| Back to Workflows build report for BioC 3.22 |
This page was generated on 2025-12-02 16:30 -0500 (Tue, 02 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4878 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4664 |
| 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 16/29 | Hostname | OS / Arch | INSTALL | BUILD | ||||||||
| maEndToEnd 2.30.0 (landing page) Stefanie Reisenauer
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK |  | |||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | |||||||||
|
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. |
| Package: maEndToEnd |
| Version: 2.30.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data maEndToEnd |
| StartedAt: 2025-12-02 13:19:48 -0500 (Tue, 02 Dec 2025) |
| EndedAt: 2025-12-02 13:25:21 -0500 (Tue, 02 Dec 2025) |
| EllapsedTime: 332.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/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 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'
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'
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2209_B.CEL'
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'
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'
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'
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/255_II.CEL'
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'
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'
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'
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'
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'
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'
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'
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3262_II.CEL'
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'
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'
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'
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
2025-12-02 13:25:15.860 R[42343:82330532] XType: com.apple.fonts is not accessible.
2025-12-02 13:25:15.860 R[42343:82330532] XType: XTFontStaticRegistry is enabled.
Quitting from MA-Workflow.Rmd:367-372 [importCelfiles]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! These do not exist:
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/164_I_.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/2209_A.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/2209_B.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/2400_I.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/2424_A.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/255_I.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/255_II.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/2826_II.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/2987_II.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/2992_II.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/321_II.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/3222_II.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/3259_I.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/3262_I.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/3262_II.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/3271_I.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/3302_II.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/848_A.CEL
---
Backtrace:
▆
1. └─oligo::read.celfiles(...)
2. └─oligo:::checkValidFilenames(filenames)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'MA-Workflow.Rmd' failed with diagnostics:
These do not exist:
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/164_I_.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/2209_A.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/2209_B.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/2400_I.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/2424_A.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/255_I.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/255_II.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/2826_II.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/2987_II.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/2992_II.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/321_II.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/3222_II.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/3259_I.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/3262_I.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/3262_II.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/3271_I.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/3302_II.CEL
/Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/848_A.CEL
--- failed re-building ‘MA-Workflow.Rmd’
SUMMARY: processing the following file failed:
‘MA-Workflow.Rmd’
Error: Vignette re-building failed.
Execution halted