Multiple platform build/check report for BioC 3.12 - CHECK report for MicrobiotaProcess on tokay1

Package: MicrobiotaProcess

Version: 1.2.2

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MicrobiotaProcess.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MicrobiotaProcess_1.2.2.tar.gz

StartedAt: 2021-05-06 04:38:28 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 04:46:52 -0400 (Thu, 06 May 2021)

EllapsedTime: 503.7 seconds

RetCode: 0

Status: WARNINGS

CheckDir: MicrobiotaProcess.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MicrobiotaProcess.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MicrobiotaProcess_1.2.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MicrobiotaProcess.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.2.2'
* 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpM9LAwq/R.INSTALL26d05a9e479b/MicrobiotaProcess/man/ggordpoint.Rd:52: file link 'scale_starshape_manual' in package 'ggstar' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MicrobiotaProcess.Rcheck/00install.out' for details.
* 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
ggrarecurve         22.08   0.00   22.07
as.data.frame       15.37   0.25   15.74
diff_analysis       13.81   0.10   13.90
ggdiffclade         12.25   0.11   12.35
ggdiffbox           11.98   0.08   12.07
get_rarecurve        9.74   0.00    9.73
convert_to_treedata  5.24   0.03    5.26
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
ggrarecurve   19.83   0.00   19.83
ggdiffclade   12.69   0.09   12.78
diff_analysis 12.27   0.04   12.31
as.data.frame 11.77   0.04   11.83
ggdiffbox     10.80   0.08   10.88
get_rarecurve  8.15   0.01    8.17
* 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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/MicrobiotaProcess.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/MicrobiotaProcess_1.2.2.tar.gz && rm -rf MicrobiotaProcess.buildbin-libdir && mkdir MicrobiotaProcess.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MicrobiotaProcess.buildbin-libdir MicrobiotaProcess_1.2.2.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL MicrobiotaProcess_1.2.2.zip && rm MicrobiotaProcess_1.2.2.tar.gz MicrobiotaProcess_1.2.2.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  401k  100  401k    0     0  8502k      0 --:--:-- --:--:-- --:--:-- 8735k

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  
    as.treedata                             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  
    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  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpM9LAwq/R.INSTALL26d05a9e479b/MicrobiotaProcess/man/ggordpoint.Rd:52: file link 'scale_starshape_manual' in package 'ggstar' does not exist and so has been treated as a topic
    ggrarecurve                             html  
    finding level-2 HTML links ... done

    import_dada2                            html  
    import_qiime2                           html  
    multi_compare                           html  
    ordplotClass-class                      html  
    pcasample-class                         html  
    pcoa-class                              html  
    prcomp-class                            html  
    read_qza                                html  
    reexports                               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

install for x64

* installing *source* package 'MicrobiotaProcess' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MicrobiotaProcess' as MicrobiotaProcess_1.2.2.zip
* DONE (MicrobiotaProcess)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'MicrobiotaProcess' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
> 
> proc.time()
   user  system elapsed 
  30.09    1.09   31.57


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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")
> 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 
  26.60    0.37   27.09

name	user	system	elapsed
as.data.frame	15.37	0.25	15.74
as.treedata	0.61	0.00	0.61
build_tree	0	0	0
convert_to_treedata	5.24	0.03	5.26
data-hmp_aerobiosis_small	0.00	0.01	0.02
data-kostic2012crc	0.11	0.08	0.19
data-test_otu_data	0	0	0
diff_analysis	13.81	0.10	13.90
drop_taxa	0.39	0.00	0.39
generalizedFC	0.01	0.00	0.02
get_alltaxadf	1.07	0.00	1.06
get_alphaindex	1.72	0.03	1.75
get_clust	0	0	0
get_coord	0.01	0.00	0.01
get_count	0.03	0.00	0.03
get_dist	0.28	0.00	0.29
get_mean_median	0.13	0.00	0.12
get_pca	0	0	0
get_pcoa	0.31	0.03	0.34
get_pvalue	0.14	0.02	0.18
get_rarecurve	9.74	0.00	9.73
get_sampledflist	0.03	0.00	0.03
get_taxadf	0.75	0.00	0.75
get_upset	0.29	0.00	0.30
get_varct	0.33	0.00	0.33
get_vennlist	0.22	0.02	0.23
ggbartax	0.27	0.01	0.28
ggbox	0.39	0.00	0.39
ggclust	0	0	0
ggdiffbox	11.98	0.08	12.07
ggdiffclade	12.25	0.11	12.35
ggdifftaxbar	0.39	0.09	0.49
ggeffectsize	1.00	0.05	1.05
ggordpoint	0	0	0
ggrarecurve	22.08	0.00	22.07
import_dada2	0.09	0.01	0.11
import_qiime2	2.21	0.02	2.22
multi_compare	0	0	0
read_qza	0.09	0.02	0.11
show-methods	0	0	0
split_data	0.00	0.01	0.02
split_str_to_list	0.02	0.00	0.01
theme_taxbar	0.25	0.00	0.25

name	user	system	elapsed
as.data.frame	11.77	0.04	11.83
as.treedata	0.40	0.00	0.41
build_tree	0	0	0
convert_to_treedata	4.92	0.00	4.93
data-hmp_aerobiosis_small	0.02	0.00	0.01
data-kostic2012crc	0.12	0.10	0.22
data-test_otu_data	0	0	0
diff_analysis	12.27	0.04	12.31
drop_taxa	0.28	0.00	0.28
generalizedFC	0	0	0
get_alltaxadf	0.95	0.02	0.97
get_alphaindex	1.69	0.05	1.74
get_clust	0	0	0
get_coord	0.01	0.00	0.01
get_count	0.04	0.00	0.03
get_dist	0.21	0.00	0.22
get_mean_median	0.13	0.00	0.13
get_pca	0	0	0
get_pcoa	0.89	0.00	0.89
get_pvalue	0.08	0.00	0.09
get_rarecurve	8.15	0.01	8.17
get_sampledflist	0.04	0.00	0.04
get_taxadf	0.75	0.00	0.75
get_upset	0.48	0.02	0.50
get_varct	0.28	0.01	0.29
get_vennlist	0.22	0.02	0.24
ggbartax	0.27	0.00	0.26
ggbox	0.32	0.00	0.33
ggclust	0	0	0
ggdiffbox	10.80	0.08	10.88
ggdiffclade	12.69	0.09	12.78
ggdifftaxbar	0.40	0.03	0.43
ggeffectsize	0.41	0.06	0.47
ggordpoint	0	0	0
ggrarecurve	19.83	0.00	19.83
import_dada2	0.09	0.00	0.10
import_qiime2	2.96	0.04	3.01
multi_compare	0	0	0
read_qza	0.10	0.00	0.11
show-methods	0	0	0
split_data	0	0	0
split_str_to_list	0.02	0.00	0.01
theme_taxbar	0.34	0.00	0.35

CHECK report for MicrobiotaProcess on tokay1

Summary

Command output

Installation output

Tests output

Example timings