bedtools-2.24.0 make command

[ara...@bu.edu]

Hi,

I'm getting the following error when I try to run make to install bedtools-2.24.0.  I'm running 32-bit Ubuntu computer and I'm used to easily installing BEDTools.  I'm not sure why I'm getting the following:

Building BEDTools:
=========================================================
DETECTED_VERSION = v2.24.0
CURRENT_VERSION  =
Updating version file.
 * Creating BamTools API
- Building in src/utils/bedFile
  * compiling bedFile.cpp
- Building in src/utils/BinTree
  * compiling BinTree.cpp
In file included from BinTree.h:16:0,
                 from BinTree.cpp:1:
../../utils//general/QuickString.h:41:15: error: ‘QuickString& QuickString::operator=(size_t)’ cannot be overloaded
  QuickString &operator = (size_t);
               ^
../../utils//general/QuickString.h:40:15: error: with ‘QuickString& QuickString::operator=(uint32_t)’
  QuickString &operator = (uint32_t);
               ^
../../utils//general/QuickString.h:50:15: error: ‘QuickString& QuickString::operator+=(size_t)’ cannot be overloaded
  QuickString &operator += (size_t);
               ^
../../utils//general/QuickString.h:49:15: error: with ‘QuickString& QuickString::operator+=(uint32_t)’
  QuickString &operator += (uint32_t);
               ^
../../utils//general/QuickString.h:76:7: error: ‘void QuickString::append(size_t)’ cannot be overloaded
  void append(size_t num);
       ^
../../utils//general/QuickString.h:75:7: error: with ‘void QuickString::append(uint32_t)’
  void append(uint32_t num);
       ^
make[1]: *** [../../../obj//BinTree.o] Error 1
make: *** [src/utils/BinTree] Error 2


I downloaded the bedtools-2.24.0.tar.gz from:
https://github.com/arq5x/bedtools2/releases/tag/v2.24.0

Has anyone dealt with this issue?
Andy

[Aaron Quinlan]

Hi Andy,

This issue was addressed in the Github repository (https://github.com/arq5x/bedtools2/issues/271), but I have not yet cut a formal release with these changes (shooting for this week).  If you compile a fresh clone from github, you should be in business.

Aaron

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[ara...@bu.edu]

Hi Aaron,

Thanks for letting me know. I was able to successfully install bedtools-2.24.0 using the following instructions if anyone is interested:

https://www.digitalocean.com/community/tutorials/how-to-install-git-on-ubuntu-14-04

#Need to install git:
sudo apt-get update
sudo apt-get install git
#Here's the BEDTools GitHub page:
#https://github.com/arq5x/bedtools2
#Get the address of the ZIP:
#https://github.com/arq5x/bedtools2/archive/master.zip
#Use the following to download the file:
wget https://github.com/arq5x/bedtools2/archive/master.zip -O BEDTools_fresh_clone.zip
#Right-click to unzip
make
#Looks like it works:
/bedtools --version
#bedtools v2.24.0

I'm fine with using this fresh clone until the formal release is available.  Thanks for your help.

Andy