matthew-ackerman
commented
5 years ago It is giving an error that gsl_cdf_chisq_P can't be linked, which means that the linker can't find the gsl libraries. I assume these were found during configuration, (that is ./config set HAVE_GSL=yes in the make file) and the linker flags necessary to find gsl weren't passed to the compiler by the Makefile. Try adding the line "LDFLAGS=@LDFLAGS@" to Makefile.in and re-running ./configure. I think that should work, so I pushed the change to git hub.
-Matt
On Mon, Feb 4, 2019 at 9:15 PM Tejas Sevak notifications@github.com wrote:
I m trying to install under ubuntu:bionic docker container and getting below error.
g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/read_pheno.o commands/read_pheno.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/fastview.o commands/fastview.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/relatedness.o commands/relatedness.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/test_keys.o commands/test_keys.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/reml.o commands/reml.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/read_bed.o commands/read_bed.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/relatedness_test.o commands/relatedness_test.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/binomial.o math_functions/binomial.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/individual_likelihood.o individual_likelihood.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/lnmultinomial.o math_functions/lnmultinomial.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/newton-method-theta.o newton-method-theta.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/newton-method-ld.o newton-method-ld.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/map_file.o io/map_file.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/models.o math_functions/models.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/pooled_likelihood.o pooled_likelihood.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/tmp_buffer.o stream_tools/tmp_buffer.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/stream_tools.o stream_tools/stream_tools.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/genotype.o raw/genotype.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/quartet.o raw/quartet.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/genotype_pair.o raw/genotype_pair.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/region.o raw/region.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/constants.o raw/constants.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/base.o raw/base.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/data.o data_types/data.cc data_types/data.cc: In destructor 'Registry_initalizer::~Registry_initalizer()': data_types/data.cc:37:31: warning: attempt to free a non-heap object 'm_data_ctor' [-Wfree-nonheap-object] if(nifty_counter-- == 0) free(&m_data_ctor);
g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/allele.o data_types/allele.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/file_index.o data_types/file_index.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/linkage_data.o data_types/linkage_data.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/pooled_data.o data_types/pooled_data.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/population.o data_types/population.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/sample_gof.o data_types/sample_gof.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/phenotype.o data_types/phenotype.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/plink_pheno.o data_conversion/plink_pheno.cc data_conversion/plink_pheno.cc: In member function 'void Plink_file::read(Plink_data&)': data_conversion/plink_pheno.cc:27:168: warning: format '%d' expects argument of type 'int', but argument 5 has type 'size_t {aka long unsigned int}' [-Wformat=] fprintf(stderr, gettext("mapgd:%s:%d: attempt to read from file failed. Expected %d columns, got %d.\n"), __FILE__, __LINE__, plink.trait_size()+2, fields.size()+2 ); ~~~~~~~~~~~~~~~~~~~~ ^ data_conversion/plink_pheno.cc:27:168: warning: format '%d' expects argument of type 'int', but argument 6 has type 'std::vector<std::__cxx11::basic_string<char> >::size_type {aka long unsigned int}' [-Wformat=] data_conversion/plink_pheno.cc:30:165: warning: format '%d' expects argument of type 'int', but argument 5 has type 'size_t {aka long unsigned int}' [-Wformat=] fprintf(stderr, gettext("mapgd:%s:%d: attempt to read from file failed. Expected %d columns, got %d.\n"), __FILE__, __LINE__, plink.trait_size()+2, fields.size() ); ~~~~~~~~~~~~~~~~~~~~ ^ data_conversion/plink_pheno.cc:30:165: warning: format '%d' expects argument of type 'int', but argument 6 has type 'std::vector<std::__cxx11::basic_string<char> >::size_type {aka long unsigned int}' [-Wformat=] g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/relatedness_data.o data_types/relatedness_data.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/bcf2pro_file.o data_conversion/bcf2pro_file.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/bed_file.o data_conversion/bed_file.cc data_conversion/bed_file.cc: In member function 'void Bed_file::open(const char*, const openmode&)': data_conversion/bed_file.cc:157:99: warning: too many arguments for format [-Wformat-extra-args] fprintf(stderr, gettext("mapgd:%s:%d: Magick bits not set.\n"), __FILE__, __LINE__, file_name ); ^ g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/locus.o data_types/locus.cc data_types/locus.cc: In constructor 'Locus::Locus(const count_t&)': data_types/locus.cc:30:40: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t {aka long unsigned int}' [-Wformat=] snprintf(buffer, 20, "Sample_%d", x+1); ~~~^ g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/key.o data_types/key.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/sample_name.o data_types/sample_name.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -c -o objs/system.o system/system.cc g++ -g -O2 -DVERSION=\"0.4.38\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -DNOSQL -fopenmp -DNOGSL -DNOHTS -DNOLZ4 -DNOMPI mapgd.o objs/allele_cmd.o objs/estimate_pooled.o objs/mapgd_help.o objs/sam2idx.o objs/proview.o objs/interface.o objs/map2genotype.o objs/linkage_disequilibrium.o objs/filter.o objs/filter_genotype.o objs/filter_pool.o objs/read_pheno.o objs/fastview.o objs/relatedness.o objs/test_keys.o objs/reml.o objs/read_bed.o objs/relatedness_test.o objs/binomial.o objs/individual_likelihood.o objs/lnmultinomial.o objs/newton-method-theta.o objs/newton-method-ld.o objs/map_file.o objs/models.o objs/pooled_likelihood.o objs/tmp_buffer.o objs/stream_tools.o objs/genotype.o objs/quartet.o objs/genotype_pair.o objs/region.o objs/constants.o objs/base.o objs/data.o objs/allele.o objs/file_index.o objs/linkage_data.o objs/pooled_data.o objs/population.o objs/sample_gof.o objs/phenotype.o objs/plink_pheno.o objs/relatedness_data.o objs/bcf2pro_file.o objs/bed_file.o objs/locus.o objs/key.o objs/sample_name.o objs/system.o -o ../../bin/mapgd -lgzstream -lz -L ./gzstream/ -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi objs/individual_likelihood.o: In function `get_bias(Locus const&, Allele&, unsigned short const&)': /root/MAPGD/src/mapgd_0.4/individual_likelihood.cc:636: undefined reference to `gsl_cdf_chisq_P' collect2: error: ld returned 1 exit status Makefile:245: recipe for target 'mapgd' failed make[2]: *** [mapgd] Error 1 make[2]: Leaving directory '/root/MAPGD/src/mapgd_0.4' Makefile:10: recipe for target 'mapgd_0.4' failed make[1]: *** [mapgd_0.4] Error 2 make[1]: Leaving directory '/root/MAPGD/src' Makefile:61: recipe for target 'src' failed make: *** [src] Error 2 root@b94f0a06a0c4:~/MAPGD# — You are receiving this because you are subscribed to this thread. 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tej4pnfr
I m trying to install under ubuntu:bionic docker container and getting below error.