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CHECK report for viper on malbec2

This page was generated on 2019-10-16 12:04:13 -0400 (Wed, 16 Oct 2019).

Package 1715/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
viper 1.18.1
Mariano J Alvarez
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/viper
Branch: RELEASE_3_9
Last Commit: cb31cee
Last Changed Date: 2019-05-30 12:29:09 -0400 (Thu, 30 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: viper
Version: 1.18.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:viper.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings viper_1.18.1.tar.gz
StartedAt: 2019-10-16 05:42:31 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:46:28 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 237.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: viper.Rcheck
Warnings: 2

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:viper.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings viper_1.18.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/viper.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘viper/DESCRIPTION’ ... OK
* this is package ‘viper’ version ‘1.18.1’
* 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 ‘viper’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
TFmode1: no visible global function definition for ‘cor’
TFmode2: no visible global function definition for ‘cor’
TFscore : : no visible global function definition for
  ‘pnorm’
aREA: no visible global function definition for ‘qnorm’
aREA: no visible global function definition for ‘txtProgressBar’
aREA : : no visible global function definition for
  ‘setTxtProgressBar’
aecdf: no visible global function definition for ‘quantile’
aecdf: no visible global function definition for ‘ecdf’
aecdf: no visible global function definition for ‘lm’
aecdf: no visible global function definition for ‘approxfun’
aecdf : dnull: no visible global function definition for ‘predict’
aecdf : dnull: no visible global function definition for ‘qnorm’
aecdf1: no visible global function definition for ‘quantile’
aecdf1: no visible global function definition for ‘ecdf’
aecdf1: no visible binding for global variable ‘tl2’
aecdf1: no visible binding for global variable ‘iq2’
aecdf1: no visible global function definition for ‘epd’
aecdf1: no visible global function definition for ‘lm’
aecdf1: no visible global function definition for ‘predict’
aecdf1: no visible global function definition for ‘qnorm’
approxk2d: no visible binding for global variable ‘quantile’
bootstrapViper :  : : no visible global function
  definition for ‘qnorm’
bootstrapViper : : no visible global function definition for
  ‘txtProgressBar’
bootstrapViper :  : : no visible global function
  definition for ‘setTxtProgressBar’
bootstrapmsviper: no visible binding for global variable ‘median’
bootstrapmsviper: no visible global function definition for ‘pnorm’
distMode: no visible global function definition for ‘density’
groupPwea3: no visible global function definition for ‘qnorm’
groupPwea3: no visible global function definition for ‘txtProgressBar’
groupPwea3 : : no visible global function definition for
  ‘setTxtProgressBar’
groupPwea3 : : no visible global function definition for
  ‘qnorm’
groupPwea3: no visible global function definition for ‘pnorm’
msviper: no visible global function definition for ‘txtProgressBar’
msviper : : no visible global function definition for
  ‘setTxtProgressBar’
msviper: no visible global function definition for ‘pnorm’
msviperClass: no visible global function definition for ‘pnorm’
msviperCombinatorial: no visible global function definition for ‘combn’
msviperSynergy : : no visible global function definition for
  ‘qnorm’
msviperSynergy : : no visible global function definition for
  ‘quantile’
msviperSynergy : : no visible global function definition for
  ‘ecdf’
msviperSynergy : : no visible global function definition for
  ‘knots’
msviperSynergy : : no visible global function definition for
  ‘smooth.spline’
msviperSynergy : : no visible global function definition for
  ‘predict’
msviperSynergy: no visible global function definition for
  ‘txtProgressBar’
msviperSynergy : : no visible global function definition for
  ‘setTxtProgressBar’
plot.msviper: no visible global function definition for ‘par’
plot.msviper: no visible global function definition for ‘layout’
plot.msviper: no visible global function definition for ‘rgb2hsv’
plot.msviper: no visible global function definition for ‘col2rgb’
plot.msviper: no visible global function definition for ‘plot’
plot.msviper: no visible global function definition for ‘hsv’
plot.msviper: no visible global function definition for ‘lines’
plot.msviper: no visible global function definition for ‘smooth.spline’
plot.msviper: no visible global function definition for ‘text’
plot.msviper: no visible global function definition for ‘axis’
plot.msviper: no visible global function definition for ‘abline’
plot.msviper: no visible global function definition for ‘image’
plot.msviper: no visible global function definition for ‘box’
plot.msviper: no visible global function definition for ‘grid’
ppwea3NULLf :  : : no visible global function
  definition for ‘pnorm’
pwea3NULLf : : no visible global function definition for
  ‘quantile’
pwea3NULLf : : no visible global function definition for
  ‘ecdf’
pwea3NULLf : : no visible global function definition for
  ‘knots’
pwea3NULLf : : no visible global function definition for
  ‘smooth.spline’
pwea3NULLf :  : : no visible global function
  definition for ‘predict’
pwea3NULLf :  : : no visible global function
  definition for ‘qnorm’
pwea3NULLf: no visible global function definition for ‘txtProgressBar’
pwea3NULLf : : no visible global function definition for
  ‘setTxtProgressBar’
pwea3NULLgroups: no visible global function definition for ‘qnorm’
pwea3NULLgroups: no visible global function definition for
  ‘txtProgressBar’
pwea3NULLgroups : : no visible global function definition
  for ‘setTxtProgressBar’
regulonDist : : no visible global function definition for
  ‘fisher.test’
scaleGroups : : no visible global function definition for
  ‘qnorm’
scaleGroups: no visible global function definition for ‘runif’
selectTFs : : no visible global function definition for
  ‘combn’
shadow: no visible global function definition for ‘combn’
shadow : : no visible global function definition for
  ‘quantile’
shadow : : no visible global function definition for ‘ecdf’
shadow : : no visible global function definition for ‘knots’
shadow : : no visible global function definition for
  ‘smooth.spline’
shadow : : no visible global function definition for
  ‘predict’
shadow: no visible global function definition for ‘txtProgressBar’
shadow : : no visible global function definition for
  ‘setTxtProgressBar’
shadowRegulon: no visible global function definition for ‘pnorm’
shadowRegulon : : no visible global function definition for
  ‘qnorm’
shadowRegulon : : no visible global function definition for
  ‘pnorm’
shadowRegulon: no visible global function definition for ‘combn’
signatureDistance: no visible global function definition for ‘qnorm’
summary.msviper: no visible global function definition for ‘p.adjust’
viper: no visible global function definition for ‘punif’
viper : : no visible global function definition for ‘median’
viper : : no visible global function definition for ‘mad’
viper : : no visible global function definition for
  ‘txtProgressBar’
viper :  : : no visible global function
  definition for ‘setTxtProgressBar’
viperRPT : : no visible global function definition for
  ‘residuals’
viperRPT : : no visible global function definition for ‘lm’
viperRPT : : no visible global function definition for
  ‘smooth.spline’
viperSimilarity: no visible global function definition for ‘qnorm’
bootstrapTtest,matrix : : no visible global function
  definition for ‘qnorm’
bootstrapTtest,matrix : : no visible global function
  definition for ‘pt’
bootstrapTtest,matrix: no visible global function definition for
  ‘txtProgressBar’
bootstrapTtest,matrix : : no visible global function
  definition for ‘setTxtProgressBar’
rowTtest,matrix: no visible global function definition for ‘pt’
ttestNull,matrix : : no visible global function definition
  for ‘qnorm’
ttestNull,matrix : : no visible global function definition
  for ‘pt’
ttestNull,matrix: no visible global function definition for
  ‘txtProgressBar’
ttestNull,matrix : : no visible global function definition
  for ‘setTxtProgressBar’
viperSignature,matrix : : no visible global function
  definition for ‘qnorm’
viperSignature,matrix: no visible global function definition for
  ‘txtProgressBar’
viperSignature,matrix :  : : no visible global
  function definition for ‘qnorm’
viperSignature,matrix : : no visible global function
  definition for ‘setTxtProgressBar’
viperSignature,matrix: no visible global function definition for
  ‘combn’
Undefined global functions or variables:
  abline approxfun axis box col2rgb combn cor density ecdf epd
  fisher.test grid hsv image iq2 knots layout lines lm mad median
  p.adjust par plot pnorm predict pt punif qnorm quantile residuals
  rgb2hsv runif setTxtProgressBar smooth.spline text tl2 txtProgressBar
Consider adding
  importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
  importFrom("graphics", "abline", "axis", "box", "grid", "image",
             "layout", "lines", "par", "plot", "text")
  importFrom("stats", "approxfun", "cor", "density", "ecdf",
             "fisher.test", "knots", "lm", "mad", "median", "p.adjust",
             "pnorm", "predict", "pt", "punif", "qnorm", "quantile",
             "residuals", "runif", "smooth.spline")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
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 ... WARNING
Codoc mismatches from documentation object 'pruneRegulon':
pruneRegulon
  Code: function(regulon, cutoff = 50, adaptive = TRUE, eliminate =
                 FALSE, wm = NULL)
  Docs: function(regulon, cutoff = 50, adaptive = TRUE, eliminate =
                 FALSE)
  Argument names in code not in docs:
    wm

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'viper'
  ‘mvws’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
bootstrapViper         21.239  1.063  22.308
viperSignature-methods 21.942  0.043  21.994
shadow                 16.127  0.076  16.203
msviperSynergy         11.575  0.072  11.649
viperRPT               10.414  0.041  10.455
msviperCombinatorial    8.942  0.027   8.968
viper                   8.810  0.016   8.833
msviper                 8.670  0.020   8.690
plot.msviper            6.708  0.036   6.744
ledge                   6.433  0.036   6.470
bootstrapmsviper        6.345  0.040   6.396
ttestNull-methods       5.198  0.024   5.224
bootstrapTtest-methods  5.179  0.040   5.219
* 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 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/viper.Rcheck/00check.log’
for details.



Installation output

viper.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL viper
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘viper’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (viper)

Tests output


Example timings

viper.Rcheck/viper-Ex.timings

nameusersystemelapsed
approxk2d0.0610.0000.061
aracne2regulon2.7940.0322.934
aracne2regulon4cnv2.7760.0282.804
bootstrapTtest-methods5.1790.0405.219
bootstrapViper21.239 1.06322.308
bootstrapmsviper6.3450.0406.396
distMode1.5070.0161.523
fcvarna1.2610.0081.269
filterCV-methods1.2760.0081.284
frcv1.4040.0201.424
frvarna1.5590.0281.587
integrateSignatures2.6790.0282.707
ledge6.4330.0366.470
msviper8.670.028.69
msviperAnnot3.2330.0243.258
msviperClass3.0500.0283.081
msviperCombinatorial8.9420.0278.968
msviperSynergy11.575 0.07211.649
plot.msviper6.7080.0366.744
pruneRegulon1.2080.0121.220
rowTtest-methods2.3510.0402.391
scaleGroups1.6220.0121.634
shadow16.127 0.07616.203
signatureDistance2.5570.0202.590
ttestNull-methods5.1980.0245.224
viper8.8100.0168.833
viperRPT10.414 0.04110.455
viperSignature-methods21.942 0.04321.994
viperSimilarity2.2460.0242.278