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This page was generated on 2021-10-23 15:51:47 -0400 (Sat, 23 Oct 2021).

CHECK results for HMP2Data on nebbiolo2

To the developers/maintainers of the HMP2Data package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 181/408HostnameOS / ArchINSTALLBUILDCHECK
HMP2Data 1.7.0  (landing page)
John Stansfield , Ekaterina Smirnova
Snapshot Date: 2021-10-23 09:30:01 -0400 (Sat, 23 Oct 2021)
git_url: https://git.bioconductor.org/packages/HMP2Data
git_branch: master
git_last_commit: 581f6a4
git_last_commit_date: 2021-05-19 12:08:33 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: HMP2Data
Version: 1.7.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:HMP2Data.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings HMP2Data_1.7.0.tar.gz
StartedAt: 2021-10-23 12:24:16 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 12:27:34 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 198.1 seconds
RetCode: 0
Status:   OK  
CheckDir: HMP2Data.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:HMP2Data.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings HMP2Data_1.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/HMP2Data.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.7.0’
* 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-3.14-data-experiment/meat/HMP2Data.Rcheck/00check.log’
for details.



Installation output

HMP2Data.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL HMP2Data
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-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)

Tests output

HMP2Data.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
 12.722   1.071  13.775 

Example timings

HMP2Data.Rcheck/HMP2Data-Ex.timings

nameusersystemelapsed
IBD16S0.0700.0080.079
T2D16S1.2590.1361.395
momspi16S1.8680.2762.144
momspiCytokines0.0450.0040.048
momspiMultiAssay2.2170.2722.488
patient_table2.7870.4323.220
table_two2.7670.3963.164
visit_table2.6820.4563.138