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CHECK report for hmdbQuery on tokay2

This page was generated on 2020-10-17 11:56:50 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE hmdbQuery PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 828/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hmdbQuery 1.8.0
VJ Carey
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/hmdbQuery
Branch: RELEASE_3_11
Last Commit: 1cbb9ae
Last Changed Date: 2020-04-27 15:12:58 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: hmdbQuery
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hmdbQuery.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings hmdbQuery_1.8.0.tar.gz
StartedAt: 2020-10-17 04:57:39 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:04:46 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 427.4 seconds
RetCode: 0
Status:  OK  
CheckDir: hmdbQuery.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hmdbQuery.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings hmdbQuery_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/hmdbQuery.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'hmdbQuery/DESCRIPTION' ... OK
* this is package 'hmdbQuery' version '1.8.0'
* 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 'hmdbQuery' 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
* 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 ... 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 ... NOTE
  Note: found 121 marked UTF-8 strings
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/hmdbQuery.Rcheck/00check.log'
for details.



Installation output

hmdbQuery.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/hmdbQuery_1.8.0.tar.gz && rm -rf hmdbQuery.buildbin-libdir && mkdir hmdbQuery.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hmdbQuery.buildbin-libdir hmdbQuery_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL hmdbQuery_1.8.0.zip && rm hmdbQuery_1.8.0.tar.gz hmdbQuery_1.8.0.zip
###
##############################################################################
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  % 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  513k  100  513k    0     0  8327k      0 --:--:-- --:--:-- --:--:-- 9508k

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'hmdbQuery' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'hmdbQuery'
    finding HTML links ... done
    HmdbEntry-class                         html  
    HmdbEntry                               html  
    biospecimens-HmdbEntry-method           html  
    diseases-HmdbEntry-method               html  
    hmdb1                                   html  
    hmdb_disease                            html  
    hmdb_gene                               html  
    hmdb_omim                               html  
    hmdb_protein                            html  
    store-HmdbEntry-method                  html  
    tissues-HmdbEntry-method                html  
** 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

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'hmdbQuery' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hmdbQuery' as hmdbQuery_1.8.0.zip
* DONE (hmdbQuery)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'hmdbQuery' successfully unpacked and MD5 sums checked

Tests output

hmdbQuery.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(hmdbQuery)
Loading required package: XML
>  
> test_check("hmdbQuery")
== testthat results  ===========================================================
[ OK: 6 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   3.46    0.29    4.06 

hmdbQuery.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(hmdbQuery)
Loading required package: XML
>  
> test_check("hmdbQuery")
== testthat results  ===========================================================
[ OK: 6 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   3.34    0.14    3.84 

Example timings

hmdbQuery.Rcheck/examples_i386/hmdbQuery-Ex.timings

nameusersystemelapsed
HmdbEntry0.800.071.65
biospecimens-HmdbEntry-method0.030.010.05
diseases-HmdbEntry-method0.050.020.07
store-HmdbEntry-method0.000.030.03
tissues-HmdbEntry-method0.020.000.01

hmdbQuery.Rcheck/examples_x64/hmdbQuery-Ex.timings

nameusersystemelapsed
HmdbEntry0.860.031.21
biospecimens-HmdbEntry-method0.010.010.03
diseases-HmdbEntry-method0.040.000.05
store-HmdbEntry-method0.020.000.01
tissues-HmdbEntry-method0.020.000.02