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This page was generated on 2025-07-26 12:10 -0400 (Sat, 26 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4795
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4534
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4577
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4518
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4512
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 2130/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
systemPipeTools 1.17.0  (landing page)
Daniela Cassol
Snapshot Date: 2025-07-25 13:25 -0400 (Fri, 25 Jul 2025)
git_url: https://git.bioconductor.org/packages/systemPipeTools
git_branch: devel
git_last_commit: 83b911f
git_last_commit_date: 2025-04-15 12:33:06 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for systemPipeTools on lconway

To the developers/maintainers of the systemPipeTools package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/systemPipeTools.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: systemPipeTools
Version: 1.17.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:systemPipeTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings systemPipeTools_1.17.0.tar.gz
StartedAt: 2025-07-26 00:03:47 -0400 (Sat, 26 Jul 2025)
EndedAt: 2025-07-26 00:08:40 -0400 (Sat, 26 Jul 2025)
EllapsedTime: 293.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: systemPipeTools.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:systemPipeTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings systemPipeTools_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/systemPipeTools.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 ‘systemPipeTools/DESCRIPTION’ ... OK
* this is package ‘systemPipeTools’ version ‘1.17.0’
* 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 ‘systemPipeTools’ 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 ... WARNING
Missing or unexported object: ‘BiocGenerics::rowSums’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
heatMaplot     12.519  0.120  12.720
volcanoplot     9.678  0.060   9.818
MAplot          9.650  0.058   9.746
exploreDDSplot  8.394  0.040   8.467
GLMplot         6.602  0.232   6.870
* 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/systemPipeTools.Rcheck/00check.log’
for details.


Installation output

systemPipeTools.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘systemPipeTools’ ...
** this is package ‘systemPipeTools’ version ‘1.17.0’
** using staged installation
** R
** 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 (systemPipeTools)

Tests output

systemPipeTools.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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(systemPipeTools)
> 
> test_check("systemPipeTools")
using ntop=500 top features by variance
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 14 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
 34.399   1.145  35.737 

Example timings

systemPipeTools.Rcheck/systemPipeTools-Ex.timings

nameusersystemelapsed
GLMplot6.6020.2326.870
MAplot9.6500.0589.746
MDSplot3.3410.0193.373
PCAplot3.2210.0513.285
exploreDDS2.1090.0132.131
exploreDDSplot8.3940.0408.467
hclustplot3.4540.0213.492
heatMaplot12.519 0.12012.720
showDT0.0780.0310.111
tSNEplot0.2020.0040.208
volcanoplot9.6780.0609.818