Back to Workflows build report for BioC 3.22

This page was generated on 2025-12-09 16:30 -0500 (Tue, 09 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4879
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4670
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 16/29HostnameOS / ArchINSTALLBUILD
maEndToEnd 2.30.0  (landing page)
Stefanie Reisenauer
Snapshot Date: 2025-12-09 12:45 -0500 (Tue, 09 Dec 2025)
git_url: https://git.bioconductor.org/packages/maEndToEnd
git_branch: RELEASE_3_22
git_last_commit: 11f1e93
git_last_commit_date: 2025-10-29 09:47:14 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK  NO, package depends on 'arrayQualityMetrics' which is not available
merida1macOS 12.7.6 Monterey / x86_64  OK    ERROR  

BUILD results for maEndToEnd on merida1

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: 2.30.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data maEndToEnd
StartedAt: 2025-12-09 13:20:40 -0500 (Tue, 09 Dec 2025)
EndedAt: 2025-12-09 13:25:55 -0500 (Tue, 09 Dec 2025)
EllapsedTime: 315.8 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### 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'
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/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/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/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/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_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/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_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/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_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/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/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/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/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/848_A.CEL'
Content type 'unknown' length 11136167 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

2025-12-09 13:24:08.077 R[64571:107840611] XType: com.apple.fonts is not accessible.
2025-12-09 13:24:08.077 R[64571:107840611] XType: XTFontStaticRegistry is enabled.

Quitting from MA-Workflow.Rmd:443-464 [qualityControlRawDataPCA]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `svd()`:
! infinite or missing values in 'x'
---
Backtrace:
    ▆
 1. ├─stats::prcomp(t(exp_raw), scale. = FALSE)
 2. └─stats:::prcomp.default(t(exp_raw), scale. = FALSE)
 3.   └─base::svd(x, nu = 0, nv = k)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MA-Workflow.Rmd' failed with diagnostics:
infinite or missing values in 'x'
--- failed re-building ‘MA-Workflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted