Package: MMUPHin

Version: 1.0.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MMUPHin.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MMUPHin_1.0.0.tar.gz

StartedAt: 2020-04-15 07:02:38 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 07:04:34 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 115.2 seconds

RetCode: 0

Status:  OK

CheckDir: MMUPHin.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MMUPHin.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MMUPHin_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/MMUPHin.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MMUPHin/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MMUPHin’ version ‘1.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MMUPHin’ 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 ... NOTE
Maaslin2_wrapper: no visible binding for global variable
  ‘feature_rename’
Maaslin2_wrapper: no visible binding for global variable ‘name’
check_exposure: no visible binding for global variable ‘lvl_batch’
diagnostic_adjust_batch: no visible binding for global variable
  ‘Adjustment’
diagnostic_adjust_batch: no visible binding for global variable ‘batch’
diagnostic_adjust_batch: no visible binding for global variable
  ‘mean_overall’
diagnostic_adjust_batch: no visible binding for global variable
  ‘mean_batch’
diagnostic_adjust_batch: no visible binding for global variable
  ‘Feature’
diagnostic_continuous_discover: no visible binding for global variable
  ‘community’
diagnostic_continuous_discover: no visible binding for global variable
  ‘correlation’
diagnostic_continuous_discover: no visible binding for global variable
  ‘batch’
diagnostic_discrete_discover: no visible binding for global variable
  ‘k’
Undefined global functions or variables:
  Adjustment Feature batch community correlation feature_rename k
  lvl_batch mean_batch mean_overall name
* 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 ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
continuous_discover 25.288  1.868  27.275
lm_meta             17.820  0.176  18.054
discrete_discover   15.000  0.124  15.147
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/MMUPHin.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL MMUPHin
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘MMUPHin’ ...
** using staged installation
** R
** data
** 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 (MMUPHin)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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)
> library(MMUPHin)
> 
> test_check("MMUPHin")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 41 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  3.216   0.076   3.301 

name	user	system	elapsed
CRC_abd	0.048	0.012	0.063
CRC_meta	0.012	0.000	0.012
adjust_batch	2.976	0.048	3.028
continuous_discover	25.288	1.868	27.275
discrete_discover	15.000	0.124	15.147
lm_meta	17.820	0.176	18.054
vaginal_abd	0.004	0.004	0.008
vaginal_meta	0.004	0.000	0.004