Cannot compile sambamba v0.6.7 on LInux

[Emilio Palumbo]

Hi,

I am trying to compile sambamba v0.6.7 on Scientific Linux 7 but I get the following error:

gcc -Wl,--gc-sections -o build/sambamba build/sambamba.o -Lhtslib -Llz4/lib -Wl,-Bstatic -lhts -llz4 -Wl,-Bdynamic -l:libphobos2-ldc.a -l:libdruntime-ldc.a  -lrt -lpthread -lm
build/sambamba.o: In function `_D6undead6stream6Stream16doFormatCallbackMFwZv':
/no_backup_isis/rg/epalumbo/tmp/bamsort-test/sambamba/undeaD/src/undead/stream.d:1217: undefined reference to `_D6undead3utf6toUTF8FNaNbNiNfNkJG4awZAa'
collect2: error: ld returned 1 exit status
make: *** [sambamba-ldmd2-64] Error 1

I also tried with the undeaD master branch from GitHub but I had no lock.

Here is the info about ldc version:

immutable LDC_VERSION_STRING = "1.7.0";

immutable BOOTSTRAP_VERSION_STRING = "LDC - the LLVM D compiler (1.7.0)";

immutable DMD_VERSION_STRING = "v2.077.1";

immutable LLVM_VERSION_STRING = "5.0.1";

Could you please help me?

Thanks

Best,

Emilio

[Pjotr Prins]

On Mon, Feb 05, 2018 at 02:56:43AM -0800, Emilio Palumbo wrote:
> Hi,
> I am trying to compile sambamba v0.6.7 on Scientific Linux 7 but I get
> the following error:
> gcc -Wl,--gc-sections -o build/sambamba build/sambamba.o -Lhtslib
> -Llz4/lib -Wl,-Bstatic -lhts -llz4 -Wl,-Bdynamic -l:libphobos2-ldc.a

> -l:libdruntime-ldc.a  -lrt -lpthread -lm

> build/sambamba.o: In function
> `_D6undead6stream6Stream16doFormatCallbackMFwZv':
> /no_backup_isis/rg/epalumbo/tmp/bamsort-test/sambamba/undeaD/src/undead
> /stream.d:1217: undefined reference to
> `_D6undead3utf6toUTF8FNaNbNiNfNkJG4awZAa'
> collect2: error: ld returned 1 exit status
> make: *** [sambamba-ldmd2-64] Error 1
> I also tried with the undeaD master branch from GitHub but I had no
> lock.
> Here is the info about ldc version:
> immutable LDC_VERSION_STRING = "1.7.0";
>
> immutable BOOTSTRAP_VERSION_STRING = "LDC - the LLVM D compiler
> (1.7.0)";
>
> immutable DMD_VERSION_STRING = "v2.077.1";
>
> immutable LLVM_VERSION_STRING = "5.0.1";
> Could you please help me?

I have simplified the Makefile and updated the build instructions at
https://github.com/biod/sambamba#compiling-sambamba

Do not forget to use the --recursive switch with git.

See if this works for you.

Pj.

(commit
https://github.com/biod/sambamba/commit/c77803f78e603044cdeab938dd68a6e930b38f76)