Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:21:49 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 MicrobiotaProcess on palomino3


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? 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 1176/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MicrobiotaProcess 1.8.2  (landing page)
Shuangbin Xu
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/MicrobiotaProcess
git_branch: RELEASE_3_15
git_last_commit: 48b0eec
git_last_commit_date: 2022-09-18 22:59:44 -0400 (Sun, 18 Sep 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MicrobiotaProcess
Version: 1.8.2
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MicrobiotaProcess.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MicrobiotaProcess_1.8.2.tar.gz
StartedAt: 2022-10-19 01:52:18 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 01:57:48 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 329.8 seconds
RetCode: 0
Status:   OK  
CheckDir: MicrobiotaProcess.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MicrobiotaProcess.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MicrobiotaProcess_1.8.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/MicrobiotaProcess.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.8.2'
* 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 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_abundance-methods     10.22   0.11   10.61
mp_cal_rarecurve-methods      7.73   0.13    7.91
mp_plot_diff_boxplot-methods  6.28   0.12    6.41
mp_diff_analysis-methods      4.91   0.11    5.03
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MicrobiotaProcess
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MicrobiotaProcess' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'taxonomy<-' with signature 'x="MPSE",value="taxonomyTable"': no definition for class "taxonomyTable"
Creating a generic function for 'rownames<-' from package 'base' in package 'MicrobiotaProcess'
in method for 'get_alltaxadf' with signature '"phyloseq"': no definition for class "phyloseq"
in method for 'get_taxadf' with signature '"phyloseq"': no definition for class "phyloseq"
in method for 'get_alphaindex' with signature '"phyloseq"': no definition for class "phyloseq"
in method for 'get_NRI_NTI' with signature '"phyloseq"': no definition for class "phyloseq"
in method for 'get_rarecurve' with signature '"phyloseq"': no definition for class "phyloseq"
in method for 'get_upset' with signature '"phyloseq"': no definition for class "phyloseq"
in method for 'get_vennlist' with signature '"phyloseq"': no definition for class "phyloseq"
in method for 'drop_taxa' with signature '"phyloseq"': no definition for class "phyloseq"
** 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 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
MicrobiotaProcess v1.8.2 For help:
https://github.com/YuLab-SMU/MicrobiotaProcess/issues

If you use MicrobiotaProcess in published research, please cite the
paper:

S Xu, L Zhan, W Tang, Z Dai, L Zhou, T Feng, M Chen, S Liu, X Fu, T Wu,
E Hu, G Yu. MicrobiotaProcess: A comprehensive R package for managing
and analyzing microbiome and other ecological data within the tidy
framework. 04 February 2022, PREPRINT (Version 1) available at Research
Square [https://doi.org/10.21203/rs.3.rs-1284357/v1]

This message can be suppressed by:
suppressPackageStartupMessages(library(MicrobiotaProcess))

Attaching package: 'MicrobiotaProcess'

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

    filter

> test_check("MicrobiotaProcess")
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 13 ]

[ FAIL 0 | WARN 9 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
  14.14    1.12   15.28 

Example timings

MicrobiotaProcess.Rcheck/MicrobiotaProcess-Ex.timings

nameusersystemelapsed
ImportDada21.560.091.70
ImportQiime23.310.083.45
MPSE0.090.000.09
as.treedata000
build_tree000
convert_to_treedata000
data-hmp_aerobiosis_small0.010.000.01
data-kostic2012crc0.050.000.05
data-test_otu_data000
diff_analysis000
dr_extract000
drop_taxa000
generalizedFC000
get_alltaxadf000
get_alphaindex000
get_clust000
get_coord000
get_count000
get_dist000
get_mean_median000
get_pca000
get_pcoa000
get_pvalue0.040.000.07
get_rarecurve000
get_sampledflist000
get_taxadf000
get_upset000
get_varct000
get_vennlist000
ggbartax000
ggbox000
ggclust000
ggdiffbox000
ggdiffclade0.000.010.02
ggdifftaxbar000
ggeffectsize000
ggordpoint000
ggrarecurve000
mp_adonis-methods0.120.000.12
mp_aggregate-methods000
mp_aggregate_clade-methods000
mp_anosim-methods1.370.051.42
mp_balance_clade-methods000
mp_cal_abundance-methods10.22 0.1110.61
mp_cal_alpha-methods1.380.001.40
mp_cal_cca-methods0.930.051.02
mp_cal_clust-methods0.500.000.55
mp_cal_dist-methods2.020.042.08
mp_cal_nmds-methods0.230.020.25
mp_cal_pca-methods1.610.011.62
mp_cal_pcoa-methods0.740.000.73
mp_cal_pd_metric-methods000
mp_cal_rarecurve-methods7.730.137.91
mp_cal_rda-methods0.740.000.74
mp_cal_upset-methods1.250.031.31
mp_cal_venn-methods1.620.092.97
mp_decostand-methods0.610.020.62
mp_diff_analysis-methods4.910.115.03
mp_diff_clade-methods000
mp_envfit-methods1.730.061.80
mp_filter_taxa-methods0.980.051.03
mp_import_metaphlan2.940.012.98
mp_mantel-methods0.310.020.33
mp_mrpp-methods0.240.000.23
mp_plot_abundance-methods000
mp_plot_alpha-methods000
mp_plot_diff_boxplot-methods6.280.126.41
mp_plot_diff_cladogram000
mp_plot_dist-methods000
mp_plot_ord-methods000
mp_plot_rarecurve-methods000
mp_plot_upset-methods000
mp_plot_venn-methods000
mp_rrarefy-methods0.410.000.40
mp_select_as_tip-methods000
mp_stat_taxa-methods1.050.021.06
multi_compare000
read_qza000
show-methods000
split_data000
split_str_to_list000
theme_taxbar000