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This page was generated on 2024-07-16 17:42 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4742
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4484
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4513
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4462
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: 2024-07-14 14:00 -0400 (Sun, 14 Jul 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
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
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 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: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2024-07-16 01:19:54 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 01:25:45 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 350.1 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_1.16.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/MicrobiotaProcess.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 13.6.6
* 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 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     8.265  0.093   8.696
mp_cal_rarecurve-methods     6.328  0.092   7.112
mp_diff_analysis-methods     5.514  0.049   5.677
mp_plot_diff_boxplot-methods 5.333  0.042   5.440
* 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-3.19-bioc/meat/MicrobiotaProcess.Rcheck/00check.log’
for details.


Installation output

MicrobiotaProcess.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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 v1.16.0 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 
 14.315   0.609  15.037 

Example timings

MicrobiotaProcess.Rcheck/MicrobiotaProcess-Ex.timings

nameusersystemelapsed
ImportDada21.4590.0661.561
ImportQiime24.0970.1014.238
MPSE0.0930.0010.094
as.treedata000
build_tree0.0000.0000.001
convert_to_treedata0.0000.0010.000
data-hmp_aerobiosis_small0.0160.0020.019
data-kostic2012crc0.0420.0040.045
data-test_otu_data0.0020.0010.004
diff_analysis0.0010.0000.001
dr_extract0.0000.0010.001
drop_taxa0.0000.0000.001
generalizedFC0.0060.0010.007
get_alltaxadf0.0000.0010.000
get_alphaindex000
get_clust000
get_coord000
get_count000
get_dist000
get_mean_median0.0000.0000.001
get_pca0.0010.0000.000
get_pcoa000
get_pvalue0.0660.0030.069
get_rarecurve000
get_sampledflist0.0000.0010.000
get_taxadf0.0010.0000.001
get_upset0.0000.0010.001
get_varct000
get_vennlist000
ggbartax000
ggbox0.0010.0000.000
ggclust000
ggdiffbox000
ggdiffclade0.0000.0000.001
ggdifftaxbar0.0000.0000.001
ggeffectsize0.0000.0000.001
ggordpoint0.0000.0000.001
ggrarecurve000
mp_adonis-methods0.1450.0040.150
mp_aggregate-methods000
mp_aggregate_clade-methods0.0000.0010.000
mp_anosim-methods0.9840.0181.003
mp_balance_clade-methods0.0000.0010.001
mp_cal_abundance-methods8.2650.0938.696
mp_cal_alpha-methods1.1910.0191.338
mp_cal_cca-methods1.0680.0231.212
mp_cal_clust-methods0.4310.0090.489
mp_cal_dist-methods3.1550.0423.549
mp_cal_divergence-methods000
mp_cal_nmds-methods0.3120.0100.361
mp_cal_pca-methods1.6000.0201.817
mp_cal_pcoa-methods0.5960.0080.663
mp_cal_pd_metric-methods0.0000.0010.001
mp_cal_rarecurve-methods6.3280.0927.112
mp_cal_rda-methods0.7320.0110.758
mp_cal_upset-methods1.0840.0131.109
mp_cal_venn-methods0.5410.0110.559
mp_decostand-methods0.3480.0040.355
mp_diff_analysis-methods5.5140.0495.677
mp_diff_clade-methods0.0000.0000.001
mp_dmn-methods0.0000.0000.001
mp_dmngroup-methods0.0000.0000.001
mp_envfit-methods3.0020.0573.102
mp_filter_taxa-methods0.9440.0100.969
mp_import_metaphlan3.0820.0203.136
mp_mantel-methods0.3130.0080.324
mp_mrpp-methods0.1750.0050.182
mp_plot_abundance-methods0.0000.0010.000
mp_plot_alpha-methods0.0000.0010.000
mp_plot_diff_boxplot-methods5.3330.0425.440
mp_plot_diff_cladogram0.0000.0010.001
mp_plot_diff_manhattan-methods2.9460.0222.997
mp_plot_dist-methods0.0000.0010.001
mp_plot_ord-methods0.0000.0010.001
mp_plot_rarecurve-methods000
mp_plot_upset-methods0.0000.0010.000
mp_plot_venn-methods0.0010.0000.000
mp_rrarefy-methods0.3530.0040.362
mp_select_as_tip-methods000
mp_stat_taxa-methods0.9160.0090.942
multi_compare0.0100.0010.013
read_qza000
show-methods0.0000.0010.000
split_data0.0020.0020.005
split_str_to_list000
theme_taxbar0.0010.0000.000