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BioC 3.5: CHECK report for viper on tokay2

This page was generated on 2017-08-16 13:23:07 -0400 (Wed, 16 Aug 2017).

Package 1362/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
viper 1.10.0
Mariano J Alvarez
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/viper
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 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
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: viper
Version: 1.10.0
Command: rm -rf viper.buildbin-libdir viper.Rcheck && mkdir viper.buildbin-libdir viper.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=viper.buildbin-libdir viper_1.10.0.tar.gz >viper.Rcheck\00install.out 2>&1 && cp viper.Rcheck\00install.out viper-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=viper.buildbin-libdir --install="check:viper-install.out" --force-multiarch --no-vignettes --timings viper_1.10.0.tar.gz
StartedAt: 2017-08-16 03:28:50 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 03:36:38 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 468.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: viper.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf viper.buildbin-libdir viper.Rcheck && mkdir viper.buildbin-libdir viper.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=viper.buildbin-libdir viper_1.10.0.tar.gz >viper.Rcheck\00install.out 2>&1 && cp viper.Rcheck\00install.out viper-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=viper.buildbin-libdir --install="check:viper-install.out" --force-multiarch --no-vignettes --timings viper_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/viper.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.10.0'
* 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 '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 ... 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 installed files from 'inst/doc' ... 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         20.64   3.43   24.06
viperSignature-methods 22.58   0.11   22.69
shadow                 14.28   0.21   14.49
msviper                11.70   0.04   11.75
msviperCombinatorial   10.65   0.08   10.74
msviperSynergy         10.21   0.23   10.44
viper                   9.22   0.05    9.27
viperRPT                8.68   0.04    8.73
bootstrapmsviper        7.94   0.28    8.22
plot.msviper            6.73   0.08    6.81
bootstrapTtest-methods  6.53   0.06    6.59
ledge                   5.83   0.06    5.89
ttestNull-methods       5.49   0.08    5.57
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
viperSignature-methods 25.99   0.26   26.25
bootstrapViper         17.50   3.34   20.85
msviperSynergy         17.86   0.56   18.43
shadow                 15.52   0.19   15.70
viperRPT               13.86   0.15   14.00
plot.msviper           10.32   0.09   10.42
msviperCombinatorial    9.97   0.05   10.01
viper                   9.67   0.10    9.78
bootstrapmsviper        7.21   0.22    7.45
msviper                 7.06   0.09    7.15
* 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-3.5-bioc/meat/viper.Rcheck/00check.log'
for details.

viper.Rcheck/00install.out:


install for i386

* installing *source* package 'viper' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'viper' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'viper' as viper_1.10.0.zip
* DONE (viper)

viper.Rcheck/examples_i386/viper-Ex.timings:

nameusersystemelapsed
approxk2d0.140.000.14
aracne2regulon4.400.084.60
aracne2regulon4cnv3.860.063.93
bootstrapTtest-methods6.530.066.59
bootstrapViper20.64 3.4324.06
bootstrapmsviper7.940.288.22
distMode1.800.031.83
fcvarna1.800.041.85
filterCV-methods1.940.082.01
frcv1.370.021.39
frvarna1.330.091.43
integrateSignatures2.390.052.43
ledge5.830.065.89
msviper11.70 0.0411.75
msviperAnnot3.030.043.06
msviperClass2.230.012.25
msviperCombinatorial10.65 0.0810.74
msviperSynergy10.21 0.2310.44
plot.msviper6.730.086.81
pruneRegulon1.690.021.70
rowTtest-methods2.860.012.88
scaleGroups1.410.031.43
shadow14.28 0.2114.49
signatureDistance2.40.02.4
ttestNull-methods5.490.085.57
viper9.220.059.27
viperRPT8.680.048.73
viperSignature-methods22.58 0.1122.69
viperSimilarity2.330.102.42

viper.Rcheck/examples_x64/viper-Ex.timings:

nameusersystemelapsed
approxk2d0.110.000.11
aracne2regulon3.420.023.44
aracne2regulon4cnv3.710.073.78
bootstrapTtest-methods4.430.054.48
bootstrapViper17.50 3.3420.85
bootstrapmsviper7.210.227.45
distMode1.430.021.45
fcvarna1.190.011.21
filterCV-methods1.240.041.26
frcv1.070.011.10
frvarna1.070.001.06
integrateSignatures1.720.101.81
ledge4.120.004.13
msviper7.060.097.15
msviperAnnot2.710.012.72
msviperClass2.140.052.19
msviperCombinatorial 9.97 0.0510.01
msviperSynergy17.86 0.5618.43
plot.msviper10.32 0.0910.42
pruneRegulon1.470.041.50
rowTtest-methods2.590.042.64
scaleGroups1.390.021.41
shadow15.52 0.1915.70
signatureDistance2.200.042.25
ttestNull-methods4.750.074.82
viper9.670.109.78
viperRPT13.86 0.1514.00
viperSignature-methods25.99 0.2626.25
viperSimilarity2.220.062.28