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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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

Package 1256/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MicrobiotaProcess 1.18.0  (landing page)
Shuangbin Xu
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/MicrobiotaProcess
git_branch: RELEASE_3_20
git_last_commit: af61750
git_last_commit_date: 2024-10-29 10:45:36 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for MicrobiotaProcess on kjohnson1

To the developers/maintainers of the MicrobiotaProcess package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: MicrobiotaProcess
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MicrobiotaProcess.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MicrobiotaProcess_1.18.0.tar.gz
StartedAt: 2024-12-21 01:12:41 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 01:18:29 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 347.8 seconds
RetCode: 0
Status:   OK  
CheckDir: MicrobiotaProcess.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MicrobiotaProcess.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MicrobiotaProcess_1.18.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MicrobiotaProcess.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MicrobiotaProcess/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MicrobiotaProcess’ version ‘1.18.0’
* 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 ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R         2.6Mb
    figures   1.9Mb
* 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 code 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 whether startup messages can be suppressed ... 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     8.487  0.135   9.378
mp_plot_diff_boxplot-methods 5.910  0.125   5.863
mp_diff_analysis-methods     5.746  0.108   5.646
mp_cal_rarecurve-methods     5.611  0.084   5.694
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/MicrobiotaProcess.Rcheck/00check.log’
for details.


Installation output

MicrobiotaProcess.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MicrobiotaProcess
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 v1.18.0 For help:
https://github.com/YuLab-SMU/MicrobiotaProcess/issues

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

Shuangbin Xu, Li Zhan, Wenli Tang, Qianwen Wang, Zehan Dai, Lang Zhou,
Tingze Feng, Meijun Chen, Tianzhi Wu, Erqiang Hu, Guangchuang Yu.
MicrobiotaProcess: A comprehensive R package for deep mining
microbiome. The Innovation. 2023, 4(2):100388. doi:
10.1016/j.xinn.2023.100388

Export the citation to BibTex by citation('MicrobiotaProcess')

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 
 15.016   0.644  16.545 

Example timings

MicrobiotaProcess.Rcheck/MicrobiotaProcess-Ex.timings

nameusersystemelapsed
ImportDada21.3650.0501.417
ImportQiime24.1360.1054.250
MPSE0.1010.0010.102
as.treedata000
build_tree000
convert_to_treedata000
data-hmp_aerobiosis_small0.0170.0020.020
data-kostic2012crc0.0440.0030.047
data-test_otu_data0.0020.0020.005
diff_analysis000
dr_extract0.0000.0000.001
drop_taxa0.0000.0010.000
generalizedFC0.0070.0010.007
get_alltaxadf000
get_alphaindex0.0000.0010.000
get_clust000
get_coord0.0000.0010.000
get_count0.0000.0000.001
get_dist0.0000.0000.001
get_mean_median000
get_pca000
get_pcoa0.0010.0000.000
get_pvalue0.0660.0030.069
get_rarecurve000
get_sampledflist000
get_taxadf000
get_upset0.0000.0010.000
get_varct000
get_vennlist000
ggbartax0.0010.0000.000
ggbox0.0000.0000.001
ggclust0.0000.0000.001
ggdiffbox0.0000.0000.001
ggdiffclade0.0000.0000.001
ggdifftaxbar0.0000.0000.001
ggeffectsize0.0000.0000.001
ggordpoint0.0000.0010.000
ggrarecurve0.0000.0000.002
mp_adonis-methods0.1150.0020.118
mp_aggregate-methods000
mp_aggregate_clade-methods0.0000.0000.001
mp_anosim-methods1.0850.0171.169
mp_balance_clade-methods0.0000.0010.001
mp_cal_abundance-methods8.4870.1359.378
mp_cal_alpha-methods1.0510.0121.064
mp_cal_cca-methods0.9330.0200.954
mp_cal_clust-methods0.4740.0090.482
mp_cal_dist-methods3.0790.0293.170
mp_cal_divergence-methods000
mp_cal_nmds-methods0.2880.0100.298
mp_cal_pca-methods1.4340.0131.447
mp_cal_pcoa-methods0.5160.0060.522
mp_cal_pd_metric-methods0.0000.0000.001
mp_cal_rarecurve-methods5.6110.0845.694
mp_cal_rda-methods0.6690.0110.681
mp_cal_upset-methods1.1980.0371.043
mp_cal_venn-methods0.6640.0340.518
mp_decostand-methods0.3140.0030.316
mp_diff_analysis-methods5.7460.1085.646
mp_diff_clade-methods0.0010.0000.001
mp_dmn-methods0.0000.0000.001
mp_dmngroup-methods000
mp_envfit-methods1.8240.0571.882
mp_filter_taxa-methods0.8260.0050.832
mp_import_metaphlan2.8460.0202.866
mp_mantel-methods0.2640.0100.274
mp_mrpp-methods0.1650.0070.172
mp_plot_abundance-methods000
mp_plot_alpha-methods0.0000.0010.001
mp_plot_diff_boxplot-methods5.9100.1255.863
mp_plot_diff_cladogram0.0000.0000.001
mp_plot_diff_manhattan-methods2.9440.0453.962
mp_plot_dist-methods0.0000.0000.001
mp_plot_ord-methods0.0000.0010.001
mp_plot_rarecurve-methods000
mp_plot_upset-methods000
mp_plot_venn-methods000
mp_rrarefy-methods0.3400.0040.390
mp_select_as_tip-methods0.0000.0010.000
mp_stat_taxa-methods1.0230.0361.992
multi_compare0.0110.0020.013
read_qza000
show-methods0.0000.0010.001
split_data0.0030.0020.004
split_str_to_list0.0000.0000.001
theme_taxbar0.0000.0000.001