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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CTDquerier.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CTDquerier_2.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CTDquerier.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '2.2.0'
* 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 ... 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
* 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 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 ...
** running examples for arch 'i386' ... 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
** running examples for arch 'x64' ... 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: 2 ERRORs, 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/CTDquerier.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/CTDquerier_2.2.0.tar.gz && rm -rf CTDquerier.buildbin-libdir && mkdir CTDquerier.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CTDquerier.buildbin-libdir CTDquerier_2.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CTDquerier_2.2.0.zip && rm CTDquerier_2.2.0.tar.gz CTDquerier_2.2.0.zip
###
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
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100 2715k  100 2715k    0     0  1588k      0  0:00:01  0:00:01 --:--:-- 1588k

install for i386

* 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

install for x64

* installing *source* package 'CTDquerier' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CTDquerier' as CTDquerier_2.2.0.zip
* DONE (CTDquerier)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'CTDquerier' successfully unpacked and MD5 sums checked