Can not install ROOT

Question

Can not install ROOT

Closed this issue 6 years ago · 16 comments

Hi all, I'm on a macbook pro with macOS Sierra 10.12.6.

In any environment I create, I'm not able to setup ROOT correctly.
conda install -c nlesc root yields:

-bash: /bin/thisroot.sh: No such file or directory
Activate: ROOT has been sourced. Environment settings are ready.
ROOTSYS=

And when I root -l

dyld: Symbol not found: __cg_png_create_info_struct
Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
Expected in: /Users/fai/miniconda2/envs/workpls/lib/libPng.dylib
in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO

I tried to install with conda create -n test-root python=2.7 root=6 it yields:

Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

root=6

Current channels:

https://conda.anaconda.org/nlesc/label/dev/osx-64

https://conda.anaconda.org/nlesc/label/dev/noarch

https://repo.continuum.io/pkgs/main/osx-64

https://repo.continuum.io/pkgs/main/noarch

https://repo.continuum.io/pkgs/free/osx-64

https://repo.continuum.io/pkgs/free/noarch

https://repo.continuum.io/pkgs/r/osx-64

https://repo.continuum.io/pkgs/r/noarch

https://repo.continuum.io/pkgs/pro/osx-64

https://repo.continuum.io/pkgs/pro/noarch

I'm obviously doing something wrong, but couldn't figure out what. Would appreciate some help, very much!
Thanks in advance.

Answer 1 · 2018-03-29T12:55:53.000Z

I cannot say anything about your first issue, but for the second one:

root is not found as it is not in the anaconda repositories. But in the NLeSC-anaconda repositories. With your first command, you explicitly specify to also search inside them (-c nlesc = also include nlesc channel).

So try the following:
conda create -n test-root -c nlesc python=2.7 root=6

and see if that works

Update: your issue may be related to #2

Answer 2 · 2018-05-09T11:17:04.000Z

@guzelgun did @mayou36 's suggestion fix your issue?

Answer 3 · 2018-05-09T11:33:20.000Z

Related to #9 as well. A fix was made, but new build needs to be created for it to be effective in the conda package.

Answer 4 · 2018-05-23T11:58:08.000Z

Hi all,

I have stumbled upon problem #1 (whether on its own or in a test env, the error is the same), and I have some insight from the Anaconda community:

The root package needs to be fixed so that it reflects is actual libpng dependency. Sadly, there is not really an easy way to do this for the existing package. You can extract files, edit info/index.json, and re-upload the package, but that's pretty messy. Better to fix the recipe and rebuild. Are you in contact with the people who run the NLeSC channel? They are who you need to talk to. They would benefit greatly from using the new run_exports feature in conda-build 3. More on that in the docs at https://conda.io/docs/user-guide/tasks/build-packages/define-metadata.html#export-runtime-requirements

Most of the low-level libraries such as libpng on the defaults channel have run_exports info already. If NLeSC uses those packages rather than build their own, they may only need to update to conda-build 3 and rebuild their recipe.

See full post here
I can help testing/repackaging (but I'm fairly new to the scene) - I would really like this to work!

Thanks,
Caterina

Answer 5 · 2018-05-24T08:17:16.000Z

Hi @urania277 we are in the process of migrating low-level library dependencies to conda package dependencies, which is what is suggested above if I understand correctly. I will figure out this week what the status of this process is and let you know.

Answer 6 · 2018-05-24T08:51:34.000Z

Hi @goord,
thanks a lot, I believe that's what is suggested above (ideally ROOT should be able to pick up the conda libpng rather than the system libpng). Let me know if I can help somehow / when I can test things out.
Caterina

Answer 7 · 2018-05-24T09:02:51.000Z

If I remember correctly, this was due to the way that ROOT was built since the Makefile doesn't find the correct libpng (starting with environmental variables), but rather had some hardcoded paths. @remenska and I had seen this a few times. My information might be out of date or wrong, but maybe a ROOT patch would help?

Answer 8 · 2018-05-24T11:49:40.000Z

My information might be out of date or wrong, but maybe a ROOT patch would help?

I'm not sure this is looking too promising: https://sft.its.cern.ch/jira/browse/ROOT-9145

Meanwhile I'm following up on why the native ROOTBooks are not exporting the right paths (maybe for my case, maybe for MacOS):

https://root-forum.cern.ch/t/rootbook-and-python-kernel-on-mac-osx/29108/6

that thread also suggests a conda-less workaround (still, conda would be great if one doesn't have root access and wants to keep the environment clean, as e.g. when giving hands-on tutorials).

Answer 9 · 2018-10-16T22:10:18.000Z

Are there any developments regarding this issue?

Answer 10 · 2019-01-31T14:40:13.000Z

Thanks to the HEP Software Foundation's packaging group it seems there is a solution at least for Linux - see those slides: https://indico.cern.ch/event/790021/contributions/3301108/attachments/1787718/2911364/2019-01-30_HSF-Packaging-Conda.pdf

Haven't tried this myself but I will in a couple of weeks or so, I'll post results here :)

Answer 11 · 2019-01-31T14:55:30.000Z

Yep, those packages work now. conda install root -c conda-forge should do the trick.

Answer 12 · 2019-02-13T18:55:43.000Z

They should work on macOS too now. https://iscinumpy.gitlab.io/post/root-conda/

Answer 13 · 2019-03-08T14:31:37.000Z

Please do not use NLeSC root. It is no longer maintained and does not work properly with current conda. Use conda-forge root instead:

conda create -n myrootenv python=2 root -c conda-forge
conda activate myrootenv

or

conda config --add channels conda-forge 
conda create -n myrootenv python=2 root
conda activate myrootenv

or install in your base environment if you really want to do that (it is not ideal, but supported).

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.

Answer 14 · 2019-03-09T09:07:02.000Z

Alright thank you @henryiii
I deleted my comment from yesterday.

But there is one problem I do not manage to solve using conda-forge instead of nlesc.
When I do source activate myrootenv and then type root I get the following error message while ROOT opens :

Warning in <TClassTable::Add>: class timespec already in TClassTable
Warning in <TClassTable::Add>: class __gnu_cxx::__normal_iterator<char*,string> already in TClassTable
Warning in <TClassTable::Add>: class __gnu_cxx::__normal_iterator<const char*,string> already in TClassTable
Warning in <TClassTable::Add>: class __gnu_cxx::__normal_iterator<TString*,vector<TString> > already in TClassTable
Warning in <TClassTable::Add>: class __gnu_cxx::__normal_iterator<const TString*,vector<TString> > already in TClassTable
Warning in <TClassTable::Add>: class __gnu_cxx::__normal_iterator<string*,vector<string> > already in TClassTable
Warning in <TClassTable::Add>: class __gnu_cxx::__normal_iterator<const string*,vector<string> > already in TClassTable
Warning in <TClassTable::Add>: class __gnu_cxx::__normal_iterator<int*,vector<int> > already in TClassTable
Warning in <TClassTable::Add>: class __gnu_cxx::__normal_iterator<const int*,vector<int> > already in TClassTable
Warning in <TClassTable::Add>: class reverse_iterator<__gnu_cxx::__normal_iterator<TString*,vector<TString> > > already in TClassTable
Warning in <TClassTable::Add>: class reverse_iterator<__gnu_cxx::__normal_iterator<string*,vector<string> > > already in TClassTable
Warning in <TClassTable::Add>: class reverse_iterator<__gnu_cxx::__normal_iterator<int*,vector<int> > > already in TClassTable
Warning in <TClassTable::Add>: class TVirtualIsAProxy already in TClassTable
Warning in <TClassTable::Add>: class TIsAProxy already in TClassTable
Warning in <TClassTable::Add>: class TStorage already in TClassTable
Warning in <TClassTable::Add>: class TObject already in TClassTable
Warning in <TClassTable::Add>: class TUUID already in TClassTable
Warning in <TClassTable::Add>: class SetWindowAttributes_t already in TClassTable
Warning in <TClassTable::Add>: class WindowAttributes_t already in TClassTable
Warning in <TClassTable::Add>: class Event_t already in TClassTable
Warning in <TClassTable::Add>: class GCValues_t already in TClassTable
Warning in <TClassTable::Add>: class ColorStruct_t already in TClassTable
Warning in <TClassTable::Add>: class PictureAttributes_t already in TClassTable
Warning in <TClassTable::Add>: class Segment_t already in TClassTable
Warning in <TClassTable::Add>: class Point_t already in TClassTable
Warning in <TClassTable::Add>: class Rectangle_t already in TClassTable
Warning in <TClassTable::Add>: class TAttBBox2D already in TClassTable
Warning in <TClassTable::Add>: class TSubString already in TClassTable
Warning in <TClassTable::Add>: class TString already in TClassTable
Warning in <TClassTable::Add>: class TNamed already in TClassTable
Warning in <TClassTable::Add>: class TBrowserImp already in TClassTable
Warning in <TClassTable::Add>: class TBrowser already in TClassTable
Warning in <TClassTable::Add>: class TContextMenuImp already in TClassTable
Warning in <TClassTable::Add>: class TIterator already in TClassTable
Warning in <TClassTable::Add>: class TVirtualMutex already in TClassTable
Warning in <TClassTable::Add>: class TLockGuard already in TClassTable
Warning in <TClassTable::Add>: class ROOT::TVirtualRWMutex already in TClassTable
Warning in <TClassTable::Add>: class ROOT::TReadLockGuard already in TClassTable
Warning in <TClassTable::Add>: class ROOT::TWriteLockGuard already in TClassTable
Warning in <TClassTable::Add>: class TCollection already in TClassTable
Warning in <TClassTable::Add>: class TIter already in TClassTable
Warning in <TClassTable::Add>: class TSeqCollection already in TClassTable
Warning in <TClassTable::Add>: class TObjArray already in TClassTable
Warning in <TClassTable::Add>: class TObjArrayIter already in TClassTable
Warning in <TClassTable::Add>: class TProcessID already in TClassTable
Warning in <TClassTable::Add>: class TPoint already in TClassTable
Warning in <TClassTable::Add>: class TInetAddress already in TClassTable
Warning in <TClassTable::Add>: class TVirtualTableInterface already in TClassTable
Warning in <TClassTable::Add>: class TList already in TClassTable
Warning in <TClassTable::Add>: class TListIter already in TClassTable
Warning in <TClassTable::Add>: class TDictionary already in TClassTable
Warning in <TClassTable::Add>: class TInterpreter already in TClassTable
Warning in <TClassTable::Add>: class TQObject already in TClassTable
Warning in <TClassTable::Add>: class TQObjSender already in TClassTable
Warning in <TClassTable::Add>: class TSysEvtHandler already in TClassTable
Warning in <TClassTable::Add>: class TFileHandler already in TClassTable
Warning in <TClassTable::Add>: class TSignalHandler already in TClassTable
Warning in <TClassTable::Add>: class TStdExceptionHandler already in TClassTable
Warning in <TClassTable::Add>: class TTime already in TClassTable
Warning in <TClassTable::Add>: class TTimer already in TClassTable
Warning in <TClassTable::Add>: class TAttPad already in TClassTable
Warning in <TClassTable::Add>: class TMethodCall already in TClassTable
Warning in <TClassTable::Add>: class TPluginHandler already in TClassTable
Warning in <TClassTable::Add>: class TPluginManager already in TClassTable
Warning in <TClassTable::Add>: class TStringLong already in TClassTable
Warning in <TClassTable::Add>: class TGuiFactory already in TClassTable
Warning in <TClassTable::Add>: class TAttFill already in TClassTable
Warning in <TClassTable::Add>: class TVirtualViewer3D already in TClassTable
Warning in <TClassTable::Add>: class TBuffer3D already in TClassTable
Warning in <TClassTable::Add>: class TSystemFile already in TClassTable
Warning in <TClassTable::Add>: class TSystemDirectory already in TClassTable
Warning in <TClassTable::Add>: class FileStat_t already in TClassTable
Warning in <TClassTable::Add>: class UserGroup_t already in TClassTable
Warning in <TClassTable::Add>: class SysInfo_t already in TClassTable
Warning in <TClassTable::Add>: class CpuInfo_t already in TClassTable
Warning in <TClassTable::Add>: class MemInfo_t already in TClassTable
Warning in <TClassTable::Add>: class ProcInfo_t already in TClassTable
Warning in <TClassTable::Add>: class RedirectHandle_t already in TClassTable
Warning in <TClassTable::Add>: class TProcessEventTimer already in TClassTable
Warning in <TClassTable::Add>: class TSystem already in TClassTable
Warning in <TClassTable::Add>: class TRemoteObject already in TClassTable
Warning in <TClassTable::Add>: class TProcessUUID already in TClassTable
Warning in <TClassTable::Add>: class TAttLine already in TClassTable
Warning in <TClassTable::Add>: class TAttText already in TClassTable
Warning in <TClassTable::Add>: class TAttMarker already in TClassTable
Warning in <TClassTable::Add>: class TVirtualPS already in TClassTable
Warning in <TClassTable::Add>: class TVirtualX already in TClassTable
Warning in <TClassTable::Add>: class TVirtualPad already in TClassTable
Warning in <TClassTable::Add>: class TAttBBox already in TClassTable
Warning in <TClassTable::Add>: class TBuffer already in TClassTable
Warning in <TClassTable::Add>: class TDatime already in TClassTable
Warning in <TClassTable::Add>: class TDirectory already in TClassTable
Warning in <TClassTable::Add>: class TROOT already in TClassTable
Warning in <TClassTable::Add>: class TAtt3D already in TClassTable
Warning in <TClassTable::Add>: class THashTable already in TClassTable
Warning in <TClassTable::Add>: class THashTableIter already in TClassTable
Warning in <TClassTable::Add>: class TMap already in TClassTable
Warning in <TClassTable::Add>: class TPair already in TClassTable
Warning in <TClassTable::Add>: class TMapIter already in TClassTable
Warning in <TClassTable::Add>: class TUrl already in TClassTable
Warning in <TClassTable::Add>: class TMD5 already in TClassTable
Warning in <TClassTable::Add>: class TArray already in TClassTable
Warning in <TClassTable::Add>: class TArrayI already in TClassTable
Warning in <TClassTable::Add>: class TPRegexp already in TClassTable
Warning in <TClassTable::Add>: class TPMERegexp already in TClassTable
Warning in <TClassTable::Add>: class TStringToken already in TClassTable
Warning in <TClassTable::Add>: class TRef already in TClassTable
Warning in <TClassTable::Add>: class TFileCollection already in TClassTable
Warning in <TClassTable::Add>: class TApplicationImp already in TClassTable
Warning in <TClassTable::Add>: class TApplication already in TClassTable
Warning in <TClassTable::Add>: class TVirtualGLPainter already in TClassTable
Warning in <TClassTable::Add>: class TVirtualGLManip already in TClassTable
Warning in <TClassTable::Add>: class TGLManager already in TClassTable
Warning in <TClassTable::Add>: class TGLPaintDevice already in TClassTable
Warning in <TClassTable::Add>: class TRootIOCtor already in TClassTable
Warning in <TClassTable::Add>: class TQCommand already in TClassTable
Warning in <TClassTable::Add>: class TQUndoManager already in TClassTable
Warning in <TClassTable::Add>: class TVirtualAuth already in TClassTable
Warning in <TClassTable::Add>: class TColor already in TClassTable
Warning in <TClassTable::Add>: class TColorGradient already in TClassTable
Warning in <TClassTable::Add>: class TLinearGradient already in TClassTable
Warning in <TClassTable::Add>: class TRadialGradient already in TClassTable
Warning in <TClassTable::Add>: class TObjString already in TClassTable
Warning in <TClassTable::Add>: class TClass already in TClassTable
Warning in <TClassTable::Add>: class TQClass already in TClassTable
Warning in <TClassTable::Add>: class TMacro already in TClassTable
Warning in <TClassTable::Add>: class TStopwatch already in TClassTable
Warning in <TClassTable::Add>: class TRegexp already in TClassTable
Warning in <TClassTable::Add>: class TAttAxis already in TClassTable
Warning in <TClassTable::Add>: class TBenchmark already in TClassTable
Warning in <TClassTable::Add>: class TParameter<bool> already in TClassTable
Warning in <TClassTable::Add>: class TParameter<Long64_t> already in TClassTable
Warning in <TClassTable::Add>: class TParameter<long> already in TClassTable
Warning in <TClassTable::Add>: class TParameter<int> already in TClassTable
Warning in <TClassTable::Add>: class TParameter<double> already in TClassTable
Warning in <TClassTable::Add>: class TParameter<float> already in TClassTable
Warning in <TClassTable::Add>: class TTimeStamp already in TClassTable
Warning in <TClassTable::Add>: class TFileInfo already in TClassTable
Warning in <TClassTable::Add>: class TFileInfoMeta already in TClassTable
Warning in <TClassTable::Add>: class TCanvasImp already in TClassTable
Warning in <TClassTable::Add>: class TVirtualPerfStats already in TClassTable
Warning in <TClassTable::Add>: class TUri already in TClassTable
Warning in <TClassTable::Add>: class TInspectorImp already in TClassTable
Warning in <TClassTable::Add>: class TRedirectOutputGuard already in TClassTable
Warning in <TClassTable::Add>: class TControlBarImp already in TClassTable
Warning in <TClassTable::Add>: class TVirtualPadPainter already in TClassTable
Warning in <TClassTable::Add>: class TVirtualFFT already in TClassTable
Warning in <TClassTable::Add>: class TMemberInspector already in TClassTable
Warning in <TClassTable::Add>: class TEnvRec already in TClassTable
Warning in <TClassTable::Add>: class TEnv already in TClassTable
Warning in <TClassTable::Add>: class TTask already in TClassTable
Warning in <TClassTable::Add>: class TVirtualMonitoringWriter already in TClassTable
Warning in <TClassTable::Add>: class TVirtualMonitoringReader already in TClassTable
Warning in <TClassTable::Add>: class TExec already in TClassTable
Warning in <TClassTable::Add>: class TMessageHandler already in TClassTable
Warning in <TClassTable::Add>: class TQConnection already in TClassTable
Warning in <TClassTable::Add>: class TObjectSpy already in TClassTable
Warning in <TClassTable::Add>: class TObjectRefSpy already in TClassTable
Warning in <TClassTable::Add>: class TContextMenu already in TClassTable
Warning in <TClassTable::Add>: class TFolder already in TClassTable
Warning in <TClassTable::Add>: class TVirtualPadEditor already in TClassTable
Warning in <TClassTable::Add>: class TBase64 already in TClassTable
Warning in <TClassTable::Add>: class TStyle already in TClassTable
Warning in <TClassTable::Add>: class TRefCnt already in TClassTable
Warning in <TClassTable::Add>: class TArrayL already in TClassTable
Warning in <TClassTable::Add>: class THashList already in TClassTable
Warning in <TClassTable::Add>: class TBits already in TClassTable
Warning in <TClassTable::Add>: class TBits::TReference already in TClassTable
Warning in <TClassTable::Add>: class TArrayD already in TClassTable
Warning in <TClassTable::Add>: class TArrayC already in TClassTable
Warning in <TClassTable::Add>: class TClassRef already in TClassTable
Warning in <TClassTable::Add>: class TDataType already in TClassTable
Warning in <TClassTable::Add>: class TVirtualCollectionProxy already in TClassTable
Warning in <TClassTable::Add>: class TRefArray already in TClassTable
Warning in <TClassTable::Add>: class TRefArrayIter already in TClassTable
Warning in <TClassTable::Add>: class TClassTable already in TClassTable
Warning in <TClassTable::Add>: class TArrayL64 already in TClassTable
Warning in <TClassTable::Add>: class TArrayS already in TClassTable
Warning in <TClassTable::Add>: class TBtree already in TClassTable
Warning in <TClassTable::Add>: class TBtreeIter already in TClassTable
Warning in <TClassTable::Add>: class TExMap already in TClassTable
Warning in <TClassTable::Add>: class TExMapIter already in TClassTable
Warning in <TClassTable::Add>: class TOrdCollection already in TClassTable
Warning in <TClassTable::Add>: class TOrdCollectionIter already in TClassTable
Warning in <TClassTable::Add>: class TClonesArray already in TClassTable
Warning in <TClassTable::Add>: class TSortedList already in TClassTable
Warning in <TClassTable::Add>: class TRefTable already in TClassTable
Warning in <TClassTable::Add>: class TObjectTable already in TClassTable
Warning in <TClassTable::Add>: class TArrayF already in TClassTable
Warning in <TClassTable::Add>: class TUnixSystem already in TClassTable
Warning in <TClassTable::Add>: class TGlobal already in TClassTable
Warning in <TClassTable::Add>: class TEnum already in TClassTable
Warning in <TClassTable::Add>: class TEnumConstant already in TClassTable
Warning in <TClassTable::Add>: class TDataMember already in TClassTable
Warning in <TClassTable::Add>: class TOptionListItem already in TClassTable
Warning in <TClassTable::Add>: class TStreamerElement already in TClassTable
Warning in <TClassTable::Add>: class TStreamerBase already in TClassTable
Warning in <TClassTable::Add>: class TStreamerBasicPointer already in TClassTable
Warning in <TClassTable::Add>: class TStreamerLoop already in TClassTable
Warning in <TClassTable::Add>: class TStreamerBasicType already in TClassTable
Warning in <TClassTable::Add>: class TStreamerObject already in TClassTable
Warning in <TClassTable::Add>: class TStreamerObjectAny already in TClassTable
Warning in <TClassTable::Add>: class TStreamerObjectPointer already in TClassTable
Warning in <TClassTable::Add>: class TStreamerObjectAnyPointer already in TClassTable
Warning in <TClassTable::Add>: class TStreamerString already in TClassTable
Warning in <TClassTable::Add>: class TStreamerSTL already in TClassTable
Warning in <TClassTable::Add>: class TStreamerSTLstring already in TClassTable
Warning in <TClassTable::Add>: class ROOT::TSchemaRule already in TClassTable
Warning in <TClassTable::Add>: class ROOT::TSchemaRule::TSources already in TClassTable
Warning in <TClassTable::Add>: class TStreamerArtificial already in TClassTable
Warning in <TClassTable::Add>: class TListOfFunctionTemplates already in TClassTable
Warning in <TClassTable::Add>: class TFunction already in TClassTable
Warning in <TClassTable::Add>: class TMethod already in TClassTable
Warning in <TClassTable::Add>: class TToggle already in TClassTable
Warning in <TClassTable::Add>: class ROOT::Detail::TSchemaRuleSet already in TClassTable
Warning in <TClassTable::Add>: class ROOT::Detail::TStatusBitsChecker already in TClassTable
Warning in <TClassTable::Add>: class TClassMenuItem already in TClassTable
Warning in <TClassTable::Add>: class TListOfEnums already in TClassTable
Warning in <TClassTable::Add>: class TListOfEnumsWithLock already in TClassTable
Warning in <TClassTable::Add>: class TListOfEnumsWithLockIter already in TClassTable
Warning in <TClassTable::Add>: class TClassStreamer already in TClassTable
Warning in <TClassTable::Add>: class TMemberStreamer already in TClassTable
Warning in <TClassTable::Add>: class TFileMergeInfo already in TClassTable
Warning in <TClassTable::Add>: class TProtoClass already in TClassTable
Warning in <TClassTable::Add>: class TProtoClass::TProtoRealData already in TClassTable
Warning in <TClassTable::Add>: class TMethodArg already in TClassTable
Warning in <TClassTable::Add>: class TToggleGroup already in TClassTable
Warning in <TClassTable::Add>: class TClassGenerator already in TClassTable
Warning in <TClassTable::Add>: class TRealData already in TClassTable
Warning in <TClassTable::Add>: class TListOfFunctions already in TClassTable
Warning in <TClassTable::Add>: class TListOfFunctionsIter already in TClassTable
Warning in <TClassTable::Add>: class TDictAttributeMap already in TClassTable
Warning in <TClassTable::Add>: class TBaseClass already in TClassTable
Warning in <TClassTable::Add>: class TListOfDataMembers already in TClassTable
Warning in <TClassTable::Add>: class TVirtualStreamerInfo already in TClassTable
Warning in <TClassTable::Add>: class TFunctionTemplate already in TClassTable
<built-in>:10:9: warning: '__CLING__GNUC__' macro redefined [-Wmacro-redefined]
#define __CLING__GNUC__ 5
        ^
<built-in>:399:9: note: previous definition is here
#define __CLING__GNUC__ 7
        ^
<built-in>:11:9: warning: '__CLING__GNUC_MINOR__' macro redefined [-Wmacro-redefined]
#define __CLING__GNUC_MINOR__ 4
        ^
<built-in>:400:9: note: previous definition is here
#define __CLING__GNUC_MINOR__ 3
        ^
fatal error: malformed or corrupted AST file: 'declaration ID out-of-range for AST file'
Warning in cling::IncrementalParser::CheckABICompatibility():
  Possible C++ standard library mismatch, compiled with __GLIBCXX__ '20160609'
  Extraction of runtime standard library version was: '20180125'

 *** Break *** segmentation violation

Whereas if I use nlesc (and downgrade the libgcc package) root command works perfectly.
Even with nlesc, I have to downgrade manually the libgcc package otherwise root command does not work.

conda create -c nlesc python=2 -n myrootenv2 
conda install -c nlesc root -n myrootenv2 
conda install -c anaconda libgcc=5.2 -n myrootenv2

I'm trying to find a solution using conda-forge instead of nlesc.

Answer 15 · 2019-03-14T15:39:18.000Z

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.

Answer 16 · 2019-03-14T15:50:57.000Z

@romainbqt, sorry for the long delay. Have you tried in a fresh environment? It looks like you have things left over from nlesc-root. There are ~20-40 other packages both depend on, and I'm sure just uninstalling root it would not remove all the other packages. And, most importantly, you must be on the current conda's compiler stack for the new ROOT. Can you try a fresh install and see if the problem persists?