repeatseq compilation issues
0
0
Entering edit mode
10 weeks ago
adarsh_pp ▴ 40

Hi,

I am trying to compile and install repeatseq tool from

https://github.com/adaptivegenome/repeatseq.git

I have followed same instructions mentioned in the installation file.

However when I am running the make command as the final step, I am always getting the following error.

sudo make
g++ -c -O3 -Ibamtools/src repeatseq.cpp 
In file included from bamtools/src/api/BamAux.h:19,
                 from bamtools/src/api/BamAlignment.h:18,
                 from bamtools/src/api/BamReader.h:14,
                 from repeatseq.h:18,
                 from repeatseq.cpp:27:
bamtools/src/api/api_global.h:13:10: fatal error: api/bamtools_api_export.h: No such file or directory
   13 | #include "api/bamtools_api_export.h"
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [makefile:13: repeatseq.o] Error 1

I have tried rebuildig bamtools by following instructions from https://github.com/pezmaster31/bamtools

However the issue is still there. I am running this in Ubuntu 22.04.4

cmake version 3.22.1

GNU Make 4.3

g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0

NGS Repeats repeatseq repeatexpansion Genomics • 341 views
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1
Entering edit mode

Hi, can you locate this file in your sourcetree: either with find or locate bamtools_api_export.h. Also, don't run make via sudo (your environment may be different and it's not safe), the only step you should run with sudo is make install, and only if you install globally. The INSTALL instructions don't mention sudo either.

Remove the src folder completely (with sudo if you have to), check out the code again and run make as a normal user.

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0
Entering edit mode

Hi

The file is located in the following directory

/bamtools/build/src/api/bamtools_api_export.h

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0
Entering edit mode

Ok, then try again without sudo, most likely this will fix it already.

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1
Entering edit mode

sudo make

using 'sudo' is usually a very bad idea

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