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!