Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-07-12 17:42 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
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 680/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
escape 2.0.0  (landing page)
Nick Borcherding
Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 2024)
git_url: https://git.bioconductor.org/packages/escape
git_branch: RELEASE_3_19
git_last_commit: d314a29
git_last_commit_date: 2024-04-30 11:25:33 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.4 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 escape on kjohnson1

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: 2.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:escape.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings escape_2.0.0.tar.gz
StartedAt: 2024-07-11 19:07:09 -0400 (Thu, 11 Jul 2024)
EndedAt: 2024-07-11 19:15:19 -0400 (Thu, 11 Jul 2024)
EllapsedTime: 490.4 seconds
RetCode: 0
Status:   OK  
CheckDir: escape.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:escape.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings escape_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/escape.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘escape/DESCRIPTION’ ... OK
* this is package ‘escape’ version ‘2.0.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
getGeneSets 6.609   0.11   6.759
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/escape.Rcheck/00check.log’
for details.


Installation output

escape.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.204   0.070   0.265 

escape.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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.

> # 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..."
Picking joint bandwidth of 9.72
[1] "Using sets of 1000 cells. Running 1 times."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Using sets of 1000 cells. Running 1 times."
[1] "Using sets of 1000 cells. Running 1 times."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
Notch went outside hinges
ℹ Do you want `notch = FALSE`?
Notch went outside hinges
ℹ Do you want `notch = FALSE`?
[ FAIL 0 | WARN 3 | SKIP 7 | PASS 18 ]

══ 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'

[ FAIL 0 | WARN 3 | SKIP 7 | PASS 18 ]
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
> 
> proc.time()
   user  system elapsed 
116.591   9.148 126.980 

Example timings

escape.Rcheck/escape-Ex.timings

nameusersystemelapsed
densityEnrichment0.7100.0250.739
escape.matrix0.3860.0110.398
getGeneSets6.6090.1106.759
geyserEnrichment0.9970.0251.033
heatmapEnrichment0.5170.0040.528
pcaEnrichment0.5460.0370.585
performNormalization1.7510.0121.768
performPCA0.3800.0020.382
ridgeEnrichment0.7830.0220.806
runEscape0.3290.0020.331
scatterEnrichment0.5020.0040.510
splitEnrichment0.7970.0100.810