cannot find -llib

[stsmall]

Hi, I followed the instructions on the github page. I also have jemalloc installed. When I run: cmake -D CMAKE_CXX_COMPILER=g++ -D MALLOC_LIBRARY=/afs/crc.nd.edu/user/s/ssmall2/programs_that_work/jemalloc-4.2.1/lib It finishes without an error. When I run "make -j 4" it get to about 90% then starts printing the error: /usr/bin/ld: cannot find -llib

cmake: 3.4.1 gcc: 4.8.2 operating system: gnu/linux

Probably something on my end, but before I bother IT I thought I would check here. Also in case someone has a similar issue in the future. thank you! -scott

[gonzalogacc]

Hi scott! Seems to be a linker problem. Please try to compile with gcc 5.1+ and let me know how it goes. Best. Gonza.-

[stsmall]

Hi Gonza, I tried it again with gcc 5.2.0. Same error (here are the lines from 83% onward):

[ 83%] Building CXX object CMakeFiles/01_unipaths.dir/src/paths/long/ShortKmerReadPather.cc.o [ 83%] Building CXX object CMakeFiles/02_qgraph.dir/src/FastaVerifier.cc.o [ 84%] Building CXX object CMakeFiles/02_qgraph.dir/src/Misc.cc.o [ 84%] Building CXX object CMakeFiles/02_qgraph.dir/src/paths/long/BuildReadQGraph.cc.o [ 85%] Linking CXX executable bin/03_clean /usr/bin/ld: cannot find -llib collect2: error: ld returned 1 exit status make[2]: * [bin/03_clean] Error 1 make[1]: * [CMakeFiles/03_clean.dir/all] Error 2 make[1]: * Waiting for unfinished jobs.... [ 85%] Building CXX object CMakeFiles/02_qgraph.dir/src/paths/long/ExtendReadPath.cc.o [ 85%] Building CXX object CMakeFiles/01_unipaths.dir/src/paths/long/large/ExtractReads.cc.o [ 85%] Building CXX object CMakeFiles/04_patching.dir/src/paths/long/large/GapToyTools2.cc.o [ 86%] Building CXX object CMakeFiles/02_qgraph.dir/src/paths/long/ShortKmerReadPather.cc.o [ 87%] Building CXX object CMakeFiles/04_patching.dir/src/paths/long/large/GapToyTools4.cc.o [ 88%] Building CXX object CMakeFiles/01_unipaths.dir/src/paths/long/large/ReadNameLookup.cc.o [ 88%] Building CXX object CMakeFiles/02_qgraph.dir/src/paths/long/large/Repath.cc.o [ 88%] Building CXX object CMakeFiles/04_patching.dir/src/paths/long/large/GapToyTools5.cc.o [ 88%] Building CXX object CMakeFiles/01_unipaths.dir/src/paths/long/large/Samples.cc.o [ 89%] Building CXX object CMakeFiles/01_unipaths.dir/src/system/Crash.cc.o [ 90%] Building CXX object CMakeFiles/02_qgraph.dir/src/system/Crash.cc.o [ 91%] Building CXX object CMakeFiles/04_patching.dir/src/paths/long/large/Unsat.cc.o [ 91%] Linking CXX executable bin/02_qgraph /usr/bin/ld: cannot find -llib collect2: error: ld returned 1 exit status make[2]: * [bin/02_qgraph] Error 1 make[1]: * [CMakeFiles/02_qgraph.dir/all] Error 2 [ 91%] Linking CXX executable bin/01_unipaths /usr/bin/ld: cannot find -llib collect2: error: ld returned 1 exit status make[2]: * [bin/01_unipaths] Error 1 make[1]: * [CMakeFiles/01_unipaths.dir/all] Error 2 [ 91%] Linking CXX executable bin/04_patching /usr/bin/ld: cannot find -llib collect2: error: ld returned 1 exit status make[2]: * [bin/04_patching] Error 1 make[1]: * [CMakeFiles/04_patching.dir/all] Error 2 make: * [all] Error 2

[gonzalogacc]

Hi Scott. Please try set the complete path to the libjemalloc.so file should look something like this: -D MALLOC_LIBRARY=/afs/crc.nd.edu/user/s/ssmall2/programs_that_work/jemalloc-4.2.1/lib/libjemalloc.so Let me know how it goes. Best Gonza.-

[stsmall]

Hi Gonza, That worked. Compiled with no errors and I now have: 01_unipaths 02_qgraph 03_clean 04_patching 05_simplify 06_scaffolding, in bin. thank you, Scott