Failed to compile

[shenwei356]

Hi Massimiliano, I failed to compile moni with the given installation step.

git clone https://github.com/maxrossi91/moni

mkdir build
cd build
cmake ..
make

[ 44%] Built target rlbwt2lcp
[ 44%] Building CXX object _deps/bwt2lcp-build/CMakeFiles/bwt2lcp.dir/bwt2lcp.cpp.o
In file included from /home/shenwei/Downloads/moni/build/_deps/bwt2lcp-src/internal/dna_bwt.hpp:15,
                 from /home/shenwei/Downloads/moni/build/_deps/bwt2lcp-src/internal/lcp.hpp:26,
                 from /home/shenwei/Downloads/moni/build/_deps/bwt2lcp-src/bwt2lcp.cpp:14:
/home/shenwei/Downloads/moni/build/_deps/bwt2lcp-src/internal/include.hpp:15:14: error: ‘uint64_t’ was not declared in this scope
   15 | typedef pair<uint64_t,uint64_t> range_t;
      |              ^~~~~~~~
/home/shenwei/Downloads/moni/build/_deps/bwt2lcp-src/internal/include.hpp:12:1: note: ‘uint64_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstd
int>’?
   11 | #include <algorithm>
  +++ |+#include <cstdint>
   12 | 
/home/shenwei/Downloads/moni/build/_deps/bwt2lcp-src/internal/include.hpp:15:23: error: ‘uint64_t’ was not declared in this scope
   15 | typedef pair<uint64_t,uint64_t> range_t;
      |                       ^~~~~~~~
/home/shenwei/Downloads/moni/build/_deps/bwt2lcp-src/internal/include.hpp:15:23: note: ‘uint64_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cst
dint>’?
/home/shenwei/Downloads/moni/build/_deps/bwt2lcp-src/internal/include.hpp:15:31: error: template argument 1 is invalid
   15 | typedef pair<uint64_t,uint64_t> range_t;
      |                               ^
/home/shenwei/Downloads/moni/build/_deps/bwt2lcp-src/internal/include.hpp:15:31: error: template argument 2 is invalid
/home/shenwei/Downloads/moni/build/_deps/bwt2lcp-src/internal/include.hpp:32:9: error: ‘uint64_t’ does not name a type
   32 |         uint64_t first_TERM;

Here's some information you might find useful.

$ uname -a
Linux mBio 6.1.55-1-MANJARO #1 SMP PREEMPT_DYNAMIC Sat Sep 23 12:13:56 UTC 2023 x86_64 GNU/Linux

$ cmake --version 
cmake version 3.27.7
$ gcc --version
gcc (GCC) 13.2.1 20230801
$ g++ --version
g++ (GCC) 13.2.1 20230801

Or, can you support installation with conda: https://github.com/bioconda/bioconda-recipes .

Thanks a lot.

Wei

[maxrossi91]

Hi, Wei,

Thank you for reporting this. I will look at this in the weekend. In the meanwhile could you try to install it from the release assets? We have three ways to install from there, i.e, using

• .sh install (https://github.com/maxrossi91/moni/releases/download/v0.2.0/moni-0.2.0-Linux.sh)
• .tar.gz package (https://github.com/maxrossi91/moni/releases/download/v0.2.0/moni-0.2.0-Linux.tar.gz)
• .deb package (https://github.com/maxrossi91/moni/releases/download/v0.2.0/moni_0.2.0_amd64.deb)

Bests,

Max

[shenwei356]

Thanks, Max, the pre-built binaries work.

[AndreaGuarracino]

Similar problem. With

uname -a
Linux guarracino-ThinkPad-P14s-Gen-4 6.5.0-44-generic #44-Ubuntu SMP PREEMPT_DYNAMIC Fri Jun  7 15:10:09 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux

cmake --version
cmake version 3.27.4

gcc --version
gcc (Ubuntu 13.2.0-4ubuntu3) 13.2.0
Copyright (C) 2023 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

g++ --version
g++ (Ubuntu 13.2.0-4ubuntu3) 13.2.0
Copyright (C) 2023 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


sudo apt-get update
sudo apt-get install -y build-essential cmake git python3 zlib1g-dev

git clone https://github.com/maxrossi91/moni
cd moni
mkdir build
cd build
cmake ..
make -j 16

I get:

[ 57%] Building CXX object _deps/sdsl-build/lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o
In file included from /home/guarracino/git/moni/build/_deps/sdsl-build/lib/../include/sdsl/wt_helper.hpp:4,
                 from /home/guarracino/git/moni/build/_deps/sdsl-src/lib/wt_helper.cpp:1:
/home/guarracino/git/moni/build/_deps/sdsl-build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
 1402 | inline auto
      |        ^~~~
/home/guarracino/git/moni/build/_deps/sdsl-build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
 1410 | inline auto
      |        ^~~~
/home/guarracino/git/moni/build/_deps/sdsl-build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
 1418 | inline auto
      |        ^~~~
/home/guarracino/git/moni/build/_deps/sdsl-build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
 1426 | inline auto
      |        ^~~~
/home/guarracino/git/moni/build/_deps/sdsl-build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
 1434 | inline auto
      |        ^~~~
/home/guarracino/git/moni/build/_deps/sdsl-build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers]
 1442 | inline auto
      |        ^~~~
[ 57%] Linking CXX static library libbenchmark.a
[ 57%] Built target benchmark
[ 57%] Linking CXX static library libgtest.a
[ 57%] Built target gtest
[ 57%] Linking CXX static library libsdsl.a
[ 57%] Built target sdsl
make: *** [Makefile:156: all] Error 2

I was able to use moni with the pre-built binary, but now I would like a binary that incorporates #9 and I can't compile it! xD

[maxrossi91]

When developing MONI I used gcc version 9.3.0. There might be issues when using more recent compilers, maybe due to old thirdparty projects.

You can try that and see if it works. I will try to make a new set of executables possibly in the weekend.

[AndreaGuarracino]

I share a hacky way to compile moni on my laptop; it might give you hints about the issues:

• Add include <array> to include/common/common.hpp
• mkdir build && cd build && cmake .. && make
• Wait for the errors
• Add #include <cstdint> to _deps/bwt2lcp-src/internal/include.hpp
• Add #include <utility> to _deps/shaped_slp-src/external/sux/sux/util/Vector.hpp
• make

[AndreaGuarracino]

@maxrossi91, I've tried your new pre-built binary (moni-0.2.2) on our cluster, but

.../moni-0.2.2/bin/newscanNT.x
.../moni-0.2.2/bin/newscanNT.x: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by .../moni-0.2.2/bin/newscanNT.x)

[maxrossi91]

@AndreaGuarracino thanks for pointing it out. It will take me some time to fix the current compile issues. In the meanwhile I released a Docker image in #13. Let me know if that might help as a workaround to your issue.

[AndreaGuarracino]

I can't help much, as I can't use Docker on our cluster ;( I could try it via conda, if you are going to deploy moni there too!

[maxrossi91]

Apologies for not replying sooner. I am slowly trying to fix the compilation issues. Thanks for pushing MONI into bioconda.