Salmon 1.10.3 build failure

[davidecarlson]

Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)? This is related to salmon.

Describe the bug When building Salmon 1.10.3 from source, I'm seeing the following error.

[ 63%] Building CXX object src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o
In file included from /usr/include/pthread.h:33,
                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/x86_64-pc-linux-gnu/bits/gthr-default.h:35,
                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/x86_64-pc-linux-gnu/bits/gthr.h:148,
                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ext/atomicity.h:35,
                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/ios_base.h:39,
                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ios:44,
                 from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/ostream:40,
                 from /gpfs/projects/hpc_support/salmon/external/install/include/boost/system/error_code.hpp:17,
                 from /gpfs/projects/hpc_support/salmon/external/install/include/boost/system/system_error.hpp:11,
                 from /gpfs/projects/hpc_support/salmon/external/install/include/boost/thread/exceptions.hpp:22,
                 from /gpfs/projects/hpc_support/salmon/external/install/include/boost/thread/pthread/thread_data.hpp:10,
                 from /gpfs/projects/hpc_support/salmon/external/install/include/boost/thread/thread_only.hpp:17,
                 from /gpfs/projects/hpc_support/salmon/external/install/include/boost/thread/thread.hpp:12,
                 from /gpfs/projects/hpc_support/salmon/include/GenomicFeature.hpp:25,
                 from /gpfs/projects/hpc_support/salmon/src/GenomicFeature.cpp:22:
/gpfs/projects/hpc_support/salmon/external/install/include/boost/thread/pthread/thread_data.hpp:60:5: error: missing binary operator before token "("
   60 | #if PTHREAD_STACK_MIN > 0
      |     ^~~~~~~~~~~~~~~~~
In file included from /gpfs/projects/hpc_support/salmon/external/install/include/boost/functional/hash.hpp:6,
                 from /gpfs/projects/hpc_support/salmon/external/install/include/boost/thread/detail/thread.hpp:41,
                 from /gpfs/projects/hpc_support/salmon/external/install/include/boost/thread/thread_only.hpp:22:
/gpfs/projects/hpc_support/salmon/external/install/include/boost/container_hash/hash.hpp:130:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  130 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /gpfs/software/gcc/13.2.0/include/c++/13.2.0/string:49,
                 from /gpfs/projects/hpc_support/salmon/external/install/include/boost/thread/exceptions.hpp:20:
/gpfs/software/gcc/13.2.0/include/c++/13.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
make[2]: *** [src/CMakeFiles/salmon_core.dir/build.make:160: src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:568: src/CMakeFiles/salmon_core.dir/all] Error 2
make: *** [Makefile:166: all] Error 2

To Reproduce

#!/usr/bin/env bash

module load cmake Bzip2/1.0.8 curl
module load oneTBB/gcc13.2/2021.13.0
module load boost/gcc13.2/1.86.0 

rm -rf CMake*

cmake .. \
-DCMAKE_C_COMPILER=gcc \
-DBOOST_ROOT=/gpfs/software/boost/xeonmax/gcc13.2/1.86.0/ \
-DTBB_INSTALL_DIR=/gpfs/software/oneTBB/xeonmax/gcc13.2.0/2021.13.0 \
-DTBB_ROOT=/gpfs/software/oneTBB/xeonmax/gcc13.2.0/2021.13.0 \
-DCMAKE_CXX_COMPILER=g++ \
-DCMAKE_C_FLAGS="-O3 -march=sapphirerapids -mtune=sapphirerapids" \
-DCMAKE_CXX_FLAGS="-O3 -march=sapphirerapids -mtune=sapphirerapids" \
-DCMAKE_INSTALL_PREFIX:PATH=/gpfs/software/salmon/xeonmax/gcc13.2.0/1.10.3

make clean
make -j 25

Specifically, please provide at least the following information:

• Which version of salmon was used? 1.10.3
• How was salmon installed (compiled, downloaded executable, through bioconda)? compiled

Expected behavior A successful build.

Desktop (please complete the following information):

• OS: Rocky Linux 9.4
• Version: Linux xm013 5.14.0-427.26.1.el9_4.x86_64 #1 SMP PREEMPT_DYNAMIC Tue Jul 23 16:00:21 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux

Additional context std err file attached. build.err.gz