refresh-bio
makefile_mac
Hi I am willing to install KMC as part of the required dependencies for IVA and I am struggling with the installation of KMC on my Mac. #1. I set the new path of gcc in the makefile_mac #2. Considering the following error message:
I removed the -fopenmp option from makefile_mac
#3. I reran make -f makefile_mac but I finally got this error I cannot fix (sorry for that...)
Any advices would be very appreciate
thanks ++ a
Hi, I will check this when I will have access to MAC, hopefully tomorrow. In the meantime, what version of gcc you have?
thanks! gcc-5.3.0 is installed on my Mac
a
On Mar 14, 2017, at 12:01 AM, marekkokot [email protected] wrote:
Hi, I will check this when I will have access to MAC, hopefully tomorrow. In the meantime, what version of gcc you have?
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Hi, I just noticed that the warning and errors you recieve are from clang, not from g++. Here is a related topic.
Unfortunatelly, for now it is not possible to compile KMC with clang, so you should install the real gcc. As far as I remember i used brew approach. I am not sure what is the newest version of gcc supported by brew, but I think it should be sufficient for KMC and KMC tools compilation.
BTW. Why you need to compile KMC on your own and cannot use precompiled version? If the only issue is disabling asmlib, I may compile KMC without asmlib and extend 3.0.0 release. Let me know.
Note: I compiled latest release of KMC on MAC with gcc-6.3.0 which I first compiled from sources using previous version of gcc (installed with homebrew). Here is the description of installing gcc from sources. You will probably do NOT need to do that.
Note2: Unfortunatelly I am not a MAC expert, so maybe it is possible to make it better.
@marekkokot Is it possible to make kmc compileable with clang? I'm trying to create a bioconda recipe for kmc. I've created one for kmc 2.3 which only builds kmc and kmc_dump . I want to add kmc_tools , but that requires a C++14 compiler. There is no bioconda recipe for a C++14 compiler, but there is a clangdev 3.9.1 recipe on conda-forge, and bioconda recipes may depend on conda-forge. But, you say there's no way to build kmc using clangdev 3.9.1.? Thanks!
@marekkokot also, the kmc website seems to be down at http://sun.aei.polsl.pl/kmc ?
Hi, I ran into a similar issue...this is the error message I received while running make -f makefile_mac:
usr/local/Cellar/gcc/10.2.0_4/bin/g++-10 -lm -fopenmp -static-libgcc -static-libstdc++ -O3 -pthread -std=c++11 -o bin/kmc kmer_counter/kmer_counter.o kmer_counter/mmer.o kmer_counter/mem_disk_file.o kmer_counter/rev_byte.o kmer_counter/bkb_writer.o kmer_counter/cpu_info.o kmer_counter/bkb_reader.o kmer_counter/fastq_reader.o kmer_counter/timer.o kmer_counter/develop.o kmer_counter/kb_completer.o kmer_counter/kb_storer.o kmer_counter/kmer.o kmer_counter/splitter.o kmer_counter/kb_collector.o kmer_counter/libs/libz.1.2.5.dylib kmer_counter/libs/libbz2.1.0.5.dylib ld: warning: direct access in function '__ZnamRKSt9nothrow_t.cold' from file '/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin17/10.2.0/../../../libstdc++.a(new_opvnt.o)' to global weak symbol '__ZnamRKSt9nothrow_t' from file '/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin17/10.2.0/../../../libstdc++.a(new_opvnt.o)' means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
I installed gcc using brew... bin/py_kmc_apipython3-config --extension-suffix does not appear
Help desperately needed
