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CHECK report for KEGGREST on tokay1

This page was generated on 2021-05-06 12:31:55 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the KEGGREST package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 941/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KEGGREST 1.30.1  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/KEGGREST
Branch: RELEASE_3_12
Last Commit: fd9970e
Last Changed Date: 2020-11-23 12:01:02 -0400 (Mon, 23 Nov 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    ERROR  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: KEGGREST
Version: 1.30.1
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KEGGREST.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings KEGGREST_1.30.1.tar.gz
StartedAt: 2021-05-06 04:03:37 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:08:27 -0400 (Thu, 06 May 2021)
EllapsedTime: 290.8 seconds
RetCode: 1
Status:   ERROR   
CheckDir: KEGGREST.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KEGGREST.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings KEGGREST_1.30.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/KEGGREST.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'KEGGREST/DESCRIPTION' ... OK
* this is package 'KEGGREST' version '1.30.1'
* 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 'KEGGREST' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
listDatabases 2.92   0.51    9.78
keggList      2.42   0.63   13.85
keggLink      0.94   0.03    6.69
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
listDatabases 2.23   0.70    9.12
keggList      1.84   0.53   12.82
keggLink      0.44   0.02    6.18
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'KEGGREST_unit_tests.R'
 ERROR
Running the tests in 'tests/KEGGREST_unit_tests.R' failed.
Last 13 lines of output:
  KEGGREST RUnit Tests - 11 test functions, 1 error, 1 failure
  FAILURE in test_keggGet_2: Error in checkTrue(class(res) == "character") : Test not TRUE
  
  ERROR in test_listDatabases: Error in .getUrl(url, .textParser) : Bad Request (HTTP 400).
  
  Test files with failing tests
  
     test_KEGGREST.R 
       test_keggGet_2 
       test_listDatabases 
  
  
  Error in BiocGenerics:::testPackage("KEGGREST") : 
    unit tests failed for package KEGGREST
  Execution halted
** running tests for arch 'x64' ...
  Running 'KEGGREST_unit_tests.R'
 ERROR
Running the tests in 'tests/KEGGREST_unit_tests.R' failed.
Last 13 lines of output:
  KEGGREST RUnit Tests - 11 test functions, 1 error, 1 failure
  FAILURE in test_keggGet_2: Error in checkTrue(class(res) == "character") : Test not TRUE
  
  ERROR in test_listDatabases: Error in .getUrl(url, .textParser) : Bad Request (HTTP 400).
  
  Test files with failing tests
  
     test_KEGGREST.R 
       test_keggGet_2 
       test_listDatabases 
  
  
  Error in BiocGenerics:::testPackage("KEGGREST") : 
    unit tests failed for package KEGGREST
  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
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/KEGGREST.Rcheck/00check.log'
for details.

Installation output

KEGGREST.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/KEGGREST_1.30.1.tar.gz && rm -rf KEGGREST.buildbin-libdir && mkdir KEGGREST.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=KEGGREST.buildbin-libdir KEGGREST_1.30.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL KEGGREST_1.30.1.zip && rm KEGGREST_1.30.1.tar.gz KEGGREST_1.30.1.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 14742  100 14742    0     0  1134k      0 --:--:-- --:--:-- --:--:-- 1199k

install for i386

* installing *source* package 'KEGGREST' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'KEGGREST'
    finding HTML links ... done
    keggConv                                html  
    keggFind                                html  
    keggGet                                 html  
    keggInfo                                html  
    keggLink                                html  
    keggList                                html  
    listDatabases                           html  
    mark.pathway.by.objects                 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

* installing *source* package 'KEGGREST' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'KEGGREST' as KEGGREST_1.30.1.zip
* DONE (KEGGREST)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'KEGGREST' successfully unpacked and MD5 sums checked

Tests output

KEGGREST.Rcheck/tests_i386/KEGGREST_unit_tests.Rout.fail


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> BiocGenerics:::testPackage("KEGGREST")
Timing stopped at: 0.09 0 0.94
Error in checkTrue(class(res) == "character") : Test not TRUE

Timing stopped at: 0.1 0.05 8.58
Error in .getUrl(url, .textParser) : Bad Request (HTTP 400).
No encoding supplied: defaulting to UTF-8.


RUNIT TEST PROTOCOL -- Thu May 06 04:07:28 2021 
*********************************************** 
Number of test functions: 11 
Number of errors: 1 
Number of failures: 1 

 
1 Test Suite : 
KEGGREST RUnit Tests - 11 test functions, 1 error, 1 failure
FAILURE in test_keggGet_2: Error in checkTrue(class(res) == "character") : Test not TRUE

ERROR in test_listDatabases: Error in .getUrl(url, .textParser) : Bad Request (HTTP 400).

Test files with failing tests

   test_KEGGREST.R 
     test_keggGet_2 
     test_listDatabases 


Error in BiocGenerics:::testPackage("KEGGREST") : 
  unit tests failed for package KEGGREST
Execution halted

KEGGREST.Rcheck/tests_x64/KEGGREST_unit_tests.Rout.fail


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> BiocGenerics:::testPackage("KEGGREST")
Timing stopped at: 0.16 0 0.97
Error in checkTrue(class(res) == "character") : Test not TRUE

Timing stopped at: 0.17 0 7.81
Error in .getUrl(url, .textParser) : Bad Request (HTTP 400).
No encoding supplied: defaulting to UTF-8.


RUNIT TEST PROTOCOL -- Thu May 06 04:08:23 2021 
*********************************************** 
Number of test functions: 11 
Number of errors: 1 
Number of failures: 1 

 
1 Test Suite : 
KEGGREST RUnit Tests - 11 test functions, 1 error, 1 failure
FAILURE in test_keggGet_2: Error in checkTrue(class(res) == "character") : Test not TRUE

ERROR in test_listDatabases: Error in .getUrl(url, .textParser) : Bad Request (HTTP 400).

Test files with failing tests

   test_KEGGREST.R 
     test_keggGet_2 
     test_listDatabases 


Error in BiocGenerics:::testPackage("KEGGREST") : 
  unit tests failed for package KEGGREST
Execution halted

Example timings

KEGGREST.Rcheck/examples_i386/KEGGREST-Ex.timings

nameusersystemelapsed
keggConv0.200.033.33
keggFind0.050.012.42
keggGet1.620.113.35
keggInfo0.000.001.64
keggLink0.940.036.69
keggList 2.42 0.6313.85
listDatabases2.920.519.78
mark.pathway.by.objects0.220.003.06

KEGGREST.Rcheck/examples_x64/KEGGREST-Ex.timings

nameusersystemelapsed
keggConv0.100.022.37
keggFind0.010.002.55
keggGet1.640.093.32
keggInfo0.030.001.32
keggLink0.440.026.18
keggList 1.84 0.5312.82
listDatabases2.230.709.12
mark.pathway.by.objects0.080.002.81