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CHECK report for microbiome on malbec2

This page was generated on 2019-04-09 11:48:46 -0400 (Tue, 09 Apr 2019).

Package 979/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiome 1.5.31
Leo Lahti
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/microbiome
Branch: master
Last Commit: a4664a10
Last Changed Date: 2019-03-30 18:21:14 -0400 (Sat, 30 Mar 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: microbiome
Version: 1.5.31
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:microbiome.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings microbiome_1.5.31.tar.gz
StartedAt: 2019-04-09 01:59:01 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:02:27 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 206.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: microbiome.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:microbiome.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings microbiome_1.5.31.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/microbiome.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘microbiome/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘microbiome’ version ‘1.5.31’
* 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 for sufficient/correct file permissions ... 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
* 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    124Kb       xz
  peerj32.rda             113Kb     87Kb       xz
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 WARNING
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/microbiome.Rcheck/00check.log’
for details.



Installation output

microbiome.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL microbiome
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘microbiome’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 (microbiome)

Tests output

microbiome.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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. <microbiome.github.io>


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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 12.745   0.235  13.116 

Example timings

microbiome.Rcheck/microbiome-Ex.timings

nameusersystemelapsed
abundances0.0150.0000.015
aggregate_taxa0.6670.0080.681
aggregate_top_taxa0.3260.0190.348
alpha0.0160.0000.016
associate0.0480.0040.052
baseline0.0320.0000.032
bfratio0.1310.0240.164
bimodality0.0140.0000.014
bimodality_sarle000
boxplot_abundance0.0490.0120.061
chunk_reorder0.0010.0000.000
cmat2table0.0890.0040.093
collapse_replicates0.0560.0080.063
core0.0270.0000.028
core_abundance0.0340.0000.033
core_matrix000
core_members0.0060.0000.007
coverage0.0350.0000.035
default_colors000
densityplot000
divergence0.6260.0000.627
diversities0.0140.0000.014
diversity0.0260.0040.030
dominance0.0090.0000.010
dominant0.010.000.01
estimate_stability000
evenness0.0070.0000.008
find_optima000
gktau0.0040.0040.009
global0.0060.0030.009
group_age0.0170.0000.017
group_bmi0.0010.0000.001
heat0.0770.0000.077
hotplot0.1420.0040.146
inequality0.030.000.03
intermediate_stability0.8480.0040.857
log_modulo_skewness0.1560.0040.162
low_abundance0.0260.0040.030
map_levels0.0550.0000.054
merge_taxa20.0310.0000.033
meta0.0060.0000.006
microbiome-package0.0140.0000.026
multimodality000
neat0.0850.0000.086
neatsort0.2020.0040.211
noncore_abundance0.0540.0000.055
noncore_members0.0210.0000.021
plot_atlas0.0660.0000.067
plot_composition0.2710.0040.283
plot_core0.1040.0040.109
plot_density0.0460.0040.050
plot_frequencies0.0160.0000.015
plot_landscape1.6800.0081.701
plot_regression0.1710.0000.171
plot_taxa_prevalence0.4310.0040.435
plot_tipping0.0960.0000.096
potential_analysis0.0420.0000.042
potential_univariate0.0010.0000.001
prevalence0.0030.0040.007
quiet0.0010.0000.001
rare_members0.0080.0000.009
rarity0.0860.0000.086
read_biom2phyloseq000
read_csv2phyloseq0.0010.0000.001
read_mothur2phyloseq0.0000.0000.001
read_phyloseq000
readcount0.0020.0040.006
remove_samples0.0130.0000.013
remove_taxa0.020.000.02
richness0.0310.0000.031
summarize_phyloseq0.020.000.02
taxa0.0050.0000.005
time_normalize0.0360.0000.036
time_sort0.1880.0000.189
timesplit0.1470.0000.147
top_taxa0.0070.0000.007
transform0.0270.0000.028
variable_members0.0480.0000.048
write_phyloseq000
ztransform000