Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-10-13 11:40:57 -0400 (Fri, 13 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4679
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4414
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4433
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4419
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 2208/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
viper 1.35.0  (landing page)
Mariano J Alvarez
Snapshot Date: 2023-10-12 14:05:06 -0400 (Thu, 12 Oct 2023)
git_url: https://git.bioconductor.org/packages/viper
git_branch: devel
git_last_commit: 8ac1760
git_last_commit_date: 2023-04-25 10:31:05 -0400 (Tue, 25 Apr 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.3.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for viper on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: viper
Version: 1.35.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:viper.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings viper_1.35.0.tar.gz
StartedAt: 2023-10-13 13:58:48 -0000 (Fri, 13 Oct 2023)
EndedAt: 2023-10-13 14:16:07 -0000 (Fri, 13 Oct 2023)
EllapsedTime: 1038.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: viper.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:viper.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings viper_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/viper.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘viper/DESCRIPTION’ ... OK
* this is package ‘viper’ version ‘1.35.0’
* 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 R 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 loading without being on the library search path ... 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 documentation object 'viper'
  ‘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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
bootstrapViper         41.022  0.303  41.398
viperSignature-methods 28.644  0.079  28.778
shadow                 19.526  0.068  19.633
msviperSynergy         14.122  0.084  14.235
msviperCombinatorial   11.251  0.107  11.382
viperRPT               10.831  0.035  10.885
plot.msviper           10.176  0.040  10.237
msviper                 9.980  0.076  10.077
viper                   9.638  0.052   9.708
bootstrapmsviper        8.124  0.056   8.197
ttestNull-methods       7.632  0.040   7.690
bootstrapTtest-methods  7.297  0.088   7.397
ledge                   5.407  0.020   5.437
aracne2regulon          5.289  0.120   5.442
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘viper.Rnw’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/viper.Rcheck/00check.log’
for details.



Installation output

viper.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL viper
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-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
approxk2d0.1030.0000.103
aracne2regulon5.2890.1205.442
aracne2regulon4cnv4.7290.0644.800
bootstrapTtest-methods7.2970.0887.397
bootstrapViper41.022 0.30341.398
bootstrapmsviper8.1240.0568.197
distMode0.9630.0080.972
fcvarna0.9280.0160.945
filterCV-methods0.9630.0080.973
frcv0.9410.0080.950
frvarna0.9370.0040.942
integrateSignatures3.0290.0363.070
ledge5.4070.0205.437
msviper 9.980 0.07610.077
msviperAnnot3.1300.0203.154
msviperClass2.2910.0282.323
msviperCombinatorial11.251 0.10711.382
msviperSynergy14.122 0.08414.235
plot.msviper10.176 0.04010.237
pruneRegulon1.0080.0121.022
rowTtest-methods1.9100.0161.930
scaleGroups1.0470.0161.064
shadow19.526 0.06819.633
signatureDistance3.3800.0083.393
ttestNull-methods7.6320.0407.690
viper9.6380.0529.708
viperRPT10.831 0.03510.885
viperSignature-methods28.644 0.07928.778
viperSimilarity3.6540.0123.671