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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:drawProteins.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings drawProteins_1.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/drawProteins.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘drawProteins/DESCRIPTION’ ... OK
* this is package ‘drawProteins’ version ‘1.31.0’
* 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 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 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: get_features
> ### Title: GET features of protein(s) from UniProt API
> ### Aliases: get_features
> 
> ### ** Examples
> 
> # Requires internet access
> prot_data <- get_features("Q04206 Q01201 Q04864 P19838 Q00653")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [www.ebi.ac.uk]:
Resolving timed out after 10001 milliseconds
Calls: get_features ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
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:
  ── Error ('test-parsers.R:57:3'): parse_gff ────────────────────────────────────
  Error in `open.connection(structure(4L, class = c("curl", "connection"), conn_id = <pointer: 0x64a7478691b0>), 
      "rb")`: cannot open the connection
  Backtrace:
      ▆
   1. ├─drawProteins::parse_gff("https://www.uniprot.org/uniprot/P0A7B8.gff") at test-parsers.R:57:3
   2. │ └─readr::read_tsv(file_or_link, comment = "##", col_names = FALSE)
   3. │   └─vroom::vroom(...)
   4. │     └─vroom:::vroom_(...)
   5. ├─base (local) `<fn>`(`<curl>`, "rb")
   6. └─base::open.connection(`<curl>`, "rb")
  
  [ FAIL 23 | WARN 2 | SKIP 0 | PASS 143 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/drawProteins.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL drawProteins
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘drawProteins’ ...
** this is package ‘drawProteins’ version ‘1.31.0’
** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 23 | WARN 2 | SKIP 0 | PASS 143 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-geoms.R:18:3'): draw_canvas ──────────────────────────────────
mode(p) not equal to "list".
1/1 mismatches
x[1]: "object"
y[1]: "list"
── Failure ('test-geoms.R:19:3'): draw_canvas ──────────────────────────────────
length(p) not equal to 11.
1/1 mismatches
[1] 1 - 11 == -10
── Failure ('test-geoms.R:47:3'): draw_chains ──────────────────────────────────
mode(p) not equal to "list".
1/1 mismatches
x[1]: "object"
y[1]: "list"
── Failure ('test-geoms.R:48:3'): draw_chains ──────────────────────────────────
length(p) not equal to 11.
1/1 mismatches
[1] 1 - 11 == -10
── Failure ('test-geoms.R:81:3'): draw_domains ─────────────────────────────────
mode(p) not equal to "list".
1/1 mismatches
x[1]: "object"
y[1]: "list"
── Failure ('test-geoms.R:82:3'): draw_domains ─────────────────────────────────
length(p) not equal to 11.
1/1 mismatches
[1] 1 - 11 == -10
── Failure ('test-geoms.R:119:3'): draw_phospho ────────────────────────────────
mode(p) not equal to "list".
1/1 mismatches
x[1]: "object"
y[1]: "list"
── Failure ('test-geoms.R:120:3'): draw_phospho ────────────────────────────────
length(p) not equal to 11.
1/1 mismatches
[1] 1 - 11 == -10
── Failure ('test-geoms.R:153:3'): draw_motif ──────────────────────────────────
mode(p) not equal to "list".
1/1 mismatches
x[1]: "object"
y[1]: "list"
── Failure ('test-geoms.R:154:3'): draw_motif ──────────────────────────────────
length(p) not equal to 11.
1/1 mismatches
[1] 1 - 11 == -10
── Failure ('test-geoms.R:198:3'): draw_regions ────────────────────────────────
mode(p) not equal to "list".
1/1 mismatches
x[1]: "object"
y[1]: "list"
── Failure ('test-geoms.R:199:3'): draw_regions ────────────────────────────────
length(p) not equal to 11.
1/1 mismatches
[1] 1 - 11 == -10
── Failure ('test-geoms.R:244:3'): draw_repeat ─────────────────────────────────
mode(p) not equal to "list".
1/1 mismatches
x[1]: "object"
y[1]: "list"
── Failure ('test-geoms.R:245:3'): draw_repeat ─────────────────────────────────
length(p) not equal to 11.
1/1 mismatches
[1] 1 - 11 == -10
── Failure ('test-geoms.R:288:3'): draw_recept_dom ─────────────────────────────
mode(p) not equal to "list".
1/1 mismatches
x[1]: "object"
y[1]: "list"
── Failure ('test-geoms.R:289:3'): draw_recept_dom ─────────────────────────────
length(p) not equal to 11.
1/1 mismatches
[1] 1 - 11 == -10
── Failure ('test-geoms.R:315:3'): draw_recept_dom ─────────────────────────────
mode(p) not equal to "list".
1/1 mismatches
x[1]: "object"
y[1]: "list"
── Failure ('test-geoms.R:316:3'): draw_recept_dom ─────────────────────────────
length(p) not equal to 11.
1/1 mismatches
[1] 1 - 11 == -10
── Failure ('test-geoms.R:373:3'): draw_folding ────────────────────────────────
mode(p) not equal to "list".
1/1 mismatches
x[1]: "object"
y[1]: "list"
── Failure ('test-geoms.R:374:3'): draw_folding ────────────────────────────────
length(p) not equal to 11.
1/1 mismatches
[1] 1 - 11 == -10
── Failure ('test-parsers.R:30:3'): parse_gff ──────────────────────────────────
mode(p) not equal to "list".
1/1 mismatches
x[1]: "object"
y[1]: "list"
── Failure ('test-parsers.R:31:3'): parse_gff ──────────────────────────────────
length(p) not equal to 11.
1/1 mismatches
[1] 1 - 11 == -10
── Error ('test-parsers.R:57:3'): parse_gff ────────────────────────────────────
Error in `open.connection(structure(4L, class = c("curl", "connection"), conn_id = <pointer: 0x64a7478691b0>), 
    "rb")`: cannot open the connection
Backtrace:
    ▆
 1. ├─drawProteins::parse_gff("https://www.uniprot.org/uniprot/P0A7B8.gff") at test-parsers.R:57:3
 2. │ └─readr::read_tsv(file_or_link, comment = "##", col_names = FALSE)
 3. │   └─vroom::vroom(...)
 4. │     └─vroom:::vroom_(...)
 5. ├─base (local) `<fn>`(`<curl>`, "rb")
 6. └─base::open.connection(`<curl>`, "rb")

[ FAIL 23 | WARN 2 | SKIP 0 | PASS 143 ]
Error: Test failures
Execution halted