Packages not found in dependent builds

[psychemedia]

I've previously successfully used the ghcr.io/r-wasm/webr:v0.3.3 image to build a set of packages where some packages are dependent on others, but trying to use build for R 4.4 I am getting dependency errors:

name: Build deployment packages

on:
  workflow_dispatch:

jobs:
  build:
    uses: ./.github/workflows/deploy-cran-repo.yml
    with:
      packages: |
        zoo
        lmtest
      webr-image: "ghcr.io/r-wasm/webr:v0.4.3"
      compress: true

and the deploy-cran-repo.yml from this repo's actions [ https://github.com/r-wasm/actions/blob/v2/.github/workflows/deploy-cran-repo.yml ] via the link on this page

trying URL 'https://packagemanager.posit.co/cran/latest/src/contrib/zoo_1.8-14.tar.gz'
Content type 'binary/octet-stream' length 780529 bytes (762 KB)
==================================================
downloaded 762 KB
i Scanning dependencies in '_site/src/contrib/zoo_1.8-14.tar.gz'
v Scanning dependencies in '_site/src/contrib/zoo_1.8-14.tar.gz' ... done
 
 
> Will download 1 package with unknown size.
  
i No downloads are needed
v :  [339ms]
* installing *source* package 'zoo' ...
** package 'zoo' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
using C compiler: 'emcc (Emscripten gcc/clang-like replacement + linker emulating GNU ld) 3.1.47 (431685f05c67f0424c11473cc16798b9587bb[536](https://github.com/ouseful-testing/webr-package-repo-demo/actions/runs/15423964294/job/43406083982#step:5:537))'
emcc -DNDEBUG -I../inst/include  -I/opt/webr/wasm/include -I/opt/webr/R/build/R-4.4.2/build/include -I/opt/webr/R/build/R-4.4.2/src/include -s USE_BZIP2=1 -s USE_ZLIB=1  -fpic  -Oz -fPIC -fwasm-exceptions -s SUPPORT_LONGJMP=wasm -std=gnu11 -c coredata.c -o coredata.o
emcc -DNDEBUG -I../inst/include  -I/opt/webr/wasm/include -I/opt/webr/R/build/R-4.4.2/build/include -I/opt/webr/R/build/R-4.4.2/src/include -s USE_BZIP2=1 -s USE_ZLIB=1  -fpic  -Oz -fPIC -fwasm-exceptions -s SUPPORT_LONGJMP=wasm -std=gnu11 -c init.c -o init.o
emcc -DNDEBUG -I../inst/include  -I/opt/webr/wasm/include -I/opt/webr/R/build/R-4.4.2/build/include -I/opt/webr/R/build/R-4.4.2/src/include -s USE_BZIP2=1 -s USE_ZLIB=1  -fpic  -Oz -fPIC -fwasm-exceptions -s SUPPORT_LONGJMP=wasm -std=gnu11 -c lag.c -o lag.o
emcc -s SIDE_MODULE=1 -s WASM_BIGINT -s ASSERTIONS=1 -L/opt/webr/wasm/lib -L/opt/webr/wasm/R-4.4.2/lib/R/lib -s USE_BZIP2=1 -s USE_ZLIB=1 -fwasm-exceptions -s SUPPORT_LONGJMP=wasm -Oz -o zoo.so coredata.o init.o lag.o
installing to /tmp/RtmpQuQx9u/file1365c7a3a/zoo/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
* creating tarball
packaged installation of 'zoo' as 'zoo_1.8-14_R_x86_64-pc-linux-gnu.tar.gz'
* DONE (zoo)
Appending virtual filesystem metadata for: _site/bin/emscripten/contrib/4.4/zoo_1.8-14.tgz
trying URL 'https://packagemanager.posit.co/cran/latest/src/contrib/lmtest_0.9-40.tar.gz'
Content type 'application/x-tar' length 230467 bytes (225 KB)
==================================================
downloaded 225 KB
i Scanning dependencies in '_site/src/contrib/lmtest_0.9-40.tar.gz'
v Scanning dependencies in '_site/src/contrib/lmtest_0.9-40.tar.gz' ... done
 
 
> Will download 1 package with unknown size.
  
i No downloads are needed
v :  [359ms]
ERROR: dependency 'zoo' is not available for package 'lmtest'
* removing '/tmp/RtmpQuQx9u/file12e92779e/lmtest'

Here's an example of the error log from my actual code: https://github.com/ouseful-testing/webr-package-repo-demo/actions/runs/15423964294/job/43406083982

[georgestagg]

I think this is probably related to r-lib/pak#784. I'll see what I can do about working around it for now.

[psychemedia]

Thanks.. I can compile things okay locally in a container, it was just the action seemed to be confusing itself somewhere...

I also noticed that my previously working version had packages I wanted to build listed out of order (i.e. not in a linear dependency order) and the resolver had worked out what order to build things in.

[psychemedia]

I swee there was an update to r-lib/pak#784 but I still get a build error e.g. here:

** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
* creating tarball
packaged installation of 'zoo' as 'zoo_1.8-14_R_x86_64-pc-linux-gnu.tar.gz'
* DONE (zoo)
Appending virtual filesystem metadata for: _site/bin/emscripten/contrib/4.5/zoo_1.8-14.tgz
trying URL 'https://packagemanager.posit.co/cran/latest/src/contrib/lmtest_0.9-40.tar.gz'
Content type 'application/x-tar' length 230467 bytes (225 KB)
==================================================
downloaded 225 KB

i Scanning dependencies in '_site/src/contrib/lmtest_0.9-40.tar.gz'
v Scanning dependencies in '_site/src/contrib/lmtest_0.9-40.tar.gz' ... done


 
 
> Will download 1 package with unknown size.
  
i No downloads are needed
v :  [332ms]
ERROR: dependency 'zoo' is not available for package 'lmtest'
Perhaps try a variation of:
install.packages('zoo')
* removing '/tmp/RtmpuhLNps/file165b6c195/lmtest'

[psychemedia]

Noting that is is duplucated in r-wasm/webr#556 which sems to suggest pak has been updated, but things just need to flow through CRAN etc.

[psychemedia]

@georgestagg I',m still seeing an issue with this? Do you know of a workaround?

[UPDATE - ah, maybe this is just now an issue with older versions of webR <0.5]