Package: hmdbQuery

Version: 1.0.1

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hmdbQuery.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings hmdbQuery_1.0.1.tar.gz

StartedAt: 2018-10-17 02:41:52 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 02:47:40 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 347.9 seconds

RetCode: 1

Status:  ERROR

CheckDir: hmdbQuery.Rcheck

Warnings: NA

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hmdbQuery.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings hmdbQuery_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/hmdbQuery.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.0.1'
* 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' ... ERROR
Running examples in 'hmdbQuery-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HmdbEntry
> ### Title: Constructor for HmdbEntry instance
> ### Aliases: HmdbEntry
> 
> ### ** Examples
> 
> HmdbEntry()
Start tag expected, '<' not found
Error: 1: Start tag expected, '<' not found
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
HmdbEntry 0.64      0   29.89
* 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'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
             cat(msg)
         if (length(msg) == 0) {
             e = simpleError(paste(1:length(messages), messages, sep = ": ", collapse = ""))
             class(e) = c(class, class(e))
             stop(e)
         }
         messages <<- c(messages, msg)
     })(character(0))
  
  == testthat results  ===========================================================
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Error: query resolves (@tests.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
* 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 ERRORs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/hmdbQuery.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/hmdbQuery_1.0.1.tar.gz && rm -rf hmdbQuery.buildbin-libdir && mkdir hmdbQuery.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hmdbQuery.buildbin-libdir hmdbQuery_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL hmdbQuery_1.0.1.zip && rm hmdbQuery_1.0.1.tar.gz hmdbQuery_1.0.1.zip
###
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100  512k  100  512k    0     0  7829k      0 --:--:-- --:--:-- --:--:-- 8844k

install for i386

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  restoring symbolic link as a file copy
* installing *source* package 'hmdbQuery' ...
** 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
In R CMD INSTALL

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_1.0.1.zip
* DONE (hmdbQuery)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'hmdbQuery' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   2.89    0.09   51.31 

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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")
Document is empty
-- 1. Error: query resolves (@tests.R#6)  --------------------------------------
1: Document is empty
1: HmdbEntry() at testthat/tests.R:6
2: hmxToList(prefix = prefix, id = id)
3: xmlToList(.hmxPath(prefix = prefix, id = id, ...))
4: xmlParse(node)
5: (function (msg, ...) 
   {
       if (length(grep("\\\n$", msg)) == 0) 
           paste(msg, "\n", sep = "")
       if (immediate) 
           cat(msg)
       if (length(msg) == 0) {
           e = simpleError(paste(1:length(messages), messages, sep = ": ", collapse = ""))
           class(e) = c(class, class(e))
           stop(e)
       }
       messages <<- c(messages, msg)
   })(character(0))

== testthat results  ===========================================================
OK: 2 SKIPPED: 0 FAILED: 1
1. Error: query resolves (@tests.R#6) 

Error: testthat unit tests failed
Execution halted