bcgsc / ntCard

Estimating k-mer coverage histogram of genomics data
http://www.bcgsc.ca/platform/bioinfo/software/ntcard
MIT License
76 stars 9 forks source link

problem with make #2

Closed zjlahey closed 7 years ago

zjlahey commented 7 years ago

Trying to make and receive the following error:

g++ -Wall -O3 -fopenmp -Ilib -ldl -o ntcard ntcard.cpp lib/Uncompress.cpp lib/SignalHandler.cpp lib/Fcontrol.cpp
/usr/bin/ld: /tmp/cczwFT7G.o: undefined reference to symbol 'dlsym@@GLIBC_2.2.5'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libdl.so: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
Makefile:12: recipe for target 'ntcard' failed
make: *** [ntcard] Error 1

Any help would be appreciated. Thank you!

sjackman commented 7 years ago

There's a bug in the Makefile. The -l options need to appear after the source file ntcard.cpp

g++ -Wall -O3 -fopenmp -o ntcard ntcard.cpp lib/Uncompress.cpp lib/SignalHandler.cpp lib/Fcontrol.cpp -Ilib -ldl
sjackman commented 7 years ago

You may want to try using Linuxbrew to install ntcard See http://linuxbrew.sh then brew install homebrew/science/ntcard

zjlahey commented 7 years ago

Thanks for you help, but I still can't get it to work. I installed linuxbrew and it doesn't recognize ntcard:

brew install homebrew/science/ntcard
Error: No available formula with the name "homebrew/science/ntcard" 
==> Searching for similarly named formulae...
Error: No similarly named formulae found.
==> Searching taps...
Error: No formulae found in taps.

I've also tried editing the make file to no avail.

mohamadi commented 7 years ago

I just pushed the AUTOTOOLS version to build ntCard. Please follow the instruction in README.md to build ntcard and let me know if it works.

zjlahey commented 7 years ago

It works, thanks!

sjackman commented 7 years ago

My mistake, ntcard wasn't yet in Homebrew, but it is now! See https://github.com/Homebrew/homebrew-science/pull/4846 Try once again

brew install homebrew/science/ntcard