Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:03 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 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 442/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
corral 1.14.0 (landing page) Lauren Hsu
| nebbiolo1 | Linux (Ubuntu 22.04.3 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 | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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: 1.14.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:corral.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings corral_1.14.0.tar.gz |
StartedAt: 2024-07-21 23:07:01 -0400 (Sun, 21 Jul 2024) |
EndedAt: 2024-07-21 23:24:24 -0400 (Sun, 21 Jul 2024) |
EllapsedTime: 1043.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: corral.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:corral.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings corral_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/corral.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘corral/DESCRIPTION’ ... OK * this is package ‘corral’ version ‘1.14.0’ * 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 loading without being on the library search path ... 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed biplot_corral 58.846 5.928 64.945 corral 12.553 1.704 14.473 corralm 11.685 1.339 13.245 add_embeddings2scelist 10.809 1.367 12.601 plot_embedding_sce 6.389 0.656 7.155 sce2matlist 5.899 0.692 6.698 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/corral.Rcheck/00check.log’ for details.
corral.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL corral ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘corral’ ... ** 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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 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. > > proc.time() user system elapsed 0.146 0.040 0.174
corral.Rcheck/corral-Ex.timings
name | user | system | elapsed | |
add_embeddings2scelist | 10.809 | 1.367 | 12.601 | |
all_are | 0.001 | 0.000 | 0.001 | |
biplot_corral | 58.846 | 5.928 | 64.945 | |
compsvd | 0.002 | 0.004 | 0.006 | |
corral | 12.553 | 1.704 | 14.473 | |
corral_preproc | 0.010 | 0.000 | 0.009 | |
corralm | 11.685 | 1.339 | 13.245 | |
earthmover_dist | 0.021 | 0.000 | 0.021 | |
get_pct_var_exp_svd | 0.001 | 0.000 | 0.001 | |
get_weights | 0.001 | 0.000 | 0.001 | |
list2mat | 0.001 | 0.000 | 0.001 | |
na2zero | 0.014 | 0.024 | 0.038 | |
pairwise_rv | 0.002 | 0.000 | 0.002 | |
plot_embedding | 0.597 | 0.204 | 0.801 | |
plot_embedding_sce | 6.389 | 0.656 | 7.155 | |
rv | 0 | 0 | 0 | |
scal_var | 0.202 | 0.004 | 0.205 | |
scal_var_mat | 0.014 | 0.000 | 0.015 | |
sce2matlist | 5.899 | 0.692 | 6.698 | |
trim_matdist | 0.045 | 0.001 | 0.046 | |
var_stabilize | 0.000 | 0.000 | 0.001 | |