Failed compiling cview

[MinS1]

Compiling stdin2beta... SUCCESS Compiling mask_pat... SUCCESS Compiling pat_sampler... SUCCESS Compiling patter... SUCCESS Compiling bp_patter... SUCCESS Compiling snp_patter... SUCCESS Compiling match_maker... SUCCESS Compiling segmentor... SUCCESS Compiling cview... FAIL Failed compilation. Command: g++ -std=c++11 -c -o src/cview/cview.o src/cview/cview.cpp && g++ -std=c++11 -c -o src/pipeline_wgbs/patter_utils.o src/pipeline_wgbs/patter_utils.cpp && g++ -std=c++11 -o src/cview/cview src/cview/cview.o src/pipeline_wgbs/patter_utils.o return code: 1 stderr:

stdout: src/cview/cview.cpp: In member function ‘void Cview::parse()’: src/cview/cview.cpp:178:78: error: cannot pass objects of non-trivially-copyable type ‘std::string {aka class std::basic_string}’ through ‘...’ if (verbose) fprintf(stderr, "finished %s reads\n", addCommas(line_i)); ^

Failed compiling cview Compiling homog... SUCCESS Compiling add_cpg_counts... SUCCESS Compiling add_loci... SUCCESS

[MinS1]

The problem has been solved. But init_genome doesn't seem to work

[AzlanNI]

Hey MinS1, Would u mind telling how u solved this? I am currently having the same problem with cview failed

[AndreiWCansor]

@MinS1 Same - having issues compiling cview.. please share how you get around with it please!

[AzlanNI]

@AndreiWCansor i change a little line in src/cview/cview.cpp line 178 from if (verbose) fprintf(stderr, "finished %s reads\n", addCommas(line_i)); to if (verbose) fprintf(stderr, "finished %s reads\n", addCommas(line_i).c_str()); After that all succeded but i still cant call wgbstools but maybe it helps u!

Edit:was able to call wgbstools after so it worked for me

[AndreiWCansor]

@AzlanNI Great it's sorted; all SUCCESS - but the same I cannot call wgbstools..

[AzlanNI]

@AndreiWCansor It is C++ compiled so i was working on Mac i had to use ./wgbstools in the directory $HOME/wbgs_tools then i added it to my Home $PATH and could use wgbstools from everywhere :) I hope that helps u out!