Package: viper

Version: 1.20.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:viper.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings viper_1.20.0.tar.gz

StartedAt: 2020-04-15 07:22:41 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 07:30:32 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 471.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: viper.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:viper.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings viper_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/viper.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'viper/DESCRIPTION' ... OK
* this is package 'viper' version '1.20.0'
* package encoding: UTF-8
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 : <anonymous>: no visible global function definition for
  'pnorm'
aREA: no visible global function definition for 'qnorm'
aREA: no visible global function definition for 'txtProgressBar'
aREA : <anonymous>: 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 : <anonymous> : <anonymous>: no visible global function
  definition for 'qnorm'
bootstrapViper : <anonymous>: no visible global function definition for
  'txtProgressBar'
bootstrapViper : <anonymous> : <anonymous>: 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 : <anonymous>: no visible global function definition for
  'setTxtProgressBar'
groupPwea3 : <anonymous>: no visible global function definition for
  'qnorm'
groupPwea3: no visible global function definition for 'pnorm'
msviper: no visible global function definition for 'txtProgressBar'
msviper : <anonymous>: 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 : <anonymous>: no visible global function definition for
  'qnorm'
msviperSynergy : <anonymous>: no visible global function definition for
  'quantile'
msviperSynergy : <anonymous>: no visible global function definition for
  'ecdf'
msviperSynergy : <anonymous>: no visible global function definition for
  'knots'
msviperSynergy : <anonymous>: no visible global function definition for
  'smooth.spline'
msviperSynergy : <anonymous>: no visible global function definition for
  'predict'
msviperSynergy: no visible global function definition for
  'txtProgressBar'
msviperSynergy : <anonymous>: 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 : <anonymous> : <anonymous>: no visible global function
  definition for 'pnorm'
pwea3NULLf : <anonymous>: no visible global function definition for
  'quantile'
pwea3NULLf : <anonymous>: no visible global function definition for
  'ecdf'
pwea3NULLf : <anonymous>: no visible global function definition for
  'knots'
pwea3NULLf : <anonymous>: no visible global function definition for
  'smooth.spline'
pwea3NULLf : <anonymous> : <anonymous>: no visible global function
  definition for 'predict'
pwea3NULLf : <anonymous> : <anonymous>: no visible global function
  definition for 'qnorm'
pwea3NULLf: no visible global function definition for 'txtProgressBar'
pwea3NULLf : <anonymous>: no visible global function definition for
  'setTxtProgressBar'
pwea3NULLgroups: no visible global function definition for 'qnorm'
pwea3NULLgroups: no visible global function definition for
  'txtProgressBar'
pwea3NULLgroups : <anonymous>: no visible global function definition
  for 'setTxtProgressBar'
regulonDist : <anonymous>: no visible global function definition for
  'fisher.test'
scaleGroups : <anonymous>: no visible global function definition for
  'qnorm'
scaleGroups: no visible global function definition for 'runif'
selectTFs : <anonymous>: no visible global function definition for
  'combn'
shadow: no visible global function definition for 'combn'
shadow : <anonymous>: no visible global function definition for
  'quantile'
shadow : <anonymous>: no visible global function definition for 'ecdf'
shadow : <anonymous>: no visible global function definition for 'knots'
shadow : <anonymous>: no visible global function definition for
  'smooth.spline'
shadow : <anonymous>: no visible global function definition for
  'predict'
shadow: no visible global function definition for 'txtProgressBar'
shadow : <anonymous>: no visible global function definition for
  'setTxtProgressBar'
shadowRegulon: no visible global function definition for 'pnorm'
shadowRegulon : <anonymous>: no visible global function definition for
  'qnorm'
shadowRegulon : <anonymous>: 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 : <anonymous>: no visible global function definition for 'median'
viper : <anonymous>: no visible global function definition for 'mad'
viper : <anonymous>: no visible global function definition for
  'txtProgressBar'
viper : <anonymous> : <anonymous>: no visible global function
  definition for 'setTxtProgressBar'
viperRPT : <anonymous>: no visible global function definition for
  'residuals'
viperRPT : <anonymous>: no visible global function definition for 'lm'
viperRPT : <anonymous>: no visible global function definition for
  'smooth.spline'
viperSimilarity: no visible global function definition for 'qnorm'
bootstrapTtest,matrix : <anonymous>: no visible global function
  definition for 'qnorm'
bootstrapTtest,matrix : <anonymous>: no visible global function
  definition for 'pt'
bootstrapTtest,matrix: no visible global function definition for
  'txtProgressBar'
bootstrapTtest,matrix : <anonymous>: no visible global function
  definition for 'setTxtProgressBar'
rowTtest,matrix: no visible global function definition for 'pt'
ttestNull,matrix : <anonymous>: no visible global function definition
  for 'qnorm'
ttestNull,matrix : <anonymous>: no visible global function definition
  for 'pt'
ttestNull,matrix: no visible global function definition for
  'txtProgressBar'
ttestNull,matrix : <anonymous>: no visible global function definition
  for 'setTxtProgressBar'
viperSignature,matrix : <anonymous>: no visible global function
  definition for 'qnorm'
viperSignature,matrix: no visible global function definition for
  'txtProgressBar'
viperSignature,matrix : <anonymous> : <anonymous>: no visible global
  function definition for 'qnorm'
viperSignature,matrix : <anonymous>: 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 ... OK
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
bootstrapViper         24.42   4.58   29.13
viperSignature-methods 23.45   0.13   23.58
shadow                 15.44   0.12   15.57
msviperSynergy          9.49   0.23    9.72
msviperCombinatorial    9.34   0.05    9.39
viperRPT                8.94   0.03    8.96
bootstrapmsviper        8.36   0.42    8.79
msviper                 8.25   0.11    8.35
bootstrapTtest-methods  7.98   0.05    8.03
viper                   7.86   0.07    7.92
ttestNull-methods       6.97   0.06    7.03
plot.msviper            6.84   0.07    6.91
ledge                   5.87   0.06    5.96
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
bootstrapViper         18.28   3.84   22.12
viperSignature-methods 19.22   0.29   19.50
shadow                 17.11   0.22   18.08
msviperSynergy         11.71   0.65   12.34
msviper                10.55   0.18   10.73
plot.msviper           10.29   0.09   10.45
msviperCombinatorial    9.67   0.15    9.83
viperRPT                9.30   0.03    9.33
viper                   6.27   0.06    6.33
bootstrapTtest-methods  5.84   0.10    5.94
bootstrapmsviper        5.38   0.17    5.55
ledge                   5.51   0.02    5.53
ttestNull-methods       5.18   0.12    5.31
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/viper.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/viper_1.20.0.tar.gz && rm -rf viper.buildbin-libdir && mkdir viper.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=viper.buildbin-libdir viper_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL viper_1.20.0.zip && rm viper_1.20.0.tar.gz viper_1.20.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 58758  100 58758    0     0  1663k      0 --:--:-- --:--:-- --:--:-- 1912k

install for i386

* installing *source* package 'viper' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'viper'
    finding HTML links ... done
    aREA                                    html  
    aecdf                                   html  
    approxk2d                               html  
    aracne2regulon                          html  
    aracne2regulon4cnv                      html  
    as.dist.signatureDistance               html  
    bootstrapTtest-methods                  html  
    bootstrapViper                          html  
    bootstrapmsviper                        html  
    comNames                                html  
    distMode                                html  
    fcvarna                                 html  
    filterCV-methods                        html  
    filterColMatrix                         html  
    filterRowMatrix                         html  
    frcv                                    html  
    frvarna                                 html  
    groupPwea3                              html  
    integrateSignatures                     html  
    ledge                                   html  
    loadExpset                              html  
    msviper-class                           html  
    msviper                                 html  
    msviperAnnot                            html  
    msviperClass                            html  
    msviperCombinatorial                    html  
    msviperSynergy                          html  
    plot.msviper                            html  
    pruneRegulon                            html  
    pwea3NULLf                              html  
    pwea3NULLgroups                         html  
    regulon-class                           html  
    rowTtest-methods                        html  
    scale.signatureDistance                 html  
    scaleGroups                             html  
    shadow                                  html  
    shadowRegulon                           html  
    sigT                                    html  
    signatureDistance-class                 html  
    signatureDistance                       html  
    summary.msviper                         html  
    ttestNull-methods                       html  
    viper                                   html  
    viperRPT                                html  
    viperSignature-class                    html  
    viperSignature-methods                  html  
    viperSimilarity                         html  
** 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

install for x64

* installing *source* package 'viper' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'viper' as viper_1.20.0.zip
* DONE (viper)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'viper' successfully unpacked and MD5 sums checked