Comments (9)
In order to use C++11 features I added -stdlib=libc++ to the compile flags and the previous error disappeared but there is a new one.
g++ -std=c++11 -stdlib=libc++ read_kmc.cpp -o read_kmc
In file included from read_kmc.cpp:3:
In file included from ./KMC-3.0.1/kmc_api/kmc_file.h:14:
./KMC-3.0.1/kmc_api/kmer_defs.h:36:11: fatal error: 'ext/algorithm' file not found
#include <ext/algorithm>
^
1 error generated.
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Hi,
I finally have access to MAC and compliled your code with following command:
/usr/local/gcc-6.3.0/bin/g++ -std=c++11 ../KMC-3.0.1/kmc_api/*.cpp read_db.cpp -o read_db
Could you try this (remember replace g++ path to yours).
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Hi,
For mac you should use makefile_mac.
make -f makefile_mac
From your warnings I assume you are using clang not g++, please refer #21
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I noticed that right after I posted the issue. It's working my mac. I've been trying to install it on Linux too with no luck.
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What's the problem on Linux?
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I updated the issue. I figured out the installation. Now I get this compilation error when I try using the C++ API (kmc_file.h).
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Could you please try to compile with:
-stdlib=libstdc++
You may also try other flags that are present in makefile_mac
Currently I have no access to MAC OS so I cannot check this by myself.
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I get the following error after using -stdlib=libstdc++
g++ -stdlib=libstdc++ -std=c++11 read_kmc.cpp -o read_kmc
In file included from read_kmc.cpp:2:
./KMC-3.0.1/kmc_api/kmc_file.h:90:41: error: no member named 'tuple' in namespace 'std'
using super_kmers_t = std::vector<std::tuple<uint32, uint32, uint32>>;//start_pos, len, bin_no
~~~~~^
./KMC-3.0.1/kmc_api/kmc_file.h:90:47: error: unexpected type name 'uint32': expected expression
using super_kmers_t = std::vector<std::tuple<uint32, uint32, uint32>>;//start_pos, len, bin_no
^
./KMC-3.0.1/kmc_api/kmc_file.h:91:58: error: unknown type name 'super_kmers_t'
void GetSuperKmers(const std::string& transformed_read, super_kmers_t& super_kmers);
^
3 errors generated.
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That worked! Thanks!
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Related Issues (20)
- Small suggestion HOT 3
- Run stages separately HOT 3
- kmc_tools dump not creating file HOT 3
- how to create multiple kmc db output as per @input_file_list. HOT 1
- kmc_tools filter does not accept large FASTA input HOT 1
- KMC abrubtly not working HOT 13
- Empty output HOT 2
- smudge pairs install HOT 1
- kmc_tools simple intersect & union, not considering reverse complement? HOT 3
- kff to jf (or vice versa) HOT 2
- munmap_chunk(): invalid pointer on ubam file - KMC crashes on BAM with long reads HOT 4
- when trying use kmc analyze .fasta file HOT 2
- T2T genome kmer count problem HOT 2
- Dump with empty output HOT 2
- Not processing all reads when limiting number of threads HOT 3
- Storing k-mers without counters HOT 2
- How to merge k-mer frequencies HOT 9
- v3.2.4 stalls on very large dataset but v3.2.1 does not HOT 2
- Seems that only one-line FASTA files are supported HOT 2
- smudge_pairs: command not found Error HOT 2
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