Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLMNOPQRSTU[V]WXYZ

This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 2204/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
vissE 1.13.0  (landing page)
Dharmesh D. Bhuva
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/vissE
git_branch: devel
git_last_commit: 418c085
git_last_commit_date: 2024-04-30 11:34:37 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for vissE on merida1

To the developers/maintainers of the vissE package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/vissE.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: vissE
Version: 1.13.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:vissE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings vissE_1.13.0.tar.gz
StartedAt: 2024-06-10 11:44:15 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 11:48:08 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 233.4 seconds
RetCode: 0
Status:   OK  
CheckDir: vissE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:vissE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings vissE_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/vissE.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 ‘vissE/DESCRIPTION’ ... OK
* this is package ‘vissE’ version ‘1.13.0’
* 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 ‘vissE’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
checkGroups: no visible global function definition for ‘na.omit’
plotGeneStats: no visible binding for global variable ‘Count’
plotGeneStats: no visible binding for global variable ‘GeneStat’
plotGeneStats: no visible binding for global variable ‘Gene’
plotMsigNetwork: no visible binding for global variable ‘Size’
plotMsigNetwork: no visible binding for global variable ‘Category’
plotMsigNetwork: no visible binding for global variable ‘x’
plotMsigNetwork: no visible binding for global variable ‘y’
plotMsigNetwork: no visible binding for global variable ‘NodeGroup’
plotMsigPPI: no visible binding for global variable ‘weight’
plotMsigPPI: no visible binding for global variable ‘Degree’
plotMsigPPI: no visible binding for global variable ‘label’
plotMsigPPI: no visible binding for global variable ‘Label’
plotMsigWordcloud: no visible binding for global variable ‘word’
plotMsigWordcloud: no visible binding for global variable ‘freq’
plotMsigWordcloud: no visible binding for global variable ‘angle’
Undefined global functions or variables:
  Category Count Degree Gene GeneStat Label NodeGroup Size angle freq
  label na.omit weight word x y
Consider adding
  importFrom("stats", "na.omit")
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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... NOTE
  'LazyDataCompression' is specified without 'LazyData'
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
plotMsigPPI         16.254  0.477  19.213
computeMsigWordFreq 13.630  2.076  17.894
plotMsigWordcloud   13.594  0.820  15.675
characteriseGeneset  8.528  0.405   9.594
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/vissE.Rcheck/00check.log’
for details.


Installation output

vissE.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘vissE’ ...
** using staged installation
** R
** data
** 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 (vissE)

Tests output

vissE.Rcheck/tests/testthat.Rout


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(vissE)
> 
> test_check("vissE")
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 63 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 63 ]
> 
> proc.time()
   user  system elapsed 
 57.427   3.608  64.784 

Example timings

vissE.Rcheck/vissE-Ex.timings

nameusersystemelapsed
bhuvad_theme0.2260.0120.247
characteriseGeneset8.5280.4059.594
computeMsigNetwork0.7370.0270.836
computeMsigOverlap0.0490.0060.061
computeMsigWordFreq13.630 2.07617.894
findMsigClusters0.0790.0070.099
getMsigExclusionList0.0010.0010.001
plotGeneStats1.7930.0471.996
plotMsigNetwork1.8750.1972.209
plotMsigPPI16.254 0.47719.213
plotMsigWordcloud13.594 0.82015.675