make compile error - Githubissues

sjads commented 2 years ago

When I follow the readme download to make compile, it reports an error, missing file

configure.ac: error: required file 'config.sub' not found configure.ac: error: required file 'config.guess' not found configure.ac: try running autoreconf --install cd lib/htslib && \ ./configure --disable-bz2 --disable-lzma --enable-libcurl configure: error: cannot find required auxiliary files: config.guess config.sub make: *** [Makefile:75：htslib] 错误 1

liujiaxin7 commented 2 years ago

I encontered the same question!

sjads commented 2 years ago

Have you solved it now？

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Date	09/18/2022 15:58
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Subject	Re: [arq5x/lumpy-sv] make compile error (Issue #384)

I encontered the same question!

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Stikus commented 11 months ago

@sjads same problem here, do you find a solution?

q-wind commented 11 months ago

@Stikus I encountered the same problem, and then I run "autoreconf --install" in the path "lumpy-sv/lib/htslib", the missing config.sub and config.guess be generated, and I can come back and make. And I meet another problem: the host type is unrecognized when running "make" at the time it run "./configure ...", then I edit the Makefile at Line76 and add "--host=\<myhosttype>" parameter and finally the make can work. I also realize that it cannot be compile by gcc-11, but gcc-9 can work.

Stikus commented 9 months ago

@q-wind great thanks for advice, autoreconf --install and --host= helped. And about compilation problem with gcc-11 - its origin is in bamtools - https://github.com/pezmaster31/bamtools/issues/213 and was fixed 3 years ago, but lumpy packages are too old: https://github.com/arq5x/lumpy-sv/tree/master/src/utils/BamTools

arq5x / lumpy-sv

make compile error #384