Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:06 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 nebbiolo1


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 352/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clustifyr 1.8.0  (landing page)
Kent Riemondy
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/clustifyr
git_branch: RELEASE_3_15
git_last_commit: 0aa93bc
git_last_commit_date: 2022-04-26 12:02:34 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 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
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: clustifyr
Version: 1.8.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings clustifyr_1.8.0.tar.gz
StartedAt: 2022-10-18 19:05:37 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 19:10:45 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 307.7 seconds
RetCode: 0
Status:   OK  
CheckDir: clustifyr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings clustifyr_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/clustifyr.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clustifyr/DESCRIPTION’ ... OK
* this is package ‘clustifyr’ version ‘1.8.0’
* 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 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 ... NOTE
assess_rank_bias : <anonymous>: no visible binding for '<<-' assignment
  to ‘res3’
assess_rank_bias: no visible binding for global variable ‘res3’
average_clusters : <anonymous>: no visible binding for global variable
  ‘pbmc_matrix_small’
Undefined global functions or variables:
  pbmc_matrix_small res3
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/clustifyr.Rcheck/00check.log’
for details.



Installation output

clustifyr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL clustifyr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 175 ]
> 
> proc.time()
   user  system elapsed 
117.933   3.651 121.587 

Example timings

clustifyr.Rcheck/clustifyr-Ex.timings

nameusersystemelapsed
append_genes0.6500.0280.679
assess_rank_bias0.0010.0000.000
average_clusters0.0660.0160.082
binarize_expr0.0410.0040.044
build_atlas0.0720.0040.077
calc_distance0.0040.0000.004
calculate_pathway_gsea2.6450.0282.674
call_consensus0.3110.0040.316
call_to_metadata0.1780.2280.406
check_raw_counts1.4150.0761.491
clustify0.1670.0320.199
clustify_lists0.0670.0080.074
clustify_nudge0.5530.0280.581
clustifyr_methods0.0010.0000.000
collapse_to_cluster1.1330.1041.237
compare_lists0.1260.0160.143
cor_to_call0.0640.0000.065
cor_to_call_rank0.0690.0000.069
cor_to_call_topn0.0690.0000.069
downsample_matrix0.10.00.1
feature_select_PCA0.0070.0040.010
file_marker_parse0.0020.0000.002
find_rank_bias0.0380.0000.038
gene_pct_markerm0.3510.0000.352
get_ucsc_reference000
get_vargenes0.0000.0010.001
gmt_to_list0.3120.0100.338
insert_meta_object000
make_comb_ref0.0090.0030.012
marker_select0.0220.0000.021
matrixize_markers0.0270.0120.039
object_data0.0270.0160.043
object_ref0.0060.0040.009
overcluster1.5950.1281.723
overcluster_test0.9980.0441.042
parse_loc_object0.0000.0000.001
plot_best_call0.5070.0260.533
plot_cor0.5100.0120.522
plot_cor_heatmap0.8900.0120.902
plot_dims0.2540.0040.257
plot_gene0.4690.0040.473
plot_pathway_gsea4.1810.0324.217
plot_rank_bias000
pos_neg_marker0.0080.0000.008
pos_neg_select0.0690.0040.073
query_rank_bias0.0450.0000.045
ref_feature_select0.0400.0030.043
ref_marker_select0.1690.0040.173
reverse_marker_matrix0.0070.0000.007
run_clustifyr_app0.0010.0000.000
seurat_meta0.0010.0000.001
seurat_ref0.0030.0000.003
write_meta0.0870.0000.087