BioC 3.2: CHECK report for KEGGREST on windows1.bioconductor.org

Package: KEGGREST

Version: 1.10.0

Command: rm -rf KEGGREST.buildbin-libdir KEGGREST.Rcheck && mkdir KEGGREST.buildbin-libdir KEGGREST.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGREST.buildbin-libdir KEGGREST_1.10.0.tar.gz >KEGGREST.Rcheck\00install.out 2>&1 && cp KEGGREST.Rcheck\00install.out KEGGREST-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=KEGGREST.buildbin-libdir --install="check:KEGGREST-install.out" --force-multiarch --no-vignettes --timings KEGGREST_1.10.0.tar.gz

StartedAt: 2015-10-27 03:00:24 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:06:38 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 374.7 seconds

RetCode: 1

Status:  ERROR

CheckDir: KEGGREST.Rcheck

Warnings: NA

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### Running command:
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###   rm -rf KEGGREST.buildbin-libdir KEGGREST.Rcheck && mkdir KEGGREST.buildbin-libdir KEGGREST.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGREST.buildbin-libdir KEGGREST_1.10.0.tar.gz >KEGGREST.Rcheck\00install.out 2>&1 && cp KEGGREST.Rcheck\00install.out KEGGREST-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=KEGGREST.buildbin-libdir --install="check:KEGGREST-install.out" --force-multiarch --no-vignettes --timings KEGGREST_1.10.0.tar.gz
###
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/KEGGREST.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.10.0'
* 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 ... NOTE
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Unexported object imported by a ':::' call: 'BiocGenerics:::testPackage'
  See the note in ?`:::` about the use of this operator.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'KEGGREST-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: keggConv
> ### Title: Convert KEGG identifiers to/from outside identifiers
> ### Aliases: keggConv conv bconv
> ### Keywords: conv
> 
> ### ** Examples
> 
> head(keggConv("eco", "ncbi-geneid")) ## conversion from NCBI GeneID to 
Error in FUN(X[[i]], ...) : subscript out of bounds
Calls: head ... .getUrl -> do.call -> <Anonymous> -> sapply -> lapply
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'KEGGREST-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: keggConv
> ### Title: Convert KEGG identifiers to/from outside identifiers
> ### Aliases: keggConv conv bconv
> ### Keywords: conv
> 
> ### ** Examples
> 
> head(keggConv("eco", "ncbi-geneid")) ## conversion from NCBI GeneID to 
Error in FUN(X[[i]], ...) : subscript out of bounds
Calls: head ... .getUrl -> do.call -> <Anonymous> -> sapply -> lapply
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'KEGGREST_unit_tests.R' [136s]
Warning message:
running command '"C:/biocbld/BBS-3˜1.2-B/R/bin/i386/R" CMD BATCH --vanilla  "KEGGREST_unit_tests.R" "KEGGREST_unit_tests.Rout"' had status 1 
 ERROR
Running the tests in 'tests/KEGGREST_unit_tests.R' failed.
Last 13 lines of output:
  
  Test files with failing tests
  
     test_KEGGREST.R 
       test_keggConv 
  
  
  Error in BiocGenerics:::testPackage("KEGGREST") : 
    unit tests failed for package KEGGREST
  In addition: Warning message:
  In download.file(url, t, quiet = TRUE) :
    downloaded length 265738 != reported length 200
  Execution halted
** running tests for arch 'x64' ...
  Running 'KEGGREST_unit_tests.R' [156s]
 [157s] 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: 3 ERRORs, 1 NOTE
See
  'C:/biocbld/bbs-3.2-bioc/meat/KEGGREST.Rcheck/00check.log'
for details.

R version 3.2.2 Patched (2015-08-16 r69094) -- "Fire Safety"
Copyright (C) 2015 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: 0.05 0 0.51 
Error in FUN(X[[i]], ...) : subscript out of bounds


RUNIT TEST PROTOCOL -- Tue Oct 27 03:03:58 2015 
*********************************************** 
Number of test functions: 10 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
KEGGREST RUnit Tests - 10 test functions, 1 error, 0 failures
ERROR in test_keggConv: Error in FUN(X[[i]], ...) : subscript out of bounds

Test files with failing tests

   test_KEGGREST.R 
     test_keggConv 


Error in BiocGenerics:::testPackage("KEGGREST") : 
  unit tests failed for package KEGGREST
In addition: Warning message:
In download.file(url, t, quiet = TRUE) :
  downloaded length 265738 != reported length 200
Execution halted

install for i386

* installing *source* package 'KEGGREST' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'KEGGREST' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'KEGGREST' as KEGGREST_1.10.0.zip
* DONE (KEGGREST)

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