Back to Workflows build report for BioC 3.24

This page was generated on 2026-05-06 14:17 -0400 (Wed, 06 May 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 RC (2026-04-17 r89917) -- "Because it was There" 4878
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 16/28HostnameOS / ArchINSTALLBUILD
maEndToEnd 2.33.0  (landing page)
Stefanie Reisenauer
Snapshot Date: 2026-05-05 12:45 -0400 (Tue, 05 May 2026)
git_url: https://git.bioconductor.org/packages/maEndToEnd
git_branch: devel
git_last_commit: 09ef1b0
git_last_commit_date: 2026-04-28 08:43:24 -0400 (Tue, 28 Apr 2026)
nebbiolo2Linux (Ubuntu 24.04.4 LTS) / x86_64  OK    ERROR  

BUILD results for maEndToEnd on nebbiolo2

To the developers/maintainers of the maEndToEnd package:
- 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.

raw results


Summary

Package: maEndToEnd
Version: 2.33.0
Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data maEndToEnd
StartedAt: 2026-05-05 13:06:16 -0400 (Tue, 05 May 2026)
EndedAt: 2026-05-05 13:19:36 -0400 (Tue, 05 May 2026)
EllapsedTime: 800.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data maEndToEnd
###
##############################################################################
##############################################################################


* checking for file ‘maEndToEnd/DESCRIPTION’ ... OK
* preparing ‘maEndToEnd’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘MA-Workflow.Rmd’ using rmarkdown
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/164_I_.CEL'
Content type 'unknown' length 11127291 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/164_II.CEL'
Content type 'unknown' length 11140543 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/183_I.CEL'
Content type 'unknown' length 11132883 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/183_II.CEL'
Content type 'unknown' length 11143643 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2114_I.CEL'
Content type 'unknown' length 11153863 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2114_II.CEL'
Content type 'unknown' length 11145363 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2209_A.CEL'
Content type 'unknown' length 11149595 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2209_B.CEL'
Content type 'unknown' length 11139827 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2255_I.CEL'
Content type 'unknown' length 11129107 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2255_II.CEL'
Content type 'unknown' length 11149443 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2400_I.CEL'
Content type 'unknown' length 11141903 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2400_II.CEL'
Content type 'unknown' length 11145051 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2424_A.CEL'
Content type 'unknown' length 11142087 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2424_B.CEL'
Content type 'unknown' length 11152051 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/255_I.CEL'
Content type 'unknown' length 11134823 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/255_II.CEL'
Content type 'unknown' length 11148839 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2826_I.CEL'
Content type 'unknown' length 11172699 bytes (10.7 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2826_II.CEL'
Content type 'unknown' length 11167763 bytes (10.7 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2853_I.CEL'
Content type 'unknown' length 11139691 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2853_II.CEL'
Content type 'unknown' length 11156107 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2978_I.CEL'
Content type 'unknown' length 11158567 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2978_II.CEL'
Content type 'unknown' length 11159179 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2987_I.CEL'
Content type 'unknown' length 11151579 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2987_II.CEL'
Content type 'unknown' length 11161519 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2992_I.CEL'
Content type 'unknown' length 11137547 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2992_II.CEL'
Content type 'unknown' length 11144255 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2995_I.CEL'
Content type 'unknown' length 11129827 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2995_II.CEL'
Content type 'unknown' length 11139707 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/321_I.CEL'
Content type 'unknown' length 11145439 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/321_II.CEL'
Content type 'unknown' length 11174727 bytes (10.7 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3222_I.CEL'
Content type 'unknown' length 11137815 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3222_II.CEL'
Content type 'unknown' length 11132307 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3223_I.CEL'
Content type 'unknown' length 11142335 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3223_II.CEL'
Content type 'unknown' length 11156763 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3226_I.CEL'
Content type 'unknown' length 11129139 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3226_II.CEL'
Content type 'unknown' length 11141699 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3233_I.CEL'
Content type 'unknown' length 11132907 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3233_II.CEL'
Content type 'unknown' length 11141551 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3258_I.CEL'
Content type 'unknown' length 11162219 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3258_II.CEL'
Content type 'unknown' length 11142571 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3259_I.CEL'
Content type 'unknown' length 11139091 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3259_II.CEL'
Content type 'unknown' length 11134395 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3262_I.CEL'
Content type 'unknown' length 11158059 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3262_II.CEL'
Content type 'unknown' length 11167211 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3266_I.CEL'
Content type 'unknown' length 11155675 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3266_II.CEL'
Content type 'unknown' length 11154755 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3269_I.CEL'
Content type 'unknown' length 11152163 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3269_II.CEL'
Content type 'unknown' length 11140091 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3271_I.CEL'
Content type 'unknown' length 11159931 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3271_II.CEL'
Content type 'unknown' length 11158883 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3302_I.CEL'
Content type 'unknown' length 11145911 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3302_II.CEL'
Content type 'unknown' length 11170603 bytes (10.7 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3332_I.CEL'
Content type 'unknown' length 11142627 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3332_II.CEL'
Content type 'unknown' length 11187423 bytes (10.7 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/848_A.CEL'
Content type 'unknown' length 11136167 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/848_B.CEL'
Content type 'unknown' length 11156799 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/888_I.CEL'
Content type 'unknown' length 11154163 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/888_II.CEL'
Content type 'unknown' length 11138831 bytes (10.6 MB)
==================================================
trying URL 'https://www.ebi.ac.uk/biostudies/files/E-MTAB-2967/E-MTAB-2967.sdrf.txt'
Content type 'text/plain; charset=UTF-8' length 22516 bytes (21 KB)
==================================================
downloaded 21 KB


Quitting from MA-Workflow.Rmd:1799-1802 [createTopGODataSet]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to open database file
---
Backtrace:
     ▆
  1. └─methods::new(...)
  2.   ├─methods::initialize(value, ...)
  3.   └─topGO::initialize(value, ...)
  4.     └─topGO (local) .local(.Object, ...)
  5.       └─topGO (local) annotationFun(ontology, .Object@allGenes, ...)
  6.         ├─DBI::dbGetQuery(get(paste(affyLib, "dbconn", sep = "_"))(), .sql)
  7.         └─DBI::dbGetQuery(get(paste(affyLib, "dbconn", sep = "_"))(), .sql)
  8.           └─DBI (local) .local(conn, statement, ...)
  9.             ├─DBI::dbFetch(rs, n = n, ...)
 10.             └─RSQLite::dbFetch(rs, n = n, ...)
 11.               └─RSQLite (local) .local(res, n, ...)
 12.                 └─RSQLite:::result_fetch(res@ptr, n = n)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MA-Workflow.Rmd' failed with diagnostics:
unable to open database file
--- failed re-building ‘MA-Workflow.Rmd’

SUMMARY: processing the following file failed:
  ‘MA-Workflow.Rmd’

Error: Vignette re-building failed.
Execution halted