| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-14 11:35 -0400 (Tue, 14 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4924 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4655 |
| 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 1989/2394 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scTypeEval 0.99.30 (landing page) Josep Garnica
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| See other builds for scTypeEval in R Universe. | ||||||||||||||
|
To the developers/maintainers of the scTypeEval package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scTypeEval.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: scTypeEval |
| Version: 0.99.30 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:scTypeEval.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings scTypeEval_0.99.30.tar.gz |
| StartedAt: 2026-04-14 05:15:16 -0400 (Tue, 14 Apr 2026) |
| EndedAt: 2026-04-14 05:19:29 -0400 (Tue, 14 Apr 2026) |
| EllapsedTime: 253.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: scTypeEval.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:scTypeEval.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings scTypeEval_0.99.30.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/scTypeEval.Rcheck’
* using R version 4.6.0 alpha (2026-04-05 r89794)
* 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: 2026-04-14 09:15:16 UTC
* checking for file ‘scTypeEval/DESCRIPTION’ ... OK
* this is package ‘scTypeEval’ version ‘0.99.30’
* 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 ‘scTypeEval’ 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 ... WARNING
Found the following significant warnings:
Warning in .local(x, ...) : 'findMarkers' is deprecated.
Warning in .local(x, ...) : 'pairwiseTTests' is deprecated.
Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
load_single_cell_object 5.484 0.513 5.997
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
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[ FAIL 1 | WARN 103 | SKIP 0 | PASS 537 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-Run-GeneMarkers.R:147:3'): run_gene_markers handles verbose parameter ──
Expected `... <- NULL` to run silently.
Actual noise: warnings.
[ FAIL 1 | WARN 103 | SKIP 0 | PASS 537 ]
Error:
! Test failures.
Execution halted
* 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: 1 ERROR, 1 WARNING
See
‘/home/biocbuild/bbs-3.23-bioc/meat/scTypeEval.Rcheck/00check.log’
for details.
scTypeEval.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL scTypeEval ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘scTypeEval’ ... ** this is package ‘scTypeEval’ version ‘0.99.30’ ** 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 (scTypeEval)
scTypeEval.Rcheck/tests/testthat.Rout.fail
R version 4.6.0 alpha (2026-04-05 r89794)
Copyright (C) 2026 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.
> library(testthat)
> library(scTypeEval)
>
> test_check("scTypeEval")
Not using black gene list
Filtering gene list...
Filtering empty rows and cols...
Running distance for euclidean...
Computing cell type markers for celltype...
Saving _problems/test-Run-GeneMarkers-154.R
Not using black gene list
Using HVG gene list.
Not using black gene list
Filtering gene list...
Filtering empty rows and cols...
Computing PCA space...
> Returning 5 dimensions for PCA
# Computing PCA data for pseudobulk ...
Filtering gene list...
Filtering empty rows and cols...
Computing PCA space...
> Returning 5 dimensions for PCA
Transforming and filtering count matrix...
Normalizing count matrix via Log1p...
# Processing data for pseudobulk ...
Transforming and filtering count matrix...
Normalizing count matrix via Log1p...
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[ FAIL 1 | WARN 103 | SKIP 0 | PASS 537 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-Run-GeneMarkers.R:147:3'): run_gene_markers handles verbose parameter ──
Expected `... <- NULL` to run silently.
Actual noise: warnings.
[ FAIL 1 | WARN 103 | SKIP 0 | PASS 537 ]
Error:
! Test failures.
Execution halted
scTypeEval.Rcheck/scTypeEval-Ex.timings
| name | user | system | elapsed | |
| add_dim_reduction | 0.062 | 0.000 | 0.062 | |
| add_gene_list | 0.104 | 0.000 | 0.104 | |
| add_processed_data | 0.013 | 0.000 | 0.013 | |
| black_list | 0.066 | 0.155 | 0.221 | |
| create_scTypeEval | 0.014 | 0.000 | 0.014 | |
| get_consistency | 0.626 | 0.063 | 0.687 | |
| get_hierarchy | 0.055 | 0.018 | 0.070 | |
| get_nn | 0.050 | 0.018 | 0.066 | |
| load_single_cell_object | 5.484 | 0.513 | 5.997 | |
| plot_heatmap | 1.635 | 0.253 | 1.886 | |
| plot_mds | 0.135 | 0.028 | 0.159 | |
| plot_pca | 0.658 | 0.099 | 0.755 | |
| run_dissimilarity | 0.058 | 0.044 | 0.100 | |
| run_gene_markers | 1.017 | 0.106 | 1.122 | |
| run_hvg | 0.073 | 0.024 | 0.093 | |
| run_pca | 0.066 | 0.023 | 0.088 | |
| run_processing_data | 0.027 | 0.005 | 0.031 | |
| set_active_ident | 0.050 | 0.034 | 0.083 | |
| wrapper_scTypeEval | 0.329 | 0.093 | 0.419 | |