Back to Multiple platform build/check report for BioC 3.13
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-06-18 14:06:39 -0400 (Fri, 18 Jun 2021).

CHECK results for clustifyr on machv2

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 336/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clustifyr 1.4.0  (landing page)
Rui Fu
Snapshot Date: 2021-06-17 06:50:12 -0400 (Thu, 17 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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings clustifyr_1.4.0.tar.gz
StartedAt: 2021-06-17 17:16:15 -0400 (Thu, 17 Jun 2021)
EndedAt: 2021-06-17 17:23:45 -0400 (Thu, 17 Jun 2021)
EllapsedTime: 449.8 seconds
RetCode: 0
Status:   OK  
CheckDir: clustifyr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings clustifyr_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/clustifyr.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-apple-darwin17.0 (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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
plot_pathway_gsea 6.176  0.047    6.23
* 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
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/clustifyr.Rcheck/00check.log’
for details.



Installation output

clustifyr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL clustifyr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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-apple-darwin17.0 (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 
166.963   4.722 171.812 

Example timings

clustifyr.Rcheck/clustifyr-Ex.timings

nameusersystemelapsed
append_genes0.0750.0100.085
assess_rank_bias0.0000.0010.001
average_clusters0.6810.0140.695
binarize_expr0.0490.0050.053
build_atlas0.0980.0200.118
calculate_pathway_gsea4.8570.0674.930
call_consensus0.2440.0070.251
call_to_metadata0.2650.2340.499
check_raw_counts1.2350.0441.280
clustify0.2500.0240.274
clustify_lists0.1870.0150.203
clustify_nudge0.9800.0110.992
clustifyr_methods000
collapse_to_cluster1.8330.0761.911
compare_lists0.2090.0160.225
cor_to_call0.1170.0050.123
cor_to_call_rank0.0910.0020.093
cor_to_call_topn0.0740.0010.075
downsample_matrix0.1060.0020.108
feature_select_PCA0.0100.0040.014
file_marker_parse0.0020.0010.003
find_rank_bias0.0740.0040.079
gene_pct_markerm0.6320.0040.636
get_ucsc_reference0.0010.0010.000
get_vargenes0.0010.0010.001
gmt_to_list0.2910.0240.316
insert_meta_object000
install_clustifyr_app0.0000.0000.001
make_comb_ref0.0200.0010.022
marker_select0.0300.0010.032
matrixize_markers0.0430.0130.056
object_data0.0810.0010.082
object_ref0.0070.0130.021
overcluster2.3380.0852.425
overcluster_test1.4710.0711.544
parse_loc_object0.0010.0010.001
plot_best_call0.7860.0410.829
plot_cor0.7450.0590.805
plot_cor_heatmap1.3480.0311.381
plot_dims0.4280.0090.438
plot_gene0.6490.0180.669
plot_pathway_gsea6.1760.0476.230
plot_rank_bias0.0000.0000.001
pos_neg_marker0.0090.0010.010
pos_neg_select0.1400.0020.143
query_rank_bias0.0700.0030.072
ref_feature_select0.0420.0010.043
ref_marker_select0.3720.0010.373
reverse_marker_matrix0.0080.0050.013
run_clustifyr_app0.0000.0000.001
run_gsea1.0170.0101.027
seurat_meta000
seurat_ref0.0020.0010.002
write_meta0.5270.0020.530