Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2025-03-20 12:06 -0400 (Thu, 20 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4756
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4487
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4514
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4441
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4406
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 676/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
escape 2.2.3  (landing page)
Nick Borcherding
Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 Mar 2025)
git_url: https://git.bioconductor.org/packages/escape
git_branch: RELEASE_3_20
git_last_commit: cc80db9
git_last_commit_date: 2025-01-24 15:23:16 -0400 (Fri, 24 Jan 2025)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  

CHECK results for escape on palomino8

To the developers/maintainers of the escape package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/escape.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: escape
Version: 2.2.3
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:escape.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings escape_2.2.3.tar.gz
StartedAt: 2025-03-18 01:14:50 -0400 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 01:21:21 -0400 (Tue, 18 Mar 2025)
EllapsedTime: 390.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: escape.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:escape.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings escape_2.2.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/escape.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'escape/DESCRIPTION' ... OK
* this is package 'escape' version '2.2.3'
* 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 whether package 'escape' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... OK
* 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 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
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'spelling.R'
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  • pcaEnrichment/pcaenrichment-facetby-plot.svg
  • pcaEnrichment/pcaenrichment-hex-plot.svg
  • ridgeEnrichment/ridgeenrichment-facet-plot.svg
  • ridgeEnrichment/ridgeenrichment-gradient-facet-plot.svg
  • ridgeEnrichment/ridgeenrichment-gradient-plot.svg
  • ridgeEnrichment/ridgeenrichment-gradient-reorder-plot.svg
  • ridgeEnrichment/ridgeenrichment-order-plot.svg
  • ridgeEnrichment/ridgeenrichment-rugadded-plot.svg
  • scatterEnrichment/scatterenrichment-facet-plot.svg
  • scatterEnrichment/scatterenrichment-hex-plot.svg
  • scatterEnrichment/scatterenrichment-scale-plot.svg
  • splitEnrichment/splitenrichment-facet-plot.svg
  • splitEnrichment/splitenrichment-mean-plot.svg
  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, 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/escape.Rcheck/00check.log'
for details.

Installation output

escape.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL escape
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'escape' ...
** using staged installation
** R
** data
** inst
** 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 (escape)

Tests output

escape.Rcheck/tests/spelling.Rout


R version 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
   0.18    0.06    0.42

escape.Rcheck/tests/testthat.Rout.fail


R version 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(escape)
> 
> test_check("escape")
[1] "Calculating features per cell..."
[1] "Normalizing enrichment scores per cell..."
[1] "Calculating features per cell..."
[1] "Normalizing enrichment scores per cell..."
[1] "Calculating features per cell..."
[1] "Normalizing enrichment scores per cell..."
[1] "Calculating features per cell..."
[1] "Normalizing enrichment scores per cell..."
Picking joint bandwidth of 9.72
[1] "Using sets of 1000 cells. Running 1 times."
[1] "Using sets of 1000 cells. Running 1 times."
[1] "Using sets of 1000 cells. Running 1 times."
Notch went outside hinges
ℹ Do you want `notch = FALSE`?
Notch went outside hinges
ℹ Do you want `notch = FALSE`?
[ FAIL 3 | WARN 2 | SKIP 7 | PASS 16 ]

══ Skipped tests (7) ═══════════════════════════════════════════════════════════
• On CRAN (7): 'test-densityEnrichment.R:9:3', 'test-geyserEnrichment.R:8:3',
  'test-heatmapEnrichment.R:7:3', 'test-pcaEnrichment.R:9:3',
  'test-ridgeEnrichment.R:8:3', 'test-scatterEnrichment.R:7:3',
  'test-splitEnrichment.R:7:3'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-getGeneSets.R:12:3'): getGeneSets works ──────────────────────
`hallmark.default` not equal to getdata("getGeneSets", "getGeneSets_default").
Component "HALLMARK-ANDROGEN-RESPONSE": Lengths (101, 100) differ (string compare on first 100)
Component "HALLMARK-ANDROGEN-RESPONSE": 13 string mismatches
Component "HALLMARK-APICAL-JUNCTION": 11 string mismatches
Component "HALLMARK-ESTROGEN-RESPONSE-EARLY": 61 string mismatches
Component "HALLMARK-ESTROGEN-RESPONSE-LATE": 60 string mismatches
Component "HALLMARK-IL2-STAT5-SIGNALING": 19 string mismatches
Component "HALLMARK-INTERFERON-GAMMA-RESPONSE": 140 string mismatches
Component "HALLMARK-MTORC1-SIGNALING": 62 string mismatches
Component "HALLMARK-MYC-TARGETS-V1": 1 string mismatch
...
── Failure ('test-getGeneSets.R:15:3'): getGeneSets works ──────────────────────
`mouse.hallmark.default` not equal to getdata("getGeneSets", "getGeneSets_mouse").
Component "HALLMARK-APICAL-JUNCTION": 11 string mismatches
Component "HALLMARK-APOPTOSIS": Lengths (160, 161) differ (string compare on first 160)
Component "HALLMARK-APOPTOSIS": 17 string mismatches
Component "HALLMARK-ESTROGEN-RESPONSE-EARLY": 61 string mismatches
Component "HALLMARK-ESTROGEN-RESPONSE-LATE": 64 string mismatches
Component "HALLMARK-IL2-STAT5-SIGNALING": 19 string mismatches
Component "HALLMARK-INTERFERON-GAMMA-RESPONSE": Lengths (205, 206) differ (string compare on first 205)
Component "HALLMARK-INTERFERON-GAMMA-RESPONSE": 167 string mismatches
Component "HALLMARK-MTORC1-SIGNALING": 63 string mismatches
...
── Failure ('test-getGeneSets.R:18:3'): getGeneSets works ──────────────────────
`C5.GO.default` not equal to getdata("getGeneSets", "getGeneSets_C5").
Names: 5 string mismatches
Length mismatch: comparison on first 5 components
Component 1: Lengths (5, 6) differ (string compare on first 5)
Component 1: 5 string mismatches
Component 2: Lengths (22, 6) differ (string compare on first 6)
Component 2: 6 string mismatches
Component 3: Lengths (65, 17) differ (string compare on first 17)
Component 3: 17 string mismatches
Component 4: Lengths (10, 6) differ (string compare on first 6)
...

[ FAIL 3 | WARN 2 | SKIP 7 | PASS 16 ]
Deleting unused snapshots:
• densityEnrichment/denistyenrichment-group-by-plot.svg
• geyserEnrichment/geyserenrichment-facet-plot.svg
• geyserEnrichment/geyserenrichment-gradient-facet-plot.svg
• geyserEnrichment/geyserenrichment-gradient-plot.svg
• geyserEnrichment/geyserenrichment-gradient-reorder-plot.svg
• geyserEnrichment/geyserenrichment-order-plot.svg
• geyserEnrichment/geyserenrichment-scale-plot.svg
• heatmapEnrichment/heatmapenrichment-clustercolumns-plot.svg
• heatmapEnrichment/heatmapenrichment-clusterrows-plot.svg
• heatmapEnrichment/heatmapenrichment-facet-plot.svg
• heatmapEnrichment/heatmapenrichment-scale-plot.svg
• pcaEnrichment/pcaenrichment-addfactors-plot.svg
• pcaEnrichment/pcaenrichment-facetby-addfactors-plot.svg
• pcaEnrichment/pcaenrichment-facetby-plot.svg
• pcaEnrichment/pcaenrichment-hex-plot.svg
• ridgeEnrichment/ridgeenrichment-facet-plot.svg
• ridgeEnrichment/ridgeenrichment-gradient-facet-plot.svg
• ridgeEnrichment/ridgeenrichment-gradient-plot.svg
• ridgeEnrichment/ridgeenrichment-gradient-reorder-plot.svg
• ridgeEnrichment/ridgeenrichment-order-plot.svg
• ridgeEnrichment/ridgeenrichment-rugadded-plot.svg
• scatterEnrichment/scatterenrichment-facet-plot.svg
• scatterEnrichment/scatterenrichment-hex-plot.svg
• scatterEnrichment/scatterenrichment-scale-plot.svg
• splitEnrichment/splitenrichment-facet-plot.svg
• splitEnrichment/splitenrichment-mean-plot.svg
Error: Test failures
Execution halted

Example timings

escape.Rcheck/escape-Ex.timings

nameusersystemelapsed
densityEnrichment0.750.010.80
escape.matrix0.420.030.45
getGeneSets0.390.050.51
geyserEnrichment2.280.012.30
heatmapEnrichment0.630.000.62
pcaEnrichment0.620.070.69
performNormalization0.470.000.47
performPCA0.490.000.48
ridgeEnrichment0.940.010.96
runEscape0.370.000.37
scatterEnrichment0.640.000.64
splitEnrichment0.910.050.96