search

gymrek-lab / LongTR

Tandem repeat genotyping with long reads
GNU General Public License v2.0
19 stars 0 forks source link

Compiling gives fatal errors #2

Closed davidlougheed closed 5 months ago

davidlougheed commented 5 months ago

When compiling LongTR, I get the following error:

fatal error: gtest/gtest.h: No such file or directory

This indicates a dependency on googletest, but no dependency is listed in the README.

When I load the module (googletest/1.13.0) on a cluster, I then get a different error:

bgzf.c:1354: error: undefined reference to 'libdeflate_crc32'
bgzf.c:719: error: undefined reference to 'libdeflate_alloc_decompressor'
bgzf.c:725: error: undefined reference to 'libdeflate_deflate_decompress'
bgzf.c:726: error: undefined reference to 'libdeflate_free_decompressor'
bgzf.c:733: error: undefined reference to 'libdeflate_crc32'
bgzf.c:602: error: undefined reference to 'libdeflate_crc32'
bgzf.c:577: error: undefined reference to 'libdeflate_alloc_compressor'
bgzf.c:582: error: undefined reference to 'libdeflate_deflate_compress'
bgzf.c:594: error: undefined reference to 'libdeflate_free_compressor'
bgzf.c:588: error: undefined reference to 'libdeflate_free_compressor'
cram/cram_io.c:990: error: undefined reference to 'libdeflate_crc32'
cram/cram_io.c:1122: error: undefined reference to 'libdeflate_alloc_compressor'
cram/cram_io.c:1137: error: undefined reference to 'libdeflate_gzip_compress'
cram/cram_io.c:1138: error: undefined reference to 'libdeflate_free_compressor'
cram/cram_io.c:1133: error: undefined reference to 'libdeflate_free_compressor'
cram/cram_io.c:1068: error: undefined reference to 'libdeflate_alloc_decompressor'
cram/cram_io.c:1085: error: undefined reference to 'libdeflate_gzip_decompress'
cram/cram_io.c:1102: error: undefined reference to 'libdeflate_free_decompressor'
cram/cram_io.c:1106: error: undefined reference to 'libdeflate_free_decompressor'
heliziii commented 5 months ago

Hi David,

Thank you for your interest in our tool! gtest is used by spoa, which is part of the LongTR package, I will add their dependencies too, sorry for the confusion.

For the second issue, I guess something went wrong with installing htslib. Can you please attach the whole log file of compiling LongTR? Thank you!

Best, Helia

davidlougheed commented 5 months ago

For the second issue, here is the log: make-longTR.log

heliziii commented 5 months ago

Thank you! I searched for the error and according to htslib team, this is a problem when htslib can't find libdeflate package. Please check their answer: https://github.com/samtools/htslib/issues/688#issuecomment-383542683

Can you please check if libdeflate is already installed in your system? There is guidance to install and point htslib to it in this response. please let me know if the issue doesn't get resolved.

Best, Helia

davidlougheed commented 5 months ago

what I ended up having to do was add -ldeflate to the end of the LIBS variable in the Makefile, since my system did indeed already have libdeflate installed. Thanks for your help!

heliziii commented 5 months ago

Great! Let me know if you have further questions!