Warning in <TClassTable::Add> and known solutions don't work

Frigorifico · June 11, 2019, 4:49pm

_ROOT Version: 6.16
_Platform: OS 10.14.3
_Compiler: Cling

EDIT: I solved it?

What I did was to change the name of my directories, I had named the directory for root “myRoot” and the build directory “builddir” so I changed them to simply “root” and “build” and now it works I think.

I didn’t know the names were so important since in the instructions they don’t direct you to give them those exact names.

Also I had to go back and update my bash with the new names.

Check this out:

eduroam-int-dhcp-98-97-107:~ Fer$ root
   ------------------------------------------------------------
  | Welcome to ROOT 6.19/01                  https://root.cern |
  |                               (c) 1995-2019, The ROOT Team |
  | Built for macosx64 on Jun 10 2019, 22:42:00                |
  | From heads/master@v6-19-01-160-g5b6222a249                 |
  | Try '.help', '.demo', '.license', '.credits', '.quit'/'.q' |
   ------------------------------------------------------------

root [0] .q
eduroam-int-dhcp-98-97-107:~ Fer$ python
Python 2.7.10 (default, Aug 17 2018, 19:45:58) 
[GCC 4.2.1 Compatible Apple LLVM 10.0.0 (clang-1000.0.42)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import ROOT
Warning in <TClassTable::Add>: class TFileMerger already in TClassTable
Warning in <TClassTable::Add>: class TDirectoryFile already in TClassTable
Warning in <TClassTable::Add>: class TFile already in TClassTable
Warning in <TClassTable::Add>: class TMemFile already in TClassTable
Warning in <TClassTable::Add>: class ROOT::Experimental::TBufferMerger already in TClassTable
Warning in <TClassTable::Add>: class ROOT::Experimental::TBufferMergerFile already in TClassTable
Warning in <TClassTable::Add>: class TArchiveFile already in TClassTable
Warning in <TClassTable::Add>: class TArchiveMember already in TClassTable
Warning in <TClassTable::Add>: class TBufferIO already in TClassTable
Warning in <TClassTable::Add>: class TBufferFile already in TClassTable
Warning in <TClassTable::Add>: class TBufferText already in TClassTable
Warning in <TClassTable::Add>: class TBufferJSON already in TClassTable
Warning in <TClassTable::Add>: class TGenCollectionProxy already in TClassTable
Warning in <TClassTable::Add>: class TGenCollectionProxy::Value already in TClassTable
Warning in <TClassTable::Add>: class TGenCollectionProxy::Method already in TClassTable
Warning in <TClassTable::Add>: class TCollectionProxyFactory already in TClassTable
Warning in <TClassTable::Add>: class TCollectionStreamer already in TClassTable
Warning in <TClassTable::Add>: class TCollectionClassStreamer already in TClassTable
Warning in <TClassTable::Add>: class TCollectionMemberStreamer already in TClassTable
Warning in <TClassTable::Add>: class TEmulatedCollectionProxy already in TClassTable
Warning in <TClassTable::Add>: class TEmulatedMapProxy already in TClassTable
Warning in <TClassTable::Add>: class TFileCacheRead already in TClassTable
Warning in <TClassTable::Add>: class TFree already in TClassTable
Warning in <TClassTable::Add>: class TFileCacheWrite already in TClassTable
Warning in <TClassTable::Add>: class TFPBlock already in TClassTable
Warning in <TClassTable::Add>: class TFilePrefetch already in TClassTable
Warning in <TClassTable::Add>: class TKey already in TClassTable
Warning in <TClassTable::Add>: class TKeyMapFile already in TClassTable
Warning in <TClassTable::Add>: class TLockFile already in TClassTable
Warning in <TClassTable::Add>: class TMapFile already in TClassTable
Warning in <TClassTable::Add>: class TMapRec already in TClassTable
Warning in <TClassTable::Add>: class TStreamerInfo already in TClassTable
Warning in <TClassTable::Add>: class TVirtualArray already in TClassTable
Warning in <TClassTable::Add>: class TStreamerInfoActions::TConfiguration already in TClassTable
Warning in <TClassTable::Add>: class TStreamerInfoActions::TConfiguredAction already in TClassTable
Warning in <TClassTable::Add>: class TStreamerInfoActions::TActionSequence already in TClassTable
Warning in <TClassTable::Add>: class TVirtualObject already in TClassTable
Warning in <TClassTable::Add>: class TZIPFile already in TClassTable
Warning in <TClassTable::Add>: class TZIPMember already in TClassTable
>>>

This is very similar to this topic.

To cite Willie-E-Coyote:

It seems you also have two ROOT versions mixed (one set of libraries in “/opt/root/lib/” and another one in “/opt/root-5.34.30.patches/lib/”).

And I did in fact had to sets of libraries, one was from a previous and very old version of ROOT, so I made sure to include in my bash the absolute address of the directory with the libraries i want to use, but this still happened, so I deleted the other directory, making absolutely sure that there is no second library, and yet this still happens.

Help, I don’t know what to do.

pcanal · June 11, 2019, 5:21pm

Technically those messages indicates that libRIO is being loaded twice … which indeed is usually because there is 2 such libraries laying around.

What is the value of your LD_LIBRARY_PATH and PYTHONPATH?

In the output of otool -l $ROOTSYS/lib/libPyROOT.so look for the section about LC_RPATH. mine looks like:

Load command 16
          cmd LC_RPATH
      cmdsize 56
         path /opt/build/root_builds/rootcling.cmake/lib (offset 12)

also what is the output of

DYLD_PRINT_LIBRARIES=1 ./python
>>> import ROOT

Cheers,
Philippe.

Frigorifico · June 11, 2019, 6:15pm

Hi Philippe, this is my PYTHONPATH

export PYTHONPATH="/Users/Fer/myRoot/builddir/lib"

I’m on mac, so if I understand correctly, I don’t have an LD_LIBRARY_PATH but the equivalent should be DYLD_FALLBACK_LIBRARY_PATH, right?, so I wrote this in my bash:

export DYLD_FALLBACK_LIBRARY_PATH="/Users/Fer/myRoot/builddir/lib"

but it didn’t work.

For > otool -l $ROOTSYS/lib/libPyROOT.so I got:

eduroam-int-dhcp-98-97-107:~ Fer$ otool -l $ROOTSYS/lib/libPyROOT.so

/Library/Developer/CommandLineTools/usr/bin/objdump: '/Users/Fer/root/build/lib/libPyROOT.so': No such file or directory

And when I tried to do the last command you mention I got:

eduroam-int-dhcp-98-97-107:~ Fer$ DYLD_PRINT_LIBRARIES=1 ./python
-bash: ./python: No such file or directory

which is weird but I’m not knowledgable enough to understand what it means

pcanal · June 11, 2019, 6:27pm

which is weird but I’m not knowledgable enough to understand what it means

Sorry, I meant:

DYLD_PRINT_LIBRARIES=1 python

and also

which python

pcanal · June 11, 2019, 6:29pm

but then you have

ROOTSYS equal to /Users/Fer/root/build/lib/

Those 2 can not be right ‘together’ and the (possible) confusion might be the source of the problem.

Frigorifico · June 11, 2019, 6:30pm

Hi, check my edit at the top, I solved it, your output made me realize that I should change the names. Now I while I get no errors on the terminal, I get errors when trying to run the examples:

/usr/bin/python2.7 /Users/Fer/PycharmProjects/proton/test.py
Traceback (most recent call last):
  File "/Users/Fer/PycharmProjects/proton/test.py", line 3, in <module>
    from ROOT import TCanvas, TPaveText, gROOT
  File "/Users/Fer/root/build/lib/ROOT.py", line 24, in <module>
    import cppyy
  File "/Users/Fer/root/build/lib/cppyy.py", line 61, in <module>
    import libPyROOT as _backend
ImportError: dlopen(/Users/Fer/root/build/lib/libPyROOT.so, 2): Library not loaded: @rpath/libTree.so
  Referenced from: /Users/Fer/root/build/lib/libPyROOT.so
  Reason: image not found

Frigorifico · June 11, 2019, 6:38pm

I can finally see the output of

otool -l $ROOTSYS/lib/libPyROOT.so

it is:

Load command 16
          cmd LC_RPATH
      cmdsize 48
         path /Users/Fer/myRoot/builddir/lib (offset 12)

which now is wrong because I renamed those directories, arrrgh, I feel like I’m going in circles, I fix one thing but that somehow broke another one.

Should I add to my bash something like:

export LC_RPATH="/Users/Fer/root/build/lib"

?

pcanal · June 11, 2019, 6:44pm

Renaming/moving a build directory does not work well.

At this point I would simply recommend to start from ‘scratch’. I.e. delete all trace of both the old and new directories. Create a new build directory with the ‘right’ name and build ‘fresh’ there.

Cheers,
Philippe.

Frigorifico · June 11, 2019, 7:00pm

how do I uninstall root correctly?, I don’t want this to turn into a bigger problem

pcanal · June 11, 2019, 7:02pm

Assuming you have nothing else you want to keep on those directory, you could do

rm -r /Users/Fer/root/build
rm -r /Users/Fer/myRoot/builddir

Frigorifico · June 11, 2019, 7:11pm

thanks, one more question, should I have a root directory with the build directory inside, OR should the build directory and the root directory be alongside on the same directory?

pcanal · June 11, 2019, 7:23pm

I am guessing that my ‘root’ directory, you are referring to the directory containing the ROOT git repository/source.

Having the build directory either as subdirectory of the source directory or along side it will work as well.

Cheers,
Philippe.

system · June 25, 2019, 7:23pm

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