heck installation issue: rhub issue macos (R-devel) #5
Comments
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This issue is also on CRAN. It can be fixed by bumping the version of libR-sys. Check: https://www.r-project.org/nosvn/R.check/r-oldrel-macos-x86_64/heck-00check.html [patch.crates-io]
libR-sys = { git = "https://github.com/extendr/libR-sys", rev = "8649204b2490f3aa3732d56f4d84af7f042e5f05" }I am referencing a specific commit here in arcpbf that is after this fix went in. @CGMossa, do you think we can publish a patched version of libR-sys so this comes from crates.io? |
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I've made a new release. |
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I am getting the following error when I add libR-sys to the [patch.crates-io]
libR-sys = { git = "https://github.com/extendr/libR-sys", rev = "8649204b2490f3aa3732d56f4d84af7f042e5f05" }> rextendr::document()
✔ Saving changes in the open files.
ℹ Generating extendr wrapper functions for package: heck.
ℹ Re-compiling heck (debug build)
── R CMD INSTALL ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
─ installing *source* package ‘heck’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’
using SDK: ‘MacOSX14.4.sdk’
rm -Rf heck.so ./rust/target/release/libheck.a entrypoint.o /Users/dyfanjones/Documents/Packages/heck/src/.cargo /Users/dyfanjones/Documents/Packages/heck/src/vendor
clang -arch arm64 -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -c entrypoint.c -o entrypoint.o
if [ -f ./rust/vendor.tar.xz ]; then \
tar xf rust/vendor.tar.xz && \
mkdir -p /Users/dyfanjones/Documents/Packages/heck/src/.cargo && \
cp rust/vendor-config.toml /Users/dyfanjones/Documents/Packages/heck/src/.cargo/config.toml; \
fi
# In some environments, ~/.cargo/bin might not be included in PATH, so we need
# to set it here to ensure cargo can be invoked. It is appended to PATH and
# therefore is only used if cargo is absent from the user's PATH.
if [ "true" != "true" ]; then \
export CARGO_HOME=/Users/dyfanjones/Documents/Packages/heck/src/.cargo; \
fi && \
export PATH="/Users/dyfanjones/Library/r-miniconda-arm64/condabin:/Users/dyfanjones/Library/r-miniconda-arm64/envs/r-reticulate/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/X11/bin:/usr/local/munki:/Applications/quarto/bin:/Users/dyfanjones/.cargo/bin:/usr/ucb:/Library/TeX/texbin:/usr/texbin:/Applications/RStudio.app/Contents/Resources/app/bin/postback:/Users/dyfanjones/.cargo/bin" && \
cargo build -j 2 --offline --lib --release --manifest-path=./rust/Cargo.toml --target-dir ./rust/target && \
echo `cargo --version` && echo `rustc --version`;
Compiling extendr-api v0.7.0
error[E0425]: cannot find function, tuple struct or tuple variant `Rf_isValidString` in this scope
--> /Users/dyfanjones/Documents/Packages/heck/src/vendor/extendr-api/src/robj/rinternals.rs:358:18
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358 | unsafe { Rf_isValidString(self.get()).into() }
| ^^^^^^^^^^^^^^^^ help: a function with a similar name exists: `Rf_isBlankString`
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::: /Users/dyfanjones/Documents/Packages/heck/src/./rust/target/release/build/libR-sys-54899a8164457f5c/out/bindings.rs:1297:5
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1297 | pub fn Rf_isBlankString(arg1: *const ::std::os::raw::c_char) -> Rboolean;
| ------------------------------------------------------------------------ similarly named function `Rf_isBlankString` defined here
error[E0425]: cannot find function, tuple struct or tuple variant `Rf_isValidStringF` in this scope
--> /Users/dyfanjones/Documents/Packages/heck/src/vendor/extendr-api/src/robj/rinternals.rs:363:18
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363 | unsafe { Rf_isValidStringF(self.get()).into() }
| ^^^^^^^^^^^^^^^^^ help: a function with a similar name exists: `Rf_isBlankString`
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::: /Users/dyfanjones/Documents/Packages/heck/src/./rust/target/release/build/libR-sys-54899a8164457f5c/out/bindings.rs:1297:5
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1297 | pub fn Rf_isBlankString(arg1: *const ::std::os::raw::c_char) -> Rboolean;
| ------------------------------------------------------------------------ similarly named function `Rf_isBlankString` defined here
For more information about this error, try `rustc --explain E0425`.
error: could not compile `extendr-api` (lib) due to 2 previous errors
make: *** [rust/target/release/libheck.a] Error 101
ERROR: compilation failed for package ‘heck’
─ removing ‘/private/var/folders/sp/scbzkbwx6hbchmylsx0y52k80000gn/T/RtmpYROWtd/devtools_install_7c4deac4773/heck’
Error in `(function (command = NULL, args = character(), error_on_status = TRUE, …`:
! System command 'R' failed
---
Exit status: 1
stdout & stderr: <printed>
---
Type .Last.error to see the more details.Updated [package]
name = 'heck'
version = '0.1.0'
edition = '2021'
[lib]
crate-type = ['staticlib']
name = 'heck'
[dependencies]
extendr-api = '0.7.0'
heck = "0.5.0"
[patch.crates-io]
libR-sys = { git = "https://github.com/extendr/libR-sys", rev = "8649204b2490f3aa3732d56f4d84af7f042e5f05" }I am guessing I am missing something :) |
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Did you re-vendor the dependencies? Typically, jsut to be safe, I will delete everything that starts with |
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Aye indeed. I wonder if it is a mac arm issue 🤔 |
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I can try and check it out later today |
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I have MacOS with Arm and was able to build. Is this issue on R-hub or on your own machine? |
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I'd like to know the r version available at r_home |
Ah yeah, I think we now have a restriction of R >= 4.1, is that right? Should go in rextendr defaults. |
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@DyfanJones I can reproduce by putting
There is an extendr-api PR to address this: extendr/extendr#842 |
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Hmmm I am not sure why my mac isn't building it correctly. I might need to do a 2 stage release. First release the cran requirements (so the package doesn't get taken down) and then circle back to try and sort out my mac. |
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Hello @DyfanJones. Do you mind trying "everything" again? We just made a patch release to extendr, so the current version is 0.7.1 for extendr-api, extendr-engine, extendr-macros, and even libR-sys. If you use Also, is your Mac an Intel mac? |
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@CGMossa I have a Mac M1 (arm64). It looks all good through my rhub checks :D https://github.com/DyfanJones/heck/actions/runs/10725077185 Thanks @CGMossa @JosiahParry for replying and fixing the issue. I will close this now and release the package shortly :) |
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