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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 scifer
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* 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
Channels:
- bioconda
- conda-forge
Platform: linux-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)")': /bioconda/linux-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/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/linux-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/linux-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)")': /bioconda/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/linux-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='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/linux-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/linux-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
failed
CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/bioconda/linux-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/linux-64'
Quitting from scifer_walkthrough.Rmd:246-254 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.create_environment()`:
! failed to create conda environment at '/home/biocbuild/.cache/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 '/home/biocbuild/.cache/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
