installation: no match for ‘operator==’

[lurebgi]

Hi,

I had an issue of installing it: scaffoldgraph.cpp: In function ‘ContigSet GetContigSet(char, long int&)’: scaffoldgraph.cpp:307:12: error: no match for ‘operator==’ (operand types are ‘std::ifstream {aka std::basic_ifstream}’ and ‘long int’) if(icin==NULL){ ^ scaffoldgraph.cpp:307:12: note: candidate: operator==(int, long int) scaffoldgraph.cpp:307:12: note: no known conversion for argument 1 from ‘std::ifstream {aka std::basic_ifstream}’ to ‘int’ In file included from include/api/SamProgramChain.h:14:0, from include/api/SamHeader.h:14, from include/api/BamReader.h:16, from include/api/BamMultiReader.h:14, from scaffoldgraph.h:13, from scaffoldgraph.cpp:14:

Any clue of how to fix that?

Thanks!

[bioinfomaticsCSU]

Hi,

We test BOSS using gcc4.6.3 on Ubuntu. When using GCC6, this problem will happen. Now, we change the source code. Please download the newes BOSS. If you have any problem when using BOSS, please let us know.

Thanks!

[lurebgi]

g++ -c main.cpp -lm -ldl -I include/ -L lib/ -lbamtools -std=gnu++98 g++ -c scaffoldgraph.cpp -lm -ldl -I include/ -L lib/ -lbamtools -std=gnu++98 g++ -c scaffolding.cpp -lm -ldl -I include/ -L lib/ -lbamtools -std=gnu++98 g++ -o boss main.o scaffoldgraph.o scaffolding.o ./lp/liblpsolve55.a -lm -ldl -I include/ -L lib/ -lbamtools -std=gnu++98 /usr/bin/ld: cannot find -lbamtools collect2: error: ld returned 1 exit status makefile:7: recipe for target 'boss' failed make: *** [boss] Error 1

On Sat, May 27, 2017 at 2:08 AM, bioinfomaticsCSU notifications@github.com wrote:

Hi,

We test BOSS using gcc4.6.3 on Ubuntu. When using GCC6, this problem will happen. Now, we change the source code. Please download the newes BOSS. If you have any problem when using BOSS, please let us know.

Thanks!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/bioinfomaticsCSU/BOSS/issues/1#issuecomment-304412035, or mute the thread https://github.com/notifications/unsubscribe-auth/AE478RT1R_oOE9zYUuqatuC21ZrmXvGWks5r92mLgaJpZM4Nnui0 .

[bioinfomaticsCSU]

Hi,

Please download the newest BOSS. Add the path (the directory of BOSS) to the enviroment variable LD_LIBRARY_PATH. Then type "make all".

In addition, we upload the binary file "boss", you can use the command "boss" for running.

If you have any problem, please let us know.

Thanks

[lurebgi]

Thanks, the binary file works. One kind remind: one should create a soft link to libbamtools.so as libbamtools.so.2.3.0

[bioinfomaticsCSU]

Thanks!

[lurebgi]

Hello, it reported an error message "Open File Wrong!" when I used the binary file provided. Could you please check that? Thanks! Luohao

[lurebgi]

solved by linking to bamtools.so file of latest version under apps which allowed then to recompile it

[pawelosipowski]

Hi I have the same issue: "Open File Wrong!". How can I solve it step by step?

[lurebgi]

in scaffoldgraph.cpp, on the line 307 you can try changing 'if(icin){‘ into 'if(!icin){‘

by the way, I got an segmental fault, so in the end this tool did work out for me.

[bioinfomaticsCSU]

Hi, we update readme.md, please install BOSS again.