Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-08-21 11:42 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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: 2025-08-18 13:40 -0400 (Mon, 18 Aug 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: 2025-08-19 07:08:12 -0000 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 07:23:41 -0000 (Tue, 19 Aug 2025)
EllapsedTime: 929.7 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      22.076  0.128  22.253
calculate_pathway_gsea 19.614  0.211  19.875
* 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 
588.234   3.512 593.260 

Example timings

clustifyr.Rcheck/clustifyr-Ex.timings

nameusersystemelapsed
append_genes0.8570.0440.904
assess_rank_bias000
average_clusters0.0820.0080.090
binarize_expr0.0870.0080.095
build_atlas0.1210.0080.129
calc_distance0.0060.0000.007
calculate_pathway_gsea19.614 0.21119.875
call_consensus0.2980.0200.319
call_to_metadata0.1580.0400.198
check_raw_counts1.0550.0041.060
clustify2.8110.0762.893
clustify_lists0.9330.0040.939
clustify_nudge1.6550.0161.676
clustifyr_methods0.0000.0000.001
collapse_to_cluster2.5140.0162.533
compare_lists0.2240.0000.225
cor_to_call0.0970.0000.097
cor_to_call_rank0.1310.0040.135
cor_to_call_topn0.1090.0000.110
downsample_matrix0.0170.0000.017
feature_select_PCA0.0130.0000.013
file_marker_parse0.0020.0000.002
find_rank_bias0.0600.0000.061
gene_pct_markerm0.5290.0000.531
get_ucsc_reference0.0010.0000.000
get_vargenes000
gmt_to_list0.0450.0000.046
insert_meta_object0.3480.0000.349
make_comb_ref0.0350.0000.034
marker_select0.030.000.03
matrixize_markers0.0350.0000.036
object_data0.4980.0120.511
object_ref0.4540.0190.475
overcluster2.0720.0282.105
overcluster_test1.6200.0041.629
parse_loc_object0.3280.0320.362
plot_best_call0.6330.0120.646
plot_cor0.7900.0040.796
plot_cor_heatmap1.1380.0161.158
plot_dims0.3390.0000.340
plot_gene0.5550.0040.559
plot_pathway_gsea22.076 0.12822.253
plot_rank_bias000
pos_neg_marker0.0110.0000.010
pos_neg_select0.1130.0000.112
query_rank_bias0.0610.0000.061
ref_feature_select0.0610.0000.061
ref_marker_select0.2680.0040.273
reverse_marker_matrix0.0050.0000.005
run_clustifyr_app0.0010.0000.000
seurat_meta0.3610.0120.374
seurat_ref0.4070.0080.416
write_meta0.4250.0040.431