XML has troubles installing on R 4.2 #559
Comments
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This is a bug in pak. It might work if you drop the |
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Yes! It works as expected by dropping the |
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Closing as in pack and there is a work around |
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This is actually a relatively common error, and it needs to be fixed in pak. |
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In case it's helpful for anyone else, adding solved this for me when XML was a dependency of a dependency, but wasn't building on ubuntu. (Maybe that is obvious to others, but took me a couple of attempts to get it working). |
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In case it's useful, this was also reported at https://community.rstudio.com/t/public-rspm-presents-outdated-version-of-xml-package/130118 where it was pointed out that there are two versions of {XML} on CRAN (https://cran.r-project.org/src/contrib/Older/) and in the GitHub action context {pak} seems to be trying to get the older one. |
r-lib/actions#559 Change-Id: I5cc1399141fd1cfea471e7bb1a864726c30fa1a4
https: //github.com/r-lib/actions/issues/559 Change-Id: I0d8fd1739dc4c7bb4ae279b00008882cc4449cc6
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If you're still having trouble with |
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Note that using |
* Simplify GHA Use actions from https://github.com/grimbough/bioc-actions * Add code coverage testing * Bug fix in `build-check` job * Let BiocCheck error on Warnings * Fix XML installation in `test-coverage` Using suggestion from r-lib/actions#559 (comment) * Disable version number checking
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So the problem is that pak does not use the version numbers to decide between two candidates for a package. It relies on the dependency solver to select one candidate, which should be the one with the fewest dependencies. If they have the same (recursive) dependencies, then the choice might be arbitrary, the solver seems to choose the first one. This is OK for the CRAN repo, because the latest package is always (?) first, i.e. for XML it has But RSPM has them reversed. (IDK if this is deterministic in RSPM, it might be by chance.) This would be all fine if XML 3.99-0.3 worked on R 4.2.x, but it does not. (So it should specify So the solution is to make pkgdepends mimic what |
For r-lib/actions#559 So the problem is that pak does not use the version numbers to decide between two candidates for a package. It relies on the dependency solver to select one candidate, which should be the one with the fewest dependencies. If they have the same (recursive) dependencies, then the choice might be arbitrary, the solver seems to choose the first one. This is OK for the CRAN repo, because the latest package is always (?) first, i.e. for XML it has ``` Package: XML Version: 3.99-0.11 Depends: R (>= 4.0.0), methods, utils Suggests: bitops, RCurl License: BSD_3_clause + file LICENSE MD5sum: dccc7171ea3d8492c7bd4c8de5bbe51d NeedsCompilation: yes Package: XML Version: 3.99-0.3 Depends: R (>= 2.13.0), methods, utils Suggests: bitops, RCurl License: BSD_3_clause + file LICENSE MD5sum: 424ade48afa7ab9da1ba5b9443b565ff NeedsCompilation: yes Path: Older ``` But RSPM has them reversed. (IDK if this is deterministic in RSPM, it might be by chance.) This would be all fine if XML 3.99-0.3 worked on R 4.2.x, but it does not. (So it should specify R (< 4.2), really.) So the solution is to make pkgdepends mimic what install.packages() does and choose the latest version between candidates that have the same platform. (The platform condition is important, because we still want to be able to choose an older binary instead of a newer sources package.)
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This should be now fixed with |
This temporary fix resolves the failing website build and deployment to the gh-pages branch of the EMLassemblyline GitHub (GH) repository. This GH Action is defined in pkgdown.yml. More information on the fix is at r-lib/actions#559.
* Fix GH Action dependency issue This temporary fix resolves the failing website build and deployment to the gh-pages branch of the EMLassemblyline GitHub (GH) repository. This GH Action is defined in pkgdown.yml. More information on the fix is at r-lib/actions#559. * Tag internal only funcs for doc build Internal only use functions should be tagged or pkgdown fails.
Using suggestion from r-lib/actions#559.
Idea from: r-lib/actions#559
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This issue has been automatically locked. If you believe you have found a related problem, please file a new issue and include a link to this issue |
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The new version of pak is out, so this does not need |
Describe the bug
{XML}is being installed on ubuntu and is having issues with R >= v4.2{XML}is installing system requirements and is being built from source. This is expected. It fails during compilation.To Reproduce
Workflow run: https://github.com/rstudio/shinycoreci/runs/6458218526?check_suite_focus=true
Expected behavior
I expect
{XML}to be installed on ubuntu without error.Additional context
Reprex workflow
Failure when creating lock file
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