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 12:04 -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 439/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
corral 1.16.0 (landing page) Lauren Hsu
| 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 | ERROR | skipped | skipped | |||||||||
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: 1.16.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:corral.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings corral_1.16.0.tar.gz |
StartedAt: 2024-12-20 00:22:50 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 00:28:33 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 343.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: corral.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:corral.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings corral_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/corral.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'corral/DESCRIPTION' ... OK * this is package 'corral' version '1.16.0' * 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 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 ... 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 63.22 5.98 69.29 add_embeddings2scelist 13.48 2.60 17.83 corralm 11.89 2.28 14.33 corral 10.87 2.08 13.08 plot_embedding_sce 6.65 0.94 7.71 sce2matlist 6.09 1.13 7.28 * 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: 3 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/corral.Rcheck/00check.log' for details.
corral.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL corral ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 0.18 0.06 0.18
corral.Rcheck/corral-Ex.timings
name | user | system | elapsed | |
add_embeddings2scelist | 13.48 | 2.60 | 17.83 | |
all_are | 0 | 0 | 0 | |
biplot_corral | 63.22 | 5.98 | 69.29 | |
compsvd | 0.00 | 0.02 | 0.02 | |
corral | 10.87 | 2.08 | 13.08 | |
corral_preproc | 0.01 | 0.00 | 0.02 | |
corralm | 11.89 | 2.28 | 14.33 | |
earthmover_dist | 0.02 | 0.01 | 0.03 | |
get_pct_var_exp_svd | 0 | 0 | 0 | |
get_weights | 0 | 0 | 0 | |
list2mat | 0 | 0 | 0 | |
na2zero | 0.01 | 0.03 | 0.05 | |
pairwise_rv | 0 | 0 | 0 | |
plot_embedding | 0.72 | 0.00 | 0.72 | |
plot_embedding_sce | 6.65 | 0.94 | 7.71 | |
rv | 0 | 0 | 0 | |
scal_var | 0.31 | 0.02 | 0.33 | |
scal_var_mat | 0.02 | 0.01 | 0.03 | |
sce2matlist | 6.09 | 1.13 | 7.28 | |
trim_matdist | 0.08 | 0.00 | 0.08 | |
var_stabilize | 0 | 0 | 0 | |