Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-03-28 11:36:18 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 377/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clustifyr 1.15.1  (landing page)
Kent Riemondy
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/clustifyr
git_branch: devel
git_last_commit: 0097813
git_last_commit_date: 2023-11-07 12:27:45 -0400 (Tue, 07 Nov 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for clustifyr on nebbiolo1


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: 1.15.1
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings clustifyr_1.15.1.tar.gz
StartedAt: 2024-03-27 21:15:16 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 21:26:28 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 671.9 seconds
RetCode: 0
Status:   OK  
CheckDir: clustifyr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings clustifyr_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/clustifyr.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘clustifyr/DESCRIPTION’ ... OK
* this is package ‘clustifyr’ version ‘1.15.1’
* 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      15.796  0.428  16.226
calculate_pathway_gsea 14.036  0.639  14.678
* 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-3.19-bioc/meat/clustifyr.Rcheck/00check.log’
for details.


Installation output

clustifyr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL clustifyr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘clustifyr’ ...
** 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) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 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 6 | SKIP 0 | PASS 176 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 176 ]
> 
> proc.time()
   user  system elapsed 
415.717   4.143 419.932 

Example timings

clustifyr.Rcheck/clustifyr-Ex.timings

nameusersystemelapsed
append_genes0.0320.0160.048
assess_rank_bias000
average_clusters0.7560.0120.768
binarize_expr0.0530.0000.053
build_atlas0.0880.0270.117
calc_distance0.0050.0000.004
calculate_pathway_gsea14.036 0.63914.678
call_consensus0.2080.0200.228
call_to_metadata0.1420.1880.330
check_raw_counts0.7140.0600.774
clustify0.1450.0120.157
clustify_lists0.0620.0080.070
clustify_nudge0.4050.0120.417
clustifyr_methods000
collapse_to_cluster0.5940.0720.666
compare_lists0.7000.0440.744
cor_to_call0.0540.0000.054
cor_to_call_rank0.0570.0000.057
cor_to_call_topn0.0620.0000.062
downsample_matrix0.0220.0000.022
feature_select_PCA0.0110.0000.011
file_marker_parse0.0020.0000.002
find_rank_bias0.030.000.03
gene_pct_markerm0.270.000.27
get_ucsc_reference0.0000.0010.000
get_vargenes0.0000.0010.000
gmt_to_list0.0370.0020.041
insert_meta_object000
make_comb_ref0.0150.0040.018
marker_select0.0180.0000.019
matrixize_markers0.0250.0120.036
object_data0.0400.0000.039
object_ref0.0040.0040.009
overcluster0.8580.0640.923
overcluster_test1.4500.0921.542
parse_loc_object0.0010.0000.001
plot_best_call0.5350.0080.543
plot_cor0.8150.0080.824
plot_cor_heatmap0.8960.0040.900
plot_dims0.3070.0000.307
plot_gene1.3910.0401.431
plot_pathway_gsea15.796 0.42816.226
plot_rank_bias0.0000.0000.001
pos_neg_marker0.0090.0000.009
pos_neg_select0.0670.0040.070
query_rank_bias0.0430.0000.043
ref_feature_select0.0290.0080.036
ref_marker_select0.1710.0000.171
reverse_marker_matrix0.0060.0000.006
run_clustifyr_app0.0010.0000.001
seurat_meta0.0010.0000.000
seurat_ref0.0030.0000.003
write_meta0.070.000.07