How to solve `obj/haplotype_indexer.o error` when i `make static`.

Question

[congruisun]

My operating system is CentOS, my CPU that supports SSE 4.2 and, GCC version is 5.3.0. I have solved several problems in vcflib, dozen, and DYNAMIC construction through google and github. Now I have no idea in obj/haplotype_indexer.o errors. please help me out!

. ./source_me.sh && /usr/bin/g++ -I/data/prosium/01.program/51.vg/BUILD/vg/include -I. -I/data/prosium/01.program/51.vg/BUILD/vg/src -I/data/prosium/01.program/51.vg/BUILD/vg/src/unittest -I/data/prosium/01.program/51.vg/BUILD/vg/src/subcommand -I/data/prosium/01.program/51.vg/BUILD/vg/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -I /data/prosium/01.program/51.vg/BUILD/vg/include -I/data/prosium/01.program/51.vg/BUILD/vg/include/dynamic -I /data/prosium/01.program/51.vg/BUILD/vg/include -I/data/prosium/01.program/51.vg/BUILD/vg/include/dynamic -I /data/prosium/01.program/51.vg/BUILD/vg/include -I/data/prosium/01.program/51.vg/BUILD/vg/include/dynamic -I /data/prosium/01.program/51.vg/BUILD/vg/include -I/data/prosium/01.program/51.vg/BUILD/vg/include/dynamic -I /data/prosium/01.program/51.vg/vg-v1.25.0/include -I/data/prosium/01.program/51.vg/vg-v1.25.0/include/dynamic -I /data/prosium/01.program/51.vg/vg-v1.25.0/include -I/data/prosium/01.program/51.vg/vg-v1.25.0/include/dynamic -I /data/prosium/01.program/51.vg/vg-v1.25.0/include -I/data/prosium/01.program/51.vg/vg-v1.25.0/include/dynamic -I /data/prosium/01.program/51.vg/vg-v1.25.0/include -I/data/prosium/01.program/51.vg/vg-v1.25.0/include/dynamic -I /data/prosium/01.program/51.vg/vg-v1.25.0/include -I/data/prosium/01.program/51.vg/vg-v1.25.0/include/dynamic  -fopenmp -msse4.2 -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp
In file included from src/haplotype_indexer.cpp:13:0:
src/haplotype_indexer.hpp:79:54: error: expected ‘;’ at end of member declaration
     pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
                                                      ^
src/haplotype_indexer.hpp:79:54: error: declaration of ‘std::pair<long unsigned int, long unsigned int> vg::HaplotypeIndexer::size_t’ [-fpermissive]
In file included from /usr/include/wchar.h:51:0,
                 from /usr/include/c++/5/cwchar:44,
                 from /usr/include/c++/5/bits/postypes.h:40,
                 from /usr/include/c++/5/iosfwd:40,
                 from /usr/include/c++/5/ios:38,
                 from /usr/include/c++/5/ostream:38,
                 from /usr/include/c++/5/iostream:39,
                 from src/haplotype_indexer.cpp:5:
/usr/lib/gcc/x86_64-linux-gnu/5/include/stddef.h:216:23: error: changes meaning of ‘size_t’ from ‘typedef long unsigned int size_t’ [-fpermissive]
 typedef __SIZE_TYPE__ size_t;
                       ^
In file included from src/haplotype_indexer.cpp:13:0:
src/haplotype_indexer.hpp:79:60: error: expected unqualified-id before ‘>’ token
     pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
                                                            ^
src/haplotype_indexer.hpp:83:22: error: invalid use of non-static data member ‘vg::HaplotypeIndexer::size_t’
     map<string, pair<size_t, size_t>> regions;
                      ^
src/haplotype_indexer.hpp:79:54: note: declared here
     pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
                                                      ^
src/haplotype_indexer.hpp:83:22: error: invalid use of non-static data member ‘vg::HaplotypeIndexer::size_t’
     map<string, pair<size_t, size_t>> regions;
                      ^
src/haplotype_indexer.hpp:79:54: note: declared here
     pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
                                                      ^
src/haplotype_indexer.hpp:83:22: error: invalid use of non-static data member ‘vg::HaplotypeIndexer::size_t’
     map<string, pair<size_t, size_t>> regions;
                      ^
                                             ^
src/haplotype_indexer.hpp:161:36: error: template argument 1 is invalid
         const function<void(size_t)>& bit_width_ready, const function<void(const gbwt::vector_type&, const gbwt::size_type (&)[4])>& each_thread);
                                    ^
src/haplotype_indexer.hpp:79:46: error: wrong number of template arguments (1, should be 2)
     pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
                                              ^
In file included from /usr/include/c++/5/bits/stl_algobase.h:64:0,
                 from /usr/include/c++/5/bits/char_traits.h:39,
                 from /usr/include/c++/5/ios:40,
                 from /usr/include/c++/5/ostream:38,
                 from /usr/include/c++/5/iostream:39,
                 from src/haplotype_indexer.cpp:5:
/usr/include/c++/5/bits/stl_pair.h:96:12: note: provided for ‘template<class _T1, class _T2> struct std::pair’
     struct pair
            ^
src/haplotype_indexer.cpp:27:233: error: invalid use of non-static data member ‘vg::HaplotypeIndexer::size_t’
 size_t HaplotypeIndexer::parse_vcf(const PathHandleGraph* graph, map<string, Path>& alt_paths, const vector<path_handle_t>& contigs, vcflib::VariantCallFile& variant_file, std::vector<std::string>& sample_names, const function<void(size_t, const gbwt::VariantPaths&, gbwt::PhasingInformation&)>& handle_contig_haplotype_batch) {
                                                                                                                                                                                                                                         ^
In file included from src/haplotype_indexer.cpp:13:0:
src/haplotype_indexer.hpp:79:54: note: declared here
     pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
                                                      ^
src/haplotype_indexer.cpp:27:293: error: expression list treated as compound expression in functional cast [-fpermissive]
 size_t HaplotypeIndexer::parse_vcf(const PathHandleGraph* graph, map<string, Path>& alt_paths, const vector<path_handle_t>& contigs, vcflib::VariantCallFile& variant_file, std::vector<std::string>& sample_names, const function<void(size_t, const gbwt::VariantPaths&, gbwt::PhasingInformation&)>& handle_contig_haplotype_batch) {

In file included from src/haplotype_indexer.cpp:13:0:
src/haplotype_indexer.hpp:79:54: note: declared here
     pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
                                                      ^
src/haplotype_indexer.cpp:27:293: error: expression list treated as compound expression in functional cast [-fpermissive]
 size_t HaplotypeIndexer::parse_vcf(const PathHandleGraph* graph, map<string, Path>& alt_paths, const vector<path_handle_t>& contigs, vcflib::VariantCallFile& variant_file, std::vector<std::string>& sample_names, const function<void(size_t, const gbwt::VariantPaths&, gbwt::PhasingInformation&)>& handle_contig_haplotype_batch) {
                                                                                                                                                                                                                                                                                                     ^
src/haplotype_indexer.cpp:27:294: error: template argument 1 is invalid
 size_t HaplotypeIndexer::parse_vcf(const PathHandleGraph* graph, map<string, Path>& alt_paths, const vector<path_handle_t>& contigs, vcflib::VariantCallFile& variant_file, std::vector<std::string>& sample_names, const function<void(size_t, const gbwt::VariantPaths&, gbwt::PhasingInformation&)>& handle_contig_haplotype_batch) {
                                                                                                                                                                                                                                                                                                      ^
src/haplotype_indexer.cpp:27:233: error: invalid use of non-static data member ‘vg::HaplotypeIndexer::size_t’
 size_t HaplotypeIndexer::parse_vcf(const PathHandleGraph* graph, map<string, Path>& alt_paths, const vector<path_handle_t>& contigs, vcflib::VariantCallFile& variant_file, std::vector<std::string>& sample_names, const function<void(size_t, const gbwt::VariantPaths&, gbwt::PhasingInformation&)>& handle_contig_haplotype_batch) {
                                                                                                                                                                                                                                         ^
In file included from src/haplotype_indexer.cpp:13:0:
src/haplotype_indexer.hpp:79:54: note: declared here
     pair<size_t, size_t> sample_range = pair<size_t, size_t>(0, numeric_limits<size_t>::max());
                                                      ^
src/haplotype_indexer.cpp:27:293: error: expression list treated as compound expression in functional cast [-fpermissive]
 size_t HaplotypeIndexer::parse_vcf(const PathHandleGraph* graph, map<string, Path>& alt_paths, const vector<path_handle_t>& contigs, vcflib::VariantCallFile& variant_file, std::vector<std::string>& sample_names, const function<void(size_t, const gbwt::VariantPaths&, gbwt::PhasingInformation&)>& handle_contig_haplotype_batch) {
                                                                                                                                                                                                                                                                                                     ^
src/haplotype_indexer.cpp:27:294: error: template argument 1 is invalid
 size_t HaplotypeIndexer::parse_vcf(const PathHandleGraph* graph, map<string, Path>& alt_paths, const vector<path_handle_t>& contigs, vcflib::VariantCallFile& variant_file, std::vector<std::string>& sample_names, const function<void(size_t, const gbwt::VariantPaths&, gbwt::PhasingInformation&)>& handle_contig_haplotype_batch) {

src/haplotype_indexer.cpp:27:294: error: template argument 1 is invalid
 size_t HaplotypeIndexer::parse_vcf(const PathHandleGraph* graph, map<string, Path>& alt_paths, const vector<path_handle_t>& contigs, vcflib::VariantCallFile& variant_file, std::vector<std::string>& sample_names, const function<void(size_t, const gbwt::VariantPaths&, gbwt::PhasingInformation&)>& handle_contig_haplotype_batch) {
                                                                                                                                                                                                                                                                                                      ^
src/haplotype_indexer.cpp:27:219: error: invalid use of template-name ‘std::function’ without an argument list
 size_t HaplotypeIndexer::parse_vcf(const PathHandleGraph* graph, map<string, Path>& alt_paths, const vector<path_handle_t>& contigs, vcflib::VariantCallFile& variant_file, std::vector<std::string>& sample_names, const function<void(size_t, const gbwt::VariantPaths&, gbwt::PhasingInformation&)>& handle_contig_haplotype_batch) {
                                                                   ^
src/haplotype_indexer.cpp:513:6: error: no matching function for call to ‘vg::HaplotypeIndexer::generate_threads(const PathHandleGraph*&, std::map<std::__cxx11::basic_string<char>, vg::Path>&, bool&, const string&, const std::vector<std::__cxx11::basic_string<char> >&, const string&, vg::HaplotypeIndexer::build_gbwt(const PathHandleGraph*, std::map<std::__cxx11::basic_string<char>, vg::Path>&, bool, const string&, const std::vector<std::__cxx11::basic_string<char> >&, const string&)::<lambda(int)>, vg::HaplotypeIndexer::build_gbwt(const PathHandleGraph*, std::map<std::__cxx11::basic_string<char>, vg::Path>&, bool, const string&, const std::vector<std::__cxx11::basic_string<char> >&, const string&)::<lambda(const vector_type&, const size_type (&)[4])>)’
     });
      ^
In file included from src/haplotype_indexer.cpp:13:0:
src/haplotype_indexer.hpp:159:51: note: candidate: int vg::HaplotypeIndexer::generate_threads(const PathHandleGraph*, std::map<std::__cxx11::basic_string<char>, vg::Path>&, bool, const string&, const std::vector<std::__cxx11::basic_string<char> >&, const string&, const int&, const std::function<void(const std::vector<unsigned int>&, const long unsigned int (&)[4])>&)
     tuple<vector<string>, size_t, vector<string>> generate_threads(const PathHandleGraph* graph, map<string, Path>& alt_paths,
                                                   ^
src/haplotype_indexer.hpp:159:51: note:   no known conversion for argument 7 from ‘vg::HaplotypeIndexer::build_gbwt(const PathHandleGraph*, std::map<std::__cxx11::basic_string<char>, vg::Path>&, bool, const string&, const std::vector<std::__cxx11::basic_string<char> >&, const string&)::<lambda(int)>’ to ‘const int&’
Makefile:702: recipe for target 'obj/haplotype_indexer.o' failed
make: *** [obj/haplotype_indexer.o] Error 1

[JC]

I guess you are trying to install the VG program, for that I recommend to use bioconda.

Answer 1

[congruisun]

Wow, yes, conda is the best! thanks for your reply. It very helps for me.