Pariksheet,
dynamic linking won't work, compile a static version with PIC enabled. If the
subproject is autoconf-compatible this means using --disable-shared --with-pic.
Then you only need to add libfoo.a to your PKG_LIBS.
Cheers,
Simon
> On Oct 19, 2021, at 4:13 PM, Pariksheet Nanda <pariksheet.na...@uconn.edu>
> wrote:
>
> Hi folks,
>
> My package [1] depends on a C library libghmm-dev that's available in many
> GNU/Linux package managers. However, it's not available on all platforms and
> if this dependency is not installed, my autoconf generated configure script
> defaults to falling back to compiling and installing the dependency from my
> bundled copy of upstream's pristine source tarball [2]. Now, because
> upstream uses automake which in turn uses libtool, I also use automake and
> libtool in my build process to hook into their build artifacts using SUBDIRS
> and *-local automake rules [3].
>
> As you may know libtool appends `-version-info` to its generated shared
> libraries in the form "libfoo.so.1.2.3". I'm linking against the bundled
> library which only sets the first value, namely libghmm.so.1.
>
> The trouble is, R's installation process will only copy compiled files from
> ./libs/ that have exactly the extension ".so" and files ending with ".so.1"
> are ignored.
>
> My current workaround is to set -Wl,-rpath to the location of the generated
> ".so.1" file. This allows the installation process to complete and sneakily
> pass the 2 canonical tests:
>
>
> ** testing if installed package can be loaded from temporary location
> ---snip---
> ** testing if installed package can be loaded from final location
>
>
> However, not surprisingly, when I try to load the library from the final
> location after the temporary directory has been deleted it fails with:
>
>
> library(tsshmm)
> ...
> Error: package or namespace load failed for 'tsshmm' indyn.load(file, DLLpath
> = DLLpath, ...):
> unable to load shared object
> '/home/omsai/R/x86_64-pc-linux-gnu-library/4.1/tsshmm/libs/tsshmm.so':
> libghmm.so.1: cannot open shared object file: No such file or directory
>
>
> I can rename the dependency from ".so.1" to ".so" to also get the dependent
> library to the final location. But it still fails with the above error
> because the library links against the ".so.1" file and I would need an
> accompanying symlink. I tried creating a symlink but can't think of how to
> get the symlink to the final location. If my Makefile writes the symlink
> into ./inst/libs/libghmm.so.1 during compile time it is not actually
> installed; perhaps because the ./inst/ sub-directories are only copied
> earlier on when staging and are ignored later? If I were to create that
> dangling symlink inside ./inst/libs/ instead of generating it later during
> compile time, devtools::install() complains about the broken symlink with:
>
>
> cp: cannot stat 'tsshmm/inst/libs/libghmm.so.1': No such file or directory
>
>
> So is there some mechanism to copy arbitrary files or symlinks to the final
> install location? I prefer not to patch upstreams Makefile.am to remove
> their -version-info, but currently that's the only option I can think of. I
> can't find helpful discussion surrounding this in the mailing list archives.
>
> Last week when I've posted for help with my package on another issue on the
> Bioconductor mailing list, one adventurous soul tried installing the package
> using `remotes::install_gitlab("coregenomics/tsshmm")`. This won't work
> because I haven't committed the generated autotools files; if anyone wants to
> play with it, you'll have to follow the 2 additional steps run by the
> continuous integration script, namely, unpacking ./src/ghmm-0.9-rc3.tar.gz
> into ./src/ and running `autoreconf -ivf` in the package's top-level
> directory where configure.ac is located.
>
> Any help appreciated,
>
> Pariksheet
>
>
> [1] https://gitlab.com/coregenomics/tsshmm
>
> [2] The only patches I apply to the dependency are to fix 2 bugs for
> compiling, and to remedy a warning severe enough to be flagged by `R CMD
> check`.
>
> [3] You can see my Makefile.am here:
> https://gitlab.com/coregenomics/tsshmm/-/blob/master/src/Makefile.am
>
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