Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-04 11:45 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 446/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
corral 1.18.0 (landing page) Lauren Hsu
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | TIMEOUT | ||||||||||
To the developers/maintainers of the corral package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/corral.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: corral |
Version: 1.18.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:corral.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings corral_1.18.0.tar.gz |
StartedAt: 2025-08-01 16:15:23 -0400 (Fri, 01 Aug 2025) |
EndedAt: 2025-08-01 16:22:18 -0400 (Fri, 01 Aug 2025) |
EllapsedTime: 414.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: corral.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:corral.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings corral_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/corral.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘corral/DESCRIPTION’ ... OK * this is package ‘corral’ version ‘1.18.0’ * 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 ‘corral’ 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 ... NOTE Unexported object imported by a ':::' call: ‘ggthemes:::check_pal_n’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE biplot_corral: no visible binding for global variable ‘Name’ plot_embedding: no visible binding for global variable ‘Xdim’ plot_embedding: no visible binding for global variable ‘Ydim’ scal_var: no visible binding for global variable ‘PC_ind’ scal_var: no visible binding for global variable ‘sv’ scal_var: no visible binding for global variable ‘Batch’ Undefined global functions or variables: Batch Name PC_ind Xdim Ydim sv * checking Rd files ... NOTE prepare_Rd: corral_preproc.Rd:41-43: Dropping empty section \details * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: corral.Rd: SingleCellExperiment corralm.Rd: SingleCellExperiment plot_embedding.Rd: ggplot2 plot_embedding_sce.Rd: SingleCellExperiment, ggplot2 scal_var.Rd: ggplot2 Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed biplot_corral 129.858 4.069 134.707 add_embeddings2scelist 16.327 1.788 21.369 corralm 15.914 1.200 18.252 corral 15.006 1.283 17.572 plot_embedding_sce 8.153 0.565 9.297 sce2matlist 7.389 0.552 8.530 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/corral.Rcheck/00check.log’ for details.
corral.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL corral ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘corral’ ... ** this is package ‘corral’ version ‘1.18.0’ ** using staged installation ** R ** 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 (corral)
corral.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 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. > > proc.time() user system elapsed 0.207 0.063 0.254
corral.Rcheck/corral-Ex.timings
name | user | system | elapsed | |
add_embeddings2scelist | 16.327 | 1.788 | 21.369 | |
all_are | 0.001 | 0.000 | 0.001 | |
biplot_corral | 129.858 | 4.069 | 134.707 | |
compsvd | 0.005 | 0.003 | 0.007 | |
corral | 15.006 | 1.283 | 17.572 | |
corral_preproc | 0.009 | 0.000 | 0.010 | |
corralm | 15.914 | 1.200 | 18.252 | |
earthmover_dist | 0.024 | 0.001 | 0.025 | |
get_pct_var_exp_svd | 0.001 | 0.000 | 0.001 | |
get_weights | 0.001 | 0.000 | 0.002 | |
list2mat | 0.001 | 0.000 | 0.001 | |
na2zero | 0.016 | 0.023 | 0.041 | |
pairwise_rv | 0.001 | 0.001 | 0.002 | |
plot_embedding | 0.749 | 0.097 | 0.868 | |
plot_embedding_sce | 8.153 | 0.565 | 9.297 | |
rv | 0.000 | 0.000 | 0.001 | |
scal_var | 0.215 | 0.002 | 0.217 | |
scal_var_mat | 0.016 | 0.002 | 0.016 | |
sce2matlist | 7.389 | 0.552 | 8.530 | |
trim_matdist | 0.062 | 0.002 | 0.063 | |
var_stabilize | 0.001 | 0.000 | 0.001 | |