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I am trying to install pysam.
After excecuting:
python path/to/pysam-master/setup.py build
This error is produced:
unable to execute 'x86_64-conda_cos6-linux-gnu-gcc': No such file or directory
error: command 'x86_64-conda_cos6-linux-gnu-gcc' failed with exit status 1
There are similar threads, but they all seem to address the problem assumig administriator rights, which I do not have. Is there a way around to install the needed files?
DISCLAIMER: This question derived from a previous post of mine. manually installing pysam error: "ImportError: No module named version" But since it might require a different approach, I made it a question of its own.
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Error : error: command 'x86_64-linux-gnu-gcc' failed with exit status 1 Executing sudo apt-get install python-dev solved the error. After upgrade my computer with pip today, and check the other answers here, I can tell you that it could be ANYTHING. You should check error by error, looking for what's the specific library that you need.
Using the compiler packages The compiler packages can be installed with conda. Because they are designed with (pseudo) cross-compiling in mind, all of the executables in a compiler package are "prefixed." Instead of gcc, the executable name of the compiler you use will be something like x86_64-conda_cos6-linux-gnu-gcc.
It is used by gcc to build applications. You need to install a package called python-dev. This package includes header files, a static library and development tools for building Python modules, extending the Python interpreter or embedding Python in applications. This did not solve the problem for me: Reading state information...
Some users want to use the latest Anaconda packages but do not yet want to use the Anaconda compilers. To enable this, the latest Python package builds have a default _sysconfigdatafile. This file sets the compilers provided by the system, such as gccand g++, as the default compilers. This way allows legacy recipes to keep working.
You can also receive the same error while installing some R packages if R was installed using conda (as I had).
Then just install the package by executing: conda install gxx_linux-64 to have that command available.
Source: https://github.com/RcppCore/Rcpp/issues/770#issuecomment-346716808
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