ViennaRNA/plotting/naview.h file not found

[GuoHao150]

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

[fncnt]

Hi, thanks for reaching out!

There are a few things happening here.
First, ViennaRNA 2.5.1 changed the location of that particular header file (ViennaRNA/ViennaRNA@569f647).

Second, for some reason, even if naview.h was at the correct location, we wouldn't find it.
The cause of this is still beyond my understanding a header directory I forgot to include.
However, there is a workaround (additionally to setting LIBRNA_INCLUDE_DIR and LIBRNA_LIB_DIR:

export CPATH=$LIBRNA_INCLUDE_DIR

There's still one major caveat; while debugging, I noticed that librna-sys wouldn't build cargo test wouldn't work with ViennaRNA >=2.5.0 (although crates depending on librna-sys still can create tests with the FFI bindings!).
This is possibly related to ViennaRNA/ViennaRNA@1055687

A workaround for this would be downgrading to 2.4.18 for now and following the user-dir installation instructions, i.e.:

tar -zxvf ViennaRNA-2.4.18.tar.gz
cd ViennaRNA-2.4.18
./configure --prefix=/data01/softwares/ViennaRNA
make install
export LIBRNA_INCLUDE_DIR=/data01/softwares/ViennaRNA/include
export LIBRNA_LIB_DIR=/data01/softwares/ViennaRNA/lib
export CPATH=$LIBRNA_INCLUDE_DIR

This should work until I manage to fix the underlying issues. Sorry for the trouble!

EDIT: changed inaccuracies for future reference.

[fncnt]

Actually, the CPATH workaround might not work for you at all...
Currently I'd recommend installing ViennaRNA via one of the official packages or through bioconda until I fix it:
Have a look at this to get an idea.

[fncnt]

This should be fixed in v0.1.5 which is already live on crates.io.
Feel free to re-open if necessary.

[GuoHao150]

Thanks for your explanation, making such a crate is definitely not easy, since the ViennaRNA is a huge package. If someone just wants to use a sub-module of ViennaRNA-2.5.1 with rust, here is the tip: Follow the C API example of ViennaRNA and make a shared library with g++ then call it from rust.

[fncnt]

If someone just wants to use a sub-module of ViennaRNA-2.5.1 with rust, here is the tip: Follow the C API example of ViennaRNA and make a shared library with g++ then call it from rust.

I don't think this is necessary. The linked libRNA.a library is static and only the functions used on the Rust side will be compiled into the binaries.
However, I omitted a few header files containing new functionality since 2.4.18 to maintain backwards-compatibility until I decide how I want to include them without affecting older versions of ViennaRNA (possibly a new minor release). See #2 for details.