Multiple platform build/check report for BioC 3.11 - CHECK report for MicrobiotaProcess on tokay2

Package: MicrobiotaProcess

Version: 1.0.5

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MicrobiotaProcess.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MicrobiotaProcess_1.0.5.tar.gz

StartedAt: 2020-10-17 06:02:35 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 06:10:29 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 474.1 seconds

RetCode: 0

Status: OK

CheckDir: MicrobiotaProcess.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MicrobiotaProcess.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MicrobiotaProcess_1.0.5.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/MicrobiotaProcess.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.0.5'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
as.data.frame       13.58   0.50   14.20
ggrarecurve         12.72   0.00   12.72
diff_analysis       12.05   0.06   12.11
ggdiffclade         10.43   0.08   10.52
ggdiffbox           10.41   0.06   10.47
import_qiime2        2.52   0.05    5.11
mapply_retrieve_seq  0.06   0.01    8.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
ggrarecurve         12.35   0.00   12.34
ggdiffbox           12.20   0.07   12.27
ggdiffclade         12.10   0.04   12.14
diff_analysis       10.80   0.10   10.89
as.data.frame       10.14   0.09   10.24
mapply_retrieve_seq  0.09   0.01    7.25
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/MicrobiotaProcess_1.0.5.tar.gz && rm -rf MicrobiotaProcess.buildbin-libdir && mkdir MicrobiotaProcess.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MicrobiotaProcess.buildbin-libdir MicrobiotaProcess_1.0.5.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL MicrobiotaProcess_1.0.5.zip && rm MicrobiotaProcess_1.0.5.tar.gz MicrobiotaProcess_1.0.5.zip
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  400k  100  400k    0     0  4919k      0 --:--:-- --:--:-- --:--:-- 5646k

install for i386

* installing *source* package 'MicrobiotaProcess' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MicrobiotaProcess'
    finding HTML links ... done
    alphasample-class                       html  
    as.data.frame                           html  
    build_tree                              html  
    clustplotClass-class                    html  
    convert_to_treedata                     html  
    data-hmp_aerobiosis_small               html  
    data-kostic2012crc                      html  
    data-test_otu_data                      html  
    diffAnalysisClass-class                 html  
    diff_analysis                           html  
    drop_taxa                               html  
    generalizedFC                           html  
    geom_ord_ellipse                        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_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

    import_dada2                            html  
    import_qiime2                           html  
    mappingtaxda                            html  
    mapply_retrieve_seq                     html  
    multi_compare                           html  
    ordplotClass-class                      html  
    pcasample-class                         html  
    pcoa-class                              html  
    prcomp-class                            html  
    read_qza                                html  
    retrieve_seq                            html  
    show-methods                            html  
    split_data                              html  
    split_str_to_list                       html  
    stat_rare                               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

install for x64

* installing *source* package 'MicrobiotaProcess' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MicrobiotaProcess' as MicrobiotaProcess_1.0.5.zip
* DONE (MicrobiotaProcess)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'MicrobiotaProcess' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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")
> 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...
== testthat results  ===========================================================
[ OK: 11 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  29.60    0.92   31.15


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
> 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...
== testthat results  ===========================================================
[ OK: 11 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  27.57    0.65   28.23

name	user	system	elapsed
as.data.frame	13.58	0.50	14.20
build_tree	0	0	0
convert_to_treedata	4.25	0.02	4.27
data-hmp_aerobiosis_small	0.02	0.01	0.03
data-kostic2012crc	0.06	0.13	0.18
data-test_otu_data	0	0	0
diff_analysis	12.05	0.06	12.11
drop_taxa	0.22	0.00	0.22
generalizedFC	0	0	0
get_alltaxadf	0.72	0.00	0.72
get_alphaindex	1.64	0.05	1.74
get_clust	0	0	0
get_coord	0.00	0.01	0.01
get_count	0.04	0.00	0.05
get_dist	0.29	0.00	0.28
get_mean_median	0.12	0.02	0.14
get_pca	0	0	0
get_pcoa	0.40	0.03	0.43
get_pvalue	0.10	0.00	0.14
get_sampledflist	0.04	0.00	0.05
get_taxadf	0.92	0.00	0.92
get_upset	0.3	0.0	0.3
get_varct	0.33	0.03	0.36
get_vennlist	0.2	0.0	0.2
ggbartax	0.22	0.00	0.22
ggbox	0.33	0.02	0.34
ggclust	0	0	0
ggdiffbox	10.41	0.06	10.47
ggdiffclade	10.43	0.08	10.52
ggdifftaxbar	0.33	0.09	0.42
ggeffectsize	0.76	0.11	0.87
ggordpoint	0	0	0
ggrarecurve	12.72	0.00	12.72
import_dada2	0.08	0.00	0.08
import_qiime2	2.52	0.05	5.11
mapply_retrieve_seq	0.06	0.01	8.11
multi_compare	0.01	0.00	0.01
read_qza	0.19	0.00	0.19
retrieve_seq	0.02	0.00	0.02
show-methods	0	0	0
split_data	0.00	0.02	0.01
split_str_to_list	0.01	0.00	0.02
theme_taxbar	0.35	0.00	0.34

name	user	system	elapsed
as.data.frame	10.14	0.09	10.24
build_tree	0	0	0
convert_to_treedata	4.04	0.00	4.04
data-hmp_aerobiosis_small	0.01	0.00	0.01
data-kostic2012crc	0.08	0.06	0.14
data-test_otu_data	0.01	0.00	0.02
diff_analysis	10.80	0.10	10.89
drop_taxa	0.22	0.00	0.22
generalizedFC	0	0	0
get_alltaxadf	0.98	0.00	0.98
get_alphaindex	1.46	0.04	1.50
get_clust	0	0	0
get_coord	0.01	0.00	0.02
get_count	0.03	0.00	0.03
get_dist	0.24	0.00	0.23
get_mean_median	0.09	0.02	0.11
get_pca	0	0	0
get_pcoa	0.25	0.03	0.28
get_pvalue	0.10	0.00	0.11
get_sampledflist	0.03	0.00	0.03
get_taxadf	0.73	0.02	0.75
get_upset	0.3	0.0	0.3
get_varct	0.22	0.03	0.25
get_vennlist	0.23	0.00	0.23
ggbartax	0.25	0.00	0.25
ggbox	0.34	0.01	0.36
ggclust	0	0	0
ggdiffbox	12.20	0.07	12.27
ggdiffclade	12.10	0.04	12.14
ggdifftaxbar	0.37	0.08	0.45
ggeffectsize	0.97	0.19	1.16
ggordpoint	0	0	0
ggrarecurve	12.35	0.00	12.34
import_dada2	0.06	0.00	0.07
import_qiime2	2.02	0.00	2.03
mapply_retrieve_seq	0.09	0.01	7.25
multi_compare	0.02	0.00	0.01
read_qza	0.14	0.02	0.16
retrieve_seq	0.02	0.00	0.02
show-methods	0	0	0
split_data	0	0	0
split_str_to_list	0.01	0.00	0.01
theme_taxbar	0.41	0.02	0.42

CHECK report for MicrobiotaProcess on tokay2

Summary

Command output

Installation output

Tests output

Example timings