##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:drawProteins.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings drawProteins_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/drawProteins.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘drawProteins/DESCRIPTION’ ... OK
* this is package ‘drawProteins’ version ‘1.26.0’
* 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 ‘drawProteins’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    CHANGES VERSION 0.98.1
* 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 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘drawProteins-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: parse_gff
> ### Title: Reformat file or url in gff format to allow to draw
> ### Aliases: parse_gff
> 
> ### ** Examples
> 
> data <- parse_gff("https://www.uniprot.org/uniprot/Q04206.gff")
Warning: One or more parsing issues, call `problems()` on your data frame for details,
e.g.:
  dat <- vroom(...)
  problems(dat)
Rows: 3 Columns: 3
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (3): X1, X2, X3

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Error in `dplyr::filter()`:
ℹ In argument: `begin > 0`.
Caused by error:
! `..1` must be of size 3 or 1, not size 0.
Backtrace:
     ▆
  1. ├─drawProteins::parse_gff("https://www.uniprot.org/uniprot/Q04206.gff")
  2. │ ├─dplyr::filter(gff_data, begin > 0)
  3. │ └─dplyr:::filter.data.frame(gff_data, begin > 0)
  4. │   └─dplyr:::filter_rows(.data, dots, by)
  5. │     └─dplyr:::filter_eval(...)
  6. │       ├─base::withCallingHandlers(...)
  7. │       └─mask$eval_all_filter(dots, env_filter)
  8. │         └─dplyr (local) eval()
  9. ├─dplyr:::dplyr_internal_error(...)
 10. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
 11. │   └─rlang:::signal_abort(cnd, .file)
 12. │     └─base::signalCondition(cnd)
 13. └─dplyr (local) `<fn>`(`<dpl:::__>`)
 14.   └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    4. │   └─dplyr:::filter_rows(.data, dots, by)
    5. │     └─dplyr:::filter_eval(...)
    6. │       ├─base::withCallingHandlers(...)
    7. │       └─mask$eval_all_filter(dots, env_filter)
    8. │         └─dplyr (local) eval()
    9. ├─dplyr:::dplyr_internal_error(...)
   10. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
   11. │   └─rlang:::signal_abort(cnd, .file)
   12. │     └─base::signalCondition(cnd)
   13. └─dplyr (local) `<fn>`(`<dpl:::__>`)
   14.   └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 165 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-bioc/meat/drawProteins.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL drawProteins
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘drawProteins’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (drawProteins)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(drawProteins)
> 
> test_check("drawProteins")
[1] "Download has worked"
[1] "An error has occured. Code: 400"
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 165 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-parsers.R:57:3'): parse_gff ────────────────────────────────────
Error in `dplyr::filter(gff_data, begin > 0)`: ℹ In argument: `begin > 0`.
Caused by error:
! `..1` must be of size 6 or 1, not size 0.
Backtrace:
     ▆
  1. ├─drawProteins::parse_gff("https://www.uniprot.org/uniprot/P0A7B8.gff") at test-parsers.R:57:3
  2. │ ├─dplyr::filter(gff_data, begin > 0)
  3. │ └─dplyr:::filter.data.frame(gff_data, begin > 0)
  4. │   └─dplyr:::filter_rows(.data, dots, by)
  5. │     └─dplyr:::filter_eval(...)
  6. │       ├─base::withCallingHandlers(...)
  7. │       └─mask$eval_all_filter(dots, env_filter)
  8. │         └─dplyr (local) eval()
  9. ├─dplyr:::dplyr_internal_error(...)
 10. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
 11. │   └─rlang:::signal_abort(cnd, .file)
 12. │     └─base::signalCondition(cnd)
 13. └─dplyr (local) `<fn>`(`<dpl:::__>`)
 14.   └─rlang::abort(message, class = error_class, parent = parent, call = error_call)

[ FAIL 1 | WARN 2 | SKIP 0 | PASS 165 ]
Error: Test failures
Execution halted