Fix build-deploy errors on push to main

[gloria-trivitt]

Sequential fixes were implemented to resolve failures in the GitHub Actions build-deploy workflow that runs on push to main.

Summary of fixes

1. Fixed the R_LIBS_USER mismatch. The Verify R Packages Installation step was reading a different R_LIBS_USER value than the Install R Packages step. Packages were being installed into one library path, but later steps were looking in another. Therefore, R reported them as missing even though installation had succeeded. This was fixed by setting R_LIBS_USER once at the job level, so every step shares the same value.

2. Added missing system dependencies for ubuntu-latest. The workflow runs on GitHub Actions’ current Ubuntu image, which does not include libcurl4-openssl-dev or libuv1-dev by default. Those headers are required to compile the curl and fs R packages from source, so an explicit apt-get install step was added for both. Background: GitHub Actions' ubuntu-latest runner now uses Ubuntu 24.04 (Noble), which differs from previous Ubuntu runner images. Ubuntu 24.04 introduced the t64 runtime library transition as part of the 64-bit time_t migration along with other changes to the base system. As a result, development packages that may have been available implicitly on earlier runner images are no longer guaranteed to be present. Installing libcurl4-openssl-dev and libuv1-dev explicitly ensures the development dependencies required to compile the curl and fs R packages are available.

3. Prevented info_schema_tutorial.qmd from executing its code chunks. This tutorial calls bigrquery::bq_auth(), which requires Google credentials. The executable R/SQL chunks were converted to non-executing code blocks, so the tutorial still renders and remains copyable without trying to authenticate during site build.

4. Removed a duplicate info_schema_tutorial.qmd at the repository root. A duplicate copy outside the tutorials/ folder was being rendered a second time, which reproduced the same failure independently of the change above. That stray duplicate was removed.

Error logs

1. Mismatched R_LIBS_USER

Run Rscript -e "library(knitr, lib.loc = Sys.getenv('R_LIBS_USER'))"
  Rscript -e "library(knitr, lib.loc = Sys.getenv('R_LIBS_USER'))"
  Rscript -e "library(rmarkdown, lib.loc = Sys.getenv('R_LIBS_USER'))"
  shell: /usr/bin/bash -e {0}
  env:
    R_LIBS_USER: /home/runner/work/_temp/Library
    TZ: UTC
    _R_CHECK_SYSTEM_CLOCK_: FALSE
    NOT_CRAN: true
    RSPM: https://packagemanager.posit.co/cran/__linux__/noble/latest
    RENV_CONFIG_REPOS_OVERRIDE: https://packagemanager.posit.co/cran/__linux__/noble/latest
Error in library(knitr, lib.loc = Sys.getenv("R_LIBS_USER")) : 
  there is no package called ‘knitr’
Execution halted
Error: Process completed with exit code 1.

2. Missing libcurl

--------------------------- [ANTICONF] --------------------------------
Configuration failed because libcurl was not found. Try installing:
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
 * rpm: libcurl-devel (Fedora, CentOS, RHEL)
 * apk: curl-dev (Alpine)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
Error: MESSAGE] ---------------------------
<stdin>:1:10: fatal error: curl/curl.h: No such file or directory
compilation terminated.
--------------------------------------------------------------------

3. Missing libuv

--------------------------- [CONFIGURE] --------------------------------
Configuration failed because libuv was not found. Try installing:
 * deb: libuv1-dev (Debian, Ubuntu, etc)
 * rpm: libuv-devel (Fedora, EPEL)
 * brew: libuv (OSX)
Alternatively set environment variable USE_BUNDLED_LIBUV=1 to build a static
version of libuv that is included with this package.
Error: MESSAGE] ---------------------------
<stdin>:1:10: fatal error: uv.h: No such file or directory
compilation terminated.
--------------------------------------------------------------------

4. BigQuery authentication failure during render

processing file: info_schema_tutorial.qmd
1/9                  
2/9 [unnamed-chunk-1]
Error in `bigrquery::bq_auth()`:
! Can't get Google credentials.
ℹ Try calling `bq_auth()` directly with necessary specifics.
Backtrace:
    ▆
 1. └─bigrquery::bq_auth()
 2.   └─cli::cli_abort(...)
 3.     └─rlang::abort(...)

Quitting from info_schema_tutorial.qmd:28-37 [unnamed-chunk-1]
Execution halted
WARN: Error encountered when rendering files
ERROR: Error
    at renderFiles (file:///opt/quarto/bin/quarto.js:136597:49)
    at eventLoopTick (ext:core/01_core.js:179:7)
    at async renderProject (file:///opt/quarto/bin/quarto.js:137140:23)
    at async renderForPublish2 (file:///opt/quarto/bin/quarto.js:173346:25)
    at async renderForPublish (file:///opt/quarto/bin/quarto.js:167988:22)
    at async Object.publish2 [as publish] (file:///opt/quarto/bin/quarto.js:168527:24)
    at async publishSite (file:///opt/quarto/bin/quarto.js:173388:38)
    at async publish8 (file:///opt/quarto/bin/quarto.js:173727:58)
    at async doPublish (file:///opt/quarto/bin/quarto.js:173674:7)
    at async publishAction (file:///opt/quarto/bin/quarto.js:173693:5)
    at async _Command.actionHandler (file:///opt/quarto/bin/quarto.js:173652:9)
    at async _Command.execute (file:///opt/quarto/bin/quarto.js:102091:7)
    at async _Command.parseCommand (file:///opt/quarto/bin/quarto.js:101968:14)
    at async quarto4 (file:///opt/quarto/bin/quarto.js:187649:5)
    at async file:///opt/quarto/bin/quarto.js:187677:5
    at async file:///opt/quarto/bin/quarto.js:187532:14
    at async mainRunner (file:///opt/quarto/bin/quarto.js:187534:5)
    at async file:///opt/quarto/bin/quarto.js:187670:3
Error: Process completed with exit code 1.

[jacobmpeters]

lgtm!