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This page was generated on 2023-04-12 11:05:10 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 1198/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MicrobiotaProcess 1.10.3  (landing page)
Shuangbin Xu
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/MicrobiotaProcess
git_branch: RELEASE_3_16
git_last_commit: 048ca61
git_last_commit_date: 2023-02-08 04:38:29 -0400 (Wed, 08 Feb 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MicrobiotaProcess
Version: 1.10.3
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:MicrobiotaProcess.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings MicrobiotaProcess_1.10.3.tar.gz
StartedAt: 2023-04-10 21:57:37 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 22:04:50 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 433.5 seconds
RetCode: 0
Status:   OK  
CheckDir: MicrobiotaProcess.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:MicrobiotaProcess.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings MicrobiotaProcess_1.10.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/MicrobiotaProcess.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘MicrobiotaProcess/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MicrobiotaProcess’ version ‘1.10.3’
* 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 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 loading without being on the library search path ... 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     9.806  0.236   9.796
mp_plot_diff_boxplot-methods 7.492  0.048   7.419
mp_diff_analysis-methods     6.118  0.107   6.103
mp_cal_rarecurve-methods     6.015  0.080   6.095
* 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 ...
  ‘MicrobiotaProcess.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/MicrobiotaProcess.Rcheck/00check.log’
for details.



Installation output

MicrobiotaProcess.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL MicrobiotaProcess
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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 v1.10.3 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, Land Zhou,
Tingze Feng, Meijun Chen, Tianzhi Wu, Erqiang Hu, Guangchuang Yu.
MicrobiotaProcess: A comprehensive R package for deep mining
microbiome. The Innovation. 2023, 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 
 15.287   1.183  16.319 

Example timings

MicrobiotaProcess.Rcheck/MicrobiotaProcess-Ex.timings

nameusersystemelapsed
ImportDada21.3380.1721.511
ImportQiime23.7460.0763.826
MPSE0.120.000.12
as.treedata000
build_tree0.0000.0000.001
convert_to_treedata000
data-hmp_aerobiosis_small0.0110.0000.011
data-kostic2012crc0.0280.0000.028
data-test_otu_data0.0020.0000.002
diff_analysis000
dr_extract000
drop_taxa000
generalizedFC0.0020.0030.005
get_alltaxadf000
get_alphaindex0.0000.0000.001
get_clust000
get_coord000
get_count000
get_dist000
get_mean_median0.0010.0000.000
get_pca000
get_pcoa000
get_pvalue0.0610.0000.062
get_rarecurve000
get_sampledflist000
get_taxadf000
get_upset000
get_varct000
get_vennlist000
ggbartax000
ggbox000
ggclust000
ggdiffbox000
ggdiffclade000
ggdifftaxbar000
ggeffectsize000
ggordpoint000
ggrarecurve000
mp_adonis-methods0.1020.0000.103
mp_aggregate-methods000
mp_aggregate_clade-methods0.0000.0000.001
mp_anosim-methods1.0920.0121.104
mp_balance_clade-methods0.0000.0000.001
mp_cal_abundance-methods9.8060.2369.796
mp_cal_alpha-methods1.2320.0201.252
mp_cal_cca-methods1.0360.0041.041
mp_cal_clust-methods0.5830.0110.594
mp_cal_dist-methods3.4140.1153.529
mp_cal_divergence-methods0.0000.0000.001
mp_cal_nmds-methods0.2420.0000.242
mp_cal_pca-methods1.6590.0441.702
mp_cal_pcoa-methods0.6110.0000.611
mp_cal_pd_metric-methods0.0000.0000.001
mp_cal_rarecurve-methods6.0150.0806.095
mp_cal_rda-methods0.7270.0120.739
mp_cal_upset-methods1.1600.0081.159
mp_cal_venn-methods2.0250.1122.130
mp_decostand-methods0.3540.0040.358
mp_diff_analysis-methods6.1180.1076.103
mp_diff_clade-methods000
mp_dmn-methods000
mp_dmngroup-methods000
mp_envfit-methods1.8370.0521.890
mp_filter_taxa-methods1.0540.0001.053
mp_import_metaphlan2.6770.0482.725
mp_mantel-methods0.3610.0040.365
mp_mrpp-methods0.1600.0040.164
mp_plot_abundance-methods000
mp_plot_alpha-methods000
mp_plot_diff_boxplot-methods7.4920.0487.419
mp_plot_diff_cladogram0.0010.0000.000
mp_plot_diff_manhattan-methods3.4930.0283.400
mp_plot_dist-methods000
mp_plot_ord-methods0.0010.0000.000
mp_plot_rarecurve-methods0.0000.0000.001
mp_plot_upset-methods000
mp_plot_venn-methods000
mp_rrarefy-methods0.3750.0200.395
mp_select_as_tip-methods0.0000.0000.001
mp_stat_taxa-methods1.3250.0471.249
multi_compare0.010.000.01
read_qza000
show-methods000
split_data0.0030.0000.003
split_str_to_list0.0000.0000.001
theme_taxbar000