Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1256/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MicrobiotaProcess 1.18.0 (landing page) Shuangbin Xu
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 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 | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.18.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MicrobiotaProcess.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MicrobiotaProcess_1.18.0.tar.gz |
StartedAt: 2024-11-20 05:43:57 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 05:49:00 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 302.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MicrobiotaProcess.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MicrobiotaProcess.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MicrobiotaProcess_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/MicrobiotaProcess.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘1.18.0’ * 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 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 ... 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 6.644 0.012 6.443 * 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 ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/MicrobiotaProcess.Rcheck/00check.log’ for details.
MicrobiotaProcess.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MicrobiotaProcess ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-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)
MicrobiotaProcess.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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 v1.18.0 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 9.592 0.728 10.200
MicrobiotaProcess.Rcheck/MicrobiotaProcess-Ex.timings
name | user | system | elapsed | |
ImportDada2 | 1.000 | 0.057 | 1.062 | |
ImportQiime2 | 2.836 | 0.051 | 2.906 | |
MPSE | 0.06 | 0.00 | 0.06 | |
as.treedata | 0 | 0 | 0 | |
build_tree | 0 | 0 | 0 | |
convert_to_treedata | 0 | 0 | 0 | |
data-hmp_aerobiosis_small | 0.008 | 0.001 | 0.009 | |
data-kostic2012crc | 0.019 | 0.005 | 0.024 | |
data-test_otu_data | 0.001 | 0.000 | 0.001 | |
diff_analysis | 0 | 0 | 0 | |
dr_extract | 0 | 0 | 0 | |
drop_taxa | 0 | 0 | 0 | |
generalizedFC | 0.004 | 0.000 | 0.004 | |
get_alltaxadf | 0 | 0 | 0 | |
get_alphaindex | 0 | 0 | 0 | |
get_clust | 0 | 0 | 0 | |
get_coord | 0 | 0 | 0 | |
get_count | 0 | 0 | 0 | |
get_dist | 0 | 0 | 0 | |
get_mean_median | 0.001 | 0.000 | 0.000 | |
get_pca | 0 | 0 | 0 | |
get_pcoa | 0 | 0 | 0 | |
get_pvalue | 0.037 | 0.000 | 0.039 | |
get_rarecurve | 0 | 0 | 0 | |
get_sampledflist | 0 | 0 | 0 | |
get_taxadf | 0 | 0 | 0 | |
get_upset | 0.000 | 0.000 | 0.001 | |
get_varct | 0 | 0 | 0 | |
get_vennlist | 0 | 0 | 0 | |
ggbartax | 0 | 0 | 0 | |
ggbox | 0 | 0 | 0 | |
ggclust | 0 | 0 | 0 | |
ggdiffbox | 0 | 0 | 0 | |
ggdiffclade | 0 | 0 | 0 | |
ggdifftaxbar | 0.000 | 0.000 | 0.001 | |
ggeffectsize | 0.000 | 0.001 | 0.000 | |
ggordpoint | 0 | 0 | 0 | |
ggrarecurve | 0 | 0 | 0 | |
mp_adonis-methods | 0.067 | 0.002 | 0.069 | |
mp_aggregate-methods | 0 | 0 | 0 | |
mp_aggregate_clade-methods | 0 | 0 | 0 | |
mp_anosim-methods | 0.755 | 0.015 | 0.769 | |
mp_balance_clade-methods | 0 | 0 | 0 | |
mp_cal_abundance-methods | 6.644 | 0.012 | 6.443 | |
mp_cal_alpha-methods | 0.711 | 0.010 | 0.730 | |
mp_cal_cca-methods | 0.612 | 0.004 | 0.617 | |
mp_cal_clust-methods | 0.270 | 0.003 | 0.273 | |
mp_cal_dist-methods | 1.339 | 0.004 | 1.344 | |
mp_cal_divergence-methods | 0 | 0 | 0 | |
mp_cal_nmds-methods | 0.176 | 0.001 | 0.178 | |
mp_cal_pca-methods | 1.040 | 0.003 | 1.044 | |
mp_cal_pcoa-methods | 0.350 | 0.002 | 0.355 | |
mp_cal_pd_metric-methods | 0 | 0 | 0 | |
mp_cal_rarecurve-methods | 4.180 | 0.014 | 4.197 | |
mp_cal_rda-methods | 0.489 | 0.001 | 0.491 | |
mp_cal_upset-methods | 0.711 | 0.005 | 0.707 | |
mp_cal_venn-methods | 0.363 | 0.003 | 0.358 | |
mp_decostand-methods | 0.213 | 0.002 | 0.215 | |
mp_diff_analysis-methods | 3.259 | 0.005 | 3.152 | |
mp_diff_clade-methods | 0 | 0 | 0 | |
mp_dmn-methods | 0 | 0 | 0 | |
mp_dmngroup-methods | 0 | 0 | 0 | |
mp_envfit-methods | 1.497 | 0.038 | 1.536 | |
mp_filter_taxa-methods | 0.611 | 0.002 | 0.613 | |
mp_import_metaphlan | 2.400 | 0.001 | 2.405 | |
mp_mantel-methods | 0.201 | 0.002 | 0.203 | |
mp_mrpp-methods | 0.119 | 0.001 | 0.121 | |
mp_plot_abundance-methods | 0.001 | 0.000 | 0.000 | |
mp_plot_alpha-methods | 0 | 0 | 0 | |
mp_plot_diff_boxplot-methods | 3.928 | 0.005 | 3.817 | |
mp_plot_diff_cladogram | 0 | 0 | 0 | |
mp_plot_diff_manhattan-methods | 2.075 | 0.001 | 1.956 | |
mp_plot_dist-methods | 0 | 0 | 0 | |
mp_plot_ord-methods | 0 | 0 | 0 | |
mp_plot_rarecurve-methods | 0 | 0 | 0 | |
mp_plot_upset-methods | 0 | 0 | 0 | |
mp_plot_venn-methods | 0 | 0 | 0 | |
mp_rrarefy-methods | 0.233 | 0.001 | 0.234 | |
mp_select_as_tip-methods | 0 | 0 | 0 | |
mp_stat_taxa-methods | 0.738 | 0.002 | 0.625 | |
multi_compare | 0.006 | 0.000 | 0.006 | |
read_qza | 0.001 | 0.000 | 0.000 | |
show-methods | 0 | 0 | 0 | |
split_data | 0.001 | 0.000 | 0.002 | |
split_str_to_list | 0.000 | 0.000 | 0.001 | |
theme_taxbar | 0 | 0 | 0 | |