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jts / nanopolish

Signal-level algorithms for MinION data
MIT License
566 stars 159 forks source link

Make #159

Closed mercycarter closed 7 years ago

mercycarter commented 7 years ago

Hi,

When I go through the steps,

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

I get the error: make Makefile:109: .depend: No such file or directory if [ ! -e hdf5-1.8.14.tar.gz ]; then wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.14/src/hdf5-1.8.14.tar.gz; fi /bin/sh: wget: command not found make: *** [lib/libhdf5.a] Error 127

Not sure what I'm doing wrong?

Thanks in advance!

jts commented 7 years ago

Hi,

It looks like you are missing wget. What version of linux are you using? If you install wget using your package manager the build should continue.

Jared

mercycarter commented 7 years ago

Hi,

I'm actually running this through terminal on a Mac. I installed wget through homebrew, which seems to have worked. Now I'm trying to sort out what seems to be a Mac related issue. Instead of using gcc, it's defaulting to clang and I'm getting: error: unsupported option '-fopenmp'

Currently reading up on that and trying to find a work around, but any thoughts would be much appreciated. My lab recently acquired the Nanopore Oxford MinION technology and I was tasked with setting up the data processing system, with my 0 years of programming experience.

This has been, and continues to be, quite the adventure.

Cheers!

Meghan

On Tue, Jun 13, 2017 at 7:48 PM, Jared Simpson notifications@github.com wrote:

Hi,

It looks like you are missing wget. What version of linux are you using? If you install wget using your package manager the build should continue.

Jared

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jts_nanopolish_issues_159-23issuecomment-2D308280034&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=-Q8_fRKqRRHfYSuLpJpifg&m=M6j96-dvjUh9NCVShzdf9rDWtbA2rGbPatwMVbiBDMc&s=pbN6VzkJ88xaCQvoS1U3NmCW6E-a3ph_02ewFLVLUFs&e=, or mute the thread https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AcDIIWP8a8PHnTr-2DosXECFPxQcJm8yzoks5sDx-5FcgaJpZM4N45sv&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=-Q8_fRKqRRHfYSuLpJpifg&m=M6j96-dvjUh9NCVShzdf9rDWtbA2rGbPatwMVbiBDMc&s=UeT18UbAOxaz2faFFvoG7O7jEcjmupL84Qqh3m2ud2A&e= .

-- Meghan Lawler Graduate Student Duke University Chemistry Department- McCafferty Lab

jts commented 7 years ago

Hi,

You'll need to to install gcc-4.8 using homebrew, then nanopolish should compile with this command:

make CXX=g++-4.8

Jared

rckeerthivasan commented 3 years ago

hi,

I am facing the above problem.

fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. make[2]: [cache.o] Error 1 make[1]: [all-recursive] Error 1 make: *** [lib/libhdf5.a] Error 2

I run these commands: make CXX=g++-11, make CXX=/usr/local/bin/g++-11. No use. Any idea on this?