Installation Fails During Make

[Former user]

Hi, I am trying to install clever-toolkit 2.1, and during make I had this error:

Building CXX object src/CMakeFiles/CleverLib.dir/DefaultGapCostDistributions.cpp.o
In file included from /usr/local/lib/SV_tools/dependencies_tools/tools/clever-toolkit-v2.1/src/IndelLengthDistribution.h:26:0,
                 from /usr/local/lib/SV_tools/dependencies_tools/tools/clever-toolkit-v2.1/src/DefaultGapCostDistributions.h:23,
                 from /usr/local/lib/SV_tools/dependencies_tools/tools/clever-toolkit-v2.1/src/DefaultGapCostDistributions.cpp:21:
/usr/local/lib/SV_tools/dependencies_tools/tools/clever-toolkit-v2.1/src/HistogramBasedDistribution.h:51:7: error: ‘auto_ptr’ in namespace ‘std’ does not name a template type
  std::auto_ptr<std::vector<double> > toDistribution(double tailCu
       ^
In file included from /usr/local/lib/SV_tools/dependencies_tools/tools/clever-toolkit-v2.1/src/DefaultGapCostDistributions.cpp:21:0:
/usr/local/lib/SV_tools/dependencies_tools/tools/clever-toolkit-v2.1/src/DefaultGapCostDistributions.h:27:14: error: ‘auto_ptr’ in namespace ‘std’ does not name a template type
  static std::auto_ptr<IndelLengthDistribution> insertionCosts();
              ^
/usr/local/lib/SV_tools/dependencies_tools/tools/clever-toolkit-v2.1/src/DefaultGapCostDistributions.h:28:14: error: ‘auto_ptr’ in namespace ‘std’ does not name a template type
  static std::auto_ptr<IndelLengthDistribution> deletionCosts();
              ^
/usr/local/lib/SV_tools/dependencies_tools/tools/clever-toolkit-v2.1/src/DefaultGapCostDistributions.cpp:25:1: error: ‘auto_ptr’ does not name a type
 auto_ptr<IndelLengthDistribution> DefaultGapCostDistributions::in
 ^
/usr/local/lib/SV_tools/dependencies_tools/tools/clever-toolkit-v2.1/src/DefaultGapCostDistributions.cpp:32:1: error: ‘auto_ptr’ does not name a type
 auto_ptr<IndelLengthDistribution> DefaultGapCostDistributions::de
 ^
src/CMakeFiles/CleverLib.dir/build.make:182: recipe for target 'src/CMakeFiles/CleverLib.dir/DefaultGapCostDistributions.cpp.o' failed
make[2]: *** [src/CMakeFiles/CleverLib.dir/DefaultGapCostDistributions.cpp.o] Error 1
CMakeFiles/Makefile2:530: recipe for target 'src/CMakeFiles/CleverLib.dir/all' failed
make[1]: *** [src/CMakeFiles/CleverLib.dir/all] Error 2
Makefile:138: recipe for target 'all' failed
make: *** [all] Error 2

I have Ubuntu version 16.04, cmake 3.5.1, and installed zlib, and boost using apt-get.

Thanks in advanced for your help.

[Tobias Marschall]

Could you please try version 2.2.1? Your error seems to be related to the use of auto_ptr, which we have removed in 2.2.1. Which version of gcc are you using?

Alternatively, you could install clever via bioconda, which usually is extremely easy, i.e. just do

conda install clever-toolkit