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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:brendaDb.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings brendaDb_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/brendaDb.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘brendaDb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘brendaDb’ version ‘1.2.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
  .github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘brendaDb’ 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
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘brendaDb-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BiocycPathwayEnzymes
> ### Title: Get all EC numbers involved in a BioCyc pathway.
> ### Aliases: BiocycPathwayEnzymes
> 
> ### ** Examples
> 
> BiocycPathwayEnzymes("HUMAN", "PWY66-400")
Error in close.connection(con) : invalid connection
Calls: BiocycPathwayEnzymes ... tryCatchOne -> <Anonymous> -> close -> close.connection
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    1. testthat::expect_message(...)
    6. brendaDb::BiocycPathwayGenes(org.id = "HUMAN", pathway = "PWY66666")
    7. base::tryCatch(...)
    8. base:::tryCatchList(expr, classes, parentenv, handlers)
    9. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10. value[[3L]](cond)
   12. base::close.connection(con)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 108 | SKIPPED: 0 | WARNINGS: 113 | FAILED: 2 ]
  1. Error: Get enzymes in BioCyc pathway  (@test-biocyc.R#6) 
  2. Error: Get genes in BioCyc pathway  (@test-biocyc.R#18) 
  
  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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/brendaDb.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL brendaDb
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘brendaDb’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c read_brenda.cpp -o read_brenda.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o brendaDb.so RcppExports.o read_brenda.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-brendaDb/00new/brendaDb/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (brendaDb)

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(brendaDb)
> 
> test_check("brendaDb")
── 1. Error: Get enzymes in BioCyc pathway  (@test-biocyc.R#6)  ────────────────
invalid connection
Backtrace:
  1. testthat::expect_message(...)
  6. brendaDb::BiocycPathwayEnzymes(org.id = "HUMAN", pathway = "PWY66666")
  7. base::tryCatch(...)
  8. base:::tryCatchList(expr, classes, parentenv, handlers)
  9. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10. value[[3L]](cond)
 12. base::close.connection(con)

── 2. Error: Get genes in BioCyc pathway  (@test-biocyc.R#18)  ─────────────────
invalid connection
Backtrace:
  1. testthat::expect_message(...)
  6. brendaDb::BiocycPathwayGenes(org.id = "HUMAN", pathway = "PWY66666")
  7. base::tryCatch(...)
  8. base:::tryCatchList(expr, classes, parentenv, handlers)
  9. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10. value[[3L]](cond)
 12. base::close.connection(con)

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 108 | SKIPPED: 0 | WARNINGS: 113 | FAILED: 2 ]
1. Error: Get enzymes in BioCyc pathway  (@test-biocyc.R#6) 
2. Error: Get genes in BioCyc pathway  (@test-biocyc.R#18) 

Error: testthat unit tests failed
Execution halted