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### Running command:
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###   /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_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/drawProteins.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘drawProteins/DESCRIPTION’ ... OK
* this is package ‘drawProteins’ version ‘1.28.0’
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
get_features 0.074  0.015  29.652
* 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:
  1/1 mismatches
  [1] 1 - 11 == -10
  ── Failure ('test-parsers.R:78:3'): parse_gff ──────────────────────────────────
  mode(p) not equal to "list".
  1/1 mismatches
  x[1]: "object"
  y[1]: "list"
  ── Failure ('test-parsers.R:79:3'): parse_gff ──────────────────────────────────
  length(p) not equal to 11.
  1/1 mismatches
  [1] 1 - 11 == -10
  
  [ FAIL 24 | WARN 1 | SKIP 0 | PASS 159 ]
  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: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/drawProteins.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL drawProteins
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘drawProteins’ ...
** this is package ‘drawProteins’ version ‘1.28.0’
** 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 version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 24 | WARN 1 | SKIP 0 | PASS 159 ]

══ 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
── Failure ('test-parsers.R:78:3'): parse_gff ──────────────────────────────────
mode(p) not equal to "list".
1/1 mismatches
x[1]: "object"
y[1]: "list"
── Failure ('test-parsers.R:79:3'): parse_gff ──────────────────────────────────
length(p) not equal to 11.
1/1 mismatches
[1] 1 - 11 == -10

[ FAIL 24 | WARN 1 | SKIP 0 | PASS 159 ]
Error: Test failures
Execution halted