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root not working in macOS 11.6 #149

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mbomben opened this issue Nov 7, 2021 · 9 comments
Open
1 task done

root not working in macOS 11.6 #149

mbomben opened this issue Nov 7, 2021 · 9 comments

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@mbomben
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mbomben commented Nov 7, 2021 •
edited
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Issue:

Dear support staff, I am using miniconda in macOS 11.6. I have installed root using these instructions:
https://root.cern/install/#conda
When I launch ROOT I get these error messages (return code: 6) and same happens for python:

$ root
input_line_1:1:2: error: module 'Darwin' uses additional module map
'/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/machine.modulemap'
used when the module was built
#include
^
input_line_1:1:2: note: imported by module 'std' in '/Users/mbomben/miniconda3/envs/myroot/lib/std.pcm'
Warning in cling::IncrementalParser::CheckABICompatibility():
Failed to extract C++ standard library version.
Warning in cling::IncrementalParser::CheckABICompatibility():
Possible C++ standard library mismatch, compiled with _LIBCPP_ABI_VERSION '1'
Extraction of runtime standard library version was: ''
input_line_2:1:2: fatal error: module file '/Users/mbomben/miniconda3/envs/myroot/lib/std.pcm' is out of date
and needs to be rebuilt
#include "cling/Interpreter/RuntimeUniverse.h"
^
input_line_2:1:2: note: imported by module 'Cling_Runtime_Extra' in
'/Users/mbomben/miniconda3/envs/myroot/lib/Cling_Runtime_Extra.pcm'
input_line_2:1:2: note: imported by module 'Cling_Runtime' in
'/Users/mbomben/miniconda3/envs/myroot/lib/Cling_Runtime.pcm'
Replaced symbol atexit cannot be found in JIT!
Replaced symbol at_quick_exit cannot be found in JIT!
<<< cling interactive line includer >>>: fatal error: module file '/Users/mbomben/miniconda3/envs/myroot/lib/Darwin.pcm' is out of
date and needs to be rebuilt
Failed to load module Darwin
Failed to load module std
Failed to load module _Builtin_intrinsics
Failed to load module ROOT_Foundation_C
Failed to load module ROOT_Config
Failed to load module ROOT_Rtypes
Failed to load module ROOT_Foundation_Stage1_NoRTTI
Failed to load module Core
Failed to load module Rint
Failed to load module RIO
Failed to load module MathCore
Failed to load module Hist
Failed to load module Darwin
Failed to load module Unfold
Failed to load module Imt
Failed to load module HistPainter
Failed to load module PyMVA
Failed to load module RHTTPSniff
Failed to load module RDAVIX
Failed to load module RHTTP
Failed to load module FitPanel
Failed to load module ROOTVecOps
Failed to load module ProofDraw
Failed to load module ROOTBrowsable
Failed to load module Quadp
Failed to load module ROOT_Foundation_Stage1_NoRTTI
Failed to load module GeomPainter
Failed to load module Genetic
Failed to load module Eve
Failed to load module TreeViewer
Failed to load module Physics
Failed to load module ROOTNTuple
Failed to load module EG
Failed to load module Tree
Failed to load module HistFactory
Failed to load module Spectrum
Failed to load module Matrix
Failed to load module Html
Failed to load module Hist
Failed to load module GuiHtml
Failed to load module _Builtin_intrinsics
Failed to load module Gpad
Failed to load module TMVAGui
Failed to load module ROOTEve
Failed to load module Fumili
Failed to load module Net
Failed to load module RGL
Failed to load module Geom
Failed to load module Postscript
Failed to load module GCocoa
Failed to load module ROOTGpadv7
Failed to load module RCsg
Failed to load module Cling_Runtime
Failed to load module SPlot
Failed to load module EGPythia8
Failed to load module GeomBuilder
Failed to load module RooFit
Failed to load module ROOT_Config
Failed to load module RooFitMore
Failed to load module Rint
Failed to load module XMLParser
Failed to load module MultiProc
Failed to load module RooStats
Failed to load module Proof
Failed to load module FITSIO
Failed to load module Ged
Failed to load module Recorder
Failed to load module FFTW
Failed to load module GuiBld
Failed to load module Vc
Failed to load module ROOTWebDisplay
Failed to load module RooFitCore
Failed to load module Gui
Failed to load module SQLIO
Failed to load module XMLIO
Failed to load module ROOT_Rtypes
Failed to load module std
Failed to load module ROOTHistDraw
Failed to load module RIO
Failed to load module ProofPlayer
Failed to load module ASImage
Failed to load module ROOT_Foundation_C
Failed to load module MathMore
Failed to load module Foam
Failed to load module RSQLite
Failed to load module SpectrumPainter
Failed to load module Minuit2
Failed to load module Core
Failed to load module MLP
Failed to load module ROOTDataFrame
Failed to load module GenVector
Failed to load module NetxNG
Failed to load module ROOTBrowserv7
Failed to load module Minuit
Failed to load module RootAuth
Failed to load module Graf3d
Failed to load module TMVA
Failed to load module ASImageGui
Failed to load module Graf
Failed to load module Gdml
Failed to load module ProofBench
Failed to load module Cling_Runtime_Extra
Failed to load module MathCore
Failed to load module Gviz3d
Failed to load module WebGui6
Failed to load module ROOTTPython
Failed to load module ROOTHist
Failed to load module TreePlayer
Failed to load module ROOTGraphicsPrimitives
Failed to load module Gviz
Failed to load module ROOTFitPanelv7
Failed to load module Smatrix
Failed to load module SessionViewer
Failed to load module Thread
Assertion failed: (clingInterp.getMacro("gROOT") && "Couldn't load gROOT macro?"), function RegisterCxxModules, file /Users/runner/miniforge3/conda-bld/root_base_1630711535126/work/root-source/core/metacling/src/TCling.cxx, line 1313.


Environment (conda list): 
$ conda list

# packages in environment at /Users/mbomben/miniconda3/envs/myroot:
#
# Name                    Version                   Build  Channel
afterimage                1.21              h4dd67e6_1003    conda-forge
appnope                   0.1.2            py39h6e9494a_2    conda-forge
argon2-cffi               21.1.0           py39h89e85a6_2    conda-forge
async_generator           1.10                       py_0    conda-forge
atk-1.0                   2.36.0               he69c4ee_4    conda-forge
attrs                     21.2.0             pyhd8ed1ab_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
bleach                    4.1.0              pyhd8ed1ab_0    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
c-ares                    1.18.1               h0d85af4_0    conda-forge
c-compiler                1.3.0                h0d85af4_0    conda-forge
ca-certificates           2021.10.8            h033912b_0    conda-forge
cairo                     1.16.0            he43a7df_1008    conda-forge
cctools                   949.0.1             hd9211c8_21    conda-forge
cctools_osx-64            949.0.1             h6407bdd_21    conda-forge
cffi                      1.15.0           py39he338e87_0    conda-forge
cfitsio                   3.470                h01dc385_7    conda-forge
clang                     11.1.0               h694c41f_1    conda-forge
clang-11                  11.1.0          default_he082bbe_1    conda-forge
clang_osx-64              11.1.0               hb91bd55_4    conda-forge
clangxx                   11.1.0          default_he082bbe_1    conda-forge
clangxx_osx-64            11.1.0               h7e1b574_4    conda-forge
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
compiler-rt               11.1.0               h654b07c_0    conda-forge
compiler-rt_osx-64        11.1.0               h8c5fa43_0    conda-forge
compilers                 1.3.0                h694c41f_0    conda-forge
cxx-compiler              1.3.0                h940c156_0    conda-forge
davix                     0.7.6                h61356a0_0    conda-forge
debugpy                   1.5.1            py39h9fcab8e_0    conda-forge
decorator                 5.1.0              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
entrypoints               0.3             pyhd8ed1ab_1003    conda-forge
expat                     2.4.1                he49afe7_0    conda-forge
fftw                      3.3.10          nompi_h4024a70_101    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.13.1            h10f422b_1005    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fortran-compiler          1.3.0                h6818c3e_0    conda-forge
freetype                  2.10.4               h4cff582_1    conda-forge
fribidi                   1.0.10               hbcb3906_0    conda-forge
ftgl                      2.4.0                h508da5b_0    conda-forge
gdk-pixbuf                2.42.6               h2e6141f_0    conda-forge
gettext                   0.19.8.1          hd1a6beb_1008    conda-forge
gfortran                  9.3.0               h768ea0c_14    conda-forge
gfortran_impl_osx-64      9.3.0               h9cc0e5e_23    conda-forge
gfortran_osx-64           9.3.0               h18f7dce_14    conda-forge
giflib                    5.2.1                hbcb3906_2    conda-forge
gl2ps                     1.4.2                h4cff582_0    conda-forge
glew                      2.1.0                h046ec9c_2    conda-forge
gmp                       6.2.1                h2e338ed_0    conda-forge
graphite2                 1.3.13            h2e338ed_1001    conda-forge
graphviz                  2.49.3               h77de9ca_0    conda-forge
gsl                       2.7                  h93259b0_0    conda-forge
gtk2                      2.24.33              h675d97a_1    conda-forge
gts                       0.7.6                hccb3bdf_2    conda-forge
harfbuzz                  3.1.0                h159f659_0    conda-forge
icu                       68.2                 he49afe7_0    conda-forge
importlib-metadata        4.8.1            py39h6e9494a_1    conda-forge
importlib_resources       5.4.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.4.2            py39h71a6800_0    conda-forge
ipyparallel               7.1.0              pyhd8ed1ab_0    conda-forge
ipython                   7.29.0           py39h71a6800_1    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
isl                       0.22.1               hb1e8313_2    conda-forge
jbig                      2.1               h0d85af4_2003    conda-forge
jedi                      0.18.0           py39h6e9494a_3    conda-forge
jinja2                    3.0.2              pyhd8ed1ab_0    conda-forge
jpeg                      9d                   hbcb3906_0    conda-forge
jsonschema                4.2.1              pyhd8ed1ab_0    conda-forge
jupyter_client            7.0.6              pyhd8ed1ab_0    conda-forge
jupyter_core              4.9.1            py39h6e9494a_0    conda-forge
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
krb5                      1.19.2               hcfbf3a7_3    conda-forge
ld64                      530                 hd2e7500_21    conda-forge
ld64_osx-64               530                 he8994da_21    conda-forge
ldid                      2.1.2                h6a69015_3    conda-forge
lerc                      3.0                  he49afe7_0    conda-forge
libblas                   3.9.0           12_osx64_openblas    conda-forge
libcblas                  3.9.0           12_osx64_openblas    conda-forge
libclang-cpp11.1          11.1.0          default_he082bbe_1    conda-forge
libcurl                   7.79.1               hf45b732_1    conda-forge
libcxx                    12.0.1               habf9029_0    conda-forge
libdeflate                1.8                  h0d85af4_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libev                     4.33                 haf1e3a3_1    conda-forge
libffi                    3.4.2                he49afe7_4    conda-forge
libgd                     2.3.3                h311d3fc_0    conda-forge
libgfortran               5.0.0           9_3_0_h6c81a4c_23    conda-forge
libgfortran-devel_osx-64  9.3.0               h6c81a4c_23    conda-forge
libgfortran5              9.3.0               h6c81a4c_23    conda-forge
libglib                   2.70.0               hf1fb8c0_1    conda-forge
libiconv                  1.16                 haf1e3a3_0    conda-forge
liblapack                 3.9.0           12_osx64_openblas    conda-forge
libllvm10                 10.0.1               h009f743_3    conda-forge
libllvm11                 11.1.0               hd011deb_2    conda-forge
libllvm9                  9.0.1           default_h2671707_4    conda-forge
libnghttp2                1.43.0               h6f36284_1    conda-forge
libopenblas               0.3.18          openmp_h3351f45_0    conda-forge
libpng                    1.6.37               h7cec526_2    conda-forge
librsvg                   2.52.3               h02b643e_0    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libssh2                   1.10.0               h52ee1ee_2    conda-forge
libtiff                   4.3.0                hd146c10_2    conda-forge
libtool                   2.4.6             he49afe7_1008    conda-forge
libwebp                   1.2.1                h28dabe5_0    conda-forge
libwebp-base              1.2.1                h0d85af4_0    conda-forge
libxml2                   2.9.12               h93ec3fd_0    conda-forge
libzlib                   1.2.11            h9173be1_1013    conda-forge
llvm-openmp               12.0.1               hda6cdc1_1    conda-forge
llvm-tools                11.1.0               hd011deb_2    conda-forge
llvmlite                  0.36.0           py39h798a4f4_0    conda-forge
lz4-c                     1.9.3                he49afe7_1    conda-forge
markupsafe                2.0.1            py39h89e85a6_1    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
metakernel                0.27.5             pyhd3deb0d_0    conda-forge
mistune                   0.8.4           py39h89e85a6_1005    conda-forge
mpc                       1.2.1                hbb51d92_0    conda-forge
mpfr                      4.1.0                h0f52abe_1    conda-forge
nbclient                  0.5.4              pyhd8ed1ab_0    conda-forge
nbconvert                 6.2.0            py39h6e9494a_0    conda-forge
nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.2                  h2e338ed_4    conda-forge
nest-asyncio              1.5.1              pyhd8ed1ab_0    conda-forge
nlohmann_json             3.10.4               he49afe7_0    conda-forge
notebook                  6.4.5              pyha770c72_0    conda-forge
numba                     0.53.0           py39he2616bd_0    conda-forge
numpy                     1.21.4           py39h7eed0ac_0    conda-forge
openssl                   1.1.1l               h0d85af4_0    conda-forge
packaging                 21.0               pyhd8ed1ab_0    conda-forge
pandoc                    2.16.1               h0d85af4_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
pango                     1.48.10              h056538c_2    conda-forge
parso                     0.8.2              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 he49afe7_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pip                       21.3.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               hbcb3906_0    conda-forge
portalocker               2.3.2            py39h6e9494a_0    conda-forge
prometheus_client         0.12.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.22             pyha770c72_0    conda-forge
psutil                    5.8.0            py39h89e85a6_2    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.10.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.4              pyhd8ed1ab_0    conda-forge
pyrsistent                0.18.0           py39h89e85a6_0    conda-forge
pythia8                   8.305            py39h9fcab8e_0    conda-forge
python                    3.9.7           h1248fe1_3_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.9                      2_cp39    conda-forge
pyzmq                     22.3.0           py39h7fec2f1_1    conda-forge
readline                  8.1                  h05e3726_0    conda-forge
root                      6.24.6           py39h757cd7f_0    conda-forge
root_base                 6.24.6           py39h1d38ebb_0    conda-forge
scitokens-cpp             0.6.3                h27338ba_1    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                58.5.3           py39h6e9494a_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlite                    3.36.0               h23a322b_2    conda-forge
tapi                      1100.0.11            h9ce4665_0    conda-forge
tbb                       2021.4.0             h940c156_1    conda-forge
terminado                 0.12.1           py39h6e9494a_1    conda-forge
testpath                  0.5.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.11               h5dbffcc_1    conda-forge
tornado                   6.1              py39h89e85a6_2    conda-forge
tqdm                      4.62.3             pyhd8ed1ab_0    conda-forge
traitlets                 5.1.1              pyhd8ed1ab_0    conda-forge
tzdata                    2021e                he74cb21_0    conda-forge
vdt                       0.4.3                h046ec9c_0    conda-forge
vector-classes            1.4.2                h940c156_1    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.37.0             pyhd8ed1ab_1    conda-forge
xrootd                    5.3.2            py39heed53e9_1    conda-forge
xxhash                    0.8.0                h35c211d_3    conda-forge
xz                        5.2.5                haf1e3a3_1    conda-forge
zeromq                    4.3.4                he49afe7_1    conda-forge
zipp                      3.6.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.11            h9173be1_1013    conda-forge
zstd                      1.5.0                h582d3a0_0    conda-forge

Details about conda and system ( conda info ): 
$ conda info

     active environment : myroot
    active env location : /Users/mbomben/miniconda3/envs/myroot
            shell level : 1
       user config file : /Users/mbomben/.condarc
 populated config files : /Users/mbomben/.condarc
          conda version : 4.10.3
    conda-build version : not installed
         python version : 3.7.3.final.0
       virtual packages : __osx=10.16=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /Users/mbomben/miniconda3  (writable)
      conda av data dir : /Users/mbomben/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/mbomben/miniconda3/pkgs
                          /Users/mbomben/.conda/pkgs
       envs directories : /Users/mbomben/miniconda3/envs
                          /Users/mbomben/.conda/envs
               platform : osx-64
             user-agent : conda/4.10.3 requests/2.26.0 CPython/3.7.3 Darwin/20.6.0 OSX/10.16
                UID:GID : 502:1415430927
             netrc file : None
           offline mode : False

Any help will be greatly appreciated.

Many thanks in advance and kind regards,
Marco Bomben
@aphecetche
Copy link

I believe I'm also encountering that issue (both on 11.6 x86 as the OP, and also on 12.0.1 M1).

Environment (conda list)

$ conda list 
# packages in environment at /Users/beta/mambaforge/envs/beta:
#
# Name                    Version                   Build  Channel
afterimage                1.21              h4dd67e6_1003    conda-forge
appnope                   0.1.2            py39h6e9494a_2    conda-forge
argon2-cffi               21.1.0           py39h89e85a6_2    conda-forge
async_generator           1.10                       py_0    conda-forge
atk-1.0                   2.36.0               he69c4ee_4    conda-forge
attrs                     21.2.0             pyhd8ed1ab_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
bleach                    4.1.0              pyhd8ed1ab_0    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
c-ares                    1.18.1               h0d85af4_0    conda-forge
c-compiler                1.3.0                h0d85af4_0    conda-forge
ca-certificates           2021.10.8            h033912b_0    conda-forge
cairo                     1.16.0            he01c77b_1009    conda-forge
cctools                   949.0.1             hd9211c8_21    conda-forge
cctools_osx-64            949.0.1             h6407bdd_21    conda-forge
cffi                      1.15.0           py39he338e87_0    conda-forge
cfitsio                   3.470                h01dc385_7    conda-forge
clang                     11.1.0               h694c41f_1    conda-forge
clang-11                  11.1.0          default_he082bbe_1    conda-forge
clang_osx-64              11.1.0               hb91bd55_4    conda-forge
clangxx                   11.1.0          default_he082bbe_1    conda-forge
clangxx_osx-64            11.1.0               h7e1b574_4    conda-forge
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
compiler-rt               11.1.0               h654b07c_0    conda-forge
compiler-rt_osx-64        11.1.0               h8c5fa43_0    conda-forge
compilers                 1.3.0                h694c41f_0    conda-forge
cxx-compiler              1.3.0                h940c156_0    conda-forge
davix                     0.7.6                ha0fbd20_0    conda-forge
debugpy                   1.5.1            py39h9fcab8e_0    conda-forge
decorator                 5.1.0              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
entrypoints               0.3             py39hde42818_1002    conda-forge
expat                     2.4.1                he49afe7_0    conda-forge
fftw                      3.3.10          nompi_h4024a70_101    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.13.1            h10f422b_1005    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fortran-compiler          1.3.0                h6818c3e_0    conda-forge
freetype                  2.10.4               h4cff582_1    conda-forge
fribidi                   1.0.10               hbcb3906_0    conda-forge
ftgl                      2.4.0                h508da5b_0    conda-forge
gdk-pixbuf                2.42.6               h2e6141f_0    conda-forge
gettext                   0.19.8.1          hd1a6beb_1008    conda-forge
gfortran                  9.3.0               h768ea0c_14    conda-forge
gfortran_impl_osx-64      9.3.0               h9cc0e5e_23    conda-forge
gfortran_osx-64           9.3.0               h18f7dce_14    conda-forge
giflib                    5.2.1                hbcb3906_2    conda-forge
gl2ps                     1.4.2                h4cff582_0    conda-forge
glew                      2.1.0                h046ec9c_2    conda-forge
gmp                       6.2.1                h2e338ed_0    conda-forge
graphite2                 1.3.13            h2e338ed_1001    conda-forge
graphviz                  2.49.3               h77de9ca_0    conda-forge
gsl                       2.7                  h93259b0_0    conda-forge
gsoap_abi                 2.8.109              h694c41f_0    conda-forge
gtk2                      2.24.33              h675d97a_1    conda-forge
gts                       0.7.6                hccb3bdf_2    conda-forge
harfbuzz                  3.1.1                h447b35c_1    conda-forge
icu                       69.1                 he49afe7_0    conda-forge
importlib-metadata        4.8.2            py39h6e9494a_0    conda-forge
importlib_resources       5.4.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.5.0            py39h71a6800_0    conda-forge
ipyparallel               8.0.0              pyhd8ed1ab_0    conda-forge
ipython                   7.29.0           py39h71a6800_2    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
isl                       0.22.1               hb1e8313_2    conda-forge
jbig                      2.1               h0d85af4_2003    conda-forge
jedi                      0.18.0           py39h6e9494a_3    conda-forge
jinja2                    3.0.3              pyhd8ed1ab_0    conda-forge
jpeg                      9d                   hbcb3906_0    conda-forge
jsonschema                4.2.1              pyhd8ed1ab_0    conda-forge
jupyter_client            7.0.6              pyhd8ed1ab_0    conda-forge
jupyter_core              4.9.1            py39h6e9494a_1    conda-forge
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
krb5                      1.19.2               hcfbf3a7_3    conda-forge
ld64                      530                 hd2e7500_21    conda-forge
ld64_osx-64               530                 he8994da_21    conda-forge
ldid                      2.1.2                h6a69015_3    conda-forge
lerc                      3.0                  he49afe7_0    conda-forge
libblas                   3.9.0           12_osx64_openblas    conda-forge
libcblas                  3.9.0           12_osx64_openblas    conda-forge
libclang-cpp11.1          11.1.0          default_he082bbe_1    conda-forge
libcurl                   7.80.0               hf45b732_0    conda-forge
libcxx                    12.0.1               habf9029_0    conda-forge
libdeflate                1.8                  h0d85af4_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libev                     4.33                 haf1e3a3_1    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgd                     2.3.3                hb8742e1_1    conda-forge
libgfortran               5.0.0           9_3_0_h6c81a4c_23    conda-forge
libgfortran-devel_osx-64  9.3.0               h6c81a4c_23    conda-forge
libgfortran5              9.3.0               h6c81a4c_23    conda-forge
libglib                   2.70.0               hf1fb8c0_1    conda-forge
libiconv                  1.16                 haf1e3a3_0    conda-forge
liblapack                 3.9.0           12_osx64_openblas    conda-forge
libllvm11                 11.1.0               hd011deb_2    conda-forge
libllvm9                  9.0.1           default_h2671707_4    conda-forge
libnghttp2                1.43.0               h6f36284_1    conda-forge
libopenblas               0.3.18          openmp_h3351f45_0    conda-forge
libpng                    1.6.37               h7cec526_2    conda-forge
librsvg                   2.52.3               h02b643e_0    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libssh2                   1.10.0               h52ee1ee_2    conda-forge
libtiff                   4.3.0                hd146c10_2    conda-forge
libtool                   2.4.6             he49afe7_1008    conda-forge
libwebp                   1.2.1                h28dabe5_0    conda-forge
libwebp-base              1.2.1                h0d85af4_0    conda-forge
libxml2                   2.9.12               h7e28ab6_1    conda-forge
libzlib                   1.2.11            h9173be1_1013    conda-forge
llvm-openmp               12.0.1               hda6cdc1_1    conda-forge
llvm-tools                11.1.0               hd011deb_2    conda-forge
llvmlite                  0.37.0           py39h798a4f4_0    conda-forge
lz4-c                     1.9.3                he49afe7_1    conda-forge
markupsafe                2.0.1            py39h89e85a6_1    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
metakernel                0.27.5             pyhd3deb0d_0    conda-forge
mistune                   0.8.4           py39h89e85a6_1005    conda-forge
mpc                       1.2.1                hbb51d92_0    conda-forge
mpfr                      4.1.0                h0f52abe_1    conda-forge
nbclient                  0.5.8              pyhd8ed1ab_0    conda-forge
nbconvert                 6.3.0            py39h6e9494a_0    conda-forge
nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.2                  h2e338ed_4    conda-forge
nest-asyncio              1.5.1              pyhd8ed1ab_0    conda-forge
nlohmann_json             3.10.4               he49afe7_0    conda-forge
notebook                  6.4.5              pyha770c72_0    conda-forge
numba                     0.54.1           py39h58500fb_0    conda-forge
numpy                     1.20.3           py39h7eed0ac_1    conda-forge
openssl                   1.1.1l               h0d85af4_0    conda-forge
packaging                 21.2               pyhd8ed1ab_1    conda-forge
pandoc                    2.16.1               h0d85af4_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
pango                     1.48.10              h056538c_2    conda-forge
parso                     0.8.2              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 he49afe7_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5           py39hde42818_1002    conda-forge
pip                       21.3.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               hbcb3906_0    conda-forge
portalocker               2.3.2            py39h6e9494a_0    conda-forge
prometheus_client         0.12.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.22             pyha770c72_0    conda-forge
psutil                    5.8.0            py39h89e85a6_2    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.10.0             pyhd8ed1ab_0    conda-forge
pyparsing                 2.4.7              pyhd8ed1ab_1    conda-forge
pyrsistent                0.18.0           py39h89e85a6_0    conda-forge
pythia8                   8.305            py39h9fcab8e_0    conda-forge
python                    3.9.7           h1248fe1_3_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.9                      2_cp39    conda-forge
pyzmq                     22.3.0           py39h7fec2f1_1    conda-forge
readline                  8.1                  h05e3726_0    conda-forge
root                      6.24.6           py39h757cd7f_0    conda-forge
root_base                 6.24.6           py39h1d38ebb_0    conda-forge
scitokens-cpp             0.6.3                h27338ba_1    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                58.5.3           py39h6e9494a_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlite                    3.36.0               h23a322b_2    conda-forge
tapi                      1100.0.11            h9ce4665_0    conda-forge
tbb                       2021.4.0             h940c156_1    conda-forge
terminado                 0.12.1           py39h6e9494a_1    conda-forge
testpath                  0.5.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.11               h5dbffcc_1    conda-forge
tornado                   6.1              py39h89e85a6_2    conda-forge
tqdm                      4.62.3             pyhd8ed1ab_0    conda-forge
traitlets                 5.1.1              pyhd8ed1ab_0    conda-forge
tzdata                    2021e                he74cb21_0    conda-forge
vdt                       0.4.3                h046ec9c_0    conda-forge
vector-classes            1.4.2                h940c156_1    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.37.0             pyhd8ed1ab_1    conda-forge
xrootd                    5.3.2            py39heed53e9_1    conda-forge
xxhash                    0.8.0                h35c211d_3    conda-forge
xz                        5.2.5                haf1e3a3_1    conda-forge
zeromq                    4.3.4                he49afe7_1    conda-forge
zipp                      3.6.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.11            h9173be1_1013    conda-forge
zstd                      1.5.0                h582d3a0_0    conda-forge

Details about conda and system (conda info) :

$ conda info 

     active environment : beta
    active env location : /Users/beta/mambaforge/envs/beta
            shell level : 2
       user config file : /Users/beta/.condarc
 populated config files : /Users/beta/mambaforge/.condarc
          conda version : 4.10.3
    conda-build version : not installed
         python version : 3.9.7.final.0
       virtual packages : __osx=11.6.1=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /Users/beta/mambaforge  (writable)
      conda av data dir : /Users/beta/mambaforge/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /Users/beta/mambaforge/pkgs
                          /Users/beta/.conda/pkgs
       envs directories : /Users/beta/mambaforge/envs
                          /Users/beta/.conda/envs
               platform : osx-64
             user-agent : conda/4.10.3 requests/2.26.0 CPython/3.9.7 Darwin/20.6.0 OSX/11.6.1
                UID:GID : 503:20
             netrc file : None
           offline mode : False

@henryiii
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henryiii commented Nov 16, 2021 •
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Same issue locally, seems to have become unusable on macOS. (12, Intel)

@henryiii
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Also same issue with homebrew, FYI. It's not built for macOS 12 yet, but interestingly the same issue.

@henryiii
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Actually the problem is that Xcode 13.1 needs new binaries. See https://root-forum.cern.ch/t/problem-with-root-on-macos-error-module-darwin-uses-additional-module-map/47443 and https://root-forum.cern.ch/t/root-6-24-06-can-not-work-on-macos-monterey/47409/6.

Basically, we need a rebuild with Xcode 13.1 (which will then stop it from working with anyone using 13.0 or earlier, I expect).

@chrisburr
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chrisburr commented Nov 16, 2021 •
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Basically, we need a rebuild with Xcode 13.1 (which will then stop it from working with anyone using 13.0 or earlier, I expect).

This shouldn't ever be the case for conda-forge as we don't use compilers from XCode though new SDKs do occasioanlly require tweaks to the conda-forge compilers.

I'll try to take a look today (need to update to 11.6 first) but you might be able to avoid the issue by setting SDK_ROOT to an older SDK (I get them from https://github.com/phracker/MacOSX-SDKs).

@aphecetche
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@chrisburr sorry for the naive question, but when/where should I set the SDK_ROOT ? Before creating my environment ? (which I do with conda env create -f dev-environment.yml )

$ cat dev-environment.yml
name: m2-exp-dev
channels:
  - conda-forge
dependencies:
  - root=6.24.*
  - fmt=7.1.*
  - uproot=4.0.*
  - ipympl=0.7.*
  - boost=1.75.*
  - rapidjson=1.1.*
  - jupyter=1.0.*
  - jupyterlab>=3
  - twine=3.4.*
  - ninja>=1
  - cmake=3.19.*
  - pybind11>=2
  - pytest>=6
  - vector>=0.8

@aphecetche
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@chrisburr @henryiii any news on this one ? thanks.

@LemurPwned
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I have the same issue with Monterey 12.1 (M1). Any updates? Thanks

@chrisburr
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This can be worked around by using and a macOS 11.x SDK instead of a macOS 12.x one by setting this variable:

export CONDA_BUILD_SYSROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk/

If you've updated you should have older SDKs lying around, unfortunately the license prevents conda-forge from shipping it ourselves.

I'll work with the ROOT team to find a proper solution soon: https://root-forum.cern.ch/t/conda-root-and-macos-12-reprise/49135/10

@chrisburr chrisburr mentioned this issue Apr 5, 2022
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@chrisburr chrisburr mentioned this issue May 10, 2022
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@aphecetche @henryiii @chrisburr @LemurPwned @mbomben