Open pawelqs opened 2 years ago
mguijarr
commented
2 years ago I had the same problem with conda build. After days of struggle, I switched to boa : problem solved using the conda mambabuild command instead of conda build. Works like a charm.
pawelqs
commented
2 years ago @mguijarr It's working! Thanks a lot! So many snakes to use instead of conda :)
mguijarr
commented
2 years ago I don't think this should be closed, since it is not solved with conda itself.
pawelqs
commented
2 years ago Reopened ;)
stefdoerr
commented
2 years ago I was able to fix it by forcing higher numpy version (>=1.17) in my meta.yaml file.
boa actually highlighted the issue to me more clearly but after increasing numpy version I don't need to use boa anymore.
jehturner
commented
1 year ago See a possible workaround in https://github.com/conda/conda/issues/11442#issuecomment-1416186371.
jehturner
commented
1 year ago I was able to fix it by forcing higher numpy version (>=1.17) in my
meta.yamlfile. boa actually highlighted the issue to me more clearly but after increasing numpy version I don't need to use boa anymore.
I accidentally rediscovered this solution after running into a case that was not solved by the workaround I posted in the last comment. As of writing, it looks like building any package that has conda-forge python and numpy as build/host requirements does not work with conda-build --python=3.10 on Linux, but if the constraint is changed to numpy >=1.17 in meta.yaml it works fine. I think this bug must occur during the process of comparing available package versions, rather than due to a real dependency conflict. Specifying --numpy=<version> for conda-build makes no difference (there aren't even any numpy builds earlier than 1.21 for Python 3.10).
This issue can be reproduced by trying to build the following trivial meta.yaml with or without the numpy version uncommented:
package:
name: test
version: 0.1
build:
number: '0'
script: touch ${PREFIX}/a_file
requirements:
build:
- python
- numpy # >=1.17
run:
- python
- numpy # >=1.17It seems that some change within the conda-forge channel (probably the addition of certain builds?) has broken recipes that were previously working. I think this is really a conda problem (in fact I see @minrk says so here), but it mostly shows up when using conda-build and I'm just trying to document the manifestation a bit better. This has nothing explicitly to do with MPI.
chebee7i
commented
1 year ago Any progress on this? I'm hitting this regularly and have to use mambabuild instead.
ValueError: Incompatible component merge:
- '*mpich*'
- 'mpi_mpich_*'$ cat meta.yaml
{% set name = "bitsandbytes" %}
{% set version = "0.39.0" %}
package:
name: "{{ name|lower }}"
version: "{{ version }}"
build:
number: 0
requirements:
host:
- pip
- python {{ PY_VER }}*,>=3.6
- absl-py
- nltk
- numpy
- six>=1.14
run:
- python {{ PY_VER }}*,>=3.6
- absl-py
- nltk
- numpy
- six>=1.14
test:
imports:
- bitsandbytes
$ cat build.sh
pip install bitsandbytes==0.39.0
tazimmerman
commented
1 year ago @chebee7i Did you try using numpy >=1.17 in your recipe? I have a similar issue and that minor change actually worked for me with plain conda-build.
chebee7i
commented
1 year ago That does indeed seem to fix the issue. Very weird that we need it, since it should be picking up something much more recent than 1.17 even.
mooreniemi
commented
1 year ago Restricting to >=1.19 did not work for me.
14 requirements:
15 build:
16 - python
17 - numpy>=1.19
18 - setuptools
19 - pip
20 run:
21 - python
22 - numpy>=1.19Switching to mambabuild did work for me.
rphel
commented
1 year ago Still hitting this issue with numpy 1.22.
github-actions[bot]
commented
2 months ago Hi there, thank you for your contribution!
This issue has been automatically marked as stale because it has not had recent activity. It will be closed automatically if no further activity occurs.
If you would like this issue to remain open please:
NOTE: If this issue was closed prematurely, please leave a comment.
Thanks!
minrk
commented
2 months ago I'd appreciate it if stale bots didn't create work for people.
Still an issue, fix is known: https://github.com/conda/conda/pull/11612
> command conda create -n test --dry-run 'petsc=*=real*' 'petsc=*=real_*'
Retrieving notices: ...working... done
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/Users/minrk/conda/lib/python3.11/site-packages/conda/exception_handler.py", line 18, in __call__
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/Users/minrk/conda/lib/python3.11/site-packages/conda/cli/main.py", line 84, in main_subshell
exit_code = do_call(args, parser)
^^^^^^^^^^^^^^^^^^^^^
File "/Users/minrk/conda/lib/python3.11/site-packages/conda/cli/conda_argparse.py", line 200, in do_call
result = getattr(module, func_name)(args, parser)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/minrk/conda/lib/python3.11/site-packages/conda/notices/core.py", line 127, in wrapper
return_value = func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/Users/minrk/conda/lib/python3.11/site-packages/conda/cli/main_create.py", line 148, in execute
return install(args, parser, "create")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/minrk/conda/lib/python3.11/site-packages/conda/cli/install.py", line 368, in install
solver = solver_backend(
^^^^^^^^^^^^^^^
File "/Users/minrk/conda/lib/python3.11/site-packages/conda_libmamba_solver/solver.py", line 87, in __init__
super().__init__(
File "/Users/minrk/conda/lib/python3.11/site-packages/conda/core/solve.py", line 96, in __init__
self.specs_to_add = frozenset(MatchSpec.merge(s for s in specs_to_add))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/minrk/conda/lib/python3.11/site-packages/conda/models/match_spec.py", line 504, in merge
reduce(lambda x, y: x._merge(y, union), group)
File "/Users/minrk/conda/lib/python3.11/site-packages/conda/models/match_spec.py", line 504, in <lambda>
reduce(lambda x, y: x._merge(y, union), group)
^^^^^^^^^^^^^^^^^^
File "/Users/minrk/conda/lib/python3.11/site-packages/conda/models/match_spec.py", line 536, in _merge
final = this_component.merge(that_component)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/minrk/conda/lib/python3.11/site-packages/conda/models/match_spec.py", line 828, in merge
raise ValueError(
ValueError: Incompatible component merge:
- 'real*'
- 'real_*'
`$ /Users/minrk/conda/condabin/conda create -n test --dry-run petsc=*=real* petsc=*=real_*`
environment variables:
AUTOJUMP_ERROR_PATH=/Users/minrk/Library/autojump/errors.log
CIO_TEST=<not set>
CONDA_ALLOW_SOFTLINKS=false
CONDA_EXE=/Users/minrk/conda/bin/conda
CONDA_PYTHON_EXE=/Users/minrk/conda/bin/python
CONDA_ROOT=/Users/minrk/conda
CONDA_SHLVL=0
CURL_CA_BUNDLE=<not set>
INFOPATH=/opt/homebrew/share/info:
LD_PRELOAD=<not set>
PATH=/Users/minrk/.local/bin:/Users/minrk/dev/mine/git-stuff/bin:/Users/min
rk/dev/mine/dotfiles/bin:/Users/minrk/conda/condabin:/Users/minrk/.kre
w/bin:/Users/minrk/conda/bin:/opt/homebrew/bin:/opt/homebrew/Caskroom/
google-cloud-sdk/latest/google-cloud-sdk/bin:/opt/homebrew/sbin:/usr/l
ocal/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/
var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/b
in:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin
:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/apple
internal/bin:/opt/X11/bin:/Library/Apple/usr/bin:/usr/local/MacGPG2/bi
n:/Library/TeX/texbin:/Applications/Wireshark.app/Contents/MacOS:/Libr
ary/Frameworks/Mono.framework/Versions/Current/Commands
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
active environment : None
shell level : 0
user config file : /Users/minrk/.condarc
populated config files : /Users/minrk/conda/.condarc
/Users/minrk/.condarc
conda version : 24.7.1
conda-build version : 24.5.2.dev60
python version : 3.11.9.final.0
solver : libmamba (default)
virtual packages : __archspec=1=m1
__conda=24.7.1=0
__osx=14.6.1=0
__unix=0=0
base environment : /Users/minrk/conda (writable)
conda av data dir : /Users/minrk/conda/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/foo/osx-arm64
https://conda.anaconda.org/foo/noarch
https://conda.anaconda.org/conda-forge/osx-arm64
https://conda.anaconda.org/conda-forge/noarch
package cache : /Users/minrk/conda/pkgs
/Users/minrk/.conda/pkgs
envs directories : /Users/minrk/conda/envs
/Users/minrk/.conda/envs
platform : osx-arm64
user-agent : conda/24.7.1 requests/2.31.0 CPython/3.11.9 Darwin/23.6.0 OSX/14.6.1 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.8
UID:GID : 501:20
netrc file : /Users/minrk/.netrc
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
If you suspect this error is being caused by a malfunctioning plugin,
consider using the --no-plugins option to turn off plugins.
Example: conda --no-plugins install <package>
Alternatively, you can set the CONDA_NO_PLUGINS environment variable on
the command line to run the command without plugins enabled.
Example: CONDA_NO_PLUGINS=true conda install <package>Interestingly, mamba doesn't appear to have this problem.
Actual Behavior
Hi, I'm trying to build R package which I would like to upload to anaconda. I am following the instructions from here: https://stackoverflow.com/questions/52061664/install-r-package-from-github-using-conda
conda skeleton cran https://github.com/pawel125/clonalityParsersworks fine, although I have to correct the names of two packages: r-genomeinfodb -> bioconductor-genomeinfodb and r-plyranges -> bioconductor-plyrangesUnfortunatelly
conda build --R=4.2.0 r-clonalityparsersresults in the following error:Could you help me to solve this issue? Thanks!
Expected Behavior
Conda builds the package.
Steps to Reproduce
Replace package names in meta.yaml: r-genomeinfodb -> bioconductor-genomeinfodb r-plyranges -> bioconductor-plyranges
Output of conda infoI am using conda version 4.12.0