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This page was generated on 2022-04-13 12:05:36 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 nebbiolo2


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 1146/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MicrobiotaProcess 1.6.6  (landing page)
Shuangbin Xu
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/MicrobiotaProcess
git_branch: RELEASE_3_14
git_last_commit: 1623d4f
git_last_commit_date: 2022-04-06 09:09:04 -0400 (Wed, 06 Apr 2022)
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: MicrobiotaProcess
Version: 1.6.6
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MicrobiotaProcess.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MicrobiotaProcess_1.6.6.tar.gz
StartedAt: 2022-04-12 08:13:43 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 08:17:58 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 254.9 seconds
RetCode: 0
Status:   OK  
CheckDir: MicrobiotaProcess.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MicrobiotaProcess.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MicrobiotaProcess_1.6.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/MicrobiotaProcess.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.6.6’
* 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_abundance-methods 6.300  0.027   6.087
mp_cal_rarecurve-methods 5.089  0.032   5.121
* 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-3.14-bioc/R/bin/R CMD INSTALL MicrobiotaProcess
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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")
MicrobiotaProcess v1.6.6 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 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 11.432   0.564  11.864 

Example timings

MicrobiotaProcess.Rcheck/MicrobiotaProcess-Ex.timings

nameusersystemelapsed
ImportDada21.2690.0641.333
ImportQiime23.3960.1083.509
MPSE0.1210.0000.121
as.treedata000
build_tree000
convert_to_treedata000
data-hmp_aerobiosis_small0.0070.0030.012
data-kostic2012crc0.0160.0120.028
data-test_otu_data0.0020.0000.002
diff_analysis000
dr_extract0.0000.0000.001
drop_taxa000
generalizedFC0.0060.0000.006
get_alltaxadf000
get_alphaindex0.0000.0000.001
get_clust000
get_coord000
get_count000
get_dist000
get_mean_median000
get_pca000
get_pcoa0.0000.0000.001
get_pvalue0.1050.0040.110
get_rarecurve0.0000.0000.001
get_sampledflist000
get_taxadf000
get_upset000
get_varct000
get_vennlist000
ggbartax0.0010.0000.000
ggbox000
ggclust000
ggdiffbox0.0000.0000.001
ggdiffclade000
ggdifftaxbar000
ggeffectsize000
ggordpoint000
ggrarecurve000
mp_adonis-methods0.1150.0000.115
mp_aggregate-methods0.0000.0000.001
mp_aggregate_clade-methods000
mp_anosim-methods0.9300.0270.959
mp_balance_clade-methods0.0010.0000.000
mp_cal_abundance-methods6.3000.0276.087
mp_cal_alpha-methods0.9900.0010.991
mp_cal_cca-methods0.7410.0040.745
mp_cal_clust-methods0.3930.0000.393
mp_cal_dist-methods1.5260.0041.530
mp_cal_nmds-methods0.2260.0120.238
mp_cal_pca-methods1.8590.0761.935
mp_cal_pcoa-methods0.5370.0760.613
mp_cal_pd_metric-methods0.0010.0000.000
mp_cal_rarecurve-methods5.0890.0325.121
mp_cal_rda-methods0.5390.0280.566
mp_cal_upset-methods1.0080.0121.012
mp_cal_venn-methods1.5810.0401.625
mp_decostand-methods0.3820.0040.386
mp_diff_analysis-methods4.3650.0564.298
mp_diff_clade-methods000
mp_envfit-methods2.3510.0042.355
mp_filter_taxa-methods0.9870.0030.989
mp_import_metaphlan2.5140.0082.522
mp_mantel-methods0.2500.0040.254
mp_mrpp-methods0.1550.0000.155
mp_plot_abundance-methods000
mp_plot_alpha-methods000
mp_plot_dist-methods000
mp_plot_ord-methods000
mp_plot_rarecurve-methods0.0000.0000.001
mp_plot_upset-methods000
mp_plot_venn-methods000
mp_rrarefy-methods0.3730.0010.374
mp_select_as_tip-methods000
mp_stat_taxa-methods0.8320.0030.721
multi_compare0.0080.0000.008
read_qza000
show-methods000
split_data0.0030.0000.003
split_str_to_list000
theme_taxbar000