Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-08 12:08 -0400 (Fri, 08 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4815 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4550 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4592 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4534 |
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 1271/2315 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MicrobiotaProcess 1.21.0 (landing page) Shuangbin Xu
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
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. |
Package: MicrobiotaProcess |
Version: 1.21.0 |
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_1.21.0.tar.gz |
StartedAt: 2025-08-07 22:17:45 -0400 (Thu, 07 Aug 2025) |
EndedAt: 2025-08-07 22:23:58 -0400 (Thu, 07 Aug 2025) |
EllapsedTime: 372.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MicrobiotaProcess.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/MicrobiotaProcess.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MicrobiotaProcess/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MicrobiotaProcess’ version ‘1.21.0’ * 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 ... INFO 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 ... NOTE Non-topic package-anchored link(s) in Rd file 'reexports.Rd': ‘[magrittr:compound]{%<>%}’ ‘[magrittr:pipe]{%>%}’ ‘[magrittr:aliases]{extract}’ See section 'Cross-references' in the 'Writing R Extensions' manual. 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 9.054 0.081 9.202 mp_cal_rarecurve-methods 7.059 0.072 7.169 mp_plot_diff_boxplot-methods 6.174 0.043 6.249 mp_diff_analysis-methods 5.063 0.051 5.166 * 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-3.22-bioc/meat/MicrobiotaProcess.Rcheck/00check.log’ for details.
MicrobiotaProcess.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MicrobiotaProcess ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘MicrobiotaProcess’ ... ** this is package ‘MicrobiotaProcess’ version ‘1.21.0’ ** 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)
MicrobiotaProcess.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-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 v1.21.0 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 14.311 0.775 15.217
MicrobiotaProcess.Rcheck/MicrobiotaProcess-Ex.timings
name | user | system | elapsed | |
ImportDada2 | 1.459 | 0.051 | 1.521 | |
ImportQiime2 | 3.928 | 0.120 | 4.097 | |
MPSE | 0.093 | 0.001 | 0.094 | |
as.treedata | 0.000 | 0.001 | 0.000 | |
build_tree | 0 | 0 | 0 | |
convert_to_treedata | 0.000 | 0.000 | 0.001 | |
data-hmp_aerobiosis_small | 0.009 | 0.002 | 0.010 | |
data-kostic2012crc | 0.022 | 0.003 | 0.025 | |
data-test_otu_data | 0.002 | 0.002 | 0.003 | |
diff_analysis | 0.000 | 0.000 | 0.001 | |
dr_extract | 0.000 | 0.000 | 0.001 | |
drop_taxa | 0.000 | 0.000 | 0.001 | |
generalizedFC | 0.006 | 0.000 | 0.006 | |
get_alltaxadf | 0 | 0 | 0 | |
get_alphaindex | 0.000 | 0.001 | 0.000 | |
get_clust | 0.000 | 0.000 | 0.001 | |
get_coord | 0 | 0 | 0 | |
get_count | 0.000 | 0.001 | 0.000 | |
get_dist | 0.000 | 0.000 | 0.001 | |
get_mean_median | 0.000 | 0.000 | 0.001 | |
get_pca | 0.000 | 0.001 | 0.001 | |
get_pcoa | 0.000 | 0.000 | 0.001 | |
get_pvalue | 0.065 | 0.002 | 0.068 | |
get_rarecurve | 0.000 | 0.001 | 0.001 | |
get_sampledflist | 0 | 0 | 0 | |
get_taxadf | 0 | 0 | 0 | |
get_upset | 0.000 | 0.001 | 0.001 | |
get_varct | 0 | 0 | 0 | |
get_vennlist | 0.001 | 0.000 | 0.000 | |
ggbartax | 0.000 | 0.001 | 0.000 | |
ggbox | 0.000 | 0.000 | 0.001 | |
ggclust | 0.001 | 0.000 | 0.000 | |
ggdiffbox | 0.000 | 0.001 | 0.001 | |
ggdiffclade | 0.001 | 0.000 | 0.001 | |
ggdifftaxbar | 0 | 0 | 0 | |
ggeffectsize | 0 | 0 | 0 | |
ggordpoint | 0 | 0 | 0 | |
ggrarecurve | 0 | 0 | 0 | |
mp_adonis-methods | 0.117 | 0.003 | 0.121 | |
mp_aggregate-methods | 0 | 0 | 0 | |
mp_aggregate_clade-methods | 0.001 | 0.000 | 0.000 | |
mp_anosim-methods | 1.193 | 0.026 | 1.228 | |
mp_balance_clade-methods | 0.000 | 0.000 | 0.001 | |
mp_cal_abundance-methods | 9.054 | 0.081 | 9.202 | |
mp_cal_alpha-methods | 1.981 | 0.029 | 2.054 | |
mp_cal_cca-methods | 1.047 | 0.034 | 1.131 | |
mp_cal_clust-methods | 0.496 | 0.011 | 0.518 | |
mp_cal_dist-methods | 2.349 | 0.026 | 2.414 | |
mp_cal_divergence-methods | 0 | 0 | 0 | |
mp_cal_nmds-methods | 0.305 | 0.010 | 0.319 | |
mp_cal_pca-methods | 1.792 | 0.015 | 1.818 | |
mp_cal_pcoa-methods | 0.650 | 0.006 | 0.659 | |
mp_cal_pd_metric-methods | 0.000 | 0.000 | 0.001 | |
mp_cal_rarecurve-methods | 7.059 | 0.072 | 7.169 | |
mp_cal_rda-methods | 0.801 | 0.010 | 0.814 | |
mp_cal_upset-methods | 1.204 | 0.014 | 1.224 | |
mp_cal_venn-methods | 0.518 | 0.011 | 0.532 | |
mp_decostand-methods | 0.401 | 0.004 | 0.410 | |
mp_diff_analysis-methods | 5.063 | 0.051 | 5.166 | |
mp_diff_clade-methods | 0.000 | 0.000 | 0.001 | |
mp_dmn-methods | 0 | 0 | 0 | |
mp_dmngroup-methods | 0.000 | 0.000 | 0.001 | |
mp_envfit-methods | 2.103 | 0.052 | 2.166 | |
mp_filter_taxa-methods | 0.989 | 0.006 | 0.999 | |
mp_import_metaphlan | 3.285 | 0.024 | 3.325 | |
mp_mantel-methods | 0.320 | 0.005 | 0.326 | |
mp_mrpp-methods | 0.178 | 0.004 | 0.184 | |
mp_plot_abundance-methods | 0.000 | 0.001 | 0.001 | |
mp_plot_alpha-methods | 0.000 | 0.000 | 0.001 | |
mp_plot_diff_boxplot-methods | 6.174 | 0.043 | 6.249 | |
mp_plot_diff_cladogram | 0.000 | 0.001 | 0.001 | |
mp_plot_diff_manhattan-methods | 3.308 | 0.024 | 3.366 | |
mp_plot_dist-methods | 0.000 | 0.001 | 0.000 | |
mp_plot_ord-methods | 0.000 | 0.001 | 0.001 | |
mp_plot_rarecurve-methods | 0.000 | 0.001 | 0.000 | |
mp_plot_upset-methods | 0 | 0 | 0 | |
mp_plot_venn-methods | 0 | 0 | 0 | |
mp_rrarefy-methods | 0.424 | 0.003 | 0.430 | |
mp_select_as_tip-methods | 0 | 0 | 0 | |
mp_stat_taxa-methods | 1.074 | 0.011 | 1.090 | |
multi_compare | 0.010 | 0.002 | 0.012 | |
read_qza | 0.000 | 0.001 | 0.000 | |
show-methods | 0.001 | 0.000 | 0.001 | |
split_data | 0.003 | 0.002 | 0.005 | |
split_str_to_list | 0.000 | 0.000 | 0.001 | |
theme_taxbar | 0.000 | 0.000 | 0.001 | |