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CHECK report for BridgeDbR on tokay1

This page was generated on 2020-04-15 12:24:02 -0400 (Wed, 15 Apr 2020).

Package 200/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BridgeDbR 1.20.3
Egon Willighagen
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/BridgeDbR
Branch: RELEASE_3_10
Last Commit: 4673e45
Last Changed Date: 2020-02-14 11:42:27 -0400 (Fri, 14 Feb 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BridgeDbR
Version: 1.20.3
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BridgeDbR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings BridgeDbR_1.20.3.tar.gz
StartedAt: 2020-04-15 01:43:43 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:44:30 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 46.8 seconds
RetCode: 1
Status:  ERROR  
CheckDir: BridgeDbR.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BridgeDbR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings BridgeDbR_1.20.3.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/BridgeDbR.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BridgeDbR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BridgeDbR' version '1.20.3'
* 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 'BridgeDbR' 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' ... ERROR
Running examples in 'BridgeDbR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getDatabase
> ### Title: Downloads a identifier mapping database for the given organism.
> ### Aliases: getDatabase
> 
> ### ** Examples
> 
> location <- getDatabase("Bacillus subtilis")
Error in function (type, msg, asError = TRUE)  : 
  error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Calls: getDatabase ... getBridgeNames -> curlPerform -> <Anonymous> -> fun
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'BridgeDbR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getDatabase
> ### Title: Downloads a identifier mapping database for the given organism.
> ### Aliases: getDatabase
> 
> ### ** Examples
> 
> location <- getDatabase("Bacillus subtilis")
Error in function (type, msg, asError = TRUE)  : 
  error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Calls: getDatabase ... getBridgeNames -> curlPerform -> <Anonymous> -> fun
Execution halted
* 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 ERRORs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/BridgeDbR.Rcheck/00check.log'
for details.


Installation output

BridgeDbR.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/BridgeDbR_1.20.3.tar.gz && rm -rf BridgeDbR.buildbin-libdir && mkdir BridgeDbR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BridgeDbR.buildbin-libdir BridgeDbR_1.20.3.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL BridgeDbR_1.20.3.zip && rm BridgeDbR_1.20.3.tar.gz BridgeDbR_1.20.3.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 2407k  100 2407k    0     0  27.7M      0 --:--:-- --:--:-- --:--:-- 29.0M

install for i386

* installing *source* package 'BridgeDbR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BridgeDbR'
    finding HTML links ... done
    BridgeDbR                               html  
    fullNameExists                          html  
    getAttributes                           html  
    getBridgeNames                          html  
    getDataSource                           html  
    getDatabase                             html  
    getFullName                             html  
    getMatchingSources                      html  
    getOrganismCode                         html  
    getSystemCode                           html  
    loadDatabase                            html  
    map                                     html  
    registerDataSource                      html  
    systemCodeExists                        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 'BridgeDbR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BridgeDbR' as BridgeDbR_1.20.3.zip
* DONE (BridgeDbR)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'BridgeDbR' successfully unpacked and MD5 sums checked

Tests output

BridgeDbR.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(BridgeDbR)
Loading required package: rJava
> 
> test_check("BridgeDbR")
== testthat results  ===========================================================
[ OK: 20 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> 
> proc.time()
   user  system elapsed 
   1.87    0.14    1.95 

BridgeDbR.Rcheck/tests_x64/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(BridgeDbR)
Loading required package: rJava
> 
> test_check("BridgeDbR")
== testthat results  ===========================================================
[ OK: 20 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> 
> proc.time()
   user  system elapsed 
   2.09    0.12    2.07 

Example timings

BridgeDbR.Rcheck/examples_i386/BridgeDbR-Ex.timings

nameusersystemelapsed
fullNameExists000
getAttributes000
getBridgeNames000
getDataSource000

BridgeDbR.Rcheck/examples_x64/BridgeDbR-Ex.timings

nameusersystemelapsed
fullNameExists000
getAttributes000
getBridgeNames000
getDataSource000