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pkg_install()
fails for GitHub package in subdirectory
#431
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netbsd-srcmastr
pushed a commit
to NetBSD/pkgsrc
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Feb 19, 2023
# pak 0.4.0 * pak has much improved and more informative error messages now. This work is not yet finished, so if you find an unclear error message, please open an issue. Thank you! * The solver is now more robust for non-canonical input (e.g. `DESCRIPTION` files) (r-lib/pak#423). * Better installation output. Standard output and error are now collected together (r-lib/pkgdepends@0669f0f8c). * The solver is now doing a better job when multiple versions of the same package are present in the same repository (r-lib/actions#559). * `pkg_name_check()` now works again, it needed a fix after changes at https://crandb.r-pkg.org. * Explicit package names in local and URL package sources, as in `package=local::...` or `package=url::...` are now parsed correctly in dependencies. * pak is now more robust to `Archs` fields missing from the CRAN metadata for packages with compiled code (r-lib/pak#448). * `url::` packages now always work correctly, even if the digest package is not installed (r-lib/pak#433). * pak is now more robust when installing packages from subdirectories of GitHub repositories (r-lib/pak#431, @paleolimbot). * Parameters `?reinstall`, `?source` and `?ignore` now work correctly when specified in the `package=?parameter` format (#294). * The `?ignore` parameter works correctly now. * Dependency resolution now does not fail if a package is not found. * pak can now install `url::` remotes from GitHub. * pak now does not fail when the package of a `.tar.gz` GitHub snapshot is in a subdirectory, or in a subdirectory of a subdirectory. * pak now errors early if it cannot deduce the name of the package from a `Remotes` or `Config/Needs/*` entry. * Solver failures now include details in some cases where previously they did not. * pak can now update packages in Docker containers where the old version was installed in the different Docker later (r-lib/pak#251) * Update R version -> Bioconductor version mapping. R 4.2.x now maps to Bioconductor 3.16.
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When trying to install from a package in a subdirectory, I get:
The equivalent call for remotes seems to work:
** using staged installation
Fetched bundled nanoarrow from https://github.com/apache/arrow-nanoarrow/tree/main/dist
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c altrep.c -o altrep.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c array.c -o array.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c array_convert_vector.c -o array_convert_vector.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c array_stream.c -o array_stream.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c array_view.c -o array_view.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c buffer.c -o buffer.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c build_id.c -o build_id.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c materialize.c -o materialize.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nanoarrow.c -o nanoarrow.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pointers.c -o pointers.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pointers_cpp.cc -o pointers_cpp.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c schema.c -o schema.o
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o nanoarrow.so altrep.o array.o array_convert_vector.o array_stream.o array_view.o buffer.o build_id.o init.o materialize.o nanoarrow.o pointers.o pointers_cpp.o schema.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-nanoarrow/00new/nanoarrow/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
This would be rather helpful for running CI with a nanoarrow dependency since all those workflows use pak for the dependency install!
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