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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1249/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MicrobiotaProcess 1.19.0  (landing page)
Shuangbin Xu
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/MicrobiotaProcess
git_branch: devel
git_last_commit: b30acb4
git_last_commit_date: 2024-10-29 10:45:36 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for MicrobiotaProcess on nebbiolo1

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: 1.19.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MicrobiotaProcess.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MicrobiotaProcess_1.19.0.tar.gz
StartedAt: 2024-12-23 23:47:44 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 23:54:24 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 399.5 seconds
RetCode: 0
Status:   OK  
CheckDir: MicrobiotaProcess.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MicrobiotaProcess.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MicrobiotaProcess_1.19.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MicrobiotaProcess.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MicrobiotaProcess/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MicrobiotaProcess’ version ‘1.19.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 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 loading without being on the library search path ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggrarecurve.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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     8.774  0.184   8.749
mp_cal_rarecurve-methods     5.723  0.119   5.843
mp_plot_diff_boxplot-methods 5.024  0.060   4.966
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/MicrobiotaProcess.Rcheck/00check.log’
for details.


Installation output

MicrobiotaProcess.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL MicrobiotaProcess
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 v1.19.0 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 
 12.144   0.719  12.738 

Example timings

MicrobiotaProcess.Rcheck/MicrobiotaProcess-Ex.timings

nameusersystemelapsed
ImportDada22.1040.0032.108
ImportQiime22.7860.0532.841
MPSE0.0790.0000.080
as.treedata0.0000.0010.000
build_tree000
convert_to_treedata000
data-hmp_aerobiosis_small0.0080.0030.012
data-kostic2012crc0.0250.0020.027
data-test_otu_data0.0020.0010.002
diff_analysis000
dr_extract0.0000.0000.001
drop_taxa0.0000.0010.000
generalizedFC0.0040.0000.005
get_alltaxadf0.0000.0000.001
get_alphaindex0.0000.0010.000
get_clust000
get_coord000
get_count0.0000.0000.001
get_dist000
get_mean_median0.0010.0000.000
get_pca0.0000.0010.001
get_pcoa000
get_pvalue0.0490.0010.051
get_rarecurve000
get_sampledflist0.0010.0000.000
get_taxadf000
get_upset0.0000.0010.001
get_varct0.0000.0010.000
get_vennlist000
ggbartax000
ggbox0.0000.0010.001
ggclust0.0000.0010.001
ggdiffbox000
ggdiffclade0.0000.0010.000
ggdifftaxbar000
ggeffectsize0.0010.0000.000
ggordpoint0.0000.0000.001
ggrarecurve0.0000.0010.001
mp_adonis-methods0.0970.0010.098
mp_aggregate-methods000
mp_aggregate_clade-methods0.0000.0010.001
mp_anosim-methods0.9760.0040.980
mp_balance_clade-methods0.0010.0000.000
mp_cal_abundance-methods8.7740.1848.749
mp_cal_alpha-methods0.9860.1211.108
mp_cal_cca-methods0.8760.0120.889
mp_cal_clust-methods0.3520.0020.354
mp_cal_dist-methods1.9130.0201.934
mp_cal_divergence-methods0.0000.0010.001
mp_cal_nmds-methods0.2490.0040.253
mp_cal_pca-methods1.4590.0041.464
mp_cal_pcoa-methods0.5380.0230.561
mp_cal_pd_metric-methods000
mp_cal_rarecurve-methods5.7230.1195.843
mp_cal_rda-methods0.6550.0040.659
mp_cal_upset-methods1.0110.0351.038
mp_cal_venn-methods0.4780.0220.493
mp_decostand-methods0.3160.0070.323
mp_diff_analysis-methods4.4230.0294.268
mp_diff_clade-methods000
mp_dmn-methods000
mp_dmngroup-methods000
mp_envfit-methods2.5460.0892.635
mp_filter_taxa-methods0.8040.0020.806
mp_import_metaphlan2.6150.0282.644
mp_mantel-methods0.2410.0070.249
mp_mrpp-methods0.1430.0020.145
mp_plot_abundance-methods0.0010.0000.000
mp_plot_alpha-methods0.0010.0000.000
mp_plot_diff_boxplot-methods5.0240.0604.966
mp_plot_diff_cladogram000
mp_plot_diff_manhattan-methods2.6940.0072.585
mp_plot_dist-methods0.0000.0010.001
mp_plot_ord-methods0.0010.0000.000
mp_plot_rarecurve-methods000
mp_plot_upset-methods000
mp_plot_venn-methods0.0000.0000.001
mp_rrarefy-methods0.290.000.29
mp_select_as_tip-methods0.0000.0000.001
mp_stat_taxa-methods0.9020.0340.822
multi_compare0.0110.0000.011
read_qza0.0000.0010.000
show-methods0.0000.0010.000
split_data0.0020.0010.002
split_str_to_list000
theme_taxbar000