cc1plus: error: unrecognized command line option "-std=c++11"

[xuemin....@gmail.com]

Hi bedtools developers and fellow users,

I installed bedtools on a HPC platform, but getting error as attached when typing "make" into the command line. 

Here is the code to install bedtools

wget https://github.com/arq5x/bedtools2/releases/tag/v2.27.1/bedtools-2.27.1.tar.gz
$ tar -zxvf bedtools-2.27.1.tar.gz
$ cd bedtools2
$ make

So when I typed "bedtools" after setting-up as indicated in http://quinlanlab.org/tutorials/bedtools/bedtools.html, it indicated "-bash: bedtools: command not found".

gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) was installed in the HPC platform. 

Was this due the lower version of gcc used? How can I fix this error?

Many thanks,

Xuemin

[Aaron Quinlan]

The bedtools binary file that is created after “make” (stored in the “bin” subdirectory of the “bedtools” directory you created below) needs to be moved into a directory that is in your PATH.  Typically, one creates a “bin” directory in one’s home directory, copies the bedtools binary file to that bin directory, and then adds the "~/bin” directory to one’s PATH environment variable.  The PATH environment variable is what your shell uses to look for binaries that you type on the command line.

Further details and examples can be found here:

https://askubuntu.com/questions/402353/how-to-add-home-username-bin-to-path

https://unix.stackexchange.com/questions/26047/how-to-correctly-add-a-path-to-path

(slides -17): https://docs.google.com/presentation/d/1W7bwMLAqCIB9unbv4Kswc8P7cE5ATkMhHYJfwBa64L0/edit#slide=id.p

Aaron

--
You received this message because you are subscribed to the Google Groups "bedtools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to bedtools-discu...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[xuemin wang]

Hi Aaron,

thanks for your reply. 

The problem is there was an error (below) when I typed "make":

cc1plus: error: unrocognized command line option "-std=c++11"

make[1]: *** [../../../obj//FileRecordMgr.o] Error 1

make: *** [src/utils/FileRecordTools] Error 2

Do you have any idea how to fix this?

Regards,

xuemin

To unsubscribe from this group and stop receiving emails from it, send an email to bedtools-discuss+unsubscribe@googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

--

Xuemin Wang

PhD Candidate

Queensland Alliance for Agriculture and Food Innovation (QAAFI)

The University of Queensland

Hermitage Research Facility, 604 Yangan Rd

Warwick, QLD 4370

Australia

Mobile (+61) 423 097 394

Email xuemin....@gmail.com

[xuemin wang]

The issue has been solved after upgrading gcc. Thanks Aaron.

Regards,

Xuemin