Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:45 -0400 (Fri, 15 Oct 2021).
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1130/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MicrobiotaProcess 1.4.4 (landing page) Shuangbin Xu
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: MicrobiotaProcess |
Version: 1.4.4 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MicrobiotaProcess.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MicrobiotaProcess_1.4.4.tar.gz |
StartedAt: 2021-10-14 10:35:36 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 10:40:11 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 275.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MicrobiotaProcess.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MicrobiotaProcess.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MicrobiotaProcess_1.4.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/MicrobiotaProcess.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MicrobiotaProcess/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MicrobiotaProcess’ version ‘1.4.4’ * 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 ... 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 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 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_rarecurve-methods 6.742 0.151 6.894 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
MicrobiotaProcess.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL MicrobiotaProcess ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘MicrobiotaProcess’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘rownames<-’ from package ‘base’ in package ‘MicrobiotaProcess’ ** 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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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") Attaching package: 'MicrobiotaProcess' The following object is masked from 'package:stats': filter > test_check("MicrobiotaProcess") Processing map file... Processing otu/tax file... Reading file into memory prior to parsing... Detecting first header line... Header is on line 2 Converting input file to a table... Defining OTU table... Parsing taxonomy table... [ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ] > > proc.time() user system elapsed 20.508 1.536 22.036
MicrobiotaProcess.Rcheck/MicrobiotaProcess-Ex.timings
name | user | system | elapsed | |
ImportDada2 | 1.462 | 0.024 | 1.487 | |
ImportQiime2 | 2.150 | 0.097 | 2.247 | |
as.MPSE | 0.605 | 0.107 | 0.713 | |
as.treedata | 0.323 | 0.020 | 0.343 | |
build_tree | 0.000 | 0.000 | 0.001 | |
convert_to_treedata | 0.001 | 0.000 | 0.000 | |
data-hmp_aerobiosis_small | 0.006 | 0.004 | 0.010 | |
data-kostic2012crc | 0.081 | 0.000 | 0.082 | |
data-test_otu_data | 0.001 | 0.000 | 0.001 | |
diff_analysis | 0 | 0 | 0 | |
dr_extract | 0 | 0 | 0 | |
drop_taxa | 0.000 | 0.000 | 0.001 | |
generalizedFC | 0.002 | 0.003 | 0.006 | |
get_alltaxadf | 0 | 0 | 0 | |
get_alphaindex | 0.000 | 0.000 | 0.001 | |
get_clust | 0.000 | 0.000 | 0.001 | |
get_coord | 0.000 | 0.001 | 0.000 | |
get_count | 0.000 | 0.001 | 0.000 | |
get_dist | 0 | 0 | 0 | |
get_mean_median | 0 | 0 | 0 | |
get_pca | 0.000 | 0.000 | 0.001 | |
get_pcoa | 0.000 | 0.001 | 0.000 | |
get_pvalue | 0.061 | 0.002 | 0.065 | |
get_rarecurve | 0.000 | 0.001 | 0.001 | |
get_sampledflist | 0.000 | 0.001 | 0.000 | |
get_taxadf | 0 | 0 | 0 | |
get_upset | 0 | 0 | 0 | |
get_varct | 0 | 0 | 0 | |
get_vennlist | 0.000 | 0.001 | 0.001 | |
ggbartax | 0.000 | 0.001 | 0.001 | |
ggbox | 0.000 | 0.001 | 0.001 | |
ggclust | 0.000 | 0.001 | 0.001 | |
ggdiffbox | 0.000 | 0.001 | 0.001 | |
ggdiffclade | 0.000 | 0.001 | 0.001 | |
ggdifftaxbar | 0 | 0 | 0 | |
ggeffectsize | 0 | 0 | 0 | |
ggordpoint | 0 | 0 | 0 | |
ggrarecurve | 0 | 0 | 0 | |
mp_adonis-methods | 0.149 | 0.000 | 0.148 | |
mp_aggregate-methods | 0 | 0 | 0 | |
mp_anosim-methods | 1.071 | 0.052 | 1.123 | |
mp_cal_abundance-methods | 4.543 | 0.091 | 4.634 | |
mp_cal_alpha-methods | 1.839 | 0.092 | 1.933 | |
mp_cal_cca-methods | 0.612 | 0.008 | 0.620 | |
mp_cal_clust-methods | 0.469 | 0.023 | 0.493 | |
mp_cal_dist-methods | 0.623 | 0.028 | 0.651 | |
mp_cal_nmds-methods | 0.252 | 0.017 | 0.268 | |
mp_cal_pca-methods | 1.103 | 0.004 | 1.107 | |
mp_cal_pcoa-methods | 0.506 | 0.004 | 0.510 | |
mp_cal_rarecurve-methods | 6.742 | 0.151 | 6.894 | |
mp_cal_rda-methods | 0.504 | 0.008 | 0.512 | |
mp_cal_upset-methods | 0.950 | 0.024 | 0.974 | |
mp_cal_venn-methods | 1.462 | 0.096 | 1.594 | |
mp_decostand-methods | 0.351 | 0.000 | 0.351 | |
mp_diff_analysis-methods | 3.454 | 0.084 | 3.539 | |
mp_envfit-methods | 2.497 | 0.076 | 2.574 | |
mp_filter_taxa-methods | 0.982 | 0.000 | 0.982 | |
mp_import_metaphlan | 2.232 | 0.024 | 2.258 | |
mp_mantel-methods | 0.305 | 0.000 | 0.305 | |
mp_mrpp-methods | 0.196 | 0.000 | 0.196 | |
mp_plot_abundance-methods | 0.001 | 0.000 | 0.001 | |
mp_plot_alpha-methods | 0.000 | 0.000 | 0.001 | |
mp_plot_dist-methods | 0.000 | 0.001 | 0.001 | |
mp_plot_ord-methods | 0.000 | 0.001 | 0.001 | |
mp_plot_rarecurve-methods | 0.000 | 0.001 | 0.001 | |
mp_plot_upset-methods | 0.000 | 0.001 | 0.001 | |
mp_plot_venn-methods | 0.001 | 0.000 | 0.000 | |
mp_rrarefy-methods | 0.321 | 0.000 | 0.321 | |
mp_stat_taxa-methods | 0.66 | 0.00 | 0.66 | |
multi_compare | 0.006 | 0.004 | 0.010 | |
read_qza | 0.000 | 0.001 | 0.001 | |
show-methods | 0.000 | 0.001 | 0.001 | |
split_data | 0.001 | 0.002 | 0.003 | |
split_str_to_list | 0.000 | 0.000 | 0.001 | |
theme_taxbar | 0.000 | 0.000 | 0.001 | |