Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-14 11:40 -0400 (Fri, 14 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4781 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4537 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4567 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4519 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4451 |
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 1588/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
poem 0.99.7 (landing page) Siyuan Luo
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | ERROR | skipped | ||||||||||
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. |
Package: poem |
Version: 0.99.7 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:poem.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings poem_0.99.7.tar.gz |
StartedAt: 2025-03-14 00:58:03 -0400 (Fri, 14 Mar 2025) |
EndedAt: 2025-03-14 01:08:58 -0400 (Fri, 14 Mar 2025) |
EllapsedTime: 654.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: poem.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:poem.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings poem_0.99.7.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/poem.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * 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 ‘poem/DESCRIPTION’ ... OK * this is package ‘poem’ version ‘0.99.7’ * 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 loading without being on the library search path ... 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 ... NOTE Unknown packages ‘FuzzyPartitionMetrics()’, ‘fuzzyHardMetrics()’ in Rd xrefs * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.21-bioc/meat/poem.Rcheck/00check.log’ for details.
poem.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL poem ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘poem’ ... ** this is package ‘poem’ version ‘0.99.7’ ** 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)
poem.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 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. > # 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... Comparing between a fuzzy truth and a hard prediction... [ FAIL 0 | WARN 14 | SKIP 0 | PASS 56 ] [ FAIL 0 | WARN 14 | SKIP 0 | PASS 56 ] > > proc.time() user system elapsed 17.745 1.023 18.758
poem.Rcheck/poem-Ex.timings
name | user | system | elapsed | |
CDbw | 0.027 | 0.000 | 0.028 | |
CHAOS | 0.009 | 0.003 | 0.013 | |
ELSA | 0.180 | 0.013 | 0.193 | |
PAS | 0.096 | 0.004 | 0.102 | |
dbcv | 0.101 | 0.001 | 0.102 | |
emb2knn | 0.003 | 0.002 | 0.005 | |
emb2snn | 0.01 | 0.00 | 0.01 | |
findSpatialKNN | 0.012 | 0.011 | 0.023 | |
fuzzyHardMetrics | 0.036 | 0.000 | 0.036 | |
fuzzyHardMetrics2 | 0.023 | 0.001 | 0.023 | |
fuzzyHardSpotConcordance | 0.003 | 0.001 | 0.003 | |
fuzzyPartitionMetrics | 0 | 0 | 0 | |
fuzzySpotConcordance | 0.000 | 0.001 | 0.001 | |
getEmbeddingMetrics | 0.033 | 0.001 | 0.033 | |
getFuzzyLabel | 0.046 | 0.005 | 0.051 | |
getFuzzyPartitionMetrics | 0.081 | 0.000 | 0.081 | |
getGraphMetrics | 0.057 | 0.003 | 0.059 | |
getNeighboringPairConcordance | 0.038 | 0.000 | 0.040 | |
getPartitionMetrics | 0.009 | 0.000 | 0.009 | |
getSpatialExternalMetrics | 0.422 | 0.022 | 0.445 | |
getSpatialInternalMetrics | 0.268 | 0.002 | 0.270 | |
knnComposition | 0.029 | 0.003 | 0.032 | |
mockData | 0.000 | 0.000 | 0.001 | |