Package: viper

Version: 1.18.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:viper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings viper_1.18.1.tar.gz

StartedAt: 2019-10-16 07:41:56 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:48:36 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 400.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: viper.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:viper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings viper_1.18.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/viper.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
viperSignature-methods 33.797 13.172  46.983
bootstrapViper         35.009  5.186  40.331
shadow                 24.540  6.807  31.373
msviperSynergy         17.467  4.537  22.027
msviperCombinatorial   14.241  3.857  18.137
plot.msviper           13.254  3.821  17.104
viperRPT               12.093  4.046  16.149
msviper                12.215  3.445  15.677
viper                  11.265  4.305  15.574
bootstrapmsviper        9.203  3.249  12.465
ttestNull-methods       6.787  2.489   9.287
bootstrapTtest-methods  6.046  1.701   7.983
ledge                   6.154  0.815   7.173
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/viper.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL viper
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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	0.153	0.012	0.165
aracne2regulon	3.697	0.843	4.544
aracne2regulon4cnv	3.081	0.769	3.850
bootstrapTtest-methods	6.046	1.701	7.983
bootstrapViper	35.009	5.186	40.331
bootstrapmsviper	9.203	3.249	12.465
distMode	1.437	0.094	1.532
fcvarna	1.321	0.071	1.392
filterCV-methods	1.397	0.082	1.479
frcv	1.449	0.086	1.615
frvarna	1.405	0.078	1.547
integrateSignatures	2.814	0.815	3.700
ledge	6.154	0.815	7.173
msviper	12.215	3.445	15.677
msviperAnnot	3.843	0.346	4.191
msviperClass	3.489	0.239	3.731
msviperCombinatorial	14.241	3.857	18.137
msviperSynergy	17.467	4.537	22.027
plot.msviper	13.254	3.821	17.104
pruneRegulon	1.505	0.091	1.597
rowTtest-methods	2.749	0.158	2.908
scaleGroups	1.392	0.108	1.500
shadow	24.540	6.807	31.373
signatureDistance	3.089	0.370	3.459
ttestNull-methods	6.787	2.489	9.287
viper	11.265	4.305	15.574
viperRPT	12.093	4.046	16.149
viperSignature-methods	33.797	13.172	46.983
viperSimilarity	2.936	0.347	3.288