Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2025-08-06 13:52 -0400 (Wed, 06 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4813
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 1560/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhosR 1.19.0  (landing page)
Taiyun Kim
Snapshot Date: 2025-08-05 13:25 -0400 (Tue, 05 Aug 2025)
git_url: https://git.bioconductor.org/packages/PhosR
git_branch: devel
git_last_commit: b93efd8
git_last_commit_date: 2025-04-15 12:09:35 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.1 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: 1.19.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:PhosR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings PhosR_1.19.0.tar.gz
StartedAt: 2025-08-06 01:24:41 -0400 (Wed, 06 Aug 2025)
EndedAt: 2025-08-06 01:33:11 -0400 (Wed, 06 Aug 2025)
EllapsedTime: 510.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: PhosR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:PhosR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings PhosR_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/PhosR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘PhosR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PhosR’ version ‘1.19.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  PhosphoExperiment-operate.Rd: SummarizedExperiment-class
  PhosphoExperiment.Rd: SummarizedExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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           26.419  0.188  26.607
kinaseSubstratePred    26.290  0.285  26.575
minmax                 16.631  0.046  16.677
kinaseSubstrateScore   16.579  0.067  16.646
kinaseSubstrateProfile 10.236  0.115  10.351
matANOVA                9.309  0.070   9.379
standardise             9.284  0.026   9.310
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(PhosR)
  > 
  > test_check("PhosR")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 57 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-pathwayAnalysis.R:74:5'): Case B.2: Expected output ──────────
  `result1` not identical to pathwayOverrepresent(geneSet, annotation, universe, alter1).
  1/12 mismatches
  x[3]: "0.100641107506833"
  y[3]: "0.100641107506832"
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 57 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/PhosR.Rcheck/00check.log’
for details.


Installation output

PhosR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL PhosR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘PhosR’ ...
** this is package ‘PhosR’ version ‘1.19.0’
** 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.fail


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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 1 | WARN 0 | SKIP 0 | PASS 57 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-pathwayAnalysis.R:74:5'): Case B.2: Expected output ──────────
`result1` not identical to pathwayOverrepresent(geneSet, annotation, universe, alter1).
1/12 mismatches
x[3]: "0.100641107506833"
y[3]: "0.100641107506832"

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 57 ]
Error: Test failures
Execution halted

Example timings

PhosR.Rcheck/PhosR-Ex.timings

nameusersystemelapsed
PhosphoExperiment-methods0.2890.0000.289
PhosphoExperiment-operate0.4220.0030.425
PhosphoExperiment0.2300.0020.232
RUVphospho0.2910.0060.297
Signalomes0.0000.0000.001
createFrequencyMat0.1030.0020.106
frequencyScoring0.3030.0030.306
getSPS2.0010.1502.151
kinaseSubstrateHeatmap000
kinaseSubstratePred26.290 0.28526.575
kinaseSubstrateProfile10.236 0.11510.351
kinaseSubstrateScore16.579 0.06716.646
mIntersect0.9640.0050.969
matANOVA9.3090.0709.379
meanAbundance0.2530.0060.259
medianScaling0.2030.0110.214
minmax16.631 0.04616.677
pathwayOverrepresent000
pathwayRankBasedEnrichment000
phosCollapse0.7730.0100.783
plotQC3.8300.0653.897
ptImpute0.2330.0020.235
scImpute0.4630.0060.468
selectGrps0.1280.0040.131
selectLocalisedSites0.0750.0030.078
selectOverallPercent0.0420.0010.043
selectTimes0.0100.0000.009
siteAnnotate26.419 0.18826.607
standardise9.2840.0269.310
tImpute0.1420.0070.149