Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:01 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for clustifyr on nebbiolo2


To the developers/maintainers of the clustifyr package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 355/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clustifyr 1.10.0  (landing page)
Kent Riemondy
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/clustifyr
git_branch: RELEASE_3_16
git_last_commit: 768cfde
git_last_commit_date: 2022-11-01 11:21:20 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: clustifyr
Version: 1.10.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings clustifyr_1.10.0.tar.gz
StartedAt: 2023-04-10 19:48:28 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 19:54:15 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 347.6 seconds
RetCode: 0
Status:   OK  
CheckDir: clustifyr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings clustifyr_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/clustifyr.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘clustifyr/DESCRIPTION’ ... OK
* this is package ‘clustifyr’ version ‘1.10.0’
* 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 ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘clustifyr.Rmd’ using ‘UTF-8’... OK
  ‘geo-annotations.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

clustifyr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL clustifyr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-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 version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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")

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[ FAIL 0 | WARN 7 | SKIP 0 | PASS 176 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 176 ]
> 
> proc.time()
   user  system elapsed 
121.492   3.245 124.757 

Example timings

clustifyr.Rcheck/clustifyr-Ex.timings

nameusersystemelapsed
append_genes0.1590.0200.179
assess_rank_bias000
average_clusters0.9170.0881.004
binarize_expr0.0430.0040.047
build_atlas0.0560.0120.068
calc_distance0.0040.0000.005
calculate_pathway_gsea2.8030.0442.847
call_consensus0.2490.0200.269
call_to_metadata0.1680.0320.201
check_raw_counts1.6400.1161.756
clustify0.1860.0000.186
clustify_lists0.0670.0120.079
clustify_nudge0.5990.0080.607
clustifyr_methods0.0000.0000.001
collapse_to_cluster1.3080.0871.394
compare_lists0.1290.0120.141
cor_to_call0.0640.0000.065
cor_to_call_rank0.0730.0000.072
cor_to_call_topn0.0770.0000.076
downsample_matrix0.1310.0040.135
feature_select_PCA0.0080.0080.017
file_marker_parse0.0020.0000.003
find_rank_bias0.0690.0120.082
gene_pct_markerm0.3260.0120.339
get_ucsc_reference0.0010.0000.000
get_vargenes000
gmt_to_list0.3620.0210.396
insert_meta_object000
make_comb_ref0.0160.0000.016
marker_select0.0150.0040.019
matrixize_markers0.0280.0040.032
object_data0.0360.0040.040
object_ref0.0040.0000.004
overcluster1.6820.0681.750
overcluster_test1.1490.0081.157
parse_loc_object0.0010.0000.001
plot_best_call0.6180.0080.626
plot_cor0.5580.0200.578
plot_cor_heatmap0.8590.0120.871
plot_dims0.3230.0000.322
plot_gene0.5220.0080.530
plot_pathway_gsea4.1920.0364.229
plot_rank_bias0.0010.0000.001
pos_neg_marker0.010.000.01
pos_neg_select0.1020.0120.113
query_rank_bias0.0410.0000.042
ref_feature_select0.0330.0000.033
ref_marker_select0.1660.0040.170
reverse_marker_matrix0.0040.0000.004
run_clustifyr_app0.0000.0000.001
seurat_meta000
seurat_ref0.0020.0000.002
write_meta0.0880.0000.089