Ziyi Li
| Snapshot Date: 2026-05-12 13:45 -0400 (Tue, 12 May 2026) |
| git_url: https://git.bioconductor.org/packages/TOAST |
| git_branch: devel |
| git_last_commit: a6f2209 |
| git_last_commit_date: 2026-04-28 08:50:25 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-13 11:33 -0400 (Wed, 13 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4893 |
| 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 2243/2374 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TOAST 1.27.0 (landing page) Ziyi Li
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for TOAST in R Universe. | ||||||||||||||
|
To the developers/maintainers of the TOAST package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TOAST.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: TOAST |
| Version: 1.27.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:TOAST.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings TOAST_1.27.0.tar.gz |
| StartedAt: 2026-05-13 05:33:56 -0400 (Wed, 13 May 2026) |
| EndedAt: 2026-05-13 05:42:08 -0400 (Wed, 13 May 2026) |
| EllapsedTime: 491.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TOAST.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:TOAST.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings TOAST_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/TOAST.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-13 09:33:57 UTC
* checking for file ‘TOAST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TOAST’ version ‘1.27.0’
* 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 ‘TOAST’ 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 ... 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
csDeconv 53.679 1.716 59.306
plotCorr 4.839 0.003 6.491
cedar 3.078 0.261 63.504
* 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: OK
TOAST.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL TOAST ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’ * installing *source* package ‘TOAST’ ... ** this is package ‘TOAST’ version ‘1.27.0’ ** 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 (TOAST)
TOAST.Rcheck/TOAST-Ex.timings
| name | user | system | elapsed | |
| CBS_PBMC_array | 0.007 | 0.001 | 0.008 | |
| ChooseMarker | 0.027 | 0.005 | 0.032 | |
| DEVarSelect | 0.761 | 0.066 | 0.827 | |
| GetPrior | 0 | 0 | 0 | |
| MDeconv | 0.031 | 0.000 | 0.031 | |
| RA_100samples | 0.158 | 0.000 | 0.158 | |
| Tsisal | 4.857 | 0.119 | 4.976 | |
| assignCellType | 0.001 | 0.000 | 0.001 | |
| beta_emp | 0.012 | 0.001 | 0.013 | |
| cedar | 3.078 | 0.261 | 63.504 | |
| csDeconv | 53.679 | 1.716 | 59.306 | |
| csTest | 0.190 | 0.004 | 0.388 | |
| findRefinx | 0.015 | 0.000 | 0.030 | |
| fitModel | 0.106 | 0.000 | 0.215 | |
| makeDesign | 0.007 | 0.000 | 0.015 | |
| plotCorr | 4.839 | 0.003 | 6.491 | |