Comments (21)
langmm
commented on June 25, 2024
2
Using flexible causes conda to install r-base from defaults (conda 4.7.5) which I'm unsure will work since I am using reticulate to call python functions from R and if python and R use different C compilers and shared libraries, segfaults are the result. Are the issues with C++ exceptions why the libcxx 4.0.1 package was marked broken on osx? There are many packages that pin libcxx to 4.0.1, so a fix to libcxx 4.0.1 would help a lot.
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langmm
commented on June 25, 2024
1
Strangely, conda reports that r is not a registered channel. I'm also confused because I never explicitly added the r channel.
conda config --remove channels r
CondaKeyError: 'channels': 'r' is not in the 'channels' key of the config file
This is my .condarc
channels:
- conda-forge
- defaults
show_channel_urls: true
channel_priority: strict
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ocefpaf
commented on June 25, 2024
1
@jdblischak the r channel is part of defaults, together with free and main.
(Free was removed recently, see https://www.anaconda.com/why-we-removed-the-free-channel-in-conda-4-7/)
@langmm did you try an older version? Like 4.7.5? You may need to do
CONDA_AUTO_UPDATE_CONDA=0 conda install conda=4.7.5 --no-deps --yes
to be able to downgrade.
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isuruf
commented on June 25, 2024
1
I added 4.0.1 to conda-forge temporarily. 4.0.1 has serious issues with C++ exceptions and we should fix the compiler package. I'd appreciate a PR to https://github.com/AnacondaRecipes/aggregate/blob/ece8f31125a17cc8187706c4ba18779ca4fc2fc0/llvm-compilers-feedstock/recipe/meta.yaml
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isuruf
commented on June 25, 2024
1
Opened AnacondaRecipes/aggregate#162. It takes a few weeks for PRs in AnacondaRecipes to get reviewed, so let's keep 4.0.1 in conda-forge for now.
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langmm
commented on June 25, 2024
As a note, I also replicated this error in a Python 2.7 environment and verified that it is only for r-base (i.e. other packages install correctly)
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dpryan79
commented on June 25, 2024
I wonder if this is a bug in conda 4.7.7, which hasn't been marked as being ready for general use yet (last I looked it was only in the conda-canary channel for this reason).
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ocefpaf
commented on June 25, 2024
I wonder if this is a bug in conda 4.7.7, which hasn't been marked as being ready for general use yet (last I looked it was only in the conda-canary channel for this reason).
BTW, I was unable to duplicate this with conda 4.7.5 on Linux.
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jdblischak
commented on June 25, 2024
Some more more data points: I was able to install r-base on linux and macOS using conda 4.7.5 and conda 4.7.8.
@langmm Could you please update conda and try again?
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langmm
commented on June 25, 2024
I updated to conda 4.7.8,
$ conda info
active environment : conda36
active env location : /Users/langmm/miniconda3/envs/conda36
shell level : 2
user config file : /Users/langmm/.condarc
populated config files : /Users/langmm/.condarc
conda version : 4.7.8
conda-build version : 3.18.7
python version : 3.7.3.final.0
virtual packages :
base environment : /Users/langmm/miniconda3 (writable)
channel URLs : https://conda.anaconda.org/conda-forge/osx-64
https://conda.anaconda.org/conda-forge/noarch
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/langmm/miniconda3/pkgs
/Users/langmm/.conda/pkgs
envs directories : /Users/langmm/miniconda3/envs
/Users/langmm/.conda/envs
platform : osx-64
user-agent : conda/4.7.8 requests/2.22.0 CPython/3.7.3 Darwin/17.5.0 OSX/10.13.4
UID:GID : 501:20
netrc file : None
offline mode : False
but I'm still getting an error (although its a different one now). I've gotten this error before, but it was transient and went away so I had assumed it was a connectivity error. Maybe not?
conda install -c conda-forge r-base
Collecting package metadata (current_repodata.json): done
Solving environment: failed with current_repodata.json, will retry with next repodata source.
Initial quick solve with frozen env failed. Unfreezing env and trying again.
Solving environment: failed with current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/Users/langmm/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1062, in __call__
return func(*args, **kwargs)
File "/Users/langmm/miniconda3/lib/python3.7/site-packages/conda/cli/main.py", line 84, in _main
exit_code = do_call(args, p)
File "/Users/langmm/miniconda3/lib/python3.7/site-packages/conda/cli/conda_argparse.py", line 82, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/Users/langmm/miniconda3/lib/python3.7/site-packages/conda/cli/main_install.py", line 20, in execute
install(args, parser, 'install')
File "/Users/langmm/miniconda3/lib/python3.7/site-packages/conda/cli/install.py", line 256, in install
force_reinstall=context.force_reinstall or context.force,
File "/Users/langmm/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 112, in solve_for_transaction
force_remove, force_reinstall)
File "/Users/langmm/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 150, in solve_for_diff
force_remove)
File "/Users/langmm/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 262, in solve_final_state
ssc = self._run_sat(ssc)
File "/Users/langmm/miniconda3/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
return f(*args, **kwds)
File "/Users/langmm/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 780, in _run_sat
repodata_fn=self._repodata_fn)
File "/Users/langmm/miniconda3/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
return f(*args, **kwds)
File "/Users/langmm/miniconda3/lib/python3.7/site-packages/conda/resolve.py", line 1219, in solve
self.find_conflicts(specs, specs_to_add, history_specs)
File "/Users/langmm/miniconda3/lib/python3.7/site-packages/conda/resolve.py", line 336, in find_conflicts
bad_deps = self.build_conflict_map(specs, specs_to_add, history_specs)
File "/Users/langmm/miniconda3/lib/python3.7/site-packages/conda/resolve.py", line 425, in build_conflict_map
deps = set.union(*[set(self.ms_depends_.get(prec)) for prec in precs])
File "/Users/langmm/miniconda3/lib/python3.7/site-packages/conda/resolve.py", line 425, in <listcomp>
deps = set.union(*[set(self.ms_depends_.get(prec)) for prec in precs])
TypeError: 'NoneType' object is not iterable
`$ /Users/langmm/miniconda3/bin/conda install -c conda-forge r-base`
environment variables:
CIO_TEST=<not set>
CONDA_BACKUP_AR=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-darwin13.4.0-ar
CONDA_BACKUP_AS=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-darwin13.4.0-as
CONDA_BACKUP_CC=x86_64-apple-darwin13.4.0-clang
CONDA_BACKUP_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE
-fstack-protector-strong -O2 -pipe
CONDA_BACKUP_CHECKSYMS=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
darwin13.4.0-checksyms
CONDA_BACKUP_CLANG=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
darwin13.4.0-clang
CONDA_BACKUP_CLANGXX=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
darwin13.4.0-clang++
CONDA_BACKUP_CODESIGN_ALLOCATE=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
darwin13.4.0-codesign_allocate
CONDA_BACKUP_CONDA_BUILD_SYSROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/D
eveloper/SDKs/MacOSX10.13.sdk
CONDA_BACKUP_CPPFLAGS=-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9
CONDA_BACKUP_CXX=x86_64-apple-darwin13.4.0-clang++
CONDA_BACKUP_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE
-fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-
inlines-hidden -std=c++14 -fmessage-length=0
CONDA_BACKUP_DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE
-fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra
CONDA_BACKUP_DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE
-fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-
inlines-hidden -std=c++14 -fmessage-length=0 -Og -g -Wall -Wextra
CONDA_BACKUP_DEBUG_FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector
-O2 -pipe
CONDA_BACKUP_DEBUG_FORTRANFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector
-O2 -pipe
CONDA_BACKUP_FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector
-O2 -pipe
CONDA_BACKUP_FORTRANFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector
-O2 -pipe
CONDA_BACKUP_GFORTRAN=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
darwin13.4.0-gfortran
CONDA_BACKUP_HOST=x86_64-apple-darwin13.4.0
CONDA_BACKUP_INDR=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-darwin13.4.0-indr
CONDA_BACKUP_INSTALL_NAME_TOOL=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
darwin13.4.0-install_name_tool
CONDA_BACKUP_LD=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-darwin13.4.0-ld
CONDA_BACKUP_LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs
CONDA_BACKUP_LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs
CONDA_BACKUP_LIBTOOL=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
darwin13.4.0-libtool
CONDA_BACKUP_LIPO=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-darwin13.4.0-lipo
CONDA_BACKUP_NM=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-darwin13.4.0-nm
CONDA_BACKUP_NMEDIT=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
darwin13.4.0-nmedit
CONDA_BACKUP_OTOOL=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
darwin13.4.0-otool
CONDA_BACKUP_PAGESTUFF=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
darwin13.4.0-pagestuff
CONDA_BACKUP_RANLIB=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
darwin13.4.0-ranlib
CONDA_BACKUP_REDO_PREBINDING=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
darwin13.4.0-redo_prebinding
CONDA_BACKUP_SEGEDIT=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
darwin13.4.0-segedit
CONDA_BACKUP_SEG_ADDR_TABLE=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
darwin13.4.0-seg_addr_table
CONDA_BACKUP_SEG_HACK=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
darwin13.4.0-seg_hack
CONDA_BACKUP_SIZE=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-darwin13.4.0-size
CONDA_BACKUP_STRINGS=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
darwin13.4.0-strings
CONDA_BACKUP_STRIP=/Users/langmm/miniconda3/envs/test2/bin/x86_64-apple-
darwin13.4.0-strip
CONDA_BACKUP__CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0
CONDA_DEFAULT_ENV=conda36
CONDA_EXE=/Users/langmm/miniconda3/bin/conda
CONDA_PREFIX=/Users/langmm/miniconda3/envs/conda36
CONDA_PREFIX_1=/Users/langmm/miniconda3
CONDA_PROMPT_MODIFIER=(conda36)
CONDA_PYTHON_EXE=/Users/langmm/miniconda3/bin/python
CONDA_ROOT=/Users/langmm/miniconda3
CONDA_SHLVL=2
PATH=/Users/langmm/miniconda3/bin:/Users/langmm/miniconda3/envs/conda36/bin
:/Users/langmm/miniconda3/condabin:/Users/langmm/anaconda/bin:/usr/loc
al/opt/openssl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Libra
ry/TeX/texbin:/opt/X11/bin:/Users/langmm/Library/Android/sdk/tools:/Us
ers/langmm/Library/Android/sdk/tools/bin:/Users/langmm/Library/Android
/sdk/platform-tools:/Applications/MATLAB_R2018b.app/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
active environment : conda36
active env location : /Users/langmm/miniconda3/envs/conda36
shell level : 2
user config file : /Users/langmm/.condarc
populated config files : /Users/langmm/.condarc
conda version : 4.7.8
conda-build version : 3.18.7
python version : 3.7.3.final.0
virtual packages :
base environment : /Users/langmm/miniconda3 (writable)
channel URLs : https://conda.anaconda.org/conda-forge/osx-64
https://conda.anaconda.org/conda-forge/noarch
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/langmm/miniconda3/pkgs
/Users/langmm/.conda/pkgs
envs directories : /Users/langmm/miniconda3/envs
/Users/langmm/.conda/envs
platform : osx-64
user-agent : conda/4.7.8 requests/2.22.0 CPython/3.7.3 Darwin/17.5.0 OSX/10.13.4
UID:GID : 501:20
netrc file : None
offline mode : False
I should note that conda 4.7.7 is the one that was installed by the miniconda for mac installer. Maybe this is in error?
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jdblischak
commented on June 25, 2024
@langmm I noticed that you have the r channel in your channel list. Everything you need should be either in conda-forge and/or defaults. Try removing it:
conda config --remove channels r
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jdblischak
commented on June 25, 2024
I am able to replicate the error on macOS when I include the r channel and set strict channel priority. Strangely, when I don't specify strict channel priority, r-base gets installed from the r channel even though that channel has the lowest priority (and the version of R is older).
$ conda config --get channels
--add channels 'r' # lowest priority
--add channels 'defaults'
--add channels 'conda-forge' # highest priority
$ conda install -c conda-forge r-base
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /Users/jdblischak/miniconda3
added / updated specs:
- r-base
The following packages will be downloaded:
package | build
---------------------------|-----------------
libgcc-4.8.5 | hdbeacc1_10 302 KB conda-forge
r-base-3.3.1 | 0 45.3 MB
------------------------------------------------------------
Total: 45.6 MB
The following NEW packages will be INSTALLED:
_r-mutex conda-forge/noarch::_r-mutex-1.0.1-anacondar_1
curl conda-forge/osx-64::curl-7.65.2-h22ea746_0
gsl conda-forge/osx-64::gsl-2.5-ha2d443c_0
jpeg conda-forge/osx-64::jpeg-9c-h1de35cc_1001
krb5 conda-forge/osx-64::krb5-1.16.3-hcfa6398_1001
libblas conda-forge/osx-64::libblas-3.8.0-10_openblas
libcblas conda-forge/osx-64::libcblas-3.8.0-10_openblas
libcurl conda-forge/osx-64::libcurl-7.65.2-h16faf7d_0
libedit conda-forge/osx-64::libedit-3.1.20170329-hcfe32e1_1001
libgcc conda-forge/osx-64::libgcc-4.8.5-hdbeacc1_10
libgfortran conda-forge/osx-64::libgfortran-3.0.1-0
libopenblas conda-forge/osx-64::libopenblas-0.3.6-hd44dcd8_4
libpng conda-forge/osx-64::libpng-1.6.37-h2573ce8_0
libssh2 conda-forge/osx-64::libssh2-1.8.2-hcdc9a53_2
libtiff conda-forge/osx-64::libtiff-4.0.10-hd08fb8f_1003
openblas conda-forge/osx-64::openblas-0.3.6-hd44dcd8_4
pcre conda-forge/osx-64::pcre-8.41-h0a44026_1003
r-base pkgs/r/osx-64::r-base-3.3.1-0
Proceed ([y]/n)? n
CondaSystemExit: Exiting.
$ conda install --strict-channel-priority -c conda-forge r-base
Collecting package metadata (current_repodata.json): done
Solving environment: failed with current_repodata.json, will retry with next repodata source.
Initial quick solve with frozen env failed. Unfreezing env and trying again.
Solving environment: failed with current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/Users/jdblischak/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1062, in __call__
return func(*args, **kwargs)
File "/Users/jdblischak/miniconda3/lib/python3.7/site-packages/conda/cli/main.py", line 84, in _main
exit_code = do_call(args, p)
File "/Users/jdblischak/miniconda3/lib/python3.7/site-packages/conda/cli/conda_argparse.py", line 82, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/Users/jdblischak/miniconda3/lib/python3.7/site-packages/conda/cli/main_install.py", line 20, in execute
install(args, parser, 'install')
File "/Users/jdblischak/miniconda3/lib/python3.7/site-packages/conda/cli/install.py", line 256, in install
force_reinstall=context.force_reinstall or context.force,
File "/Users/jdblischak/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 112, in solve_for_transaction
force_remove, force_reinstall)
File "/Users/jdblischak/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 150, in solve_for_diff
force_remove)
File "/Users/jdblischak/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 262, in solve_final_state
ssc = self._run_sat(ssc)
File "/Users/jdblischak/miniconda3/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
return f(*args, **kwds)
File "/Users/jdblischak/miniconda3/lib/python3.7/site-packages/conda/core/solve.py", line 780, in _run_sat
repodata_fn=self._repodata_fn)
File "/Users/jdblischak/miniconda3/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
return f(*args, **kwds)
File "/Users/jdblischak/miniconda3/lib/python3.7/site-packages/conda/resolve.py", line 1219, in solve
self.find_conflicts(specs, specs_to_add, history_specs)
File "/Users/jdblischak/miniconda3/lib/python3.7/site-packages/conda/resolve.py", line 336, in find_conflicts
bad_deps = self.build_conflict_map(specs, specs_to_add, history_specs)
File "/Users/jdblischak/miniconda3/lib/python3.7/site-packages/conda/resolve.py", line 425, in build_conflict_map
deps = set.union(*[set(self.ms_depends_.get(prec)) for prec in precs])
File "/Users/jdblischak/miniconda3/lib/python3.7/site-packages/conda/resolve.py", line 425, in <listcomp>
deps = set.union(*[set(self.ms_depends_.get(prec)) for prec in precs])
TypeError: 'NoneType' object is not iterable
`$ /Users/jdblischak/miniconda3/bin/conda install --strict-channel-priority -c conda-forge r-base`
environment variables:
CIO_TEST=<not set>
CONDA_BACKUP_AR=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-ar
CONDA_BACKUP_AS=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-as
CONDA_BACKUP_CC=x86_64-apple-darwin13.4.0-clang
CONDA_BACKUP_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE
-fstack-protector-strong -O2 -pipe
CONDA_BACKUP_CHECKSYMS=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-checksyms
CONDA_BACKUP_CLANG=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-clang
CONDA_BACKUP_CLANGXX=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-clang++
CONDA_BACKUP_CODESIGN_ALLOCATE=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-codesign_allocate
CONDA_BACKUP_CPPFLAGS=-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9
CONDA_BACKUP_CXX=x86_64-apple-darwin13.4.0-clang++
CONDA_BACKUP_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE
-fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-
inlines-hidden -std=c++14 -fmessage-length=0
CONDA_BACKUP_DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE
-fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra
CONDA_BACKUP_DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE
-fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-
inlines-hidden -std=c++14 -fmessage-length=0 -Og -g -Wall -Wextra
CONDA_BACKUP_DEBUG_FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector
-O2 -pipe
CONDA_BACKUP_DEBUG_FORTRANFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector
-O2 -pipe
CONDA_BACKUP_FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector
-O2 -pipe
CONDA_BACKUP_FORTRANFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector
-O2 -pipe
CONDA_BACKUP_GFORTRAN=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-gfortran
CONDA_BACKUP_HOST=x86_64-apple-darwin13.4.0
CONDA_BACKUP_INDR=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-indr
CONDA_BACKUP_INSTALL_NAME_TOOL=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-install_name_tool
CONDA_BACKUP_LD=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-ld
CONDA_BACKUP_LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs
CONDA_BACKUP_LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs
CONDA_BACKUP_LIBTOOL=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-libtool
CONDA_BACKUP_LIPO=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-lipo
CONDA_BACKUP_NM=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-nm
CONDA_BACKUP_NMEDIT=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-nmedit
CONDA_BACKUP_OTOOL=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-otool
CONDA_BACKUP_PAGESTUFF=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-pagestuff
CONDA_BACKUP_RANLIB=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-ranlib
CONDA_BACKUP_REDO_PREBINDING=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-redo_prebinding
CONDA_BACKUP_SEGEDIT=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-segedit
CONDA_BACKUP_SEG_ADDR_TABLE=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-seg_addr_table
CONDA_BACKUP_SEG_HACK=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-seg_hack
CONDA_BACKUP_SIZE=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-size
CONDA_BACKUP_STRINGS=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-strings
CONDA_BACKUP_STRIP=/Users/jdblischak/miniconda3/envs/test-rbase/bin/x86_64-apple-
darwin13.4.0-strip
CONDA_BACKUP__CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0
CONDA_DEFAULT_ENV=base
CONDA_EXE=/Users/jdblischak/miniconda3/bin/conda
CONDA_PREFIX=/Users/jdblischak/miniconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/Users/jdblischak/miniconda3/bin/python
CONDA_ROOT=/Users/jdblischak/miniconda3
CONDA_SHLVL=1
PATH=/Users/jdblischak/miniconda3/bin:/Users/jdblischak/miniconda3/bin:/Use
rs/jdblischak/miniconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/sb
in:/sbin:/opt/X11/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
active environment : base
active env location : /Users/jdblischak/miniconda3
shell level : 1
user config file : /Users/jdblischak/.condarc
populated config files : /Users/jdblischak/.condarc
conda version : 4.7.8
conda-build version : not installed
python version : 3.7.3.final.0
virtual packages :
base environment : /Users/jdblischak/miniconda3 (writable)
channel URLs : https://conda.anaconda.org/conda-forge/osx-64
https://conda.anaconda.org/conda-forge/noarch
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
https://conda.anaconda.org/r/osx-64
https://conda.anaconda.org/r/noarch
package cache : /Users/jdblischak/miniconda3/pkgs
/Users/jdblischak/.conda/pkgs
envs directories : /Users/jdblischak/miniconda3/envs
/Users/jdblischak/.conda/envs
platform : osx-64
user-agent : conda/4.7.8 requests/2.22.0 CPython/3.7.3 Darwin/14.5.0 OSX/10.10.5
UID:GID : 501:20
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers?
[y/N]: n
No report sent. To permanently opt-out, use
$ conda config --set report_errors false
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langmm
commented on June 25, 2024
Downgrading causes a UnsatisfiableError
conda info
active environment : conda36
active env location : /Users/langmm/miniconda3/envs/conda36
shell level : 2
user config file : /Users/langmm/.condarc
populated config files : /Users/langmm/.condarc
conda version : 4.7.5
conda-build version : 3.18.7
python version : 3.7.3.final.0
virtual packages :
base environment : /Users/langmm/miniconda3 (writable)
channel URLs : https://conda.anaconda.org/conda-forge/osx-64
https://conda.anaconda.org/conda-forge/noarch
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/langmm/miniconda3/pkgs
/Users/langmm/.conda/pkgs
envs directories : /Users/langmm/miniconda3/envs
/Users/langmm/.conda/envs
platform : osx-64
user-agent : conda/4.7.5 requests/2.22.0 CPython/3.7.3 Darwin/17.5.0 OSX/10.13.4
UID:GID : 501:20
netrc file : None
offline mode : False
conda install -c conda-forge r-base
Collecting package metadata (current_repodata.json): done
Solving environment: failed
Collecting package metadata (repodata.json): done
Solving environment: failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
- r-base -> _r-mutex=1[build=anacondar_1]
- r-base -> bwidget -> tk -> zlib[version='>=1.2.11,<1.3.0a0']
- r-base -> bzip2[version='>=1.0.6,<2.0a0']
- r-base -> cairo[version='>=1.16.0,<1.17.0a0'] -> freetype[version='>=2.9.1,<3.0a0'] -> libpng[version='>=1.6.35,<1.7.0a0']
- r-base -> cairo[version='>=1.16.0,<1.17.0a0'] -> icu[version='>=58.2,<59.0a0'] -> libcxx[version='>=4.0.1'] -> libcxxabi==8.0.0=4
- r-base -> clang_osx-64=4 -> clang -> compiler-rt==4.0.1=hcfea43d_1
- r-base -> clang_osx-64=4 -> clang -> llvm==4.0.1=1 -> cctools==895=1
- r-base -> clang_osx-64=4 -> clang -> llvm==4.0.1=1 -> ld64==274.2=1 -> llvm-lto-tapi==4.0.1=1
- r-base -> clangxx_osx-64=4 -> clangxx
- r-base -> curl -> krb5[version='>=1.16.3,<1.17.0a0'] -> openssl[version='>=1.1.1a,<1.1.2a']
- r-base -> curl -> libcurl==7.65.2=h16faf7d_0 -> libssh2[version='>=1.8.2,<1.9.0a0']
- r-base -> gcc
- r-base -> gfortran_osx-64=4 -> libgfortran[version='>=3.0.1,<4.0.0.a0']
- r-base -> gsl[version='>=2.5,<2.6.0a0'] -> libblas[version='>=3.8.0,<4.0a0'] -> blis[version='>=0.5.2,<0.5.3.0a0']
- r-base -> gsl[version='>=2.5,<2.6.0a0'] -> libblas[version='>=3.8.0,<4.0a0'] -> libcblas==3.8.0=10_mkl -> liblapack==3.8.0=10_mkl -> liblapacke==3.8.0=10_mkl -> blas=[build=mkl]
- r-base -> gsl[version='>=2.5,<2.6.0a0'] -> libblas[version='>=3.8.0,<4.0a0'] -> mkl[version='>=2019.0,<2020.0a0'] -> intel-openmp
- r-base -> gsl[version='>=2.5,<2.6.0a0'] -> libblas[version='>=3.8.0,<4.0a0'] -> openblas[version='>=0.3.6,<0.3.7.0a0'] -> libopenblas==0.3.6=hd44dcd8_4
- r-base -> gsl[version='>=2.5,<2.6.0a0'] -> libblas[version='>=3.8.0,<4.0a0'] -> openblas[version='>=0.3.6,<0.3.7.0a0'] -> nomkl==3.0=0
- r-base -> gsl[version='>=2.5,<2.6.0a0'] -> libblas[version='>=3.8.0,<4.0a0'] -> openblas[version='>=0.3.6,<0.3.7.0a0'] -> openblas-devel==0.3.6=1
- r-base -> jpeg[version='>=9c,<10a']
- r-base -> libgcc
- r-base -> libiconv[version='>=1.15,<1.16.0a0']
- r-base -> libtiff[version='>=4.0.9,<5.0a0'] -> xz[version='>=5.2.4,<5.3.0a0']
- r-base -> libxml2[version='>=2.9.9,<2.10.0a0']
- r-base -> llvm-openmp[version='>=8.0.0']
- r-base -> make
- r-base -> pango[version='>=1.40.14,<1.41.0a0']
- r-base -> pcre[version='>=8.41,<9.0a0']
- r-base -> readline[version='>=8.0,<9.0a0'] -> ncurses[version='>=6.1,<6.2.0a0']
- r-base -> tktable
Note that strict channel priority may have removed packages required for satisfiability.
conda list
# packages in environment at /Users/langmm/miniconda3/envs/conda36:
#
# Name Version Build Channel
appnope 0.1.0 py36_1000 conda-forge
backcall 0.1.0 py_0 conda-forge
ca-certificates 2019.6.16 hecc5488_0 conda-forge
certifi 2019.6.16 py36_0 conda-forge
decorator 4.4.0 py_0 conda-forge
ipython 7.6.1 py36h5ca1d4c_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
jedi 0.14.1 py36_0 conda-forge
libcxx 8.0.0 4 conda-forge
libcxxabi 8.0.0 4 conda-forge
libffi 3.2.1 h6de7cb9_1006 conda-forge
ncurses 6.1 h0a44026_1002 conda-forge
openssl 1.1.1c h01d97ff_0 conda-forge
parso 0.5.0 py_0 conda-forge
pexpect 4.7.0 py36_0 conda-forge
pickleshare 0.7.5 py36_1000 conda-forge
pip 19.1.1 py36_0 conda-forge
prompt_toolkit 2.0.9 py_0 conda-forge
ptyprocess 0.6.0 py_1001 conda-forge
pygments 2.4.2 py_0 conda-forge
python 3.6.7 h94afb7f_1005 conda-forge
readline 8.0 hcfe32e1_0 conda-forge
setuptools 41.0.1 py36_0 conda-forge
six 1.12.0 py36_1000 conda-forge
sqlite 3.29.0 hb7d70f7_0 conda-forge
tk 8.6.9 h2573ce8_1002 conda-forge
traitlets 4.3.2 py36_1000 conda-forge
wcwidth 0.1.7 py_1 conda-forge
wheel 0.33.4 py36_0 conda-forge
xz 5.2.4 h1de35cc_1001 conda-forge
zlib 1.2.11 h01d97ff_1005 conda-forge
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langmm
commented on June 25, 2024
This looks to be due to the pinning of the llvm packages at 4.0.1 and is an issue I've run into with the python libraries on conda 4.7.5.
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ocefpaf
commented on June 25, 2024
This looks to be due to the pinning of the llvm packages at 4.0.1 and is an issue I've run into with the python libraries on conda 4.7.5.
Thanks for the report. IMO strict has a bug that, when a package is tightly pinned strict won't pull it from another channel even when that is the right thing to do.
You can try flexible for now but I'm thinking that maybe we should vender libcxx 4.0.1 to prevent that. @isuruf what do you think?
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ocefpaf
commented on June 25, 2024
I added 4.0.1 to conda-forge temporarily. 4.0.1 has serious issues with C++ exceptions and we should fix the compiler package. I'd appreciate a PR to AnacondaRecipes/aggregate:llvm-compilers-feedstock/recipe/meta.yaml@
ece8f31
Thanks!
Using flexible causes conda to install r-base from defaults (conda 4.7.5) which I'm unsure will work since I am using reticulate to call python functions from R and if python and R use different C compilers and shared libraries, segfaults are the result. Are the issues with C++ exceptions why the libcxx 4.0.1 package was marked broken on osx? There are many packages that pin libcxx to 4.0.1, so a fix to libcxx 4.0.1 would help a lot.
I added libcxxabi 4.0.1 hcfea43d_1, a missing dependency, and it should be installable with strict in ~40 min (the CDN sync time).
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isuruf
commented on June 25, 2024
There are many packages that pin libcxx to 4.0.1, so a fix to libcxx 4.0.1 would help a lot.
Which ones?
Are the issues with C++ exceptions why the libcxx 4.0.1 package was marked broken on osx?
Yes, there was an attempt to fix this, but it resulted in more issues. moving to libcxx 8 works. I don't have the time nor access to osx to backport the PR to 4.0.1
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langmm
commented on June 25, 2024
It looks like I was wrong, I'm currently only seeing r-base as requiring 4.0.1 strictly (at least in the packages I work with).
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langmm
commented on June 25, 2024
Great, thank you! (and sorry for any notifications due to my clumsy selection of the incorrect reaction)
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medb
commented on June 25, 2024
I still face this issue in fresh Anaconda 2020.07 environment when installing r-base 4.0.2 from conda-forge channel:
conda install -c conda-forge --strict-channel-priority r-base=4.0.2
Are there any workarounds to install latest version of r-base?
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isuruf
commented on June 25, 2024
Outdated issue. Please open a new issue if this issue still exists.
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Related Issues (20)
- Prepare for R 4.1 HOT 6
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- R-base 4.2 integration HOT 4
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- ETA for Windows r-base > 4.1.3? HOT 10
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- Cannot install r-base and imagmagick in the same environment on Ubuntu 22.04 HOT 2
- BLAS/LAPACK linked libraries not delivered in build variants HOT 5
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