTA.singleestimate : lossfct: no visible global function definition for
  ‘median’
DTA.singleestimate: no visible global function definition for
  ‘optimize’
DTA.singleestimate: no visible global function definition for ‘lm’
DTA.singleestimate: no visible global function definition for
  ‘coefficients’
DTA.singleestimate: no visible global function definition for
  ‘quantile’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘par’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘points’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘abline’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘median’
DTA.singleestimate: no visible binding for global variable ‘median’
DTA.singleestimate : plotsfkt: no visible binding for global variable
  ‘median’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘plot’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘hist’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘text’
DTA.singleestimate: no visible global function definition for ‘cor’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘layout’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘image’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘colorRampPalette’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘axis’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘box’
DTA.singleestimate: no visible binding for global variable ‘sd’
DTA.singleestimate: no visible global function definition for ‘loess’
DTA.singleestimate : <anonymous>: no visible global function definition
  for ‘optimize’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘persp’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘polygon’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘trans3d’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘lines’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘dgamma’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘mtext’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘legend’
DTA.singleestimate : <anonymous>: no visible global function definition
  for ‘rnorm’
DTA.singleestimate : <anonymous>: no visible global function definition
  for ‘quantile’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘quantile’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘coefficients’
DTA.singleestimate : plotsfkt: no visible global function definition
  for ‘density’
DTA.singlegenerate: no visible global function definition for ‘median’
DTA.singlegenerate: no visible global function definition for ‘rnorm’
gridfkt: no visible global function definition for ‘abline’
gridfkt: no visible global function definition for ‘text’
likelihood: no visible global function definition for ‘dnorm’
likelihood: no visible global function definition for ‘dgamma’
medctr: no visible binding for global variable ‘median’
medctr: no visible global function definition for ‘median’
mediancenter: no visible binding for global variable ‘median’
mediancenter: no visible global function definition for ‘median’
mtextfkt: no visible global function definition for ‘mtext’
parfkt: no visible global function definition for ‘par’
pcor: no visible global function definition for ‘cor’
scor: no visible global function definition for ‘cor’
tls: no visible global function definition for ‘model.response’
tls: no visible global function definition for ‘model.matrix’
tls: no visible binding for global variable ‘contrasts’
toquantiles: no visible global function definition for ‘quantile’
wtls.solve: no visible global function definition for ‘lm’
wtls.solve: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  abline aggregate axis bmp box coefficients colorRampPalette contrasts
  cor density dev.new dev.off dgamma dnorm hist image jpeg layout
  legend lines lm loess median model.matrix model.response mtext
  optimize par pdf persp plot png points polygon postscript qchisq
  quantile rf rnorm sd text tiff trans3d uniroot
Consider adding
  importFrom("grDevices", "bmp", "colorRampPalette", "dev.new",
             "dev.off", "jpeg", "pdf", "png", "postscript", "tiff",
             "trans3d")
  importFrom("graphics", "abline", "axis", "box", "hist", "image",
             "layout", "legend", "lines", "mtext", "par", "persp",
             "plot", "points", "polygon", "text")
  importFrom("stats", "aggregate", "coefficients", "contrasts", "cor",
             "density", "dgamma", "dnorm", "lm", "loess", "median",
             "model.matrix", "model.response", "optimize", "qchisq",
             "quantile", "rf", "rnorm", "sd", "uniroot")
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 sizes of PDF files under ‘inst/doc’ ... 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
DTA.dynamic.generate 67.282  4.742  72.048
DTA.estimate         47.687  2.022  49.736
DTA.generate         42.911  1.684  44.622
DTA.dynamic.estimate 38.778  0.382  39.177
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/DTA.Rcheck/00check.log’
for details.


DTA.Rcheck/00install.out:

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

DTA.Rcheck/DTA-Ex.timings:

nameusersystemelapsed
DTA-package0.0010.0000.001
DTA.dynamic.estimate38.778 0.38239.177
DTA.dynamic.generate67.282 4.74272.048
DTA.estimate47.687 2.02249.736
DTA.generate42.911 1.68444.622
DTA.map.it0.0010.0000.000
DTA.normalize000
DTA.phenomat0.0020.0010.002
DTA.plot.it0.0490.0160.069
tls0.6350.2530.889