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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Moonlight2R.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Moonlight2R_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Moonlight2R.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘Moonlight2R/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Moonlight2R’ 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Moonlight2R’ 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 code 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Moonlight2R-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GLS
> ### Title: GLS This function carries out gene literature search.
> ### Aliases: GLS
> 
> ### ** Examples
> 
> genes_query <- "BRCA1"
> dataGLS <- GLS(genes = genes_query,
+                query_string = "AND cancer AND driver",
+ 	  max_records = 2)
Killing the request! Something is not working. Please, try again later
Error in `map()`:
ℹ In index: 1.
Caused by error in `if (count_pubmed > 0) ...`:
! argument is of length zero
Backtrace:
     ▆
  1. ├─Moonlight2R::GLS(...)
  2. │ ├─map(genes, search_pubmed) %>% bind_rows()
  3. │ └─purrr::map(genes, search_pubmed)
  4. │   └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  5. │     ├─purrr:::with_indexed_errors(...)
  6. │     │ └─base::withCallingHandlers(...)
  7. │     ├─purrr:::call_with_cleanup(...)
  8. │     └─Moonlight2R (local) .f(.x[[i]], ...)
  9. ├─dplyr::bind_rows(.)
 10. │ └─rlang::list2(...)
 11. └─base::.handleSimpleError(...)
 12.   └─purrr (local) h(simpleError(msg, call))
 13.     └─cli::cli_abort(...)
 14.       └─rlang::abort(...)
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:
    4. │   └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
    5. │     ├─purrr:::with_indexed_errors(...)
    6. │     │ └─base::withCallingHandlers(...)
    7. │     ├─purrr:::call_with_cleanup(...)
    8. │     └─Moonlight2R (local) .f(.x[[i]], ...)
    9. ├─dplyr::bind_rows(.)
   10. │ └─rlang::list2(...)
   11. └─base::.handleSimpleError(...)
   12.   └─purrr (local) h(simpleError(msg, call))
   13.     └─cli::cli_abort(...)
   14.       └─rlang::abort(...)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 39 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘Moonlight2R.Rmd’ using rmarkdown
trying URL 'https://egg2.wustl.edu/roadmap/data/byFileType/chromhmmSegmentations/ChmmModels/core_K27ac/jointModel/final/E096_18_core_K27ac_hg38lift_mnemonics.bed.gz'
Content type 'application/x-gzip' length 3835377 bytes (3.7 MB)
==================================================
downloaded 3.7 MB


Quitting from lines 761-766 [unnamed-chunk-21] (Moonlight2R.Rmd)
Error: processing vignette 'Moonlight2R.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `if (count_pubmed > 0) ...`:
! argument is of length zero
--- failed re-building ‘Moonlight2R.Rmd’

SUMMARY: processing the following file failed:
  ‘Moonlight2R.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/Moonlight2R.Rcheck/00check.log’
for details.