Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-09-18 11:38 -0400 (Thu, 18 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R 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 387/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clustifyr 1.20.0  (landing page)
Rui Fu
Snapshot Date: 2025-09-15 13:40 -0400 (Mon, 15 Sep 2025)
git_url: https://git.bioconductor.org/packages/clustifyr
git_branch: RELEASE_3_21
git_last_commit: 88a6a55
git_last_commit_date: 2025-04-15 11:54:38 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  


CHECK results for clustifyr on merida1

To the developers/maintainers of the clustifyr package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/clustifyr.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.

raw results


Summary

Package: clustifyr
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings clustifyr_1.20.0.tar.gz
StartedAt: 2025-09-16 01:27:11 -0400 (Tue, 16 Sep 2025)
EndedAt: 2025-09-16 01:48:48 -0400 (Tue, 16 Sep 2025)
EllapsedTime: 1297.0 seconds
RetCode: 0
Status:   OK  
CheckDir: clustifyr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings clustifyr_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/clustifyr.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clustifyr/DESCRIPTION’ ... OK
* this is package ‘clustifyr’ version ‘1.20.0’
* 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 ‘clustifyr’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... 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 LazyData ... 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
plot_pathway_gsea      24.810  0.141  26.171
calculate_pathway_gsea 21.848  0.129  23.834
overcluster_test        4.656  0.211   5.345
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/clustifyr.Rcheck/00check.log’
for details.


Installation output

clustifyr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL clustifyr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘clustifyr’ ...
** this is package ‘clustifyr’ version ‘1.20.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (clustifyr)

Tests output

clustifyr.Rcheck/tests/testthat.Rout


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(clustifyr)
> 
> test_check("clustifyr")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 183 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 183 ]
> 
> proc.time()
   user  system elapsed 
683.313   9.872 732.290 

Example timings

clustifyr.Rcheck/clustifyr-Ex.timings

nameusersystemelapsed
append_genes0.0430.0100.061
assess_rank_bias0.0000.0020.002
average_clusters0.0840.0180.115
binarize_expr0.1320.0070.144
build_atlas0.7970.0270.866
calc_distance0.0070.0010.009
calculate_pathway_gsea21.848 0.12923.834
call_consensus0.3980.0150.429
call_to_metadata0.3660.4850.891
check_raw_counts0.8860.0580.982
clustify3.2330.1193.558
clustify_lists0.1030.0120.119
clustify_nudge1.8630.0482.040
clustifyr_methods0.0000.0010.000
collapse_to_cluster2.0180.0832.207
compare_lists0.2340.0090.256
cor_to_call0.1290.0080.145
cor_to_call_rank0.1100.0010.114
cor_to_call_topn0.1170.0020.128
downsample_matrix0.0220.0010.025
feature_select_PCA0.0160.0080.023
file_marker_parse0.0030.0030.007
find_rank_bias0.0720.0050.078
gene_pct_markerm0.5450.0060.557
get_ucsc_reference0.0000.0020.002
get_vargenes0.0010.0020.003
gmt_to_list0.0760.0070.091
insert_meta_object0.5120.0150.557
make_comb_ref0.0300.0040.036
marker_select0.0380.0110.062
matrixize_markers0.0570.0220.087
object_data0.6680.0230.724
object_ref1.3920.3361.797
overcluster2.0450.0912.228
overcluster_test4.6560.2115.345
parse_loc_object0.4970.0110.534
plot_best_call1.2460.0221.330
plot_cor1.9680.0562.109
plot_cor_heatmap2.1020.0802.412
plot_dims0.8990.0130.954
plot_gene1.5260.0241.576
plot_pathway_gsea24.810 0.14126.171
plot_rank_bias0.0000.0020.002
pos_neg_marker0.0170.0010.022
pos_neg_select0.1890.0040.199
query_rank_bias0.0790.0040.092
ref_feature_select0.0380.0020.040
ref_marker_select0.5130.0050.571
reverse_marker_matrix0.0100.0220.043
run_clustifyr_app0.0010.0010.002
seurat_meta0.5670.0130.627
seurat_ref0.5370.0150.655
write_meta0.6930.0400.872