cling error missing libraries

[sidebo]

After what appears to be a successful install (sudo conda install root) on an slc6 machine, I cannot run root. I get the following:

[psidebo@gluino ~]$ root
ERROR in cling::CIFactory::createCI(): cannot extract standard library include paths!
Invoking:
    echo | LC_ALL=C c++  -pipe -m64 -Wall -W -Woverloaded-virtual -fsigned-char -fPIC -pthread -std=c++11 -Wno-deprecated-declarations -Wno-comment -Wno-unused-parameter -Wno-maybe-uninitialized -Wno-unused-but-set-variable -Wno-missing-field-initializers -fPIC -fvisibility-inlines-hidden -std=c++11 -ffunction-sections -fdata-sections -fno-common -Woverloaded-virtual -Wcast-qual -fno-strict-aliasing -pedantic -Wno-long-long -Wall -W -Wno-unused-parameter -Wwrite-strings -Wno-unused-local-typedefs -O2 -DNDEBUG -xc++ -E -v - 2>&1 >/dev/null | awk '/^#include </,/^End of search/{if (!/^#include </ && !/^End of search/){ print }}' | grep -E "(c|g)\+\+"
results in
with exit code 256
input_line_1:1:10: fatal error: 'new' file not found
#include <new>
         ^
input_line_3:38:10: fatal error: 'string' file not found
#include <string>
         ^
input_line_8:1:10: fatal error: 'iostream' file not found
#include <iostream>
         ^

Any help would be appreciated.

[egpbos]

Usually, conda is run as a regular user, i.e. without sudo. Is there any specific reason why you install using sudo?

Installing in the default conda environment is also problematic. Could you try installing in a new environment? For instance, install + activate environment + run like this:

conda create -n root root -c nlesc
source activate root
root

[egpbos]

The NLeSC ROOT Conda package is no longer maintained and does not work properly with current Conda, modern Python, or modern ROOT. Use conda-forge ROOT instead:

Installing in a new environment:

conda create -n myrootenv python=3.7 root -c conda-forge
conda activate myrootenv
conda config --env --add channels conda-forge

From then on, use conda activate myrootenv to get in and conda deactivate to get out of the env. You should have a recent version of conda.

or

Installing in the current environment:

conda config --env --add channels conda-forge 
conda install root

Unlike the NLeSC package, this can even be the base environment if you really want to do that (it is not ideal, since it will be rather invasive, adding things like conda's compiler packages that are needed to compile with ROOT and Conda).

Conda-forge ROOT provides ROOT 6.16.00+, and supports Python 3.7, 3.6, and 2.7 on macOS and Linux. It is being tested by the ROOT team, and is automatically build by the conda-forge infrastructure. All default features and a huge number of optional features are turned on, and you can use it anywhere you would use ROOT, JupyROOT, or PyROOT.