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CHECK report for HMP2Data on riesling1

This page was generated on 2021-01-18 15:58:48 -0500 (Mon, 18 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE HMP2Data PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 178/385HostnameOS / ArchINSTALLBUILDCHECK
HMP2Data 1.5.0
John Stansfield , Ekaterina Smirnova
Snapshot Date: 2021-01-18 09:00:15 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/HMP2Data
Branch: master
Last Commit: 199fb00
Last Changed Date: 2020-10-27 10:30:12 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: HMP2Data
Version: 1.5.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HMP2Data.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings HMP2Data_1.5.0.tar.gz
StartedAt: 2021-01-18 11:27:04 -0500 (Mon, 18 Jan 2021)
EndedAt: 2021-01-18 11:31:01 -0500 (Mon, 18 Jan 2021)
EllapsedTime: 237.1 seconds
RetCode: 0
Status:  OK  
CheckDir: HMP2Data.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HMP2Data.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings HMP2Data_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/HMP2Data.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HMP2Data/DESCRIPTION' ... OK
* this is package 'HMP2Data' version '1.5.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'D:/biocbuild/bbs-3.13-data-experiment/meat/HMP2Data.Rcheck/00check.log'
for details.



Installation output

HMP2Data.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/HMP2Data_1.5.0.tar.gz && rm -rf HMP2Data.buildbin-libdir && mkdir HMP2Data.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HMP2Data.buildbin-libdir HMP2Data_1.5.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL HMP2Data_1.5.0.zip && rm HMP2Data_1.5.0.tar.gz HMP2Data_1.5.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 4764k  100 4764k    0     0  76.2M      0 --:--:-- --:--:-- --:--:-- 76.2M

install for i386

* installing *source* package 'HMP2Data' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'HMP2Data'
    finding HTML links ... done
    IBD16S                                  html  
REDIRECT:topic	 IBD16S -> IBD16S.html [ SUCCESS ]
    IBD16S_mtx                              html  
REDIRECT:topic	 IBD16S_mtx -> IBD16S_mtx.html [ SUCCESS ]
    IBD16S_samp                             html  
REDIRECT:topic	 IBD16S_samp -> IBD16S_samp.html [ SUCCESS ]
    IBD16S_tax                              html  
REDIRECT:topic	 IBD16S_tax -> IBD16S_tax.html [ SUCCESS ]
    T2D16S                                  html  
REDIRECT:topic	 T2D16S -> T2D16S.html [ SUCCESS ]
    T2D16S_mtx                              html  
REDIRECT:topic	 T2D16S_mtx -> T2D16S_mtx.html [ SUCCESS ]
    T2D16S_samp                             html  
REDIRECT:topic	 T2D16S_samp -> T2D16S_samp.html [ SUCCESS ]
    T2D16S_tax                              html  
REDIRECT:topic	 T2D16S_tax -> T2D16S_tax.html [ SUCCESS ]
    momspi16S                               html  
REDIRECT:topic	 momspi16S -> momspi16S.html [ SUCCESS ]
    momspi16S_mtx                           html  
REDIRECT:topic	 momspi16S_mtx -> momspi16S_mtx.html [ SUCCESS ]
    momspi16S_samp                          html  
REDIRECT:topic	 momspi16S_samp -> momspi16S_samp.html [ SUCCESS ]
    momspi16S_tax                           html  
REDIRECT:topic	 momspi16S_tax -> momspi16S_tax.html [ SUCCESS ]
    momspiCyto_mtx                          html  
REDIRECT:topic	 momspiCyto_mtx -> momspiCyto_mtx.html [ SUCCESS ]
    momspiCyto_samp                         html  
REDIRECT:topic	 momspiCyto_samp -> momspiCyto_samp.html [ SUCCESS ]
    momspiCytokines                         html  
REDIRECT:topic	 momspiCytokines -> momspiCytokines.html [ SUCCESS ]
    momspiMultiAssay                        html  
REDIRECT:topic	 momspiMultiAssay -> momspiMultiAssay.html [ SUCCESS ]
    patient_table                           html  
REDIRECT:topic	 patient_table -> patient_table.html [ SUCCESS ]
    table_two                               html  
REDIRECT:topic	 table_two -> table_two.html [ SUCCESS ]
    visit_table                             html  
REDIRECT:topic	 visit_table -> visit_table.html [ SUCCESS ]
** 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

install for x64

* installing *source* package 'HMP2Data' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HMP2Data' as HMP2Data_1.5.0.zip
* DONE (HMP2Data)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'HMP2Data' successfully unpacked and MD5 sums checked

Tests output

HMP2Data.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  11.60    0.84   12.43 

HMP2Data.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  11.62    0.87   12.48 

Example timings

HMP2Data.Rcheck/examples_i386/HMP2Data-Ex.timings

nameusersystemelapsed
IBD16S0.060.010.08
T2D16S1.100.031.13
momspi16S1.820.111.93
momspiCytokines0.020.040.05
momspiMultiAssay2.580.312.89
patient_table2.540.473.01
table_two2.580.292.88
visit_table2.660.212.86

HMP2Data.Rcheck/examples_x64/HMP2Data-Ex.timings

nameusersystemelapsed
IBD16S0.050.010.06
T2D16S1.010.051.06
momspi16S1.530.161.68
momspiCytokines0.030.000.03
momspiMultiAssay2.440.312.75
patient_table2.170.482.68
table_two2.170.352.52
visit_table2.220.252.47