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This page was generated on 2024-05-20 11:32:23 -0400 (Mon, 20 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4381
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Package 2196/2233HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
viper 1.39.0  (landing page)
Mariano J Alvarez
Snapshot Date: 2024-05-18 09:00:01 -0400 (Sat, 18 May 2024)
git_url: https://git.bioconductor.org/packages/viper
git_branch: devel
git_last_commit: d2d0de2
git_last_commit_date: 2024-04-30 10:35:42 -0400 (Tue, 30 Apr 2024)
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for viper on kjohnson1


To the developers/maintainers of the viper package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: viper
Version: 1.39.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:viper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings viper_1.39.0.tar.gz
StartedAt: 2024-05-20 06:16:30 -0400 (Mon, 20 May 2024)
EndedAt: 2024-05-20 06:20:55 -0400 (Mon, 20 May 2024)
EllapsedTime: 264.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: viper.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:viper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings viper_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/viper.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘viper/DESCRIPTION’ ... OK
* this is package ‘viper’ version ‘1.39.0’
* 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 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 code 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 : <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 ‘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 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", "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 Rd file 'viper.Rd'
  ‘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 (user + system) or elapsed time > 5s
                         user system elapsed
viperSignature-methods 21.563  3.886  25.638
bootstrapViper         13.973  2.038  16.341
shadow                 13.274  1.562  14.924
msviperSynergy          9.646  0.963  10.744
viperRPT                8.516  1.302   9.931
viper                   7.589  1.164   8.895
msviperCombinatorial    7.694  0.794   8.611
plot.msviper            7.353  0.569   7.953
msviper                 7.102  0.805   7.951
ttestNull-methods       5.842  0.564   6.455
bootstrapmsviper        5.504  0.784   6.312
ledge                   5.525  0.307   5.879
bootstrapTtest-methods  5.084  0.222   5.471
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/viper.Rcheck/00check.log’
for details.


Installation output

viper.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL viper
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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)

Tests output


Example timings

viper.Rcheck/viper-Ex.timings

nameusersystemelapsed
approxk2d0.0830.0040.086
aracne2regulon3.4250.2083.704
aracne2regulon4cnv2.9890.3043.413
bootstrapTtest-methods5.0840.2225.471
bootstrapViper13.973 2.03816.341
bootstrapmsviper5.5040.7846.312
distMode1.7570.0231.785
fcvarna1.7210.0211.746
filterCV-methods1.7540.0261.788
frcv1.7220.0231.760
frvarna1.7770.0221.809
integrateSignatures2.5420.1762.725
ledge5.5250.3075.879
msviper7.1020.8057.951
msviperAnnot3.2240.1803.427
msviperClass3.0000.2173.241
msviperCombinatorial7.6940.7948.611
msviperSynergy 9.646 0.96310.744
plot.msviper7.3530.5697.953
pruneRegulon1.7970.0231.824
rowTtest-methods3.4580.0423.508
scaleGroups1.7850.0431.844
shadow13.274 1.56214.924
signatureDistance2.6750.1272.823
ttestNull-methods5.8420.5646.455
viper7.5891.1648.895
viperRPT8.5161.3029.931
viperSignature-methods21.563 3.88625.638
viperSimilarity3.1870.1193.320