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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CTDquerier.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CTDquerier_2.3.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CTDquerier.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CTDquerier/DESCRIPTION' ... OK
* this is package 'CTDquerier' version '2.3.1'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'CTDquerier' can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... NOTE
  Note: found 176 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'batch_query.Rmd', 'biomed-central.csl', 'case_study.Rmd',
    'case_study.bib', 'img/01_CTDbase.png', 'img/02_XKR4_keyword.png',
    'img/03_BatchQuery.png', 'vignette.Rmd'
* checking examples ... ERROR
Running examples in 'CTDquerier-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: enrich
> ### Title: Method to perform enrichment analysis using two 'CTDdata'
> ###   objects
> ### Aliases: enrich
> 
> ### ** Examples
> 
> data("gala")
> air <- query_ctd_chem( terms = "Air Pollutants" )
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to ctdbase.org port 80: Timed out
Calls: query_ctd_chem ... download_url -> <Anonymous> -> curlPerform -> <Anonymous> -> fun
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/CTDquerier.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CTDquerier
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'CTDquerier' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CTDquerier'
    finding HTML links ... done
    CTDdata-class                           html  
    CTDquerier                              html  
    download_ctd_chem                       html  
    download_ctd_dise                       html  
    download_ctd_genes                      html  
    enrich-methods                          html  
    gala                                    html  
    get_table-methods                       html  
    get_terms-methods                       html  
    leaf_plot                               html  
    load_ctd_chem                           html  
    load_ctd_dise                           html  
    load_ctd_gene                           html  
    query_ctd_chem                          html  
    query_ctd_dise                          html  
    query_ctd_gene                          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
* DONE (CTDquerier)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'geneRecommender' is missing or broken
 done