Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 676/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
escape 2.2.2 (landing page) Nick Borcherding
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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. |
Package: escape |
Version: 2.2.2 |
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_2.2.2.tar.gz |
StartedAt: 2024-12-20 19:03:42 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 19:11:14 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 452.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: escape.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_2.2.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/escape.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘escape/DESCRIPTION’ ... OK * this is package ‘escape’ version ‘2.2.2’ * 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 ‘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 5.994 0.09 6.092 * 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-3.20-bioc/meat/escape.Rcheck/00check.log’ for details.
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)
escape.Rcheck/tests/spelling.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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 0.207 0.052 0.245
escape.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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..." [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 0 | WARN 0 | SKIP 7 | PASS 19 ] ══ 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 0 | SKIP 7 | PASS 19 ] > > proc.time() user system elapsed 104.029 10.319 115.037
escape.Rcheck/escape-Ex.timings
name | user | system | elapsed | |
densityEnrichment | 0.678 | 0.014 | 0.697 | |
escape.matrix | 0.381 | 0.012 | 0.394 | |
getGeneSets | 5.994 | 0.090 | 6.092 | |
geyserEnrichment | 0.949 | 0.021 | 0.975 | |
heatmapEnrichment | 0.493 | 0.033 | 0.526 | |
pcaEnrichment | 0.514 | 0.023 | 0.537 | |
performNormalization | 0.312 | 0.002 | 0.314 | |
performPCA | 0.309 | 0.002 | 0.311 | |
ridgeEnrichment | 1.884 | 0.033 | 1.920 | |
runEscape | 0.313 | 0.016 | 0.329 | |
scatterEnrichment | 0.501 | 0.028 | 0.529 | |
splitEnrichment | 0.622 | 0.008 | 0.630 | |