Multiple platform build/check report for BioC 3.20 - CHECK results for viper on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4764
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4495
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4522
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4449
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4426
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 kjohnson1

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: 1.40.0

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_1.40.0.tar.gz

StartedAt: 2025-04-02 12:32:57 -0400 (Wed, 02 Apr 2025)

EndedAt: 2025-04-02 12:37:14 -0400 (Wed, 02 Apr 2025)

EllapsedTime: 257.6 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_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/viper.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘viper/DESCRIPTION’ ... OK
* this is package ‘viper’ version ‘1.40.0’
* 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 21.057  4.140  25.473
bootstrapViper         14.257  2.306  16.671
shadow                 13.352  2.195  15.705
msviperSynergy         10.194  1.168  11.441
msviperCombinatorial    8.796  0.828   9.802
viperRPT                8.226  1.345   9.712
plot.msviper            7.342  0.965   8.377
viper                   6.682  1.418   8.357
ttestNull-methods       5.643  0.498   6.239
bootstrapTtest-methods  5.679  0.443   6.173
msviper                 4.735  0.301   5.146
* 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-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

name	user	system	elapsed
approxk2d	0.089	0.005	0.094
aracne2regulon	3.462	0.295	3.803
aracne2regulon4cnv	3.048	0.274	3.359
bootstrapTtest-methods	5.679	0.443	6.173
bootstrapViper	14.257	2.306	16.671
bootstrapmsviper	4.253	0.514	4.816
distMode	1.087	0.024	1.179
fcvarna	1.021	0.023	1.119
filterCV-methods	0.902	0.025	1.046
frcv	1.228	0.031	1.349
frvarna	1.459	0.028	1.519
integrateSignatures	1.504	0.097	1.625
ledge	4.323	0.268	4.646
msviper	4.735	0.301	5.146
msviperAnnot	2.401	0.136	2.565
msviperClass	1.894	0.069	2.000
msviperCombinatorial	8.796	0.828	9.802
msviperSynergy	10.194	1.168	11.441
plot.msviper	7.342	0.965	8.377
pruneRegulon	1.715	0.042	1.784
rowTtest-methods	3.254	0.059	3.345
scaleGroups	1.641	0.030	1.728
shadow	13.352	2.195	15.705
signatureDistance	2.865	0.159	3.039
ttestNull-methods	5.643	0.498	6.239
viper	6.682	1.418	8.357
viperRPT	8.226	1.345	9.712
viperSignature-methods	21.057	4.140	25.473
viperSimilarity	2.564	0.114	2.888