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CHECK report for microbiome on tokay2

This page was generated on 2019-10-16 12:39:11 -0400 (Wed, 16 Oct 2019).

Package 996/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiome 1.6.0
Leo Lahti
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/microbiome
Branch: RELEASE_3_9
Last Commit: 4a7a3ac
Last Changed Date: 2019-05-02 11:54:08 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: microbiome
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:microbiome.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings microbiome_1.6.0.tar.gz
StartedAt: 2019-10-16 05:13:02 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:17:12 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 250.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: microbiome.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:microbiome.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings microbiome_1.6.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/microbiome.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'microbiome/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'microbiome' version '1.6.0'
* 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 'microbiome' 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                       old_size new_size compress
  atlas1006.rda           233Kb    127Kb       xz
  dietswap.rda             45Kb     28Kb       xz
  hitchip.taxonomy.rda    402Kb    123Kb       xz
  peerj32.rda             113Kb     87Kb       xz
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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-3.9-bioc/meat/microbiome.Rcheck/00check.log'
for details.



Installation output

microbiome.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/microbiome_1.6.0.tar.gz && rm -rf microbiome.buildbin-libdir && mkdir microbiome.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=microbiome.buildbin-libdir microbiome_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL microbiome_1.6.0.zip && rm microbiome_1.6.0.tar.gz microbiome_1.6.0.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  689k  100  689k    0     0  10.0M      0 --:--:-- --:--:-- --:--:-- 11.2M

install for i386

* installing *source* package 'microbiome' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'microbiome'
    finding HTML links ... done
    abundances                              html  
    finding level-2 HTML links ... done

    aggregate_taxa                          html  
    aggregate_top_taxa                      html  
    alpha                                   html  
    associate                               html  
    atlas1006                               html  
    baseline                                html  
    bfratio                                 html  
    bimodality                              html  
    bimodality_sarle                        html  
    boxplot_abundance                       html  
    chunk_reorder                           html  
    cmat2table                              html  
    collapse_replicates                     html  
    core                                    html  
    core_abundance                          html  
    core_heatmap                            html  
    core_matrix                             html  
    core_members                            html  
    coverage                                html  
    default_colors                          html  
    densityplot                             html  
    dietswap                                html  
    divergence                              html  
    diversities                             html  
    diversity                               html  
    dominance                               html  
    dominant                                html  
    estimate_stability                      html  
    evenness                                html  
    find_optima                             html  
    gktau                                   html  
    global                                  html  
    group_age                               html  
    group_bmi                               html  
    heat                                    html  
    hitchip.taxonomy                        html  
    hotplot                                 html  
    inequality                              html  
    intermediate_stability                  html  
    log_modulo_skewness                     html  
    low_abundance                           html  
    map_levels                              html  
    merge_taxa2                             html  
    meta                                    html  
    microbiome-package                      html  
    multimodality                           html  
    neat                                    html  
    neatsort                                html  
    noncore_abundance                       html  
    noncore_members                         html  
    peerj32                                 html  
    plot_atlas                              html  
    plot_composition                        html  
    plot_core                               html  
    plot_density                            html  
    plot_frequencies                        html  
    plot_landscape                          html  
    plot_regression                         html  
    plot_taxa_prevalence                    html  
    plot_tipping                            html  
    potential_analysis                      html  
    potential_univariate                    html  
    prevalence                              html  
    quiet                                   html  
    radial_theta                            html  
    rare_members                            html  
    rarity                                  html  
    read_biom2phyloseq                      html  
    read_csv2phyloseq                       html  
    read_mothur2phyloseq                    html  
    read_phyloseq                           html  
    readcount                               html  
    remove_samples                          html  
    remove_taxa                             html  
    richness                                html  
    summarize_phyloseq                      html  
    taxa                                    html  
    time_normalize                          html  
    time_sort                               html  
    timesplit                               html  
    top_taxa                                html  
    transform                               html  
    variable_members                        html  
    write_phyloseq                          html  
    ztransform                              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 'microbiome' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'microbiome' as microbiome_1.6.0.zip
* DONE (microbiome)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'microbiome' successfully unpacked and MD5 sums checked

Tests output

microbiome.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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)
> test_check("microbiome")
Loading required package: microbiome
Loading required package: phyloseq
Loading required package: ggplot2

microbiome R package (microbiome.github.com)
    


 Copyright (C) 2011-2019 Leo Lahti, 
    Sudarshan Shetty et al. 


Attaching package: 'microbiome'

The following object is masked from 'package:ggplot2':

    alpha

The following object is masked from 'package:base':

    transform

== testthat results  ===========================================================
[ OK: 72 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  11.23    0.68   12.31 

microbiome.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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)
> test_check("microbiome")
Loading required package: microbiome
Loading required package: phyloseq
Loading required package: ggplot2

microbiome R package (microbiome.github.com)
    


 Copyright (C) 2011-2019 Leo Lahti, 
    Sudarshan Shetty et al. 


Attaching package: 'microbiome'

The following object is masked from 'package:ggplot2':

    alpha

The following object is masked from 'package:base':

    transform

== testthat results  ===========================================================
[ OK: 72 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  10.85    0.51   11.35 

Example timings

microbiome.Rcheck/examples_i386/microbiome-Ex.timings

nameusersystemelapsed
abundances0.010.010.03
aggregate_taxa0.250.060.31
aggregate_top_taxa0.360.090.45
alpha0.020.000.02
associate0.040.030.08
baseline0.050.000.04
bfratio0.110.020.13
bimodality000
bimodality_sarle000
boxplot_abundance0.050.010.07
chunk_reorder000
cmat2table0.070.000.07
collapse_replicates0.020.020.03
core0.030.000.03
core_abundance0.030.000.03
core_matrix000
core_members000
coverage0.030.000.04
default_colors000
densityplot000
divergence0.470.010.48
diversities0.030.000.03
diversity000
dominance000
dominant0.020.000.01
estimate_stability000
evenness000
find_optima000
gktau000
global0.020.000.01
group_age0.010.000.02
group_bmi000
heat0.070.000.06
hotplot0.090.000.10
inequality0.030.000.03
intermediate_stability0.530.000.53
log_modulo_skewness0.140.010.15
low_abundance0.000.020.02
map_levels0.060.010.08
merge_taxa20.020.020.03
meta000
microbiome-package000
multimodality000
neat0.090.020.10
neatsort0.170.000.18
noncore_abundance0.020.000.02
noncore_members0.010.020.03
plot_atlas0.050.000.05
plot_composition0.230.030.26
plot_core0.130.010.14
plot_density0.060.000.06
plot_frequencies0.020.020.04
plot_landscape1.420.001.42
plot_regression0.140.000.14
plot_taxa_prevalence0.330.020.34
plot_tipping0.090.000.10
potential_analysis0.030.000.03
potential_univariate000
prevalence0.020.000.01
quiet000
rare_members0.010.000.02
rarity0.460.000.45
read_biom2phyloseq000
read_csv2phyloseq000
read_mothur2phyloseq000
read_phyloseq000
readcount000
remove_samples0.020.000.01
remove_taxa0.010.000.02
richness000
summarize_phyloseq0.020.000.02
taxa000
time_normalize0.030.000.03
time_sort0.090.010.11
timesplit0.080.000.08
top_taxa0.010.000.01
transform0.020.000.02
variable_members0.050.000.05
write_phyloseq000
ztransform000

microbiome.Rcheck/examples_x64/microbiome-Ex.timings

nameusersystemelapsed
abundances0.020.000.02
aggregate_taxa0.230.020.25
aggregate_top_taxa0.270.000.26
alpha0.010.000.02
associate0.030.000.03
baseline0.020.010.03
bfratio0.110.020.12
bimodality0.010.000.02
bimodality_sarle000
boxplot_abundance0.030.030.06
chunk_reorder000
cmat2table0.100.030.13
collapse_replicates0.060.020.08
core0.050.000.04
core_abundance0.040.010.07
core_matrix000
core_members0.020.000.01
coverage0.050.000.05
default_colors000
densityplot000
divergence0.700.000.71
diversities0.020.000.01
diversity0.000.010.02
dominance0.010.000.01
dominant000
estimate_stability000
evenness000
find_optima000
gktau0.020.000.01
global0.010.000.02
group_age0.020.000.02
group_bmi000
heat0.080.000.08
hotplot0.160.010.17
inequality0.050.000.05
intermediate_stability0.820.000.83
log_modulo_skewness0.210.000.20
low_abundance0.010.020.03
map_levels0.080.000.08
merge_taxa20.030.000.03
meta000
microbiome-package0.020.000.02
multimodality000
neat0.080.000.07
neatsort0.180.000.19
noncore_abundance0.030.000.03
noncore_members0.020.000.02
plot_atlas0.060.000.06
plot_composition0.210.020.22
plot_core0.560.000.56
plot_density0.030.000.03
plot_frequencies0.000.020.01
plot_landscape1.050.031.08
plot_regression0.140.000.14
plot_taxa_prevalence0.450.040.50
plot_tipping0.120.020.14
potential_analysis0.050.020.07
potential_univariate000
prevalence000
quiet000
rare_members000
rarity0.130.000.13
read_biom2phyloseq000
read_csv2phyloseq000
read_mothur2phyloseq000
read_phyloseq000
readcount0.000.020.01
remove_samples0.030.000.04
remove_taxa0.030.000.03
richness0.020.000.01
summarize_phyloseq0.030.000.03
taxa000
time_normalize0.030.010.05
time_sort0.220.020.23
timesplit0.110.010.13
top_taxa000
transform0.030.000.03
variable_members0.030.020.05
write_phyloseq000
ztransform000