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This page was generated on 2024-06-18 17:59 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 1266/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MicrobiotaProcess 1.16.0  (landing page)
Shuangbin Xu
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/MicrobiotaProcess
git_branch: RELEASE_3_19
git_last_commit: 7a3d7c5
git_last_commit_date: 2024-04-30 11:22:53 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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 12.7.4 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 palomino3

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: 1.16.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MicrobiotaProcess.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings MicrobiotaProcess_1.16.0.tar.gz
StartedAt: 2024-06-17 06:46:49 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 06:56:14 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 564.6 seconds
RetCode: 0
Status:   OK  
CheckDir: MicrobiotaProcess.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MicrobiotaProcess.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings MicrobiotaProcess_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/MicrobiotaProcess.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MicrobiotaProcess/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MicrobiotaProcess' version '1.16.0'
* 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 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     8.11   0.29    8.41
mp_cal_rarecurve-methods     5.27   0.22    5.48
mp_plot_diff_boxplot-methods 4.84   0.19    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 ... 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
  'F:/biocbuild/bbs-3.19-bioc/meat/MicrobiotaProcess.Rcheck/00check.log'
for details.


Installation output

MicrobiotaProcess.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL MicrobiotaProcess
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 v1.16.0 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 
  12.48    9.23   21.67 

Example timings

MicrobiotaProcess.Rcheck/MicrobiotaProcess-Ex.timings

nameusersystemelapsed
ImportDada21.320.191.50
ImportQiime23.930.234.17
MPSE0.060.020.07
as.treedata000
build_tree000
convert_to_treedata000
data-hmp_aerobiosis_small0.020.000.02
data-kostic2012crc0.030.020.04
data-test_otu_data000
diff_analysis000
dr_extract000
drop_taxa000
generalizedFC000
get_alltaxadf000
get_alphaindex0.000.020.01
get_clust000
get_coord000
get_count000
get_dist000
get_mean_median000
get_pca000
get_pcoa000
get_pvalue0.070.030.13
get_rarecurve000
get_sampledflist000
get_taxadf000
get_upset000
get_varct000
get_vennlist000
ggbartax000
ggbox000
ggclust000
ggdiffbox0.020.000.00
ggdiffclade000
ggdifftaxbar000
ggeffectsize000
ggordpoint000
ggrarecurve000
mp_adonis-methods0.150.000.16
mp_aggregate-methods000
mp_aggregate_clade-methods000
mp_anosim-methods1.220.071.29
mp_balance_clade-methods000
mp_cal_abundance-methods8.110.298.41
mp_cal_alpha-methods1.100.011.12
mp_cal_cca-methods1.120.171.33
mp_cal_clust-methods0.350.070.41
mp_cal_dist-methods2.260.092.36
mp_cal_divergence-methods000
mp_cal_nmds-methods0.360.080.44
mp_cal_pca-methods2.410.062.46
mp_cal_pcoa-methods0.540.050.60
mp_cal_pd_metric-methods000
mp_cal_rarecurve-methods5.270.225.48
mp_cal_rda-methods0.800.110.90
mp_cal_upset-methods1.030.031.10
mp_cal_venn-methods0.520.030.61
mp_decostand-methods0.420.010.44
mp_diff_analysis-methods4.360.214.58
mp_diff_clade-methods000
mp_dmn-methods000
mp_dmngroup-methods0.020.000.01
mp_envfit-methods2.450.172.63
mp_filter_taxa-methods0.840.010.86
mp_import_metaphlan2.300.082.50
mp_mantel-methods0.250.110.36
mp_mrpp-methods0.160.000.15
mp_plot_abundance-methods000
mp_plot_alpha-methods0.000.000.02
mp_plot_diff_boxplot-methods4.840.195.03
mp_plot_diff_cladogram000
mp_plot_diff_manhattan-methods2.770.102.84
mp_plot_dist-methods000
mp_plot_ord-methods000
mp_plot_rarecurve-methods000
mp_plot_upset-methods000
mp_plot_venn-methods000
mp_rrarefy-methods0.340.010.36
mp_select_as_tip-methods000
mp_stat_taxa-methods0.830.040.86
multi_compare0.020.000.02
read_qza000
show-methods000
split_data0.000.030.03
split_str_to_list000
theme_taxbar000