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This page was generated on 2025-08-11 12:10 -0400 (Mon, 11 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4532
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 1590/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
poem 1.1.2  (landing page)
Siyuan Luo
Snapshot Date: 2025-08-10 13:45 -0400 (Sun, 10 Aug 2025)
git_url: https://git.bioconductor.org/packages/poem
git_branch: devel
git_last_commit: 7367e0d
git_last_commit_date: 2025-06-04 07:34:16 -0400 (Wed, 04 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'bluster' which is only available as a source package that needs compilation
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for poem on lconway

To the developers/maintainers of the poem package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/poem.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: poem
Version: 1.1.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:poem.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings poem_1.1.2.tar.gz
StartedAt: 2025-08-10 23:18:01 -0400 (Sun, 10 Aug 2025)
EndedAt: 2025-08-10 23:23:56 -0400 (Sun, 10 Aug 2025)
EllapsedTime: 354.5 seconds
RetCode: 0
Status:   OK  
CheckDir: poem.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:poem.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings poem_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/poem.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘poem/DESCRIPTION’ ... OK
* this is package ‘poem’ version ‘1.1.2’
* 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 ‘poem’ 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 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 ‘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: OK


Installation output

poem.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘poem’ ...
** this is package ‘poem’ version ‘1.1.2’
** 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 (poem)

Tests output

poem.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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(poem)
> 
> test_check("poem")
Standard error of the mean NDC across permutations:0.00342
You might want to increase the number of permutations to increase the robustness of the adjusted metrics.
Comparing between a fuzzy truth and a fuzzy prediction...
Running 100 extra permutations.
Standard error of the mean NDC across permutations:0.00227
Comparing between a fuzzy truth and a fuzzy prediction...
Running 100 extra permutations.
Standard error of the mean NDC across permutations:0.00228
Comparing between a fuzzy truth and a fuzzy prediction...
Comparing between a fuzzy truth and a hard prediction...
Standard error of the mean NDC across permutations:0.000185
the specified variable is considered as categorical...
the specified variable is considered as categorical...
the specified variable is considered as categorical...
Comparing between a fuzzy truth and a hard prediction...
Standard error of the mean NDC across permutations:0.000889
Comparing between a fuzzy truth and a hard prediction...
Standard error of the mean NDC across permutations:0.000296
Comparing between a fuzzy truth and a hard prediction...
Standard error of the mean NDC across permutations:0.000322
Comparing between a fuzzy truth and a hard prediction...
Comparing between a fuzzy truth and a hard prediction...
[ FAIL 0 | WARN 14 | SKIP 0 | PASS 58 ]

[ FAIL 0 | WARN 14 | SKIP 0 | PASS 58 ]
> 
> proc.time()
   user  system elapsed 
 19.163   0.956  20.285 

Example timings

poem.Rcheck/poem-Ex.timings

nameusersystemelapsed
CDbw0.0270.0010.028
CHAOS0.0130.0030.016
ELSA0.3650.0400.412
PAS0.1060.0060.114
dbcv0.1620.0150.178
emb2knn0.0030.0020.005
emb2snn0.0090.0010.009
findSpatialKNN0.0170.0110.028
fuzzyHardMetrics0.0320.0010.035
fuzzyHardMetrics20.0230.0000.024
fuzzyHardSpotConcordance0.0030.0000.003
fuzzyPartitionMetrics0.0000.0010.000
getEmbeddingMetrics0.0480.0010.049
getFuzzyLabel0.0380.0050.043
getFuzzyPartitionMetrics0.1280.0030.132
getGraphMetrics0.0700.0030.074
getNeighboringPairConcordance0.0380.0040.042
getPartitionMetrics0.0390.0010.040
getSpatialExternalMetrics0.4330.0290.463
getSpatialInternalMetrics0.2710.0050.276
knnComposition0.0260.0040.029
mockData0.0010.0000.001
silhouetteWidths0.0010.0000.001
spatialARI0.0110.0020.012