installation fails on Alpine Linux: lseek64 and ftruncate64 not defined

[bastistician]

Package 'gdsfmt' currently fails installation on Alpine Linux (or, more generally, under musl libc). I get:

CoreArray/dPlatform.cpp:1212:32: error: 'lseek64' was not declared in this scope; did you mean 'lseek'?
CoreArray/dPlatform.cpp:1228:32: error: 'ftruncate64' was not declared in this scope; did you mean 'ftruncate'?

The corresponding code already seems to take care of cygwin/mac/BSD:

gdsfmt/src/CoreArray/dPlatform.cpp

Lines 1209 to 1213 in 3109e86

	#if defined(COREARRAY_CYGWIN) || defined(COREARRAY_PLATFORM_MACOS) || defined(COREARRAY_PLATFORM_BSD)
	return lseek(Handle, Offset, sk);
	#else
	return lseek64(Handle, Offset, sk);
	#endif

gdsfmt/src/CoreArray/dPlatform.cpp

Lines 1225 to 1229 in 3109e86

	#if defined(COREARRAY_CYGWIN) || defined(COREARRAY_PLATFORM_MACOS) || defined(COREARRAY_PLATFORM_BSD)
	return ftruncate(Handle, NewSize)==0;
	#else
	return ftruncate64(Handle, NewSize)==0;
	#endif

As there is no __MUSL__ macro by design, maybe add something like || (defined(COREARRAY_PLATFORM_LINUX) && !defined(__GLIBC__)) to also enter the first branch? (This assumes features.h has been included at that point, which I did not check.)

[zhengxwen]

Could you please show me sessionInfo() in R, the gcc version, and the gdsfmt version?

[bastistician]

You could reproduce the error using the rhub/r-minimal Docker image with the following oneliner:

docker run --rm -t rhub/r-minimal installr -d zhengxwen/gdsfmt

This will use the current development version from GitHub.

I have originally observed the installation failure using released 'gdsfmt' 1.42.0 in current R 4.4.2 on an Alpine Linux 3.20 system with C++ compiler g++ (Alpine 13.2.1_git20240309) 13.2.1 20240309. R.version$platform is "x86_64-pc-linux-musl", R.version$os is "linux-musl".

[bastistician]

Any chance this could be fixed in the next release? Unfortunately, I cannot install several other packages because they depend on 'gdsfmt'. Thanks!

[zhengxwen]

I am working on this issue now.

[zhengxwen]

The commit d91e2d0 should fix the issue.
gdsfmt_1.42.1 should be available on BioC release soon.