Package: HMP2Data

Version: 1.1.0

Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:HMP2Data.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings HMP2Data_1.1.0.tar.gz

StartedAt: 2020-01-27 13:27:06 -0500 (Mon, 27 Jan 2020)

EndedAt: 2020-01-27 13:30:46 -0500 (Mon, 27 Jan 2020)

EllapsedTime: 219.9 seconds

RetCode: 0

Status:  OK

CheckDir: HMP2Data.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:HMP2Data.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings HMP2Data_1.1.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.11-data-experiment/meat/HMP2Data.Rcheck’
* using R Under development (unstable) (2019-12-14 r77569)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HMP2Data/DESCRIPTION’ ... OK
* this is package ‘HMP2Data’ version ‘1.1.0’
* 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 ‘HMP2Data’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
IBD16S: no visible global function definition for ‘data’
IBD16S: no visible binding for global variable ‘IBD16S_mtx’
IBD16S: no visible binding for global variable ‘IBD16S_samp’
IBD16S: no visible binding for global variable ‘IBD16S_tax’
T2D16S: no visible global function definition for ‘data’
T2D16S: no visible binding for global variable ‘T2D16S_mtx’
T2D16S: no visible binding for global variable ‘T2D16S_samp’
T2D16S: no visible binding for global variable ‘T2D16S_tax’
momspi16S: no visible global function definition for ‘data’
momspi16S: no visible binding for global variable ‘momspi16S_mtx’
momspi16S: no visible binding for global variable ‘momspi16S_samp’
momspi16S: no visible binding for global variable ‘momspi16S_tax’
momspiCytokines: no visible global function definition for ‘data’
momspiCytokines: no visible binding for global variable
  ‘momspiCyto_mtx’
momspiCytokines: no visible binding for global variable
  ‘momspiCyto_samp’
momspiMultiAssay: no visible global function definition for ‘data’
momspiMultiAssay: no visible binding for global variable ‘file_name’
momspiMultiAssay: no visible binding for global variable
  ‘momspi16S_mtx’
momspiMultiAssay: no visible binding for global variable
  ‘momspiCyto_mtx’
patient_table: no visible binding for global variable ‘.’
table_two: no visible binding for global variable ‘.’
visit_table : <anonymous>: no visible global function definition for
  ‘quantile’
visit_table: no visible binding for global variable ‘.’
Undefined global functions or variables:
  . IBD16S_mtx IBD16S_samp IBD16S_tax T2D16S_mtx T2D16S_samp T2D16S_tax
  data file_name momspi16S_mtx momspi16S_samp momspi16S_tax
  momspiCyto_mtx momspiCyto_samp quantile
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "data")
to your NAMESPACE file.
* 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
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-data-experiment/meat/HMP2Data.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL HMP2Data
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘HMP2Data’ ...
** 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 (HMP2Data)

R Under development (unstable) (2019-12-14 r77569) -- "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)
> library(HMP2Data)
> 
> test_check("HMP2Data")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 5 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 16.120   1.135  17.259 

name	user	system	elapsed
IBD16S	0.087	0.004	0.091
T2D16S	1.365	0.080	1.446
momspi16S	2.156	0.216	2.372
momspiCytokines	0.045	0.004	0.049
momspiMultiAssay	3.376	0.324	3.700
patient_table	3.312	0.352	3.700
table_two	3.050	0.352	3.402
visit_table	3.121	0.360	3.481