Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-09-01 12:03 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 385/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clustifyr 1.21.0  (landing page)
Rui Fu
Snapshot Date: 2025-08-31 13:45 -0400 (Sun, 31 Aug 2025)
git_url: https://git.bioconductor.org/packages/clustifyr
git_branch: devel
git_last_commit: d3521c2
git_last_commit_date: 2025-04-16 16:21:04 -0400 (Wed, 16 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for clustifyr on nebbiolo2

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: 1.21.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings clustifyr_1.21.0.tar.gz
StartedAt: 2025-08-31 21:21:05 -0400 (Sun, 31 Aug 2025)
EndedAt: 2025-08-31 21:32:47 -0400 (Sun, 31 Aug 2025)
EllapsedTime: 701.7 seconds
RetCode: 0
Status:   OK  
CheckDir: clustifyr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings clustifyr_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/clustifyr.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘clustifyr/DESCRIPTION’ ... OK
* this is package ‘clustifyr’ version ‘1.21.0’
* 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      17.002  0.255  17.258
calculate_pathway_gsea 15.617  0.233  15.852
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/clustifyr.Rcheck/00check.log’
for details.


Installation output

clustifyr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL clustifyr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘clustifyr’ ...
** this is package ‘clustifyr’ version ‘1.21.0’
** 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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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(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 
418.043   6.339 424.393 

Example timings

clustifyr.Rcheck/clustifyr-Ex.timings

nameusersystemelapsed
append_genes0.0430.0080.051
assess_rank_bias000
average_clusters0.9320.0701.002
binarize_expr0.0420.0020.044
build_atlas0.0500.0120.062
calc_distance0.0040.0010.005
calculate_pathway_gsea15.617 0.23315.852
call_consensus0.1860.0210.209
call_to_metadata0.1140.0300.143
check_raw_counts0.7070.0590.767
clustify1.1700.0421.212
clustify_lists0.7640.0030.768
clustify_nudge0.8980.0190.918
clustifyr_methods0.0000.0000.001
collapse_to_cluster0.5480.0500.599
compare_lists0.1270.0090.137
cor_to_call0.0530.0010.053
cor_to_call_rank0.0830.0020.084
cor_to_call_topn0.0610.0000.061
downsample_matrix0.0120.0000.012
feature_select_PCA0.0070.0010.008
file_marker_parse0.0020.0000.002
find_rank_bias0.0310.0000.032
gene_pct_markerm0.2870.0020.290
get_ucsc_reference000
get_vargenes0.0010.0010.001
gmt_to_list0.0390.0000.040
insert_meta_object0.2140.0060.222
make_comb_ref0.0130.0010.014
marker_select0.0170.0000.017
matrixize_markers0.0250.0000.025
object_data0.2770.0020.279
object_ref0.2470.0130.260
overcluster0.8960.0110.907
overcluster_test1.8110.0801.891
parse_loc_object0.1980.0000.198
plot_best_call0.4620.0030.464
plot_cor0.5840.0020.585
plot_cor_heatmap0.8900.0600.951
plot_dims0.2210.0020.224
plot_gene0.4500.0040.455
plot_pathway_gsea17.002 0.25517.258
plot_rank_bias000
pos_neg_marker0.0080.0000.007
pos_neg_select0.0610.0050.066
query_rank_bias0.0350.0070.042
ref_feature_select0.0300.0050.035
ref_marker_select0.1570.0000.156
reverse_marker_matrix0.0020.0010.003
run_clustifyr_app000
seurat_meta0.2510.0420.292
seurat_ref0.2590.0290.288
write_meta0.2730.0190.293