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This page was generated on 2025-09-22 12:06 -0400 (Mon, 22 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 617/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
drawProteins 1.29.0  (landing page)
Paul Brennan
Snapshot Date: 2025-09-21 13:45 -0400 (Sun, 21 Sep 2025)
git_url: https://git.bioconductor.org/packages/drawProteins
git_branch: devel
git_last_commit: 3f29211
git_last_commit_date: 2025-04-15 11:16:54 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for drawProteins on taishan

To the developers/maintainers of the drawProteins package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/drawProteins.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: drawProteins
Version: 1.29.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:drawProteins.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings drawProteins_1.29.0.tar.gz
StartedAt: 2025-09-19 08:04:26 -0000 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 08:05:25 -0000 (Fri, 19 Sep 2025)
EllapsedTime: 59.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: drawProteins.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:drawProteins.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings drawProteins_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/drawProteins.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘drawProteins/DESCRIPTION’ ... OK
* this is package ‘drawProteins’ version ‘1.29.0’
* 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 ... OK
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/drawProteins.Rcheck/00check.log’
for details.


Installation output

drawProteins.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL drawProteins
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘drawProteins’ ...
** this is package ‘drawProteins’ version ‘1.29.0’
** 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)

Tests output

drawProteins.Rcheck/tests/testthat.Rout.fail


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 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

Example timings

drawProteins.Rcheck/drawProteins-Ex.timings

nameusersystemelapsed
draw_canvas0.3400.0160.358
draw_chains0.8130.0280.844
draw_domains0.6550.0000.657
draw_folding0.8650.0000.867
draw_motif0.4590.0000.459
draw_phospho0.3660.0000.366
draw_recept_dom0.5850.0000.586
draw_regions0.4950.0160.513
draw_repeat0.4170.0040.422
extract_feat_acc0.010.000.01
extract_names0.0050.0000.005
extract_transcripts0.0280.0040.031
feature_to_dataframe0.0230.0000.023
get_features0.0750.0121.796
parse_gff0.5960.0532.231
phospho_site_info0.0050.0000.005