I'm helping develop scPipe which we're currently trying to contribute to Bioconductor. Unfortunately the are build issues on Windows that I am unable to resolve. Namely the package is unable to load its own DLL.

I noticed that link2Rhtslib does not build on Windows with the error

localfunc.o:localfunc.c:(.txt+0x45): undefined reference to `bios_zlibversion'

collect2.exe: error: ld returned 1 exit status

no DLL was created

Also that Rhtslib currently skips building on Windows. So I am wondering if Rhtslib (or htslib) currently supports Windows at all or if I'm on a wild goose chase.

Wow some of the StackOverflow discussion was quite hostile!

The build system link with no Windows build shows that the Windows builds as a whole failed to report; Rhtslib is supported on Windows. For reference, several packages, e.g., csaw and bamsignals, link to Rhtslib and are available on Windows.

Remember to use the 'devel' version of Bioconductor (hence devel build reports) when developing packages.

And I know you've bounced around from your contribution to StackOverflow to here, but the _correct_ place to ask about Bioconductor package development is on the bioc-devel mailing list (the support site is meant for end-user questions).

The undefined reference is to 'bios_zlibversion' but the symbol is bioc_zlibVersion -- is that a copy-paste error?

I don't have windows access at the moment, but suggest removing the explicit reference to zlib in Makevars.win and adding Rhtslib to the Imports: field of the DESCRIPTION file. In terms of debugging, I'd get RStudio out of the way and try to build / install from the DOS / PowerShell prompt, R CMD INSTALL scPipe (R has to be on the PATH environment variable, or the full path specified).

First off, I'm not sure I can actually answer your headline question. I can install Rhtslib fine on Windows, but get the same error you do when trying to build link2Rhtslib. However I think I can at least get your package to load on Windows.

If you want to use zlibbioc then I think you should link against the pre-compiled static library on Windows. It looks like you got some decent advice on StackOverflow, and the error LoadLibrary failure: The specified module could not be found is a result of linking against the shared library during compilation, and its location can't be resolved when you then try to load scPipe.dll

You can fix this by using zlibbioc::pkgconfig("PKG_LIBS_static") in your Makevars.win

However, I think this will lead to a new set of problems, and I'm not sure you should use zlibbioc at all. In my experience I find the interaction between zlibbioc and other packages that are also ship pre-compiled Windows binaries (like Rhtslib) pretty baffling, and when I've tried to use it, I've ended up just resorting to using system versions of zlib.

In your case Rhtslib already links against a version of zlib, and includes -lz in it's compilation flags, which will probably be a system version of zlib since no path is specified. If you also include zlibbioc I think there's a good chance your compiler will complain of multiple definitions of the same functions and fail.

If you remove any reference to zlibbioc (in Makevars.win and DESCRIPTION) then your code will link to the system library. I understand the desire to use stable library versions that don't require external installation, but zlib is pretty ubiquitous and I'm not sure Rhtslib will work without it anyway, so I think that's a safe option here.