Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-09-25 11:41 -0400 (Thu, 25 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: 2025-09-22 13:40 -0400 (Mon, 22 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    OK  


CHECK results for clustifyr on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: clustifyr
Version: 1.20.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings clustifyr_1.20.0.tar.gz
StartedAt: 2025-09-23 08:26:42 -0000 (Tue, 23 Sep 2025)
EndedAt: 2025-09-23 08:42:30 -0000 (Tue, 23 Sep 2025)
EllapsedTime: 947.7 seconds
RetCode: 0
Status:   OK  
CheckDir: clustifyr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings clustifyr_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/clustifyr.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 ‘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 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 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      22.70  0.064   22.81
calculate_pathway_gsea 19.55  0.068   19.66
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/clustifyr.Rcheck/00check.log’
for details.


Installation output

clustifyr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL clustifyr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-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 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(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 
602.415   4.136 607.919 

Example timings

clustifyr.Rcheck/clustifyr-Ex.timings

nameusersystemelapsed
append_genes0.8950.0040.900
assess_rank_bias000
average_clusters0.0990.0000.099
binarize_expr0.0990.0000.099
build_atlas0.1230.0040.127
calc_distance0.0070.0000.007
calculate_pathway_gsea19.550 0.06819.660
call_consensus0.3120.0270.340
call_to_metadata0.1630.0390.203
check_raw_counts1.0880.0081.098
clustify2.9150.0522.973
clustify_lists0.9560.0040.961
clustify_nudge1.8440.0161.863
clustifyr_methods000
collapse_to_cluster2.5180.0162.537
compare_lists0.2210.0000.221
cor_to_call0.0990.0000.099
cor_to_call_rank0.1430.0000.144
cor_to_call_topn0.1110.0000.112
downsample_matrix0.0170.0000.016
feature_select_PCA0.0130.0000.013
file_marker_parse0.0020.0000.003
find_rank_bias0.0620.0000.063
gene_pct_markerm0.6350.0000.636
get_ucsc_reference000
get_vargenes000
gmt_to_list0.0480.0000.050
insert_meta_object0.3610.0000.362
make_comb_ref0.0340.0000.035
marker_select0.0260.0040.030
matrixize_markers0.0340.0000.035
object_data0.4700.0040.475
object_ref0.4150.0280.445
overcluster3.1130.0443.164
overcluster_test1.6820.0041.690
parse_loc_object0.3320.0280.362
plot_best_call0.6330.0160.650
plot_cor0.7930.0080.803
plot_cor_heatmap1.1780.0161.197
plot_dims0.3510.0080.359
plot_gene0.5800.0000.581
plot_pathway_gsea22.700 0.06422.810
plot_rank_bias000
pos_neg_marker0.0100.0000.011
pos_neg_select0.1070.0040.111
query_rank_bias0.0640.0000.064
ref_feature_select0.0600.0040.064
ref_marker_select0.2510.0040.256
reverse_marker_matrix0.0040.0000.005
run_clustifyr_app000
seurat_meta0.3600.0040.365
seurat_ref0.4060.0000.407
write_meta0.4480.0160.465