* installing to library '/home/runner/R-patched/lib'
* installing *source* package 'smoothbp' ...
** this is package 'smoothbp' version '0.2.4'
** package 'smoothbp' successfully unpacked and MD5 sums checked
** using staged installation
Using cargo 1.87.0 (99624be96 2025-05-06) (Alpine Linux 1.87.0-r1)
Using rustc 1.87.0 (17067e9ac 2025-05-09) (Alpine Linux 1.87.0-r1)
Building for CRAN.
Writing `src/Makevars`.
`tools/config.R` has finished.
** libs
using C compiler: 'gcc (Alpine 14.2.0) 14.2.0'
make[1]: Entering directory '/var/local/PKGS/CRAN/smoothbp/src'
gcc -std=gnu23 -I"/home/runner/R-patched/build/include" -DNDEBUG   -I/usr/local/include    -fpic  -O2 -mtune=native  -c entrypoint.c -o entrypoint.o
if [ -d ./vendor ]; then \
	echo "=== Using offline vendor directory ==="; \
	mkdir -p /var/local/PKGS/CRAN/smoothbp/src/.cargo && \
	printf '[source.crates-io]\nreplace-with = "vendored-sources"\n\n[source.vendored-sources]\ndirectory = "/var/local/PKGS/CRAN/smoothbp/src/vendor"\n' > /var/local/PKGS/CRAN/smoothbp/src/.cargo/config.toml; \
elif [ -f ./rust/vendor.tar.xz ]; then \
	echo "=== Using offline vendor tarball ==="; \
	tar xf rust/vendor.tar.xz && \
	mkdir -p /var/local/PKGS/CRAN/smoothbp/src/.cargo && \
	printf '[source.crates-io]\nreplace-with = "vendored-sources"\n\n[source.vendored-sources]\ndirectory = "/var/local/PKGS/CRAN/smoothbp/src/vendor"\n' > /var/local/PKGS/CRAN/smoothbp/src/.cargo/config.toml; \
fi
=== Using offline vendor tarball ===
export CARGO_HOME=/var/local/PKGS/CRAN/smoothbp/src/.cargo && \
export PATH="/bin:/sbin:/usr/bin:/usr/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin:/home/runner/.cargo/bin" && \
RUSTFLAGS=" --print=native-static-libs" cargo build -j 2 --offline --lib --release --manifest-path=./rust/Cargo.toml --target-dir ./rust/target 
   Compiling autocfg v1.5.0
   Compiling libm v0.2.16
   Compiling proc-macro2 v1.0.106
   Compiling num-traits v0.2.19
   Compiling unicode-ident v1.0.24
   Compiling quote v1.0.45
   Compiling libc v0.2.186
   Compiling paste v1.0.15
   Compiling zerocopy v0.8.48
   Compiling cfg-if v1.0.4
   Compiling bytemuck v1.25.0
   Compiling safe_arch v0.7.4
   Compiling getrandom v0.2.17
   Compiling crossbeam-utils v0.8.21
   Compiling rand_core v0.6.4
   Compiling wide v0.7.33
   Compiling approx v0.5.1
   Compiling num-complex v0.4.6
   Compiling ppv-lite86 v0.2.21
   Compiling syn v2.0.117
   Compiling matrixmultiply v0.3.10
   Compiling syn v1.0.109
   Compiling rand_chacha v0.3.1
   Compiling num-integer v0.1.46
   Compiling rawpointer v0.2.1
   Compiling extendr-ffi v0.9.0
   Compiling num-rational v0.4.2
   Compiling crossbeam-epoch v0.9.18
   Compiling rand v0.8.6
   Compiling rayon-core v1.13.0
   Compiling typenum v1.20.0
   Compiling rand_distr v0.4.3
   Compiling crossbeam-deque v0.8.6
   Compiling simba v0.6.0
   Compiling nalgebra-macros v0.1.0
   Compiling lazy_static v1.5.0
   Compiling extendr-api v0.9.0
   Compiling extendr-macros v0.9.0
   Compiling nalgebra v0.29.0
   Compiling nalgebra-macros v0.2.2
   Compiling readonly v0.2.13
   Compiling simba v0.9.1
   Compiling once_cell v1.21.4
   Compiling either v1.15.0
   Compiling rayon v1.12.0
   Compiling statrs v0.16.1
   Compiling nalgebra v0.33.3
   Compiling smoothbp v0.1.0 (/var/local/PKGS/CRAN/smoothbp/src/rust)
warning: unused import: `extendr_api::prelude`
 --> src/bridge.rs:6:5
  |
6 | use extendr_api::prelude::*;
  |     ^^^^^^^^^^^^^^^^^^^^
  |
  = note: `#[warn(unused_imports)]` on by default

warning: fields `p_b0`, `p_b1`, `p_deltas`, `p_om`, and `p_rho` are never read
  --> src/model.rs:80:9
   |
41 | pub struct Priors {
   |            ------ fields in this struct
...
80 |     pub p_b0: usize,
   |         ^^^^
81 |     pub p_b1: usize,
   |         ^^^^
82 |     pub p_deltas: Vec<usize>,
   |         ^^^^^^^^
83 |     pub p_om: Vec<usize>,
   |         ^^^^
84 |     pub p_rho: Vec<usize>,
   |         ^^^^^
   |
   = note: `#[warn(dead_code)]` on by default

note: Link against the following native artifacts when linking against this static library. The order and any duplication can be significant on some platforms.

note: native-static-libs: -lR -lgcc_s -lc

warning: `smoothbp` (lib) generated 2 warnings
    Finished `release` profile [optimized] target(s) in 6m 16s
export CARGO_HOME="/var/local/PKGS/CRAN/smoothbp/src/.cargo" && \
export PATH="/bin:/sbin:/usr/bin:/usr/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin:/home/runner/.cargo/bin" && \
cargo run -j 2 --offline --release --bin document --manifest-path=./rust/Cargo.toml --target-dir ./rust/target 
   Compiling autocfg v1.5.0
   Compiling libm v0.2.16
   Compiling proc-macro2 v1.0.106
   Compiling num-traits v0.2.19
   Compiling quote v1.0.45
   Compiling unicode-ident v1.0.24
   Compiling libc v0.2.186
   Compiling zerocopy v0.8.48
   Compiling paste v1.0.15
   Compiling cfg-if v1.0.4
   Compiling bytemuck v1.25.0
   Compiling safe_arch v0.7.4
   Compiling getrandom v0.2.17
   Compiling crossbeam-utils v0.8.21
   Compiling rand_core v0.6.4
   Compiling wide v0.7.33
   Compiling approx v0.5.1
   Compiling num-complex v0.4.6
   Compiling syn v2.0.117
   Compiling ppv-lite86 v0.2.21
   Compiling matrixmultiply v0.3.10
   Compiling syn v1.0.109
   Compiling rand_chacha v0.3.1
   Compiling num-integer v0.1.46
   Compiling extendr-ffi v0.9.0
   Compiling rawpointer v0.2.1
   Compiling num-rational v0.4.2
   Compiling crossbeam-epoch v0.9.18
   Compiling rand v0.8.6
   Compiling rayon-core v1.13.0
   Compiling typenum v1.20.0
   Compiling rand_distr v0.4.3
   Compiling crossbeam-deque v0.8.6
   Compiling simba v0.6.0
   Compiling nalgebra-macros v0.1.0
   Compiling extendr-api v0.9.0
   Compiling lazy_static v1.5.0
   Compiling extendr-macros v0.9.0
   Compiling nalgebra v0.29.0
   Compiling nalgebra-macros v0.2.2
   Compiling readonly v0.2.13
   Compiling simba v0.9.1
   Compiling either v1.15.0
   Compiling once_cell v1.21.4
   Compiling statrs v0.16.1
   Compiling rayon v1.12.0
   Compiling nalgebra v0.33.3
   Compiling smoothbp v0.1.0 (/var/local/PKGS/CRAN/smoothbp/src/rust)
warning: unused import: `extendr_api::prelude`
 --> src/bridge.rs:6:5
  |
6 | use extendr_api::prelude::*;
  |     ^^^^^^^^^^^^^^^^^^^^
  |
  = note: `#[warn(unused_imports)]` on by default

warning: fields `p_b0`, `p_b1`, `p_deltas`, `p_om`, and `p_rho` are never read
  --> src/model.rs:80:9
   |
41 | pub struct Priors {
   |            ------ fields in this struct
...
80 |     pub p_b0: usize,
   |         ^^^^
81 |     pub p_b1: usize,
   |         ^^^^
82 |     pub p_deltas: Vec<usize>,
   |         ^^^^^^^^
83 |     pub p_om: Vec<usize>,
   |         ^^^^
84 |     pub p_rho: Vec<usize>,
   |         ^^^^^
   |
   = note: `#[warn(dead_code)]` on by default

warning: `smoothbp` (lib) generated 2 warnings
error: linking with `cc` failed: exit status: 1
  |
  = note:  "cc" "-m64" "/home/runner/tmp/rustcWNUVvU/symbols.o" "<1 object files omitted>" "-Wl,--as-needed" "-Wl,-Bstatic" "/home/runner/tmp/rustcWNUVvU/{libstd-003ce02984288987.rlib}.rlib" "<sysroot>/lib/rustlib/x86_64-alpine-linux-musl/lib/{libcompiler_builtins-*}.rlib" "-Wl,-Bdynamic" "-lR" "-lgcc_s" "-lc" "-L" "/home/runner/tmp/rustcWNUVvU/raw-dylibs" "-Wl,--eh-frame-hdr" "-Wl,-z,noexecstack" "-L" "<sysroot>/lib/rustlib/x86_64-alpine-linux-musl/lib" "-o" "/var/local/PKGS/CRAN/smoothbp/src/./rust/target/release/deps/document-9b8eb44873e9d4f5" "-Wl,--gc-sections" "-pie" "-Wl,-z,relro,-z,now" "-Wl,-O1" "-Wl,--strip-debug" "-nodefaultlibs" "-Wl,--enable-new-dtags,-z,origin"
  = note: some arguments are omitted. use `--verbose` to show all linker arguments
  = note: /usr/lib/gcc/x86_64-alpine-linux-musl/14.2.0/../../../../x86_64-alpine-linux-musl/bin/ld: cannot find -lR: No such file or directory
          collect2: error: ld returned 1 exit status
          

error: could not compile `smoothbp` (bin "document") due to 1 previous error
make[1]: *** [Makevars:28: rust/target/release/libsmoothbp.a] Error 101
make[1]: Leaving directory '/var/local/PKGS/CRAN/smoothbp/src'
make[1]: Entering directory '/var/local/PKGS/CRAN/smoothbp/src'
make[1]: Leaving directory '/var/local/PKGS/CRAN/smoothbp/src'
ERROR: compilation failed for package 'smoothbp'
* removing '/home/runner/R-patched/lib/smoothbp'
* restoring previous '/home/runner/R-patched/lib/smoothbp'