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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1546/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhosR 1.16.0  (landing page)
Taiyun Kim
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/PhosR
git_branch: RELEASE_3_20
git_last_commit: 400b0f0
git_last_commit_date: 2024-10-29 10:50:46 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 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 PhosR on merida1

To the developers/maintainers of the PhosR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PhosR.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: PhosR
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PhosR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PhosR_1.16.0.tar.gz
StartedAt: 2024-12-20 07:37:06 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 07:50:40 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 813.7 seconds
RetCode: 0
Status:   OK  
CheckDir: PhosR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PhosR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PhosR_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PhosR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PhosR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PhosR’ version ‘1.16.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PhosR’ 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::replaceSlots’ ‘S4Vectors:::disableValidity’
  ‘SummarizedExperiment:::.SummarizedExperiment.charbound’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
abundPlot: no visible binding for global variable ‘.’
Undefined global functions or variables:
  .
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
kinaseSubstratePred    70.059  0.714  76.816
siteAnnotate           70.180  0.499  71.844
kinaseSubstrateScore   49.769  0.406  54.112
minmax                 49.644  0.471  52.786
standardise            26.652  0.122  27.242
matANOVA               26.581  0.096  27.833
kinaseSubstrateProfile 26.446  0.156  29.054
plotQC                 10.621  0.115  11.242
getSPS                  5.324  0.223   5.625
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/PhosR.Rcheck/00check.log’
for details.


Installation output

PhosR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘PhosR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (PhosR)

Tests output

PhosR.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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(PhosR)
> 
> test_check("PhosR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 58 ]
> 
> proc.time()
   user  system elapsed 
 18.090   1.051  19.745 

Example timings

PhosR.Rcheck/PhosR-Ex.timings

nameusersystemelapsed
PhosphoExperiment-methods0.6750.0210.707
PhosphoExperiment-operate0.9870.0271.064
PhosphoExperiment0.5490.0060.561
RUVphospho0.4460.0110.460
Signalomes0.0000.0010.001
createFrequencyMat0.1660.0050.172
frequencyScoring0.7100.0370.772
getSPS5.3240.2235.625
kinaseSubstrateHeatmap0.0000.0010.001
kinaseSubstratePred70.059 0.71476.816
kinaseSubstrateProfile26.446 0.15629.054
kinaseSubstrateScore49.769 0.40654.112
mIntersect3.2680.0283.479
matANOVA26.581 0.09627.833
meanAbundance0.5090.0150.548
medianScaling0.7230.0130.746
minmax49.644 0.47152.786
pathwayOverrepresent0.0000.0000.001
pathwayRankBasedEnrichment0.0000.0000.001
phosCollapse2.2190.0252.314
plotQC10.621 0.11511.242
ptImpute0.6550.0050.660
scImpute1.3960.0141.412
selectGrps0.1700.0060.177
selectLocalisedSites0.1120.0050.117
selectOverallPercent0.0580.0040.061
selectTimes0.0140.0040.017
siteAnnotate70.180 0.49971.844
standardise26.652 0.12227.242
tImpute0.2650.0080.286