Multiple platform build/check report for BioC 3.22 - BUILD results for ELViS on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4819
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4597
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4539
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4536
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*

BUILD results for ELViS on lconway

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

Version: 1.1.9

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ELViS

StartedAt: 2025-08-20 16:45:37 -0400 (Wed, 20 Aug 2025)

EndedAt: 2025-08-20 16:47:23 -0400 (Wed, 20 Aug 2025)

EllapsedTime: 106.1 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 ELViS
###
##############################################################################
##############################################################################


* checking for file ‘ELViS/DESCRIPTION’ ... OK
* preparing ‘ELViS’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘ELViS_Toy_Example.Rmd’ using rmarkdown
Channels:
 - conda-forge
 - bioconda
 - defaults
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='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/main/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)")': /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='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/r/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=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/r/osx-64/repodata.json.zst

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

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

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

Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Read timed out. (read timeout=9.15)")': /pkgs/r/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=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

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

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

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

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

failed

CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/conda-forge/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/conda-forge/osx-64'



Quitting from ELViS_Toy_Example.Rmd:168-199 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error creating conda environment 'env_samtools_auto' [exit code 1]
---
Backtrace:
    ▆
 1. ├─base::system.time(...)
 2. └─ELViS::get_depth_matrix(...)
 3.   └─ELViS:::get_envs_samtools_basilisk(...)
 4.     └─reticulate::conda_create(...)
 5.       └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ELViS_Toy_Example.Rmd' failed with diagnostics:
Error creating conda environment 'env_samtools_auto' [exit code 1]
--- failed re-building ‘ELViS_Toy_Example.Rmd’

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

Error: Vignette re-building failed.
Execution halted