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This page was generated on 2021-10-15 15:05:45 -0400 (Fri, 15 Oct 2021).

CHECK results for MicrobiotaProcess on nebbiolo1

To the developers/maintainers of the MicrobiotaProcess package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MicrobiotaProcess.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 1130/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MicrobiotaProcess 1.4.4  (landing page)
Shuangbin Xu
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/MicrobiotaProcess
git_branch: RELEASE_3_13
git_last_commit: 3305c9c
git_last_commit_date: 2021-09-30 21:50:40 -0400 (Thu, 30 Sep 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: MicrobiotaProcess
Version: 1.4.4
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MicrobiotaProcess.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MicrobiotaProcess_1.4.4.tar.gz
StartedAt: 2021-10-14 10:35:36 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:40:11 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 275.5 seconds
RetCode: 0
Status:   OK  
CheckDir: MicrobiotaProcess.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MicrobiotaProcess.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MicrobiotaProcess_1.4.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/MicrobiotaProcess.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MicrobiotaProcess/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MicrobiotaProcess’ version ‘1.4.4’
* 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 ‘MicrobiotaProcess’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
mp_cal_rarecurve-methods 6.742  0.151   6.894
* 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

MicrobiotaProcess.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL MicrobiotaProcess
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘MicrobiotaProcess’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘rownames<-’ from package ‘base’ in package ‘MicrobiotaProcess’
** help
*** installing help indices
** 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 (MicrobiotaProcess)

Tests output

MicrobiotaProcess.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-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("MicrobiotaProcess")

Attaching package: 'MicrobiotaProcess'

The following object is masked from 'package:stats':

    filter

> test_check("MicrobiotaProcess")
Processing map file...
Processing otu/tax file...
Reading file into memory prior to parsing...
Detecting first header line...
Header is on line 2  
Converting input file to a table...
Defining OTU table... 
Parsing taxonomy table...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
> 
> proc.time()
   user  system elapsed 
 20.508   1.536  22.036 

Example timings

MicrobiotaProcess.Rcheck/MicrobiotaProcess-Ex.timings

nameusersystemelapsed
ImportDada21.4620.0241.487
ImportQiime22.1500.0972.247
as.MPSE0.6050.1070.713
as.treedata0.3230.0200.343
build_tree0.0000.0000.001
convert_to_treedata0.0010.0000.000
data-hmp_aerobiosis_small0.0060.0040.010
data-kostic2012crc0.0810.0000.082
data-test_otu_data0.0010.0000.001
diff_analysis000
dr_extract000
drop_taxa0.0000.0000.001
generalizedFC0.0020.0030.006
get_alltaxadf000
get_alphaindex0.0000.0000.001
get_clust0.0000.0000.001
get_coord0.0000.0010.000
get_count0.0000.0010.000
get_dist000
get_mean_median000
get_pca0.0000.0000.001
get_pcoa0.0000.0010.000
get_pvalue0.0610.0020.065
get_rarecurve0.0000.0010.001
get_sampledflist0.0000.0010.000
get_taxadf000
get_upset000
get_varct000
get_vennlist0.0000.0010.001
ggbartax0.0000.0010.001
ggbox0.0000.0010.001
ggclust0.0000.0010.001
ggdiffbox0.0000.0010.001
ggdiffclade0.0000.0010.001
ggdifftaxbar000
ggeffectsize000
ggordpoint000
ggrarecurve000
mp_adonis-methods0.1490.0000.148
mp_aggregate-methods000
mp_anosim-methods1.0710.0521.123
mp_cal_abundance-methods4.5430.0914.634
mp_cal_alpha-methods1.8390.0921.933
mp_cal_cca-methods0.6120.0080.620
mp_cal_clust-methods0.4690.0230.493
mp_cal_dist-methods0.6230.0280.651
mp_cal_nmds-methods0.2520.0170.268
mp_cal_pca-methods1.1030.0041.107
mp_cal_pcoa-methods0.5060.0040.510
mp_cal_rarecurve-methods6.7420.1516.894
mp_cal_rda-methods0.5040.0080.512
mp_cal_upset-methods0.9500.0240.974
mp_cal_venn-methods1.4620.0961.594
mp_decostand-methods0.3510.0000.351
mp_diff_analysis-methods3.4540.0843.539
mp_envfit-methods2.4970.0762.574
mp_filter_taxa-methods0.9820.0000.982
mp_import_metaphlan2.2320.0242.258
mp_mantel-methods0.3050.0000.305
mp_mrpp-methods0.1960.0000.196
mp_plot_abundance-methods0.0010.0000.001
mp_plot_alpha-methods0.0000.0000.001
mp_plot_dist-methods0.0000.0010.001
mp_plot_ord-methods0.0000.0010.001
mp_plot_rarecurve-methods0.0000.0010.001
mp_plot_upset-methods0.0000.0010.001
mp_plot_venn-methods0.0010.0000.000
mp_rrarefy-methods0.3210.0000.321
mp_stat_taxa-methods0.660.000.66
multi_compare0.0060.0040.010
read_qza0.0000.0010.001
show-methods0.0000.0010.001
split_data0.0010.0020.003
split_str_to_list0.0000.0000.001
theme_taxbar0.0000.0000.001