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

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### Running command:
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###   /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.

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

name	user	system	elapsed
approxk2d	0.061	0.000	0.061
aracne2regulon	2.794	0.032	2.934
aracne2regulon4cnv	2.776	0.028	2.804
bootstrapTtest-methods	5.179	0.040	5.219
bootstrapViper	21.239	1.063	22.308
bootstrapmsviper	6.345	0.040	6.396
distMode	1.507	0.016	1.523
fcvarna	1.261	0.008	1.269
filterCV-methods	1.276	0.008	1.284
frcv	1.404	0.020	1.424
frvarna	1.559	0.028	1.587
integrateSignatures	2.679	0.028	2.707
ledge	6.433	0.036	6.470
msviper	8.67	0.02	8.69
msviperAnnot	3.233	0.024	3.258
msviperClass	3.050	0.028	3.081
msviperCombinatorial	8.942	0.027	8.968
msviperSynergy	11.575	0.072	11.649
plot.msviper	6.708	0.036	6.744
pruneRegulon	1.208	0.012	1.220
rowTtest-methods	2.351	0.040	2.391
scaleGroups	1.622	0.012	1.634
shadow	16.127	0.076	16.203
signatureDistance	2.557	0.020	2.590
ttestNull-methods	5.198	0.024	5.224
viper	8.810	0.016	8.833
viperRPT	10.414	0.041	10.455
viperSignature-methods	21.942	0.043	21.994
viperSimilarity	2.246	0.024	2.278