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20 hours ago •
mamba-org
mamba-org
micromamba env update --prune not working properly
Troubleshooting docs
- [X] My problem is not solved in the Troubleshooting docs
Anaconda default channels
- [X] I do NOT use the Anaconda default channels (pkgs/* etc.)
How did you install Mamba?
Micromamba
Search tried in issue tracker
micromamba env update
Latest version of Mamba
- [X] My problem is not solved with the latest version
Tried in Conda?
I didn't try
Describe your issue
Hello guys,
I have tried the latest release https://github.com/mamba-org/mamba/releases/tag/2023.12.14 to see if command micromamba env update -f ./conda/linux_env.yaml --prune works correctly.
Unfortunately after --prune flag is added, command sometimes fails.
.envrc file
export PATH=$HOME/micromamba:$PATH
export MAMBARC=$(realpath ./.mambarc)
export MAMBA_ROOT_PREFIX="$HOME/micromamba"
eval "$(micromamba shell hook -s posix)"
Steps to reproduce 1.1) Initial environment looks like
[environments.txt](https://github.com/mamba-org/mamba/files/14154424/environments.txt)
1.2) Execute micromamba env create -f ./conda/linux_env.yaml Note: Even if I create .mamba/pkgs at this point, at later stage I will still reproduce the issue
conda-forge/noarch 13.4MB @ 47.7MB/s 0.3s
conda-forge/linux-64 32.2MB @ 36.2MB/s 1.0s
error libmamba Could not lock non-existing path '/home/pandora/.mamba/pkgs'
Transaction
Prefix: /home/pandora/micromamba/envs/linux
Updating specs:
- rattler-build
- valgrind
Package Version Build Channel Size
───────────────────────────────────────────────────────────────────
Install:
───────────────────────────────────────────────────────────────────
+ _libgcc_mutex 0.1 conda_forge conda-forge 3kB
+ _openmp_mutex 4.5 2_gnu conda-forge 24kB
+ ca-certificates 2024.2.2 hbcca054_0 conda-forge 155kB
+ libgcc-ng 13.2.0 h807b86a_5 conda-forge 771kB
+ libgomp 13.2.0 h807b86a_5 conda-forge 420kB
+ libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge 4MB
+ libzlib 1.2.13 hd590300_5 conda-forge 62kB
+ openssl 3.2.1 hd590300_0 conda-forge 3MB
+ rattler-build 0.8.1 h614bb76_0 conda-forge 7MB
+ valgrind 3.22.0 hcd5def8_0 conda-forge 54MB
+ zlib 1.2.13 hd590300_5 conda-forge 93kB
Summary:
Install: 11 packages
Total download: 69MB
2.1) We mow add one package to environment file
name: linux
channels:
- conda-forge
- nodefaults
dependencies:
- rattler-build
- valgrind
- gxx_linux-64=13.*
2.2) Now we execute micromamba env update -f ./conda/linux_env.yaml --prune. Packages are correctly installed
Install:
─────────────────────────────────────────────────────────────────────────────
+ binutils_impl_linux-64 2.40 hf600244_0 conda-forge Cached
+ binutils_linux-64 2.40 hbdbef99_2 conda-forge Cached
+ gcc_impl_linux-64 13.2.0 h338b0a0_5 conda-forge Cached
+ gcc_linux-64 13.2.0 h112eaf3_2 conda-forge Cached
+ gxx_impl_linux-64 13.2.0 h338b0a0_5 conda-forge Cached
+ gxx_linux-64 13.2.0 hc53e3bf_2 conda-forge Cached
+ kernel-headers_linux-64 2.6.32 he073ed8_16 conda-forge Cached
+ ld_impl_linux-64 2.40 h41732ed_0 conda-forge Cached
+ libgcc-devel_linux-64 13.2.0 ha9c7c90_105 conda-forge Cached
+ libsanitizer 13.2.0 h7e041cc_5 conda-forge Cached
+ libstdcxx-devel_linux-64 13.2.0 ha9c7c90_105 conda-forge Cached
+ sysroot_linux-64 2.12 he073ed8_16 conda-forge Cached
Summary:
Install: 12 packages
3.1) Remove the package which we just added and run again
name: linux
channels:
- conda-forge
- nodefaults
dependencies:
- rattler-build
- valgrind
3.2) Run again micromamba env update -f ./conda/linux_env.yaml --prune. Package is successfully removed
Remove:
─────────────────────────────────────────────────────────────────────────────
- binutils_impl_linux-64 2.40 hf600244_0 conda-forge Cached
- binutils_linux-64 2.40 hbdbef99_2 conda-forge Cached
- gcc_impl_linux-64 13.2.0 h338b0a0_5 conda-forge Cached
- gcc_linux-64 13.2.0 h112eaf3_2 conda-forge Cached
- gxx_impl_linux-64 13.2.0 h338b0a0_5 conda-forge Cached
- gxx_linux-64 13.2.0 hc53e3bf_2 conda-forge Cached
- kernel-headers_linux-64 2.6.32 he073ed8_16 conda-forge Cached
- ld_impl_linux-64 2.40 h41732ed_0 conda-forge Cached
- libgcc-devel_linux-64 13.2.0 ha9c7c90_105 conda-forge Cached
- libsanitizer 13.2.0 h7e041cc_5 conda-forge Cached
- libstdcxx-devel_linux-64 13.2.0 ha9c7c90_105 conda-forge Cached
- sysroot_linux-64 2.12 he073ed8_16 conda-forge Cached
4.1) Add again the same package back to env file
name: linux
channels:
- conda-forge
- nodefaults
dependencies:
- rattler-build
- valgrind
- gxx_linux-64=13.*
4.2) Run again micromamba env update -f ./conda/linux_env.yaml --prune. Package is installed correctly again
Install:
─────────────────────────────────────────────────────────────────────────────
+ binutils_impl_linux-64 2.40 hf600244_0 conda-forge Cached
+ binutils_linux-64 2.40 hbdbef99_2 conda-forge Cached
+ gcc_impl_linux-64 13.2.0 h338b0a0_5 conda-forge Cached
+ gcc_linux-64 13.2.0 h112eaf3_2 conda-forge Cached
+ gxx_impl_linux-64 13.2.0 h338b0a0_5 conda-forge Cached
+ gxx_linux-64 13.2.0 hc53e3bf_2 conda-forge Cached
+ kernel-headers_linux-64 2.6.32 he073ed8_16 conda-forge Cached
+ ld_impl_linux-64 2.40 h41732ed_0 conda-forge Cached
+ libgcc-devel_linux-64 13.2.0 ha9c7c90_105 conda-forge Cached
+ libsanitizer 13.2.0 h7e041cc_5 conda-forge Cached
+ libstdcxx-devel_linux-64 13.2.0 ha9c7c90_105 conda-forge Cached
+ sysroot_linux-64 2.12 he073ed8_16 conda-forge Cached
Summary:
Install: 12 packages
Total download: 0 B
- Try to run the same command again. It will fail now
micromamba env update -f ./conda/linux_env.yaml --prune
conda-forge/linux-64 Using cache
conda-forge/noarch Using cache
critical libmamba Could not solve for environment specs
mamba info / micromamba info
libmamba version : 2.0.0
micromamba version : 2.0.0
curl version : libcurl/8.5.0 OpenSSL/3.2.1 zlib/1.2.13 zstd/1.5.5 libssh2/1.11.0 nghttp2/1.58.0
libarchive version : libarchive 3.7.2 zlib/1.2.13 bz2lib/1.0.8 libzstd/1.5.5
envs directories : /home/pandora/micromamba/envs
package cache : /home/pandora/micromamba/pkgs
/home/pandora/.mamba/pkgs
environment : linux (active)
env location : /home/pandora/micromamba/envs/linux
user config files : /home/pandora/.mambarc
populated config files : /app/cpp_training_flakes/.mambarc
virtual packages : __unix=0=0
__linux=6.5.0=0
__glibc=2.35=0
__archspec=1=x86_64-v3
__cuda=12.2=0
channels : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://conda.anaconda.org/nodefaults/linux-64
https://conda.anaconda.org/nodefaults/noarch
base environment : /home/pandora/micromamba
platform : linux-64
Logs
No response
environment.yml
name: linux
channels:
- conda-forge
- nodefaults
dependencies:
- rattler-build
- valgrind
# - gcc_linux-64=13.*
~/.condarc
channels:
- conda-forge
- nodefaults
auto_activate_base: false
channel_priority: strict
