Installing Joinx on Linux-x86_64

Question

[njbernstein]

So, I'm trying to install joinx from https://github.com/genome/joinx

I can't use git cause its not installed on the server and I don't have sudo privileges. So downloaded the zip to the server and unzipped. Then created a new directory and entered it, and then ran:

​cmake /labshare/Nick/tools/joinx-master/

Then I got this error:

CMake Error at build-common/cmake/VersionHelper.cmake:9 (list):
  list GET given empty list
Call Stack (most recent call first):
  CMakeLists.txt:18 (include)
CMake Error at build-common/cmake/VersionHelper.cmake:10 (list):
  list GET given empty list
Call Stack (most recent call first):
  CMakeLists.txt:18 (include)
CMake Error at build-common/cmake/VersionHelper.cmake:11 (list):
  list GET given empty list
Call Stack (most recent call first):
  CMakeLists.txt:18 (include)
CMake Error at build-common/cmake/VersionHelper.cmake:14 (if):
  if given arguments:
    "STREQUAL" "-unstable"
  Unknown arguments specified
Call Stack (most recent call first):
  CMakeLists.txt:18 (include)
-- Configuring incomplete, errors occurred!

Any help would be greatly appreciate. Any ideas?

[Michael]

I just did exactly what you describe with success. What's your cmake version, mine is cmake version 2.8.12.2. Please give the full output, mine below.

---

 cmake `pwd`
-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- No CMAKE_INSTALL_PREFIX specified, defaulting to /usr
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
No CMAKE_BUILD_TYPE specified, defaulting to release
-- Install path: /usr
-- Share path: share/joinx-unstable
-- Doc path: share/doc/joinx-unstable
-- Performing Test CXX11_FLAG0
-- Performing Test CXX11_FLAG0 - Failed
-- Performing Test CXX11_FLAG1
-- Performing Test CXX11_FLAG1 - Success
-- C++11 support enabled via -std=c++0x
-- Performing Test CXX11_STDLIB_FLAG0
-- Performing Test CXX11_STDLIB_FLAG0 - Success
-- Sufficient C++11 library support found with flag ' '
-- Performing Test _CAN_SORT_UNIQUE_PTR
-- Performing Test _CAN_SORT_UNIQUE_PTR - Failed
-- Performing Test _HAS_MAKE_UNIQUE
-- Performing Test _HAS_MAKE_UNIQUE - Failed
-- Looking for clock_gettime
-- Looking for clock_gettime - found
-- * clock_gettime found in library rt
-- Looking for C++ include cstdint
-- Looking for C++ include cstdint - found
-- Looking for C++ include stdint.h
-- Looking for C++ include stdint.h - found
-- Looking for C++ include tr1/tuple
-- Looking for C++ include tr1/tuple - found
-- Boost build log will be written to /export/home/michaeld/compile/joinx-master/vendor/boost/boost-src/build.log
-- Boost include directory: /export/home/michaeld/compile/joinx-master/vendor/boost/boost/include
-- Boost libraries: /export/home/michaeld/compile/joinx-master/vendor/boost/boost/lib/libboost_program_options.a;/export/home/michaeld/compile/joinx-master/vendor/boost/boost/lib/libboost_filesystem.a;/export/home/michaeld/compile/joinx-master/vendor/boost/boost/lib/libboost_system.a;/export/home/michaeld/compile/joinx-master/vendor/boost/boost/lib/libboost_iostreams.a;/export/home/michaeld/compile/joinx-master/vendor/boost/boost/lib/libboost_regex.a
-- CXX flags:  -Wall -pedantic -fPIC  -Wnon-virtual-dtor -std=c++0x  
-- Compile definitions: CXX11_CANT_SORT_UNIQUE_PTR;CXX14_NO_MAKE_UNIQUE;BOOST_CHRONO_HEADER_ONLY
-- INCLUDE DIRS:
-- Configuring done
-- Generating done
-- Build files have been written to: /export/home/michaeld/compile/joinx-master

Answer 1

[SES]

Try to grab the latest release and see what happens:

wget https://github.com/genome/joinx/archive/v1.12.0.tar.gz
tar xzf v1.12.0.tar.gz
cd joinx-1.12.0
cmake .
make

I was able to compile it but I had to update some packages.

[njbernstein]

Hello @SES,

This worked perfectly. Any chance you could explain to me what was going on, so I can troubleshoot it myself in the future?

Best

Answer 2

[Ram]

You don't need root privileges to install git. The make command can be given a prefix to install on a custom directory. The current version from https://github.com/git/git/archive/v2.6.1.tar.gz installs to ~/bin/ by default anyway.

"Installation" in Linux is just pointing the shell to the executable file - once you understand that, you can "install" anything anyway you want :)

[SES]

This is a good point but I think the compile errors may be Boost-related (at least for me updating boost-devel solved it). Boost and cmake issues are much harder to solve without admin privileges, which is why I didn't answer because I don't have a solution.

[Ram]

That's nice forethought! IMO, even if that's the case, crossing off git should help us hit the root cause with a bit more certainty, no?

[SES]

I honestly think it is a Cmake or Boost issue. That combo is a major obstacle without admin privileges. Installing git will only make your life easier though :)

Answer 3

[ernfrid]

Your lack of git is likely to be the issue. The versioning code all depends on utilizing git to grab tags from the repository. You should follow Ram's instructions and see if that fixes your problem.

[SES]

I compiled it without git, so I think there is more to it. It could be that OP didn't grab a release and is trying to compile from master or something? That may be the issue.