Bug in installation

[twesigomwedavid]

Hello, I tried following the manual for installing HISAT-genotype (https://daehwankimlab.github.io/hisat-genotype/manual) on a macOS (Python 2.7)

First, it says we should use git checkout hisatgenotype_v1.1.2_beta. However, it looks like hisatgenotype_v1.1.2_beta is no longer available.

So I tried switching to hisatgenotype_v1.1.3. When I ran make hisat2-align-s hisat2-build-s hisat2-inspect-s I got the errors below:

/usr/local/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DHISAT2_VERSION="\"cat VERSION\"" -DBUILD_HOST="\"hostname\"" -DBUILD_TIME="\"date\"" -DCOMPILER_VERSION="\"/usr/local/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -I third_party \ -o hisat2-align-s hisat2.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 qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread
In file included from /usr/local/Cellar/gcc@6/6.5.0_2/include/c++/6.5.0/stdlib.h:36:0, from hisat2.cpp:20: /usr/local/Cellar/gcc@6/6.5.0_2/include/c++/6.5.0/cstdlib:75:25: fatal error: stdlib.h: No such file or directory

include_next

                     ^

compilation terminated. In file included from /usr/local/Cellar/gcc@6/6.5.0_2/lib/gcc/6/gcc/x86_64-apple-darwin18.5.0/6.5.0/include/stdint.h:9:0, from ccnt_lut.cpp:20: /usr/local/Cellar/gcc@6/6.5.0_2/lib/gcc/6/gcc/x86_64-apple-darwin18.5.0/6.5.0/include-fixed/stdint.h:27:32: fatal error: sys/_types/_int8_t.h: No such file or directory

include <sys/_types/_int8_t.h>

                            ^

compilation terminated. In file included from /usr/local/Cellar/gcc@6/6.5.0_2/include/c++/6.5.0/bits/postypes.h:40:0, from /usr/local/Cellar/gcc@6/6.5.0_2/include/c++/6.5.0/iosfwd:40, from /usr/local/Cellar/gcc@6/6.5.0_2/include/c++/6.5.0/ios:38, from /usr/local/Cellar/gcc@6/6.5.0_2/include/c++/6.5.0/ostream:38, from /usr/local/Cellar/gcc@6/6.5.0_2/include/c++/6.5.0/iostream:39, from ref_read.h:23, from ref_read.cpp:20: /usr/local/Cellar/gcc@6/6.5.0_2/include/c++/6.5.0/cwchar:44:19: fatal error: wchar.h: No such file or directory

include

               ^

compilation terminated.`

Also it looks like hisat2-align is not present in hisatgenotype_v1.1.3

What could I be doing wrong?

Thank you.

[chbe-helix]

Hi!

Thank your for pointing out the type in my manual! You should certainly be on version 1.1.3 at this time. It looks like there is a package missing from your Mac when building HISAT2. I will consult with the HISAT2 developer to see if we can sort out the problem. Stay tuned and I'll update you as soon as we find something.

Thanks!

[parkchanhee]

@twesigomwedavid Could you compile again using xcode compiler(clang)?

[twesigomwedavid]

@parkchanhee Thank you for the suggestion. I tried to use clang but I am getting this error

` $ clang hisat2-align-s hisat2-build-s hisat2-inspect-s

clang: error: no such file or directory: 'hisat2-align-s' clang: error: no such file or directory: 'hisat2-build-s' clang: error: no such file or directory: 'hisat2-inspect-s' `

PS: I tried using make again after reinstalling xcode and CLT and got the error below:

ld: unexpected token: !tapi-tbd-v3 file '/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd' for architecture x86_64 collect2: error: ld returned 1 exit status

On Fri, Apr 3, 2020 at 4:26 AM Chanhee Park notifications@github.com wrote:

@twesigomwedavid https://github.com/twesigomwedavid Could you compile again using xcode compiler(clang)?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/DaehwanKimLab/hisat-genotype/issues/6#issuecomment-608194427, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJJNE7WEGOTBOUDYOB67Y7TRKVCORANCNFSM4LX4HDJA .

[parkchanhee]

@twesigomwedavid Try this command make CC=/usr/bin/gcc CPP=/usr/bin/g++

[twesigomwedavid]

@twesigomwedavid Try this command make CC=/usr/bin/gcc CPP=/usr/bin/g++

@parkchanhee Thank you. The command ran without errors. I would like to do CYP2D6 typing to see whether everything is now working fine. I would like to ask more specific questions about CYP2D6 typing. May you direct me on the appropriate place to ask these. I tried sending an email to hisat2.genomics@gmail.com but haven't received any response.

[chbe-helix]

Glad to hear it is working! for CYP typing information please send an email to christopher@bennett-tech.dev. I'll happily help in anyway I can.