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This page was generated on 2025-09-16 12:05 -0400 (Tue, 16 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4726
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4545
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4529
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4554
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 1907/2330HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scifer 1.11.5  (landing page)
Rodrigo Arcoverde Cerveira
Snapshot Date: 2025-09-15 13:45 -0400 (Mon, 15 Sep 2025)
git_url: https://git.bioconductor.org/packages/scifer
git_branch: devel
git_last_commit: 32aa727
git_last_commit_date: 2025-07-18 03:46:50 -0400 (Fri, 18 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

BUILD results for scifer on lconway

To the developers/maintainers of the scifer package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scifer.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.

raw results


Summary

Package: scifer
Version: 1.11.5
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data scifer
StartedAt: 2025-09-15 18:24:40 -0400 (Mon, 15 Sep 2025)
EndedAt: 2025-09-15 18:27:40 -0400 (Mon, 15 Sep 2025)
EllapsedTime: 180.2 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 scifer
###
##############################################################################
##############################################################################


* checking for file ‘scifer/DESCRIPTION’ ... OK
* preparing ‘scifer’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘scifer_walkthrough.Rmd’ using rmarkdown
2025-09-15 18:25:19.564 R[63198:290722374] XType: com.apple.fonts is not accessible.
2025-09-15 18:25:19.566 R[63198:290722374] XType: XTFontStaticRegistry is enabled.
Channels:
 - bioconda
 - conda-forge
Platform: osx-64
Collecting package metadata (repodata.json): ...working... Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/noarch/repodata.json.zst

Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /bioconda/osx-64/repodata.json.zst

Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /bioconda/noarch/repodata.json.zst

Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/osx-64/repodata.json.zst

Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/noarch/repodata.json.zst

Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/osx-64/repodata.json.zst

Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /bioconda/osx-64/repodata.json.zst

Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /bioconda/noarch/repodata.json.zst

Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/osx-64/repodata.json.zst

Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /bioconda/noarch/repodata.json.zst

Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /bioconda/osx-64/repodata.json.zst

Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/noarch/repodata.json.zst

failed

CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/bioconda/osx-64/repodata.json>
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
'https//conda.anaconda.org/bioconda/osx-64'



Quitting from scifer_walkthrough.Rmd:246-254 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.create_environment()`:
! failed to create conda environment at '/Users/biocbuild/Library/Caches/org.R-project.R/R/scifer/igblast_wrap_basilisk/1.0.0' (returned 1)
---
Backtrace:
    ▆
 1. └─scifer::igblast(...)
 2.   └─basilisk.utils::createEnvironment(...)
 3.     └─basilisk.utils:::.create_environment(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'scifer_walkthrough.Rmd' failed with diagnostics:
failed to create conda environment at '/Users/biocbuild/Library/Caches/org.R-project.R/R/scifer/igblast_wrap_basilisk/1.0.0' (returned 1)
--- failed re-building ‘scifer_walkthrough.Rmd’

SUMMARY: processing the following file failed:
  ‘scifer_walkthrough.Rmd’

Error: Vignette re-building failed.
Execution halted