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jts / nanopolish

Signal-level algorithms for MinION data
MIT License
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Make quits halfway without the nanopolish executable #1124

Open ZachChua opened 5 months ago

ZachChua commented 5 months ago

Hi, I'm currently trying to install nanopolish on a linux server and have used the following:

$git clone --recursive https://github.com/jts/nanopolish.git cd nanopolish make

After running for a few minutes, the following error appears and make quits halfway without the nanopolish executable:

/scratch/users/nus/e0540727/nanopolish/minimap2/ksw2_extz2_sse.c:97: undefined reference to __cray_sset_detect' /opt/cray/pe/cce/13.0.2/binutils/x86_64/x86_64-pc-linux-gnu/bin/ld: ./minimap2/libminimap2.a(ksw2_extd2_sse2.o):/scratch/users/nus/e0540727/nanopolish/minimap2/ksw2_extd2_sse.c:119: more undefined references to__cray_sset_detect' follow collect2: error: ld returned 1 exit status make: *** [Makefile:198: nanopolish] Error 1

May I know how to solve the issue? Could I run make again on the same nanopolish directory or do I need to delete the files and clone again?

Thanks in advance!

jts commented 5 months ago

The error message (__cray_sset_detect) suggests you are using a Cray computer. What architecture is the machine? Can you post the output of uname -a?

ZachChua commented 5 months ago

Hi, apologies for the delayed response here is the output:

Linux asp2a-login-nus02 4.18.0-305.25.1.el8_4.x86_64 #1 SMP Mon Oct 18 14:34:11 EDT 2021 x86_64 x86_64 x86_64 GNU/Linux

jts commented 5 months ago

Thanks. It looks like your development environment is based on Cray, which differs from the gnu dev environment that nanopolish expects. You should contact your sysadmins for help on compiling software on their system.