jared
342debaefa
The "Install system libraries" step was stalling indefinitely. It was not deadlocked on a config prompt and not slow-but-progressing: measured inside the live runner container, /var/cache/apt/archives stayed at 0 .deb files after 3+ minutes, with apt's http workers parked in S state waiting on the network. Root cause is the http:// mirror path being pathologically slow from this runner, not broken. Measured 2026-08-04 from inside the CI container, same index file, back to back: http://archive.ubuntu.com/ubuntu/dists/noble/Release 20.1s https://archive.ubuntu.com/ubuntu/dists/noble/Release 3.1s apt fetches many indexes serially, so ~20s apiece compounds into what looks like a hang. Rewriting the deb822 sources to https makes the step complete. Verified before committing, in the running CI container (rocker/r-ver:4.4): - ca-certificates present and apt 2.8.3 ships the https method built in, so nothing has to be installed over http first to bootstrap TLS - the sed rewrites both URIs (archive + security); the only remaining http:// is an inert comment line - '#' is used as the sed delimiter deliberately: '|' collides with the alternation and fails with "unknown option to `s'" - the regex survives YAML block-scalar parsing with backslashes intact `|| true` guards each sed because the step runs under `sh -e`, so a missing-sources-file on some other base image must not kill the job.
61 lines
2.2 KiB
YAML
61 lines
2.2 KiB
YAML
name: R-CMD-check
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on: [push, pull_request]
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jobs:
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check:
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runs-on: ubuntu-latest
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container:
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image: rocker/r-ver:4.4
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steps:
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- name: Install system libraries and Node.js (required by actions/checkout)
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run: |
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# Switch apt to HTTPS mirrors. Measured from this runner on
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# 2026-08-04: the SAME index file takes 20.1s over http:// and 3.1s
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# over https://. apt fetches many indexes serially, so http:// does
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# not read as "slow" -- it reads as a hang (zero bytes in
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# /var/cache/apt/archives after 3+ minutes, apt's http workers parked
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# in S state). rocker/r-ver:4.4 already ships ca-certificates and
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# apt 2.8.3 has the https method built in, so nothing needs to be
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# installed over http first to bootstrap this.
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# `|| true` because the step runs under `sh -e`: on an image whose
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# sources live in the other location, the missing-file sed must not
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# kill the job.
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sed -i -E 's#http://(archive|security)\.ubuntu\.com#https://\1.ubuntu.com#g' \
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/etc/apt/sources.list.d/ubuntu.sources 2>/dev/null || true
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sed -i -E 's#http://(archive|security)\.ubuntu\.com#https://\1.ubuntu.com#g' \
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/etc/apt/sources.list 2>/dev/null || true
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apt-get update -qq
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apt-get install -y --no-install-recommends \
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nodejs git \
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libcurl4-openssl-dev libssl-dev libxml2-dev \
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libfontconfig1-dev libharfbuzz-dev libfribidi-dev
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- uses: actions/checkout@v4
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- name: Install pak
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run: |
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Rscript -e 'install.packages("pak", repos = "https://r-lib.github.io/p/pak/stable/")'
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- name: Install package dependencies
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run: |
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Rscript -e 'pak::local_install_deps(dependencies = TRUE)'
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- name: Install rcmdcheck (check runner)
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run: |
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Rscript -e 'pak::pak("rcmdcheck")'
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- name: Run tests
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run: |
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Rscript -e 'testthat::test_local(stop_on_failure = TRUE)'
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- name: R CMD check
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run: |
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Rscript -e '
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rcmdcheck::rcmdcheck(
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args = c("--no-manual", "--no-vignettes"),
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error_on = "error"
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)
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'
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