Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-07-23 12:08 -0400 (Wed, 23 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4792
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4530
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4573
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4514
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4510
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 383/2311HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clustifyr 1.21.0  (landing page)
Rui Fu
Snapshot Date: 2025-07-22 13:25 -0400 (Tue, 22 Jul 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 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 lconway

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: /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_1.21.0.tar.gz
StartedAt: 2025-07-22 19:51:00 -0400 (Tue, 22 Jul 2025)
EndedAt: 2025-07-22 20:03:34 -0400 (Tue, 22 Jul 2025)
EllapsedTime: 754.7 seconds
RetCode: 0
Status:   OK  
CheckDir: clustifyr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/clustifyr.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.21.0’
* 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 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      18.148  0.118  18.372
calculate_pathway_gsea 15.162  0.107  15.347
* 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-3.22-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 ‘1.21.0’
** 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-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 
457.748   6.874 467.046 

Example timings

clustifyr.Rcheck/clustifyr-Ex.timings

nameusersystemelapsed
append_genes0.6850.0130.703
assess_rank_bias0.0000.0000.001
average_clusters0.0420.0070.051
binarize_expr0.0400.0010.042
build_atlas0.0660.0170.083
calc_distance0.0050.0000.005
calculate_pathway_gsea15.162 0.10715.347
call_consensus0.2080.0080.218
call_to_metadata0.1740.1610.336
check_raw_counts0.8220.0400.868
clustify2.0840.0892.195
clustify_lists0.0550.0040.060
clustify_nudge0.9730.0321.013
clustifyr_methods0.0010.0000.000
collapse_to_cluster1.3150.0581.378
compare_lists0.1090.0050.114
cor_to_call0.0670.0060.075
cor_to_call_rank0.0700.0020.073
cor_to_call_topn0.0680.0020.070
downsample_matrix0.0150.0000.015
feature_select_PCA0.0090.0020.011
file_marker_parse0.0020.0020.004
find_rank_bias0.0340.0020.035
gene_pct_markerm0.2900.0020.295
get_ucsc_reference000
get_vargenes0.0010.0010.001
gmt_to_list0.0440.0020.046
insert_meta_object0.2470.0150.263
make_comb_ref0.0120.0010.013
marker_select0.0240.0110.035
matrixize_markers0.0250.0040.030
object_data0.3300.0160.349
object_ref0.3080.1130.427
overcluster1.6810.1141.808
overcluster_test1.2120.0511.272
parse_loc_object0.2410.0080.252
plot_best_call0.5610.0240.591
plot_cor0.6920.0160.730
plot_cor_heatmap1.7330.0711.818
plot_dims0.2420.0120.255
plot_gene0.4930.0230.518
plot_pathway_gsea18.148 0.11818.372
plot_rank_bias0.0000.0010.002
pos_neg_marker0.0090.0010.010
pos_neg_select0.0640.0020.067
query_rank_bias0.0410.0020.045
ref_feature_select0.0270.0020.029
ref_marker_select0.1980.0010.202
reverse_marker_matrix0.0040.0110.016
run_clustifyr_app000
seurat_meta0.3340.0220.358
seurat_ref0.2670.0070.274
write_meta0.3370.0080.367