| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-25 11:41 -0400 (Thu, 25 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4581 |
| 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 310/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CellScore 1.28.0 (landing page) Nancy Mah
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the CellScore package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CellScore.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: CellScore |
| Version: 1.28.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:CellScore.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CellScore_1.28.0.tar.gz |
| StartedAt: 2025-09-23 08:07:59 -0000 (Tue, 23 Sep 2025) |
| EndedAt: 2025-09-23 08:16:44 -0000 (Tue, 23 Sep 2025) |
| EllapsedTime: 524.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CellScore.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:CellScore.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CellScore_1.28.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CellScore.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CellScore/DESCRIPTION’ ... OK
* this is package ‘CellScore’ version ‘1.28.0’
* 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 ‘CellScore’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CellScoreReport 43.213 0.215 43.542
heatmapOnOffMarkers 34.389 0.132 34.606
extractTransitions 31.707 0.084 31.871
RugplotCellScore 31.609 0.072 31.762
ScatterplotCellScoreComponents 31.144 0.107 31.331
PlotCosineSimHeatmap 24.545 0.020 24.626
BoxplotCellScore 20.886 0.176 21.120
CellScore 20.318 0.168 20.539
PcaStandards 17.659 0.180 17.885
BarplotOnOff 16.807 0.574 17.533
CosineSimScore 16.961 0.108 17.112
OnOff 12.533 0.159 12.728
* 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: OK
CellScore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL CellScore ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘CellScore’ ... ** this is package ‘CellScore’ version ‘1.28.0’ ** 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 (CellScore)
CellScore.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
> library(testthat)
> library(CellScore)
>
> test_check("CellScore")
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
To process 2 cell transitions
Now processing transition FIB -> ESC
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Now processing transition KER -> ESC
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[ FAIL 0 | WARN 1 | SKIP 0 | PASS 4 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
35.811 1.036 36.931
CellScore.Rcheck/CellScore-Ex.timings
| name | user | system | elapsed | |
| BarplotOnOff | 16.807 | 0.574 | 17.533 | |
| BoxplotCellScore | 20.886 | 0.176 | 21.120 | |
| CellScore | 20.318 | 0.168 | 20.539 | |
| CellScoreReport | 43.213 | 0.215 | 43.542 | |
| CosineSimScore | 16.961 | 0.108 | 17.112 | |
| OnOff | 12.533 | 0.159 | 12.728 | |
| PcaStandards | 17.659 | 0.180 | 17.885 | |
| PlotCosineSimHeatmap | 24.545 | 0.020 | 24.626 | |
| RugplotCellScore | 31.609 | 0.072 | 31.762 | |
| ScatterplotCellScoreComponents | 31.144 | 0.107 | 31.331 | |
| extractTransitions | 31.707 | 0.084 | 31.871 | |
| heatmapOnOffMarkers | 34.389 | 0.132 | 34.606 | |
| rugplotDonorTargetTest | 0 | 0 | 0 | |
| scatterplotDonorTargetTest | 0.000 | 0.000 | 0.001 | |