Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-17 13:05:20 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 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: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
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 20.04.4 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: 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: 2022-01-16 08:40:32 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 08:46:54 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 382.0 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
###
##############################################################################
##############################################################################


* 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     8.679  0.016   8.695
run_ancombc    7.246  0.000   7.246
plot_cladogram 6.875  0.044   6.918
plot_sl_roc    6.614  0.018   6.638
plot_heatmap   5.418  0.028   5.446
run_aldex      5.302  0.088   5.391
* 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 
 58.732   1.717  60.444 

Example timings

microbiomeMarker.Rcheck/microbiomeMarker-Ex.timings

nameusersystemelapsed
abundances-methods0.0700.0040.074
aggregate_taxa1.2760.0081.284
assign-marker_table2.4640.0922.556
effect_size-plot2.5990.0202.618
extract_posthoc_res0.130.000.13
import_dada20.0610.0070.069
import_qiime20.2030.0200.242
marker_table-methods2.3940.0002.393
microbiomeMarker0.0130.0000.013
nmarker-methods0.0010.0000.002
normalize-methods0.0930.0040.098
phyloseq2DESeq20.7660.0040.771
phyloseq2edgeR0.1350.0000.136
phyloseq2metagenomeSeq0.1720.0000.172
plot_abundance3.4510.0003.452
plot_cladogram6.8750.0446.918
plot_heatmap5.4180.0285.446
plot_postHocTest0.7830.0000.784
plot_sl_roc6.6140.0186.638
postHocTest0.0890.0000.089
run_aldex5.3020.0885.391
run_ancom000
run_ancombc7.2460.0007.246
run_deseq28.6790.0168.695
run_edger3.2390.0123.251
run_lefse4.0320.0084.039
run_limma_voom2.3660.0002.365
run_metagenomeseq3.960.003.96
run_posthoc_test0.4470.0000.447
run_simple_stat2.3710.0002.371
run_sl2.4180.0002.419
run_test_multiple_groups2.6840.0162.700
run_test_two_groups2.7590.0002.758
subset_marker2.4580.0002.459
summarize_taxa0.2930.0000.294
transform_abundances0.1360.0040.141