Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 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: 1.18.0 |
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: 2024-12-20 02:40:11 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 02:49:39 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 568.4 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 ‘/home/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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 7.231 0.091 7.036 mp_cal_rarecurve-methods 5.077 0.034 5.111 * 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-3.20-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 ‘/home/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 10.815 0.593 11.282
MicrobiotaProcess.Rcheck/MicrobiotaProcess-Ex.timings
name | user | system | elapsed | |
ImportDada2 | 1.160 | 0.042 | 1.203 | |
ImportQiime2 | 3.104 | 0.071 | 3.179 | |
MPSE | 0.072 | 0.001 | 0.073 | |
as.treedata | 0 | 0 | 0 | |
build_tree | 0 | 0 | 0 | |
convert_to_treedata | 0 | 0 | 0 | |
data-hmp_aerobiosis_small | 0.010 | 0.001 | 0.011 | |
data-kostic2012crc | 0.024 | 0.004 | 0.028 | |
data-test_otu_data | 0.001 | 0.000 | 0.001 | |
diff_analysis | 0 | 0 | 0 | |
dr_extract | 0.000 | 0.001 | 0.000 | |
drop_taxa | 0 | 0 | 0 | |
generalizedFC | 0.005 | 0.000 | 0.005 | |
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 | 0 | 0 | |
get_pca | 0.001 | 0.000 | 0.001 | |
get_pcoa | 0 | 0 | 0 | |
get_pvalue | 0.044 | 0.004 | 0.049 | |
get_rarecurve | 0 | 0 | 0 | |
get_sampledflist | 0 | 0 | 0 | |
get_taxadf | 0.001 | 0.000 | 0.000 | |
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 | 0 | 0 | |
ggeffectsize | 0 | 0 | 0 | |
ggordpoint | 0 | 0 | 0 | |
ggrarecurve | 0 | 0 | 0 | |
mp_adonis-methods | 0.088 | 0.001 | 0.089 | |
mp_aggregate-methods | 0.000 | 0.000 | 0.001 | |
mp_aggregate_clade-methods | 0 | 0 | 0 | |
mp_anosim-methods | 0.944 | 0.006 | 0.951 | |
mp_balance_clade-methods | 0 | 0 | 0 | |
mp_cal_abundance-methods | 7.231 | 0.091 | 7.036 | |
mp_cal_alpha-methods | 1.725 | 0.080 | 1.807 | |
mp_cal_cca-methods | 0.754 | 0.002 | 0.757 | |
mp_cal_clust-methods | 0.331 | 0.002 | 0.332 | |
mp_cal_dist-methods | 1.696 | 0.003 | 1.700 | |
mp_cal_divergence-methods | 0 | 0 | 0 | |
mp_cal_nmds-methods | 0.218 | 0.002 | 0.221 | |
mp_cal_pca-methods | 1.281 | 0.024 | 1.304 | |
mp_cal_pcoa-methods | 0.453 | 0.002 | 0.455 | |
mp_cal_pd_metric-methods | 0.001 | 0.000 | 0.000 | |
mp_cal_rarecurve-methods | 5.077 | 0.034 | 5.111 | |
mp_cal_rda-methods | 0.585 | 0.018 | 0.603 | |
mp_cal_upset-methods | 0.881 | 0.032 | 0.897 | |
mp_cal_venn-methods | 0.427 | 0.005 | 0.416 | |
mp_decostand-methods | 0.283 | 0.003 | 0.286 | |
mp_diff_analysis-methods | 3.880 | 0.025 | 3.737 | |
mp_diff_clade-methods | 0.001 | 0.000 | 0.000 | |
mp_dmn-methods | 0 | 0 | 0 | |
mp_dmngroup-methods | 0 | 0 | 0 | |
mp_envfit-methods | 2.260 | 0.104 | 2.364 | |
mp_filter_taxa-methods | 0.695 | 0.061 | 0.755 | |
mp_import_metaphlan | 2.414 | 0.045 | 2.460 | |
mp_mantel-methods | 0.216 | 0.002 | 0.218 | |
mp_mrpp-methods | 0.141 | 0.001 | 0.142 | |
mp_plot_abundance-methods | 0.001 | 0.000 | 0.000 | |
mp_plot_alpha-methods | 0 | 0 | 0 | |
mp_plot_diff_boxplot-methods | 4.538 | 0.039 | 4.412 | |
mp_plot_diff_cladogram | 0 | 0 | 0 | |
mp_plot_diff_manhattan-methods | 2.388 | 0.005 | 2.218 | |
mp_plot_dist-methods | 0.001 | 0.000 | 0.000 | |
mp_plot_ord-methods | 0.000 | 0.001 | 0.000 | |
mp_plot_rarecurve-methods | 0 | 0 | 0 | |
mp_plot_upset-methods | 0 | 0 | 0 | |
mp_plot_venn-methods | 0 | 0 | 0 | |
mp_rrarefy-methods | 0.269 | 0.000 | 0.269 | |
mp_select_as_tip-methods | 0 | 0 | 0 | |
mp_stat_taxa-methods | 0.870 | 0.003 | 0.698 | |
multi_compare | 0.007 | 0.000 | 0.007 | |
read_qza | 0 | 0 | 0 | |
show-methods | 0 | 0 | 0 | |
split_data | 0.002 | 0.000 | 0.002 | |
split_str_to_list | 0 | 0 | 0 | |
theme_taxbar | 0 | 0 | 0 | |