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CHECK report for viper on tokay1

This page was generated on 2019-04-13 11:23:42 -0400 (Sat, 13 Apr 2019).

Package 1624/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
viper 1.16.0
Mariano J Alvarez
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/viper
Branch: RELEASE_3_8
Last Commit: c95d6fe
Last Changed Date: 2018-10-30 11:41:53 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: viper
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:viper.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings viper_1.16.0.tar.gz
StartedAt: 2019-04-13 06:09:45 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 06:18:17 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 512.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: viper.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:viper.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings viper_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/viper.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'knots'
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 global function definition for 'knots'
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 fisher.test
  grid hsv image knots layout lines lm mad median p.adjust par plot
  pnorm predict pt punif qnorm quantile residuals rgb2hsv runif
  setTxtProgressBar smooth.spline text 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
bootstrapViper         17.76   3.30   21.06
viperSignature-methods 20.29   0.07   20.37
shadow                 14.05   0.11   14.16
msviperSynergy          9.79   0.31   10.11
viperRPT                8.58   0.07    8.64
msviperCombinatorial    8.35   0.22    8.57
msviper                 7.33   0.03    7.36
plot.msviper            6.94   0.05    6.98
viper                   6.96   0.01    6.98
ttestNull-methods       6.82   0.11    6.92
bootstrapTtest-methods  6.13   0.12    6.25
bootstrapmsviper        5.41   0.22    5.62
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
bootstrapViper         18.94   3.33   22.26
shadow                 20.80   0.28   21.08
viperSignature-methods 18.23   0.17   18.41
msviperSynergy         10.90   0.50   11.40
msviperCombinatorial   10.94   0.12   11.06
msviper                10.75   0.13   10.87
viperRPT                8.91   0.03    8.93
plot.msviper            8.66   0.09   11.50
viper                   8.11   0.06    8.18
ledge                   6.14   0.03    6.17
bootstrapmsviper        5.89   0.25    6.14
ttestNull-methods       5.42   0.11    5.53
bootstrapTtest-methods  5.25   0.09    5.35
* 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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/viper.Rcheck/00check.log'
for details.

Installation output

viper.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/viper_1.16.0.tar.gz && rm -rf viper.buildbin-libdir && mkdir viper.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=viper.buildbin-libdir viper_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL viper_1.16.0.zip && rm viper_1.16.0.tar.gz viper_1.16.0.zip
###
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##############################################################################


  % 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 58414  100 58414    0     0  1674k      0 --:--:-- --:--:-- --:--:-- 1840k

install for i386

* installing *source* package 'viper' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'viper' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'viper' as viper_1.16.0.zip
* DONE (viper)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'viper' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

viper.Rcheck/examples_i386/viper-Ex.timings

nameusersystemelapsed
approxk2d0.080.000.08
aracne2regulon3.550.123.78
aracne2regulon4cnv3.220.073.28
bootstrapTtest-methods6.130.126.25
bootstrapViper17.76 3.3021.06
bootstrapmsviper5.410.225.62
distMode1.470.041.52
fcvarna1.50.01.5
filterCV-methods1.510.081.59
frcv1.500.031.54
frvarna1.490.031.51
integrateSignatures2.440.052.49
ledge4.780.054.82
msviper7.330.037.36
msviperAnnot2.930.063.00
msviperClass2.390.002.39
msviperCombinatorial8.350.228.57
msviperSynergy 9.79 0.3110.11
plot.msviper6.940.056.98
pruneRegulon1.550.021.58
rowTtest-methods3.220.003.22
scaleGroups1.560.031.59
shadow14.05 0.1114.16
signatureDistance3.150.063.22
ttestNull-methods6.820.116.92
viper6.960.016.98
viperRPT8.580.078.64
viperSignature-methods20.29 0.0720.37
viperSimilarity2.490.022.50

viper.Rcheck/examples_x64/viper-Ex.timings

nameusersystemelapsed
approxk2d0.060.020.08
aracne2regulon3.000.083.08
aracne2regulon4cnv2.960.063.03
bootstrapTtest-methods5.250.095.35
bootstrapViper18.94 3.3322.26
bootstrapmsviper5.890.256.14
distMode1.420.001.43
fcvarna1.220.031.25
filterCV-methods1.530.031.56
frcv1.270.021.28
frvarna1.270.061.33
integrateSignatures2.500.082.58
ledge6.140.036.17
msviper10.75 0.1310.87
msviperAnnot4.290.064.36
msviperClass2.830.022.85
msviperCombinatorial10.94 0.1211.06
msviperSynergy10.9 0.511.4
plot.msviper 8.66 0.0911.50
pruneRegulon1.250.042.91
rowTtest-methods2.640.072.72
scaleGroups1.310.001.31
shadow20.80 0.2821.08
signatureDistance2.230.052.28
ttestNull-methods5.420.115.53
viper8.110.068.18
viperRPT8.910.038.93
viperSignature-methods18.23 0.1718.41
viperSimilarity2.240.032.27