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This page was generated on 2021-12-06 13:05:03 -0500 (Mon, 06 Dec 2021).

CHECK results for microbiomeMarker on nebbiolo2

To the developers/maintainers of the microbiomeMarker package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/microbiomeMarker.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 1144/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiomeMarker 1.0.1  (landing page)
Yang Cao
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/microbiomeMarker
git_branch: RELEASE_3_14
git_last_commit: d4852b9
git_last_commit_date: 2021-11-08 03:46:16 -0500 (Mon, 08 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: microbiomeMarker
Version: 1.0.1
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:microbiomeMarker.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings microbiomeMarker_1.0.1.tar.gz
StartedAt: 2021-12-05 08:41:21 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 08:47:51 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 390.4 seconds
RetCode: 0
Status:   OK  
CheckDir: microbiomeMarker.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:microbiomeMarker.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings microbiomeMarker_1.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/microbiomeMarker.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 ‘microbiomeMarker/DESCRIPTION’ ... OK
* this is package ‘microbiomeMarker’ version ‘1.0.1’
* 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 ‘microbiomeMarker’ 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 data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
run_deseq2     9.245  0.112   9.359
run_ancombc    7.450  0.091   7.547
plot_cladogram 6.902  0.079   6.982
plot_sl_roc    6.822  0.087   6.914
run_aldex      5.478  0.131   5.612
plot_heatmap   5.412  0.076   5.488
* 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

microbiomeMarker.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘microbiomeMarker’ ...
** using staged installation
** R
** data
** 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 (microbiomeMarker)

Tests output

microbiomeMarker.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(microbiomeMarker)
> 
> test_check("microbiomeMarker")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 11 | SKIP 1 | PASS 194 ]
> 
> proc.time()
   user  system elapsed 
 59.694   2.697  62.387 

Example timings

microbiomeMarker.Rcheck/microbiomeMarker-Ex.timings

nameusersystemelapsed
abundances-methods0.0690.0080.077
aggregate_taxa1.2700.0121.283
assign-marker_table2.5060.1082.614
effect_size-plot2.6010.0282.628
extract_posthoc_res0.1130.0000.113
import_dada20.0640.0050.068
import_qiime20.2080.0240.241
marker_table-methods2.3520.0082.360
microbiomeMarker0.0140.0000.013
nmarker-methods0.0020.0000.001
normalize-methods0.1060.0120.118
phyloseq2DESeq20.6980.0000.699
phyloseq2edgeR0.1250.0000.125
phyloseq2metagenomeSeq0.1590.0040.163
plot_abundance3.4130.0403.453
plot_cladogram6.9020.0796.982
plot_heatmap5.4120.0765.488
plot_postHocTest0.8480.0080.856
plot_sl_roc6.8220.0876.914
postHocTest0.0980.0040.102
run_aldex5.4780.1315.612
run_ancom000
run_ancombc7.4500.0917.547
run_deseq29.2450.1129.359
run_edger3.3710.0363.408
run_lefse4.2490.0484.297
run_limma_voom2.4770.0232.500
run_metagenomeseq4.0490.0454.094
run_posthoc_test0.4730.0120.485
run_simple_stat2.4680.0162.484
run_sl2.6490.0482.697
run_test_multiple_groups2.8090.0322.840
run_test_two_groups2.8120.0322.843
subset_marker2.3130.0122.325
summarize_taxa0.2910.0160.307
transform_abundances0.1100.0160.127