How to fix 'make" problem

[jpbreed90]

Hi. I have used shapeit4, and have been using it well without any problems. In order to use another data set this time, I access the homepage of shapeit4 and see the message to use shapeit5, so I am installing it. I modified the path of HTSSRC, BOOST in each tool's makefile file, and replaced the makefile of all tools. Then, when executing the "make" command, the following error occurs.

"make: No rule to make target src/containers/bitvector.h', needed byobj/haplotype_writer.o'. Stop." or "make -C phase_common make[1]: No rule to make target src/containers/bitvector.h', needed byobj/haplotype_writer.o'. Stop. make: *** [phase_common] Error 2"

There was no problem using shapeit4, but shapeit5 has not been installed since. I'm using the Macbook Pro Ventura version. How can we solve this problem?

[jikhashkya]

Having the same issue, it looks like bitvector.h actually has a symbolic link to the actual file which is supposed to be in xcftools folder but when git cloning the repo, the directory is just empty. In any case, you can try downloading the static binary file, convert the file to be an executable file like so chmod +x <static_file_name>.

[odelaneau]

I see the problem, it's indeed related to the symlink. I'll solve it asap. In the meantime, try to clone xcftools to get bitvector class. It's a submodule.

Olivier.

Le lun. 3 avr. 2023, 07:50, Pramesh Shakya @.***> a écrit :

Having the same issue, it looks like bitvector.h actually has a symbolic link to the actual file which is supposed to be in xcftools folder but when git cloning the repo, the directory is just empty. In any case, you can try downloading the static binary file, convert the file to be an executable file like so chmod +x .

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[LouisLeNezet]

Hi,

I was building the bioconda recipe for the new 5.1.0 version, and also ran in this problem. So it seems that xcftools is also empty in the tar.gz of the new version.

Louis

[odelaneau]

Yes, for some reasons github make releases without the submodules in it :/ There's no fix for this.