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This page was generated on 2024-05-04 11:40:55 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1561/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhosR 1.14.0  (landing page)
Taiyun Kim
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/PhosR
git_branch: RELEASE_3_19
git_last_commit: f13aba8
git_last_commit_date: 2024-04-30 11:27:23 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for PhosR on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: PhosR
Version: 1.14.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:PhosR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings PhosR_1.14.0.tar.gz
StartedAt: 2024-05-04 10:35:21 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 10:43:18 -0000 (Sat, 04 May 2024)
EllapsedTime: 476.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: PhosR.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:PhosR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings PhosR_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/PhosR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PhosR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PhosR’ version ‘1.14.0’
* 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           42.552  0.163  42.820
kinaseSubstratePred    40.896  0.296  41.282
kinaseSubstrateScore   28.263  0.148  28.472
minmax                 27.858  0.088  28.003
matANOVA               14.970  0.016  15.018
standardise            14.639  0.047  14.722
kinaseSubstrateProfile 14.529  0.067  14.629
plotQC                  6.168  0.055   6.242
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/PhosR.Rcheck/00check.log’
for details.


Installation output

PhosR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL PhosR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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.fail


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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-methods0.3500.0120.364
PhosphoExperiment-operate0.5270.0240.552
PhosphoExperiment0.2670.0040.271
RUVphospho0.2370.0040.241
Signalomes000
createFrequencyMat0.1130.0000.113
frequencyScoring0.3950.0000.395
getSPS2.9880.1393.133
kinaseSubstrateHeatmap000
kinaseSubstratePred40.896 0.29641.282
kinaseSubstrateProfile14.529 0.06714.629
kinaseSubstrateScore28.263 0.14828.472
mIntersect1.6390.0201.663
matANOVA14.970 0.01615.018
meanAbundance0.3030.0000.304
medianScaling0.3790.0040.385
minmax27.858 0.08828.003
pathwayOverrepresent0.0010.0000.000
pathwayRankBasedEnrichment000
phosCollapse1.2140.0321.249
plotQC6.1680.0556.242
ptImpute0.3360.0000.337
scImpute0.7750.0030.780
selectGrps0.1250.0000.126
selectLocalisedSites0.0840.0000.085
selectOverallPercent0.0440.0000.043
selectTimes0.0130.0000.013
siteAnnotate42.552 0.16342.820
standardise14.639 0.04714.722
tImpute0.1690.0040.174