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Unsafe low-level Rust bindings for the ViennaRNA package.

Home Page: https://crates.io/crates/librna-sys

License: Other

Rust 45.46% C 54.54%

bioinformatics ffi rna rust sys

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librna-sys's Issues

Building a crate with `librna-sys` as a dependency might fail linking against `openmp`

If you use librna-sys as a dependency you might encounter an error similar to this:

error: linking with `cc` failed: exit status: 1
  |
  = note: LC_ALL="C" PATH="~/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin:~/.cargo/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:~/.dotnet/tools:/var/lib/flatpak/exports/bin:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl:/usr/lib/rustup/bin:~/bin" VSLANG="1033" "cc" "-m64" "/tmp/rustcVe6E8r/symbols.o" "~/crate-name/target/release/deps/executable-77097ed7f3783d37.executable.acdf1c1d4c87c16c-cgu.0.rcgu.o" "-Wl,--as-needed" "-L" "~/crate-name/target/release/deps" "-L" "/usr/lib" "-L" "/usr/lib/gcc/x86_64-pc-linux-gnu/13.2.1/../../../../lib/" "-L" "~/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-Wl,-Bstatic" "/tmp/rustcVe6E8r/liblibrna_sys-9e8497eadd24f151.rlib" "~/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcompiler_builtins-b114db70ea0690b1.rlib" "-Wl,-Bdynamic" "-lc" "-lm" "-lrt" "-lpthread" "-lgcc_s" "-lutil" "-lrt" "-lpthread" "-lm" "-ldl" "-lc" "-Wl,--eh-frame-hdr" "-Wl,-z,noexecstack" "-L" "~/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-o" "~/Dev/crate-name/target/release/deps/executable-77097ed7f3783d37" "-Wl,--gc-sections" "-pie" "-Wl,-z,relro,-z,now" "-Wl,-O1" "-nodefaultlibs"
  = note: /usr/bin/ld: /tmp/rustcVe6E8r/liblibrna_sys-9e8497eadd24f151.rlib(svm.o): in function `svm_predict_values._omp_fn.0':
          ~/builddir/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:2610:(.text+0x1544): undefined reference to `GOMP_loop_nonmonotonic_guided_start'
          /usr/bin/ld: ~/builddir/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:2610:(.text+0x1555): undefined reference to `GOMP_loop_end_nowait'
          /usr/bin/ld: ~/builddir/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:2610:(.text+0x15a9): undefined reference to `GOMP_loop_nonmonotonic_guided_next'
          /usr/bin/ld: /tmp/rustcVe6E8r/liblibrna_sys-9e8497eadd24f151.rlib(svm.o): in function `svm_predict_values._omp_fn.1':
          ~/builddir/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:2629:(.text+0x165c): undefined reference to `GOMP_loop_nonmonotonic_guided_start'
          /usr/bin/ld: ~/builddir/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:2629:(.text+0x1665): undefined reference to `GOMP_loop_end_nowait'
          /usr/bin/ld: ~/builddir/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:2629:(.text+0x1699): undefined reference to `GOMP_loop_nonmonotonic_guided_next'
          /usr/bin/ld: /tmp/rustcVe6E8r/liblibrna_sys-9e8497eadd24f151.rlib(svm.o): in function `svm_predict_values':
          ~/builddir/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:2610:(.text+0x3ec8): undefined reference to `GOMP_parallel'
          /usr/bin/ld: ~/builddir/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:2629:(.text+0x3f6a): undefined reference to `GOMP_parallel'
          /usr/bin/ld: /tmp/rustcVe6E8r/liblibrna_sys-9e8497eadd24f151.rlib(svm.o): in function `SVR_Q::get_Q(int, int) const [clone ._omp_fn.0]':
          ~/builddir/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:1408:(.text._ZNK5SVR_Q5get_QEii._omp_fn.0[_ZNK5SVR_Q5get_QEii]+0x4f): undefined reference to `GOMP_loop_nonmonotonic_guided_start'
          /usr/bin/ld: ~/builddir/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:1408:(.text._ZNK5SVR_Q5get_QEii._omp_fn.0[_ZNK5SVR_Q5get_QEii]+0x58): undefined reference to `GOMP_loop_end_nowait'
          /usr/bin/ld: ~/builddir/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:1408:(.text._ZNK5SVR_Q5get_QEii._omp_fn.0[_ZNK5SVR_Q5get_QEii]+0x8a): undefined reference to `GOMP_loop_nonmonotonic_guided_next'
          /usr/bin/ld: /tmp/rustcVe6E8r/liblibrna_sys-9e8497eadd24f151.rlib(svm.o): in function `SVC_Q::get_Q(int, int) const [clone ._omp_fn.0]':
          ~/builddir/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:1290:(.text._ZNK5SVC_Q5get_QEii._omp_fn.0[_ZNK5SVC_Q5get_QEii]+0x57): undefined reference to `GOMP_loop_nonmonotonic_guided_start'
          /usr/bin/ld: ~/builddir/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:1293:(.text._ZNK5SVC_Q5get_QEii._omp_fn.0[_ZNK5SVC_Q5get_QEii]+0xee): undefined reference to `GOMP_loop_nonmonotonic_guided_next'
          /usr/bin/ld: ~/builddir/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:1293:(.text._ZNK5SVC_Q5get_QEii._omp_fn.0[_ZNK5SVC_Q5get_QEii]+0xfb): undefined reference to `GOMP_loop_end_nowait'
          /usr/bin/ld: /tmp/rustcVe6E8r/liblibrna_sys-9e8497eadd24f151.rlib(svm.o): in function `SVR_Q::get_Q(int, int) const':
          ~/builddir/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:1408:(.text._ZNK5SVR_Q5get_QEii[_ZNK5SVR_Q5get_QEii]+0x128): undefined reference to `GOMP_parallel'
          /usr/bin/ld: /tmp/rustcVe6E8r/liblibrna_sys-9e8497eadd24f151.rlib(svm.o): in function `SVC_Q::get_Q(int, int) const':
          ~/builddir/ViennaRNA-2.6.4/src/ViennaRNA/../libsvm-3.31/svm.cpp:1290:(.text._ZNK5SVC_Q5get_QEii[_ZNK5SVC_Q5get_QEii]+0x87): undefined reference to `GOMP_parallel'
          collect2: error: ld returned 1 exit status
          
  = note: some `extern` functions couldn't be found; some native libraries may need to be installed or have their path specified
  = note: use the `-l` flag to specify native libraries to link
  = note: use the `cargo:rustc-link-lib` directive to specify the native libraries to link with Cargo (see https://doc.rust-lang.org/cargo/reference/build-scripts.html#cargorustc-link-libkindname)

error: could not compile `crate-name` (bin "executable") due to previous error

The current solution to this is to add openmp-sys as a dependency to your crate as well.
I'm currently hesitating to do this internally in librna-sys but that might change in the future.

ViennaRNA/plotting/naview.h file not found

Hi,

Thank you for creating this crate, I'm not familiar with the rust calling c library. I installed the ViennaRNA at /data01/softwares/ViennaRNA-2.5.1 and the libRNA.a file can be found at /data01/softwares/ViennaRNA-2.5.1/src/ViennaRNA I want to know how to set the LIBRNA_INCLUDE_DIR variable because the cargo keeps telling me that fatal error: 'ViennaRNA/plotting/naview.h' file not found

Best wishes

Support for ViennaRNA `>= 2.5.0`

This is a meta-issue. There are a few central issues coming with some subtleties to consider.

update naview.h location in wrapper.h
- there's a deprecated ViennaRNA/naview.h pointing to ViennaRNA/plotting(/naview)/naview.h which we don't need but it is a hacky(?) way to provide backwards-compatibiltiy
- see ViennaRNA/ViennaRNA@569f647
- see ViennaRNA/ViennaRNA@400669b
- address export CPATH=$LIBRNA_INCLUDE_DIR workaround (see #1)
some dlib extern functions could not be found in the generated bindings
- see ViennaRNA/ViennaRNA@1055687
- see https://rust-lang.github.io/rust-bindgen/cpp.html
- ~~use allowlisting to fix layout tests~~
address auto-dereferenced null pointers in generated bindings (not new but should be finally addressed)
clean up wrapper.h
- remove deprecated headers
- include headers added since 2.4.18 (pk_plex.h, pf_multifold.h, subopt_zuker.h, wrap_dlib.h)
  - this is a backwards-compatibility breaking change

Ideally, these problems should be addressed in a backwards-compatible manner.
I.e. a new librna-sys release should still work with ViennaRNA <=2.4.18 because this crate is currently not explicitly tied to specific versions of ViennaRNA.
Alternatively, librna-sys 0.2 could break backwards-compatibility but the mapping between librna-sys and ViennaRNA versions needs to be clearly communicated.
Publishing librna-sys in lock-step versions with ViennaRNA comes with its own limitations (can't create independent bugfix releases). In this case it would make sense to directly publish a version-specific bindings.rs instead of build.rs + wrapper.h

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