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This page was generated on 2021-06-17 02:38:16 -0400 (Thu, 17 Jun 2021).

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? here for more information.
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raw results

Package 336/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clustifyr 1.4.0  (landing page)
Rui Fu
Snapshot Date: 2021-06-15 06:50:12 -0400 (Tue, 15 Jun 2021)
URL: https://git.bioconductor.org/packages/clustifyr
Branch: RELEASE_3_13
Last Commit: 7a53859
Last Changed Date: 2021-05-19 12:49:30 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: clustifyr
Version: 1.4.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings clustifyr_1.4.0.tar.gz
StartedAt: 2021-06-15 11:20:27 -0400 (Tue, 15 Jun 2021)
EndedAt: 2021-06-15 11:25:22 -0400 (Tue, 15 Jun 2021)
EllapsedTime: 294.5 seconds
RetCode: 0
Status:   OK  
CheckDir: clustifyr.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings clustifyr_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/clustifyr.Rcheck’
* using R version 4.1.0 (2021-05-18)
* 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 ‘1.4.0’
* 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 ... 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

clustifyr.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL clustifyr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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 162 ]
> 
> proc.time()
   user  system elapsed 
102.741   4.205 106.934 

Example timings

clustifyr.Rcheck/clustifyr-Ex.timings

nameusersystemelapsed
append_genes0.0570.0120.069
assess_rank_bias0.0000.0000.001
average_clusters0.7720.0110.785
binarize_expr0.0460.0090.054
build_atlas0.0610.0070.070
calculate_pathway_gsea2.0440.0082.052
call_consensus0.180.000.18
call_to_metadata0.1450.2590.405
check_raw_counts1.3920.0641.457
clustify0.1590.0160.175
clustify_lists0.1420.0000.142
clustify_nudge0.5900.0110.602
clustifyr_methods000
collapse_to_cluster1.2180.0471.266
compare_lists0.1180.0090.126
cor_to_call0.0700.0040.073
cor_to_call_rank0.0590.0000.059
cor_to_call_topn0.0630.0000.063
downsample_matrix0.1110.0000.111
feature_select_PCA0.0090.0000.009
file_marker_parse0.0010.0020.003
find_rank_bias0.0410.0010.041
gene_pct_markerm0.3290.0070.337
get_ucsc_reference000
get_vargenes000
gmt_to_list0.1630.0080.172
insert_meta_object000
install_clustifyr_app000
make_comb_ref0.0120.0000.012
marker_select0.0230.0000.023
matrixize_markers0.0260.0030.031
object_data0.0460.0010.045
object_ref0.0060.0030.010
overcluster1.6030.1201.723
overcluster_test0.9320.0080.941
parse_loc_object0.0010.0000.001
plot_best_call0.4650.0200.485
plot_cor0.4420.0400.483
plot_cor_heatmap0.7210.0200.741
plot_dims0.2150.0000.216
plot_gene0.4190.0000.419
plot_pathway_gsea3.1930.0243.217
plot_rank_bias0.0010.0000.001
pos_neg_marker0.0090.0000.008
pos_neg_select0.0640.0000.063
query_rank_bias0.0390.0040.043
ref_feature_select0.0390.0000.040
ref_marker_select0.1660.0000.167
reverse_marker_matrix0.0030.0040.007
run_clustifyr_app0.0010.0000.000
run_gsea1.1130.0161.128
seurat_meta0.0010.0000.000
seurat_ref0.0020.0000.002
write_meta0.2650.0040.270