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This page was generated on 2021-09-20 15:05:38 -0400 (Mon, 20 Sep 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: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/clustifyr
git_branch: RELEASE_3_13
git_last_commit: 7a53859
git_last_commit_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: 2021-09-19 17:28:37 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 17:36:05 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 448.6 seconds
RetCode: 0
Status:   OK  
CheckDir: clustifyr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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 4.1.1 (2021-08-10)
* 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 6.663  0.061    6.73
* 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

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##############################################################################
###
### 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 4.1.1 (2021-08-10) -- "Kick Things"
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 
168.382   4.452 172.957 

Example timings

clustifyr.Rcheck/clustifyr-Ex.timings

nameusersystemelapsed
append_genes0.0660.0100.075
assess_rank_bias0.0000.0000.002
average_clusters0.6940.0140.708
binarize_expr0.0540.0050.059
build_atlas0.0870.0140.101
calculate_pathway_gsea4.6870.0934.787
call_consensus0.2710.0100.280
call_to_metadata0.2570.2700.527
check_raw_counts1.2560.0461.304
clustify0.2240.0220.247
clustify_lists0.1810.0180.200
clustify_nudge0.9010.0130.918
clustifyr_methods0.0000.0010.001
collapse_to_cluster1.6450.0591.705
compare_lists0.1810.0070.188
cor_to_call0.1130.0040.117
cor_to_call_rank0.0910.0030.094
cor_to_call_topn0.0990.0050.104
downsample_matrix0.1450.0010.146
feature_select_PCA0.0140.0040.018
file_marker_parse0.0010.0010.002
find_rank_bias0.0760.0060.082
gene_pct_markerm0.6590.0050.664
get_ucsc_reference000
get_vargenes0.0010.0000.002
gmt_to_list0.5800.0230.604
insert_meta_object000
install_clustifyr_app000
make_comb_ref0.0190.0020.021
marker_select0.0310.0010.032
matrixize_markers0.0460.0100.055
object_data0.0840.0010.084
object_ref0.0080.0090.016
overcluster2.5590.1042.667
overcluster_test1.5390.0791.620
parse_loc_object0.0000.0000.001
plot_best_call0.6800.0360.719
plot_cor0.6780.0530.732
plot_cor_heatmap1.3620.0301.394
plot_dims0.3650.0070.373
plot_gene0.6180.0160.637
plot_pathway_gsea6.6630.0616.730
plot_rank_bias0.0010.0010.001
pos_neg_marker0.0150.0000.016
pos_neg_select0.1470.0020.150
query_rank_bias0.0810.0040.085
ref_feature_select0.0410.0010.042
ref_marker_select0.4180.0020.421
reverse_marker_matrix0.0070.0060.012
run_clustifyr_app000
run_gsea0.9980.0171.016
seurat_meta0.0000.0010.001
seurat_ref0.0030.0000.004
write_meta0.5300.0030.533