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BioC 3.4: CHECK report for viper on moscato1

This page was generated on 2016-09-21 03:45:42 -0700 (Wed, 21 Sep 2016).

Package 1240/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
viper 1.7.3
Mariano J Alvarez
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/viper
Last Changed Rev: 120590 / Revision: 121152
Last Changed Date: 2016-08-30 13:32:51 -0700 (Tue, 30 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: viper
Version: 1.7.3
Command: rm -rf viper.buildbin-libdir viper.Rcheck && mkdir viper.buildbin-libdir viper.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=viper.buildbin-libdir viper_1.7.3.tar.gz >viper.Rcheck\00install.out 2>&1 && cp viper.Rcheck\00install.out viper-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=viper.buildbin-libdir --install="check:viper-install.out" --force-multiarch --no-vignettes --timings viper_1.7.3.tar.gz
StartedAt: 2016-09-20 18:09:38 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 18:17:53 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 494.7 seconds
RetCode: 0
Status:  OK  
CheckDir: viper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf viper.buildbin-libdir viper.Rcheck && mkdir viper.buildbin-libdir viper.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=viper.buildbin-libdir viper_1.7.3.tar.gz >viper.Rcheck\00install.out 2>&1 && cp viper.Rcheck\00install.out viper-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=viper.buildbin-libdir --install="check:viper-install.out" --force-multiarch --no-vignettes --timings viper_1.7.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/viper.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.7.3'
* 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 : 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>: no visible global function definition for
  'qnorm'
bootstrapViper: no visible global function definition for
  'txtProgressBar'
bootstrapViper : <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: no visible global function definition for 'txtProgressBar'
viper : <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
  'combn'
viperSignature,matrix: no visible global function definition for
  'txtProgressBar'
viperSignature,matrix : <anonymous>: no visible global function
  definition for 'setTxtProgressBar'
Undefined global functions or variables:
  abline 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", "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 ... OK
* 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
viperSignature-methods 41.11   0.10   41.20
bootstrapViper         29.08   2.28   31.39
shadow                 18.69   0.12   18.82
msviperSynergy         12.37   0.15   12.53
msviperCombinatorial   11.51   0.03   11.54
viperRPT               11.11   0.08   11.18
viper                  10.76   0.06   10.82
plot.msviper           10.41   0.00   10.40
msviper                 9.49   0.10    9.58
ledge                   8.49   0.07    8.58
bootstrapmsviper        8.30   0.11    8.41
ttestNull-methods       6.82   0.01    6.90
bootstrapTtest-methods  6.10   0.04    6.20
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
viperSignature-methods 36.41   0.11   36.62
bootstrapViper         26.76   1.09   27.84
shadow                 19.49   0.08   19.58
msviperSynergy         12.26   0.21   12.46
viperRPT               12.17   0.06   12.23
msviperCombinatorial   10.84   0.09   10.94
viper                  10.17   0.08   10.25
plot.msviper            9.31   0.08    9.40
msviper                 9.19   0.06    9.25
bootstrapmsviper        6.94   0.13    7.07
ledge                   6.77   0.02    6.79
ttestNull-methods       6.19   0.06    6.25
bootstrapTtest-methods  5.52   0.09    5.64
* 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 NOTEs
See
  'D:/biocbld/bbs-3.4-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_1.7.3.zip
* DONE (viper)

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

nameusersystemelapsed
approxk2d0.140.000.14
aracne2regulon3.460.053.87
aracne2regulon4cnv3.140.003.14
bootstrapTtest-methods6.100.046.20
bootstrapViper29.08 2.2831.39
bootstrapmsviper8.300.118.41
distMode1.420.001.42
fcvarna1.400.021.42
filterCV-methods1.530.011.54
frcv1.450.001.46
frvarna1.400.061.46
integrateSignatures3.000.043.03
ledge8.490.078.58
msviper9.490.109.58
msviperAnnot4.390.034.42
msviperClass2.650.032.70
msviperCombinatorial11.51 0.0311.54
msviperSynergy12.37 0.1512.53
plot.msviper10.41 0.0010.40
pruneRegulon1.730.051.78
rowTtest-methods2.930.032.97
scaleGroups1.480.021.49
shadow18.69 0.1218.82
signatureDistance4.760.024.77
ttestNull-methods6.820.016.90
viper10.76 0.0610.82
viperRPT11.11 0.0811.18
viperSignature-methods41.11 0.1041.20
viperSimilarity2.800.002.81

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

nameusersystemelapsed
approxk2d0.190.020.21
aracne2regulon3.370.093.46
aracne2regulon4cnv3.010.023.02
bootstrapTtest-methods5.520.095.64
bootstrapViper26.76 1.0927.84
bootstrapmsviper6.940.137.07
distMode1.310.011.33
fcvarna1.200.031.23
filterCV-methods1.310.031.34
frcv1.330.001.33
frvarna1.280.001.28
integrateSignatures2.750.052.79
ledge6.770.026.79
msviper9.190.069.25
msviperAnnot3.630.063.70
msviperClass2.670.002.66
msviperCombinatorial10.84 0.0910.94
msviperSynergy12.26 0.2112.46
plot.msviper9.310.089.40
pruneRegulon1.360.011.37
rowTtest-methods2.590.052.64
scaleGroups1.340.031.37
shadow19.49 0.0819.58
signatureDistance3.980.064.04
ttestNull-methods6.190.066.25
viper10.17 0.0810.25
viperRPT12.17 0.0612.23
viperSignature-methods36.41 0.1136.62
viperSimilarity2.540.022.55