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This page was generated on 2024-06-15 12:33 -0400 (Sat, 15 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4685
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4400
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4349
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 1516/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhosR 1.15.0  (landing page)
Taiyun Kim
Snapshot Date: 2024-06-14 14:00 -0400 (Fri, 14 Jun 2024)
git_url: https://git.bioconductor.org/packages/PhosR
git_branch: devel
git_last_commit: 9a43a09
git_last_commit_date: 2024-04-30 11:27:23 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for PhosR on nebbiolo2

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: 1.15.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:PhosR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings PhosR_1.15.0.tar.gz
StartedAt: 2024-06-15 02:08:14 -0400 (Sat, 15 Jun 2024)
EndedAt: 2024-06-15 02:16:04 -0400 (Sat, 15 Jun 2024)
EllapsedTime: 469.9 seconds
RetCode: 0
Status:   OK  
CheckDir: PhosR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:PhosR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings PhosR_1.15.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/PhosR.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘PhosR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PhosR’ version ‘1.15.0’
* 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 loading without being on the library search path ... 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
siteAnnotate           26.176  0.168  26.344
kinaseSubstratePred    24.564  0.203  24.768
kinaseSubstrateScore   16.599  0.132  16.731
minmax                 16.441  0.035  16.477
matANOVA                9.134  0.099   9.234
standardise             9.048  0.032   9.079
kinaseSubstrateProfile  8.925  0.065   8.989
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/PhosR.Rcheck/00check.log’
for details.


Installation output

PhosR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL PhosR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  9.195   1.364  10.549 

Example timings

PhosR.Rcheck/PhosR-Ex.timings

nameusersystemelapsed
PhosphoExperiment-methods0.2830.0000.284
PhosphoExperiment-operate0.4090.0090.417
PhosphoExperiment0.2250.0000.225
RUVphospho0.1950.0040.200
Signalomes000
createFrequencyMat0.1100.0040.113
frequencyScoring0.2960.0040.300
getSPS2.1150.0922.206
kinaseSubstrateHeatmap0.0010.0000.000
kinaseSubstratePred24.564 0.20324.768
kinaseSubstrateProfile8.9250.0658.989
kinaseSubstrateScore16.599 0.13216.731
mIntersect0.9480.0160.964
matANOVA9.1340.0999.234
meanAbundance0.2420.0040.247
medianScaling0.2160.0040.220
minmax16.441 0.03516.477
pathwayOverrepresent000
pathwayRankBasedEnrichment000
phosCollapse0.7620.0240.787
plotQC3.7290.0323.762
ptImpute0.2070.0000.207
scImpute0.4810.0000.481
selectGrps0.1150.0000.115
selectLocalisedSites0.080.000.08
selectOverallPercent0.0430.0000.043
selectTimes0.0100.0000.009
siteAnnotate26.176 0.16826.344
standardise9.0480.0329.079
tImpute0.1460.0000.146