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bingmann / cobs

COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)
https://panthema.net/cobs
MIT License
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Fail during make -j4 (GCC8 is used) #7

Closed MinghaoYan closed 4 years ago

MinghaoYan commented 4 years ago

Hi! I'm using GCC8 for compilation and my CMake output is

-- COBS CMAKE_CXX_FLAGS: -Wpedantic -W -Wall -march=native -fPIC -- Boost version: 1.53.0 -- Found the following Boost libraries: -- system -- filesystem -- TLX CMAKE_CXX_FLAGS: -Wshadow -Wold-style-cast -std=c++17 -g -W -Wall -Wextra -fPIC -Wpedantic -W -Wall -march=native -fPIC -Wcast-qual -Winit-self -Wnoexcept -Woverloaded-virtual -Wredundant-decls -- pybind11 v2.4.3 -- Configuring done -- Generating done -- Build files have been written to: /scratch/my29/cobs/build

When I run make -j4 I would get the following error, it would drag on for thousands of more lines, here is an excerpt of the beginning of the error messages

Scanning dependencies of target gtest Scanning dependencies of target xxhash Scanning dependencies of target tlx [ 1%] Building C object extlib/xxhash/cmake_unofficial/CMakeFiles/xxhash.dir/__/xxhash.c.o [ 2%] Linking C static library libxxhash.a [ 2%] Built target xxhash Scanning dependencies of target xxhsum [ 3%] Building C object extlib/xxhash/cmake_unofficial/CMakeFiles/xxhsum.dir/__/xxhsum.c.o [ 4%] Building CXX object extlib/googletest/googlemock/gtest/CMakeFiles/gtest.dir/src/gtest-all.cc.o [ 6%] Building CXX object extlib/tlx/tlx/CMakeFiles/tlx.dir/backtrace.cpp.o [ 6%] Building CXX object extlib/tlx/tlx/CMakeFiles/tlx.dir/algorithm/parallel_multiway_merge.cpp.o [ 7%] Linking C executable xxhsum [ 7%] Built target xxhsum [ 8%] Building CXX object extlib/tlx/tlx/CMakeFiles/tlx.dir/cmdline_parser.cpp.o /tmp/ccMLvSpN.s: Assembler messages: /tmp/ccMLvSpN.s:15: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:15: Error: junk at end of line, first unrecognized character is-' /tmp/ccMLvSpN.s:17: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:17: Error: unknown pseudo-op:.lvu1' /tmp/ccMLvSpN.s:18: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:18: Error: unknown pseudo-op:.lvu2' /tmp/ccMLvSpN.s:19: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:19: Error: unknown pseudo-op:.lvu3' /tmp/ccMLvSpN.s:20: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:20: Error: unknown pseudo-op:.lvu4' /tmp/ccMLvSpN.s:21: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:21: Error: unknown pseudo-op:.lvu5' /tmp/ccMLvSpN.s:25: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:25: Error: unknown pseudo-op:.lvu6' /tmp/ccMLvSpN.s:27: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:27: Error: unknown pseudo-op:.lvu7' /tmp/ccMLvSpN.s:33: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:33: Error: unknown pseudo-op:.lvu8' /tmp/ccMLvSpN.s:37: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:37: Error: unknown pseudo-op:.lvu9' /tmp/ccMLvSpN.s:40: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:40: Error: unknown pseudo-op:.lvu10' /tmp/ccMLvSpN.s:44: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:44: Error: unknown pseudo-op:.lvu11' /tmp/ccMLvSpN.s:47: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:47: Error: unknown pseudo-op:.lvu12' /tmp/ccMLvSpN.s:48: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:48: Error: unknown pseudo-op:.lvu13' /tmp/ccMLvSpN.s:51: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:51: Error: unknown pseudo-op:.lvu14' /tmp/ccMLvSpN.s:55: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:55: Error: unknown pseudo-op:.lvu15' /tmp/ccMLvSpN.s:56: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:56: Error: unknown pseudo-op:.lvu16' /tmp/ccMLvSpN.s:59: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:59: Error: unknown pseudo-op:.lvu17' /tmp/ccMLvSpN.s:61: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:61: Error: unknown pseudo-op:.lvu18' /tmp/ccMLvSpN.s:64: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:64: Error: unknown pseudo-op:.lvu19' /tmp/ccMLvSpN.s:65: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:65: Error: unknown pseudo-op:.lvu20' /tmp/ccMLvSpN.s:84: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:84: Error: junk at end of line, first unrecognized character is-' /tmp/ccMLvSpN.s:86: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:86: Error: unknown pseudo-op:.lvu22' /tmp/ccMLvSpN.s:119: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:119: Error: unknown pseudo-op:.lvu23' /tmp/ccMLvSpN.s:120: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:120: Error: unknown pseudo-op:.lvu24' /tmp/ccMLvSpN.s:122: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:122: Error: unknown pseudo-op:.lvu25' /tmp/ccMLvSpN.s:123: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:123: Error: unknown pseudo-op:.lvu26' /tmp/ccMLvSpN.s:125: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:125: Error: unknown pseudo-op:.lvu27' /tmp/ccMLvSpN.s:128: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:128: Error: unknown pseudo-op:.lvu28' /tmp/ccMLvSpN.s:130: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:130: Error: unknown pseudo-op:.lvu29' /tmp/ccMLvSpN.s:132: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:132: Error: unknown pseudo-op:.lvu30' /tmp/ccMLvSpN.s:134: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:134: Error: unknown pseudo-op:.lvu31' /tmp/ccMLvSpN.s:138: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:138: Error: unknown pseudo-op:.lvu32' /tmp/ccMLvSpN.s:142: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:142: Error: unknown pseudo-op:.lvu33' /tmp/ccMLvSpN.s:144: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:144: Error: unknown pseudo-op:.lvu34' /tmp/ccMLvSpN.s:145: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:145: Error: unknown pseudo-op:.lvu35' /tmp/ccMLvSpN.s:148: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:148: Error: unknown pseudo-op:.lvu36' /tmp/ccMLvSpN.s:150: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:150: Error: unknown pseudo-op:.lvu37' /tmp/ccMLvSpN.s:153: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:153: Error: unknown pseudo-op:.lvu38' /tmp/ccMLvSpN.s:154: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:154: Error: unknown pseudo-op:.lvu39' /tmp/ccMLvSpN.s:163: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:163: Error: unknown pseudo-op:.lvu40' /tmp/ccMLvSpN.s:164: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:164: Error: unknown pseudo-op:.lvu41' /tmp/ccMLvSpN.s:169: Error: unknown .loc sub-directive view' /tmp/ccMLvSpN.s:169: Error: unknown pseudo-op:.lvu42' /tmp/ccMLvSpN.s:172: Error: unknown .loc sub-directive `view'

How should I fix this? Thank you very much!

bingmann commented 4 years ago

Sorry, no idea. This is a very strange error by the assembler that should never occur. I think your whole compiler setup may be broken.