Shuangbin Xu
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/MicrobiotaProcess |
| git_branch: master |
| git_last_commit: 5ec3ed3 |
| git_last_commit_date: 2022-03-01 03:04:12 -0400 (Tue, 01 Mar 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:01 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? 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 1151/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MicrobiotaProcess 1.7.8 (landing page) Shuangbin Xu
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | 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: 1.7.8 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MicrobiotaProcess.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MicrobiotaProcess_1.7.8.tar.gz |
| StartedAt: 2022-03-17 19:34:58 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:39:00 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 242.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MicrobiotaProcess.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MicrobiotaProcess.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MicrobiotaProcess_1.7.8.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MicrobiotaProcess.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MicrobiotaProcess/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MicrobiotaProcess' version '1.7.8'
* 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 ... NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
R 1.9Mb
help 1.0Mb
* 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 6.06 0.06 6.1
* 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: 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/MicrobiotaProcess.Rcheck/00check.log'
for details.
MicrobiotaProcess.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MicrobiotaProcess
###
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* installing to library 'D:/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_NRI_NTI' 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_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
converting help for package 'MicrobiotaProcess'
finding HTML links ... done
ImportDada2 html
ImportQiime2 html
MPSE-accessors html
MPSE-class html
MPSE html
alphasample-class html
as.MPSE html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-MicrobiotaProcess/00new/MicrobiotaProcess/help/as.mpse.html
as.phyloseq html
as.treedata html
build_tree html
convert_to_treedata html
data-hmp_aerobiosis_small html
data-kostic2012crc html
data-test_otu_data html
diffAnalysisClass-class html
diff_analysis html
dr_extract html
drop_taxa html
generalizedFC html
get_NRI_NTI-methods html
get_alltaxadf html
get_alphaindex html
get_clust html
get_coord html
get_count html
get_dist html
get_mean_median html
get_pca html
get_pcoa html
get_pvalue html
get_rarecurve html
get_sampledflist html
get_taxadf html
get_upset html
get_varct html
get_vennlist html
ggbartax html
ggbox html
ggclust html
ggdiffbox html
ggdiffclade html
ggdifftaxbar html
ggeffectsize html
ggordpoint html
ggrarecurve html
finding level-2 HTML links ... done
mouse.time.mpse html
mp_adonis-methods html
mp_aggregate-methods html
mp_anosim-methods html
mp_cal_NRI_NTI-methods html
mp_cal_abundance-methods html
mp_cal_alpha-methods html
mp_cal_cca-methods html
mp_cal_clust-methods html
mp_cal_dca-methods html
mp_cal_dist-methods html
mp_cal_nmds-methods html
mp_cal_pca-methods html
mp_cal_pcoa-methods html
mp_cal_rarecurve-methods html
mp_cal_rda-methods html
mp_cal_upset-methods html
mp_cal_venn-methods html
mp_decostand-methods html
mp_diff_analysis-methods html
mp_envfit-methods html
mp_extract_abundance-methods html
mp_extract_assays-methods html
mp_extract_dist-methods html
mp_extract_feature-methods html
mp_extract_internal_attr-methods html
mp_extract_rarecurve-methods html
mp_extract_refseq-methods html
mp_extract_sample-methods html
mp_extract_taxonomy-methods html
mp_extract_tree-methods html
mp_filter_taxa-methods html
mp_fortify html
mp_import_metaphlan html
mp_import_qiime html
mp_mantel-methods html
mp_mrpp-methods html
mp_plot_abundance-methods html
mp_plot_alpha-methods html
mp_plot_diff_res-methods html
mp_plot_dist-methods html
mp_plot_ord-methods html
mp_plot_rarecurve-methods html
mp_plot_upset-methods html
mp_plot_venn-methods html
mp_rrarefy-methods html
mp_stat_taxa-methods html
multi_compare html
ordplotClass-class html
pcasample-class html
pcoa-class html
prcomp-class html
print html
read_qza html
reexports html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-MicrobiotaProcess/00new/MicrobiotaProcess/help/as.treedata.html
set_scale_theme html
show-methods html
split_data html
split_str_to_list html
theme_taxbar html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'SEtools' is missing or broken
done
MicrobiotaProcess.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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 v1.7.8 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 0 | SKIP 0 | PASS 7 ]
>
> proc.time()
user system elapsed
10.26 0.92 11.11
MicrobiotaProcess.Rcheck/MicrobiotaProcess-Ex.timings
| name | user | system | elapsed | |
| ImportDada2 | 1.65 | 0.06 | 1.70 | |
| ImportQiime2 | 3.56 | 0.19 | 3.77 | |
| 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 | 0.02 | 0.00 | 0.02 | |
| data-kostic2012crc | 0.03 | 0.01 | 0.04 | |
| data-test_otu_data | 0 | 0 | 0 | |
| diff_analysis | 0 | 0 | 0 | |
| dr_extract | 0 | 0 | 0 | |
| drop_taxa | 0 | 0 | 0 | |
| generalizedFC | 0.01 | 0.00 | 0.02 | |
| 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 | 0.08 | 0.00 | 0.09 | |
| 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 | 0 | 0 | |
| ggdifftaxbar | 0 | 0 | 0 | |
| ggeffectsize | 0 | 0 | 0 | |
| ggordpoint | 0 | 0 | 0 | |
| ggrarecurve | 0 | 0 | 0 | |
| mp_adonis-methods | 0.12 | 0.02 | 0.14 | |
| mp_aggregate-methods | 0 | 0 | 0 | |
| mp_anosim-methods | 1.02 | 0.03 | 1.05 | |
| mp_cal_abundance-methods | 6.06 | 0.06 | 6.10 | |
| mp_cal_alpha-methods | 1.25 | 0.00 | 1.25 | |
| mp_cal_cca-methods | 0.78 | 0.00 | 0.83 | |
| mp_cal_clust-methods | 0.38 | 0.02 | 0.39 | |
| mp_cal_dist-methods | 1.70 | 0.00 | 1.71 | |
| mp_cal_nmds-methods | 0.28 | 0.03 | 0.31 | |
| mp_cal_pca-methods | 1.58 | 0.00 | 1.58 | |
| mp_cal_pcoa-methods | 0.53 | 0.00 | 0.53 | |
| mp_cal_rarecurve-methods | 4.36 | 0.02 | 4.37 | |
| mp_cal_rda-methods | 0.48 | 0.01 | 0.50 | |
| mp_cal_upset-methods | 0.88 | 0.02 | 0.89 | |
| mp_cal_venn-methods | 1.42 | 0.08 | 1.55 | |
| mp_decostand-methods | 0.27 | 0.01 | 0.28 | |
| mp_diff_analysis-methods | 3.81 | 0.02 | 3.85 | |
| mp_envfit-methods | 1.87 | 0.06 | 1.93 | |
| mp_filter_taxa-methods | 0.90 | 0.00 | 0.89 | |
| mp_import_metaphlan | 1.89 | 0.00 | 1.89 | |
| mp_mantel-methods | 0.31 | 0.00 | 0.32 | |
| mp_mrpp-methods | 0.12 | 0.00 | 0.12 | |
| mp_plot_abundance-methods | 0 | 0 | 0 | |
| mp_plot_alpha-methods | 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 | 0.25 | 0.02 | 0.27 | |
| mp_stat_taxa-methods | 0.55 | 0.01 | 0.56 | |
| 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 | |