-
Notifications
You must be signed in to change notification settings - Fork 15
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Bug in installation #6
Comments
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! |
@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 ***@***.***> 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
<#6 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AJJNE7WEGOTBOUDYOB67Y7TRKVCORANCNFSM4LX4HDJA>
.
|
@twesigomwedavid |
@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. |
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. |
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 <stdlib.h> ^ 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 <wchar.h> ^ compilation terminated.
Also it looks like hisat2-align is not present in hisatgenotype_v1.1.3
What could I be doing wrong?
Thank you.
The text was updated successfully, but these errors were encountered: