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

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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.

##############################################################################
##############################################################################
###
### 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)

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 

name	user	system	elapsed
abundances	0.015	0.000	0.015
aggregate_taxa	0.667	0.008	0.681
aggregate_top_taxa	0.326	0.019	0.348
alpha	0.016	0.000	0.016
associate	0.048	0.004	0.052
baseline	0.032	0.000	0.032
bfratio	0.131	0.024	0.164
bimodality	0.014	0.000	0.014
bimodality_sarle	0	0	0
boxplot_abundance	0.049	0.012	0.061
chunk_reorder	0.001	0.000	0.000
cmat2table	0.089	0.004	0.093
collapse_replicates	0.056	0.008	0.063
core	0.027	0.000	0.028
core_abundance	0.034	0.000	0.033
core_matrix	0	0	0
core_members	0.006	0.000	0.007
coverage	0.035	0.000	0.035
default_colors	0	0	0
densityplot	0	0	0
divergence	0.626	0.000	0.627
diversities	0.014	0.000	0.014
diversity	0.026	0.004	0.030
dominance	0.009	0.000	0.010
dominant	0.01	0.00	0.01
estimate_stability	0	0	0
evenness	0.007	0.000	0.008
find_optima	0	0	0
gktau	0.004	0.004	0.009
global	0.006	0.003	0.009
group_age	0.017	0.000	0.017
group_bmi	0.001	0.000	0.001
heat	0.077	0.000	0.077
hotplot	0.142	0.004	0.146
inequality	0.03	0.00	0.03
intermediate_stability	0.848	0.004	0.857
log_modulo_skewness	0.156	0.004	0.162
low_abundance	0.026	0.004	0.030
map_levels	0.055	0.000	0.054
merge_taxa2	0.031	0.000	0.033
meta	0.006	0.000	0.006
microbiome-package	0.014	0.000	0.026
multimodality	0	0	0
neat	0.085	0.000	0.086
neatsort	0.202	0.004	0.211
noncore_abundance	0.054	0.000	0.055
noncore_members	0.021	0.000	0.021
plot_atlas	0.066	0.000	0.067
plot_composition	0.271	0.004	0.283
plot_core	0.104	0.004	0.109
plot_density	0.046	0.004	0.050
plot_frequencies	0.016	0.000	0.015
plot_landscape	1.680	0.008	1.701
plot_regression	0.171	0.000	0.171
plot_taxa_prevalence	0.431	0.004	0.435
plot_tipping	0.096	0.000	0.096
potential_analysis	0.042	0.000	0.042
potential_univariate	0.001	0.000	0.001
prevalence	0.003	0.004	0.007
quiet	0.001	0.000	0.001
rare_members	0.008	0.000	0.009
rarity	0.086	0.000	0.086
read_biom2phyloseq	0	0	0
read_csv2phyloseq	0.001	0.000	0.001
read_mothur2phyloseq	0.000	0.000	0.001
read_phyloseq	0	0	0
readcount	0.002	0.004	0.006
remove_samples	0.013	0.000	0.013
remove_taxa	0.02	0.00	0.02
richness	0.031	0.000	0.031
summarize_phyloseq	0.02	0.00	0.02
taxa	0.005	0.000	0.005
time_normalize	0.036	0.000	0.036
time_sort	0.188	0.000	0.189
timesplit	0.147	0.000	0.147
top_taxa	0.007	0.000	0.007
transform	0.027	0.000	0.028
variable_members	0.048	0.000	0.048
write_phyloseq	0	0	0
ztransform	0	0	0