Installation Issue Error 1 - make

[ntorres17]

Hi, bioinformatics student working on a project using HISAT2. I tried to install using the install provided in git (thank you) but when it tried to execute "make" many fatal errors appeared. I'm using a macbook pro M2 chip, any help would be greatly appreciated!

There is a long lost of errors but here is a snippet: git clone https://github.com/DaehwanKimLab/hisat2.git cd hisat2 make Cloning into 'hisat2'... remote: Enumerating objects: 9646, done. remote: Counting objects: 100% (649/649), done. remote: Compressing objects: 100% (250/250), done. remote: Total 9646 (delta 421), reused 610 (delta 390), pack-reused 8997 Receiving objects: 100% (9646/9646), 31.72 MiB | 493.00 KiB/s, done. Resolving deltas: 100% (6337/6337), done. /usr/bin/g++ -O3 -m32 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m32 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\"" -DPOPCNT_CAPABILITY -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"cat VERSION\"" -DBUILD_HOST="\"hostname\"" -DBUILD_TIME="\"date\"" -DCOMPILER_VERSION="\"/usr/bin/g++ -v 2>&1 | tail -1\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ -I. -I third_party \ -o hisat2-build-s hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread In file included from hisat2_build.cpp:20: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/iostream:38: ./version:1:1: error: expected unqualified-id 2.2.1 ^ In file included from hisat2_build.cpp:20: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/iostream:43: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/ios:220: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/ios/fpos.h:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/iosfwd:101: ./version:1:1: error: expected unqualified-id 2.2.1 ^ In file included from hisat2_build.cpp:20: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/iostream:43: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/ios:221: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:18: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/mutex:191: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory/shared_ptr.h:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/compare/compare_three_way.h:13: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/compare/three_way_comparable.h:12: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/compare/common_comparison_category.h:15: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:41: ./version:1:1: error: expected unqualified-id 2.2.1 ^ In file included from hisat2_build.cpp:20: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/iostream:43: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/ios:221: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/locale:18: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/mutex:191: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory/shared_ptr.h:22: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory/allocation_guard.h:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory/allocator_traits.h:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/memory/construct_at.h:23: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/new:97: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/exception:92: ./version:1:1: error: expected unqualified-id 2.2.1 ^ ion:1:1: error: expected unqualified-id 2.2.1 ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. make: *** [hisat2-build-s] Error 1

[Shivani-kushwaha]

I have the same issue. Could you please help?