Multiple platform build/check report for BioC 3.20 - CHECK results for viper on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"	4672
palomino4	Windows Server 2022 Datacenter	x64	4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"	4407
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4434
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4387
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for viper on merida1

To the developers/maintainers of the viper package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/viper.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: 2024-06-06 11:30:57 -0400 (Thu, 06 Jun 2024)

EndedAt: 2024-06-06 11:38:34 -0400 (Thu, 06 Jun 2024)

EllapsedTime: 456.7 seconds

RetCode: 0

Status: WARNINGS

CheckDir: viper.Rcheck

Warnings: 1

Command output

##############################################################################
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###
### 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/meat/viper.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-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 Monterey 12.7.4
* 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 33.648  3.614  38.906
shadow                 24.748  1.593  27.010
bootstrapViper         24.852  1.423  27.347
msviperSynergy         17.128  0.936  18.765
msviperCombinatorial   14.848  0.623  16.131
msviper                13.175  0.600  14.464
plot.msviper           13.230  0.497  14.473
viperRPT               12.543  1.162  13.938
viper                  11.513  1.140  12.950
bootstrapmsviper        9.186  0.655  10.398
bootstrapTtest-methods  7.175  0.322   8.349
ledge                   7.187  0.289   7.876
ttestNull-methods       6.883  0.536   7.623
msviperAnnot            5.639  0.207   5.955
aracne2regulon          4.004  0.348   5.080
* 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/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-x86_64/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

name	user	system	elapsed
approxk2d	0.176	0.009	0.220
aracne2regulon	4.004	0.348	5.080
aracne2regulon4cnv	3.610	0.306	4.420
bootstrapTtest-methods	7.175	0.322	8.349
bootstrapViper	24.852	1.423	27.347
bootstrapmsviper	9.186	0.655	10.398
distMode	1.668	0.041	1.822
fcvarna	1.644	0.041	1.775
filterCV-methods	1.704	0.047	1.818
frcv	1.635	0.046	1.733
frvarna	1.640	0.052	1.806
integrateSignatures	3.025	0.165	3.356
ledge	7.187	0.289	7.876
msviper	13.175	0.600	14.464
msviperAnnot	5.639	0.207	5.955
msviperClass	4.237	0.204	4.706
msviperCombinatorial	14.848	0.623	16.131
msviperSynergy	17.128	0.936	18.765
plot.msviper	13.230	0.497	14.473
pruneRegulon	1.747	0.036	1.805
rowTtest-methods	3.257	0.058	3.342
scaleGroups	1.685	0.032	1.790
shadow	24.748	1.593	27.010
signatureDistance	3.477	0.149	3.684
ttestNull-methods	6.883	0.536	7.623
viper	11.513	1.140	12.950
viperRPT	12.543	1.162	13.938
viperSignature-methods	33.648	3.614	38.906
viperSimilarity	3.093	0.107	3.348