Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:04:55 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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? here 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 344/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clustifyr 1.6.0  (landing page)
Rui Fu
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/clustifyr
git_branch: RELEASE_3_14
git_last_commit: e07d1df
git_last_commit_date: 2021-10-26 12:57:20 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.6.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings clustifyr_1.6.0.tar.gz
StartedAt: 2022-01-23 06:59:34 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 07:04:54 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 319.8 seconds
RetCode: 0
Status:   OK  
CheckDir: clustifyr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings clustifyr_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/clustifyr.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.6.0’
* 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-3.14-bioc/meat/clustifyr.Rcheck/00check.log’
for details.



Installation output

clustifyr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL clustifyr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.2 (2021-11-01) -- "Bird Hippie"
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 167 ]
> 
> proc.time()
   user  system elapsed 
121.158   5.072 126.236 

Example timings

clustifyr.Rcheck/clustifyr-Ex.timings

nameusersystemelapsed
append_genes0.0440.0120.056
assess_rank_bias000
average_clusters0.1180.0080.125
binarize_expr0.0410.0000.041
build_atlas0.7020.0190.722
calculate_pathway_gsea2.2590.0202.279
call_consensus0.1750.0000.175
call_to_metadata0.1310.0510.184
check_raw_counts1.5720.0601.632
clustify0.1730.0000.172
clustify_lists0.0550.0000.055
clustify_nudge0.5640.0080.572
clustifyr_methods0.0010.0000.000
collapse_to_cluster1.3360.0361.373
compare_lists0.1370.0120.150
cor_to_call0.0650.0000.065
cor_to_call_rank0.0790.0000.079
cor_to_call_topn0.0770.0000.078
downsample_matrix0.1170.0000.117
feature_select_PCA0.0060.0030.009
file_marker_parse0.0010.0010.002
find_rank_bias0.0400.0000.041
gene_pct_markerm0.3520.0000.353
get_ucsc_reference0.0000.0000.001
get_vargenes0.0010.0000.000
gmt_to_list0.3150.0140.344
insert_meta_object000
make_comb_ref0.0380.0040.042
marker_select0.0210.0000.021
matrixize_markers0.0280.0000.028
object_data0.0520.0000.051
object_ref0.0040.0000.004
overcluster1.8410.1802.021
overcluster_test0.9450.0230.969
parse_loc_object0.0000.0000.001
plot_best_call0.4840.0080.493
plot_cor0.4240.0600.485
plot_cor_heatmap0.7460.0280.773
plot_dims0.2430.0040.246
plot_gene0.4640.0040.467
plot_pathway_gsea4.4930.1084.600
plot_rank_bias000
pos_neg_marker0.0070.0000.007
pos_neg_select0.0590.0000.059
query_rank_bias0.0410.0000.041
ref_feature_select0.0320.0040.036
ref_marker_select0.1440.0030.148
reverse_marker_matrix0.0010.0040.003
run_clustifyr_app000
run_gsea0.3390.0080.347
seurat_meta0.0010.0000.001
seurat_ref0.0020.0000.002
write_meta0.3200.0000.321