install error

[jeongmeani]

Hi,

i have installed rmats but some issues occur.

when i run cmd ./build_rmats --conda, it is done with last line

** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

• DONE (PAIRADISE)
  Loading required package: PAIRADISE

and i run python rmats.py
it prints this message
ImportError: /data/tools/rMATS_install/rmats-turbo/rmatspipeline.cpython-37m-x86_64-linux-gnu.so: undefined symbol: _ZNK8BamTools12BamAlignment10GetTagTypeERKSsRc

what can i do?

Best Regards

Jeongmin

[EricKutschera]

That error is similar to what was reported in this issue: #21

The problem in that case was that different compilers were being used for building bamtools and then building rmatspipeline. The fix was to change CC and CXX here: https://github.com/Xinglab/rmats-turbo/blob/master/rMATS_pipeline/setup.py#L11

Removing those lines may work or you could set them to match what is printed out during the bamtools part of the build for C and CXX compiler