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bioturing / hera

MIT License
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Missing files #19

Open hmontenegro opened 6 years ago

hmontenegro commented 6 years ago

I am trying to compile Hera 1.2 using the build.sh script, and compilation fails due to missing source code files. Here is the end of the compilation messages:

gcc -fgnu89-inline -O2 -w -lrt src/ssw.c src/xxhash.c src/bgzf.c src/hash_align.c src/EM.c src/bam_write.c src/fmindex.c src/genome_map.c src/main.c src/argument.c src/get_buffer.c src/read.c src/usage.c src/log.c -pthread -lm lib/zlib/libz.a -lm lib/hdf5/lib/libhdf5-static.a -lm lib/hdf5/lib/libhdf5_hl-static.a -ldl -lm lib/libdivsufsort/lib/libdivsufsort64.a -o build/hera
gcc: error: src/argument.c: No such file or directory
gcc: error: src/get_buffer.c: No such file or directory
gcc: error: src/read.c: No such file or directory
gcc: error: src/usage.c: No such file or directory
gcc: error: src/log.c: No such file or directory
make: *** [Makefile_linux:28: Hera] Error 1
thangtq139 commented 6 years ago

Hi hmontenegro, It seems that your download/uncompress is not completed. Please make sure that you clone or download the source code correctly and let us know if the problem still persists.

hmontenegro commented 6 years ago

Thanks for looking into this, and sorry for not properly describing the problem originally - I was too concise in my original post.

Indeed, I can compile if I clone the repository, but the source tarball available at the releases page (e.g., https://github.com/bioturing/hera/archive/v1.2.tar.gz ) is incomplete.

I downloaded all the github packaged source releases (1.0, 1.0.1, 1.1.1 and 1.2, both tar.gz and .zip) and all are missing the aforementioned files (argument.c, get_buffer.c, read.c, usage.c and log.c). So the problem isn't the repository, it is how the release tarball is being created