Mariano J Alvarez
| Snapshot Date: 2025-08-19 13:45 -0400 (Tue, 19 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/viper |
| git_branch: devel |
| git_last_commit: 710ec21 |
| git_last_commit_date: 2025-04-15 10:29:52 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-20 12:05 -0400 (Wed, 20 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4596 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4538 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4536 |
| 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 | ||||
| Package 2274/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| viper 1.43.0 (landing page) Mariano J Alvarez
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. |
| Package: viper |
| Version: 1.43.0 |
| 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_1.43.0.tar.gz |
| StartedAt: 2025-08-20 00:25:43 -0400 (Wed, 20 Aug 2025) |
| EndedAt: 2025-08-20 00:29:54 -0400 (Wed, 20 Aug 2025) |
| EllapsedTime: 251.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: viper.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### 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_1.43.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/viper.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘viper/DESCRIPTION’ ... OK
* this is package ‘viper’ version ‘1.43.0’
* 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 21.898 3.576 25.685
bootstrapViper 18.215 1.613 19.923
shadow 14.120 1.501 15.708
msviperSynergy 9.674 0.999 10.714
viperRPT 7.979 1.200 9.338
viper 7.789 1.298 9.150
msviperCombinatorial 8.226 0.787 9.099
msviper 7.111 0.705 7.853
plot.msviper 6.988 0.478 7.503
bootstrapmsviper 5.158 0.635 5.825
* 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-3.22-bioc/meat/viper.Rcheck/00check.log’
for details.
viper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL viper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘viper’ ... ** this is package ‘viper’ version ‘1.43.0’ ** 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)
viper.Rcheck/viper-Ex.timings
| name | user | system | elapsed | |
| approxk2d | 0.067 | 0.005 | 0.072 | |
| aracne2regulon | 2.165 | 0.315 | 2.492 | |
| aracne2regulon4cnv | 1.836 | 0.254 | 2.097 | |
| bootstrapTtest-methods | 3.613 | 0.436 | 4.072 | |
| bootstrapViper | 18.215 | 1.613 | 19.923 | |
| bootstrapmsviper | 5.158 | 0.635 | 5.825 | |
| distMode | 0.643 | 0.014 | 0.661 | |
| fcvarna | 0.701 | 0.017 | 0.725 | |
| filterCV-methods | 0.746 | 0.021 | 0.772 | |
| frcv | 0.679 | 0.018 | 0.701 | |
| frvarna | 0.683 | 0.021 | 0.708 | |
| integrateSignatures | 1.490 | 0.157 | 1.658 | |
| ledge | 3.720 | 0.275 | 4.018 | |
| msviper | 7.111 | 0.705 | 7.853 | |
| msviperAnnot | 2.331 | 0.201 | 2.546 | |
| msviperClass | 1.657 | 0.136 | 1.799 | |
| msviperCombinatorial | 8.226 | 0.787 | 9.099 | |
| msviperSynergy | 9.674 | 0.999 | 10.714 | |
| plot.msviper | 6.988 | 0.478 | 7.503 | |
| pruneRegulon | 0.745 | 0.017 | 0.768 | |
| rowTtest-methods | 1.360 | 0.029 | 1.404 | |
| scaleGroups | 0.712 | 0.013 | 0.730 | |
| shadow | 14.120 | 1.501 | 15.708 | |
| signatureDistance | 2.037 | 0.140 | 2.188 | |
| ttestNull-methods | 3.538 | 0.468 | 4.047 | |
| viper | 7.789 | 1.298 | 9.150 | |
| viperRPT | 7.979 | 1.200 | 9.338 | |
| viperSignature-methods | 21.898 | 3.576 | 25.685 | |
| viperSimilarity | 1.755 | 0.105 | 1.874 | |