| Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-10-19 13:21:49 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1176/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MicrobiotaProcess 1.8.2 (landing page) Shuangbin Xu
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MicrobiotaProcess |
| Version: 1.8.2 |
| Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MicrobiotaProcess.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MicrobiotaProcess_1.8.2.tar.gz |
| StartedAt: 2022-10-19 01:52:18 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 01:57:48 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 329.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MicrobiotaProcess.Rcheck |
| Warnings: 0 |
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### Running command:
###
### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MicrobiotaProcess.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MicrobiotaProcess_1.8.2.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/MicrobiotaProcess.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.8.2'
* 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 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_abundance-methods 10.22 0.11 10.61
mp_cal_rarecurve-methods 7.73 0.13 7.91
mp_plot_diff_boxplot-methods 6.28 0.12 6.41
mp_diff_analysis-methods 4.91 0.11 5.03
* 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: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MicrobiotaProcess ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
MicrobiotaProcess v1.8.2 For help:
https://github.com/YuLab-SMU/MicrobiotaProcess/issues
If you use MicrobiotaProcess in published research, please cite the
paper:
S Xu, L Zhan, W Tang, Z Dai, L Zhou, T Feng, M Chen, S Liu, X Fu, T Wu,
E Hu, G Yu. MicrobiotaProcess: A comprehensive R package for managing
and analyzing microbiome and other ecological data within the tidy
framework. 04 February 2022, PREPRINT (Version 1) available at Research
Square [https://doi.org/10.21203/rs.3.rs-1284357/v1]
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
14.14 1.12 15.28
MicrobiotaProcess.Rcheck/MicrobiotaProcess-Ex.timings
| name | user | system | elapsed | |
| ImportDada2 | 1.56 | 0.09 | 1.70 | |
| ImportQiime2 | 3.31 | 0.08 | 3.45 | |
| MPSE | 0.09 | 0.00 | 0.09 | |
| as.treedata | 0 | 0 | 0 | |
| build_tree | 0 | 0 | 0 | |
| convert_to_treedata | 0 | 0 | 0 | |
| data-hmp_aerobiosis_small | 0.01 | 0.00 | 0.01 | |
| data-kostic2012crc | 0.05 | 0.00 | 0.05 | |
| data-test_otu_data | 0 | 0 | 0 | |
| diff_analysis | 0 | 0 | 0 | |
| dr_extract | 0 | 0 | 0 | |
| drop_taxa | 0 | 0 | 0 | |
| generalizedFC | 0 | 0 | 0 | |
| 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 | 0 | 0 | |
| get_pcoa | 0 | 0 | 0 | |
| get_pvalue | 0.04 | 0.00 | 0.07 | |
| get_rarecurve | 0 | 0 | 0 | |
| get_sampledflist | 0 | 0 | 0 | |
| get_taxadf | 0 | 0 | 0 | |
| get_upset | 0 | 0 | 0 | |
| 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 | 0.00 | 0.01 | 0.02 | |
| ggdifftaxbar | 0 | 0 | 0 | |
| ggeffectsize | 0 | 0 | 0 | |
| ggordpoint | 0 | 0 | 0 | |
| ggrarecurve | 0 | 0 | 0 | |
| mp_adonis-methods | 0.12 | 0.00 | 0.12 | |
| mp_aggregate-methods | 0 | 0 | 0 | |
| mp_aggregate_clade-methods | 0 | 0 | 0 | |
| mp_anosim-methods | 1.37 | 0.05 | 1.42 | |
| mp_balance_clade-methods | 0 | 0 | 0 | |
| mp_cal_abundance-methods | 10.22 | 0.11 | 10.61 | |
| mp_cal_alpha-methods | 1.38 | 0.00 | 1.40 | |
| mp_cal_cca-methods | 0.93 | 0.05 | 1.02 | |
| mp_cal_clust-methods | 0.50 | 0.00 | 0.55 | |
| mp_cal_dist-methods | 2.02 | 0.04 | 2.08 | |
| mp_cal_nmds-methods | 0.23 | 0.02 | 0.25 | |
| mp_cal_pca-methods | 1.61 | 0.01 | 1.62 | |
| mp_cal_pcoa-methods | 0.74 | 0.00 | 0.73 | |
| mp_cal_pd_metric-methods | 0 | 0 | 0 | |
| mp_cal_rarecurve-methods | 7.73 | 0.13 | 7.91 | |
| mp_cal_rda-methods | 0.74 | 0.00 | 0.74 | |
| mp_cal_upset-methods | 1.25 | 0.03 | 1.31 | |
| mp_cal_venn-methods | 1.62 | 0.09 | 2.97 | |
| mp_decostand-methods | 0.61 | 0.02 | 0.62 | |
| mp_diff_analysis-methods | 4.91 | 0.11 | 5.03 | |
| mp_diff_clade-methods | 0 | 0 | 0 | |
| mp_envfit-methods | 1.73 | 0.06 | 1.80 | |
| mp_filter_taxa-methods | 0.98 | 0.05 | 1.03 | |
| mp_import_metaphlan | 2.94 | 0.01 | 2.98 | |
| mp_mantel-methods | 0.31 | 0.02 | 0.33 | |
| mp_mrpp-methods | 0.24 | 0.00 | 0.23 | |
| mp_plot_abundance-methods | 0 | 0 | 0 | |
| mp_plot_alpha-methods | 0 | 0 | 0 | |
| mp_plot_diff_boxplot-methods | 6.28 | 0.12 | 6.41 | |
| mp_plot_diff_cladogram | 0 | 0 | 0 | |
| 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 | 0.41 | 0.00 | 0.40 | |
| mp_select_as_tip-methods | 0 | 0 | 0 | |
| mp_stat_taxa-methods | 1.05 | 0.02 | 1.06 | |
| multi_compare | 0 | 0 | 0 | |
| read_qza | 0 | 0 | 0 | |
| show-methods | 0 | 0 | 0 | |
| split_data | 0 | 0 | 0 | |
| split_str_to_list | 0 | 0 | 0 | |
| theme_taxbar | 0 | 0 | 0 | |