Open mathomp4 opened 1 year ago
Interesting find, I think this is an edge case not handled by Mamba (file type change)
Can you fix it by removing the old version first?
Can you fix it by removing the old version first?
@jonashaag Well, if I do the "remove file" way, yes it works. But let me try an uninstall.
@jonashaag Doesn't seem to help. I tried and:
❯ /Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/bin/micromamba -p /Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14 remove libcxx
Transaction
Prefix: /Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14
Removing specs:
- libcxx
Package Version Build Channel Size
───────────────────────────────────────────────────────────────────────────────
Remove:
───────────────────────────────────────────────────────────────────────────────
- conda-libmamba-solver 23.5.0 py311hecd8cb5_0 pkgs/main 87kB
- libmambapy 1.4.1 py311h8c3233a_1 pkgs/main 261kB
- pybind11-abi 4 hd3eb1b0_1 pkgs/main 14kB
- libmamba 1.4.1 h8c3233a_1 pkgs/main 1MB
- yaml-cpp 0.7.0 he9d5cce_1 pkgs/main 452kB
- reproc-cpp 14.2.4 he9d5cce_1 pkgs/main 20kB
- libsolv 0.7.22 h8346a28_0 pkgs/main 407kB
- libcurl 8.1.1 hf20ceda_1 pkgs/main 369kB
- libarchive 3.6.2 h29ab7a1_2 pkgs/main 800kB
- fmt 9.1.0 ha357a0b_0 pkgs/main 190kB
- reproc 14.2.4 he9d5cce_1 pkgs/main 27kB
- pcre2 10.37 he7042d7_1 pkgs/main 843kB
- libssh2 1.10.0 h04015c4_2 pkgs/main 281kB
- libnghttp2 1.52.0 h9beae6a_1 pkgs/main 678kB
- krb5 1.20.1 h428f121_1 pkgs/main 1MB
- zstd 1.5.5 hc035e20_0 pkgs/main 622kB
- libxml2 2.10.3 h930c0e2_0 pkgs/main 681kB
- libev 4.33 h9ed2024_1 pkgs/main 108kB
- c-ares 1.19.0 h6c40b1e_0 pkgs/main 107kB
- libedit 3.1.20221030 h6c40b1e_0 pkgs/main 159kB
- lz4-c 1.9.4 hcec6c5f_0 pkgs/main 171kB
- libiconv 1.16 hca72f7f_2 pkgs/main 711kB
- icu 58.2 h0a44026_3 pkgs/main 11MB
- libcxx 14.0.6 h9765a3e_0 pkgs/main 991kB
Summary:
Remove: 24 packages
Total download: 0 B
───────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] y
Transaction starting
Unlinking conda-libmamba-solver-23.5.0-py311hecd8cb5_0
Unlinking libmambapy-1.4.1-py311h8c3233a_1
Unlinking pybind11-abi-4-hd3eb1b0_1
Unlinking libmamba-1.4.1-h8c3233a_1
Unlinking yaml-cpp-0.7.0-he9d5cce_1
Unlinking reproc-cpp-14.2.4-he9d5cce_1
Unlinking libsolv-0.7.22-h8346a28_0
Unlinking libcurl-8.1.1-hf20ceda_1
Unlinking libarchive-3.6.2-h29ab7a1_2
Unlinking fmt-9.1.0-ha357a0b_0
Unlinking reproc-14.2.4-he9d5cce_1
Unlinking pcre2-10.37-he7042d7_1
Unlinking libssh2-1.10.0-h04015c4_2
Unlinking libnghttp2-1.52.0-h9beae6a_1
Unlinking krb5-1.20.1-h428f121_1
Unlinking zstd-1.5.5-hc035e20_0
Unlinking libxml2-2.10.3-h930c0e2_0
Unlinking libev-4.33-h9ed2024_1
Unlinking c-ares-1.19.0-h6c40b1e_0
Unlinking libedit-3.1.20221030-h6c40b1e_0
Unlinking lz4-c-1.9.4-hcec6c5f_0
Unlinking libiconv-1.16-hca72f7f_2
Unlinking icu-58.2-h0a44026_3
Unlinking libcxx-14.0.6-h9765a3e_0
Transaction finished
To activate this environment, use:
micromamba activate /Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14
Or to execute a single command in this environment, use:
micromamba run -p /Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14 mycommand
~/TestMiniforgeLibcxx at 12:41:38 PM
❯ /Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/bin/micromamba -p /Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14 install esmpy
conda-forge/osx-64 Using cache
conda-forge/noarch Using cache
pkgs/main/noarch No change
pkgs/r/osx-64 No change
pkgs/r/noarch No change
pkgs/main/osx-64 No change
Pinned packages:
- python 3.11.*
Transaction
Prefix: /Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14
Updating specs:
- esmpy
Package Version Build Channel Size
──────────────────────────────────────────────────────────────────────────────────
Install:
──────────────────────────────────────────────────────────────────────────────────
+ libzlib 1.2.13 h8a1eda9_5 conda-forge Cached
+ python_abi 3.11 2_cp311 conda-forge Cached
+ libcxx 16.0.6 hd57cbcb_0 conda-forge Cached
+ llvm-openmp 16.0.6 hff08bdf_0 conda-forge Cached
+ libjpeg-turbo 2.1.5.1 hb7f2c08_0 conda-forge Cached
+ mpi 1.0 mpich conda-forge Cached
+ libiconv 1.17 hac89ed1_0 conda-forge Cached
+ icu 72.1 h7336db1_0 conda-forge Cached
+ c-ares 1.19.1 h0dc2134_0 conda-forge Cached
+ libev 4.33 haf1e3a3_1 conda-forge Cached
+ libedit 3.1.20191231 h0678c8f_2 conda-forge Cached
+ libzip 1.9.2 h6db710c_1 conda-forge Cached
+ zstd 1.5.2 h829000d_7 conda-forge Cached
+ libssh2 1.10.0 h47af595_3 conda-forge 227kB
+ libaec 1.0.6 hf0c8a7f_1 conda-forge Cached
+ lz4-c 1.9.4 hf0c8a7f_0 conda-forge Cached
+ snappy 1.1.10 h225ccf5_0 conda-forge Cached
+ libgfortran5 12.2.0 he409387_31 conda-forge Cached
+ hdf4 4.2.15 h9804679_6 conda-forge Cached
+ libxml2 2.11.4 hd95e348_0 conda-forge Cached
+ libnghttp2 1.52.0 he2ab024_0 conda-forge Cached
+ krb5 1.20.1 h049b76e_0 conda-forge Cached
+ blosc 1.21.4 heccf04b_0 conda-forge Cached
+ libgfortran 5.0.0 11_3_0_h97931a8_31 conda-forge Cached
+ libcurl 7.88.1 h6df9250_0 conda-forge 343kB
+ mpich 4.1.1 hd33e60e_100 conda-forge Cached
+ libopenblas 0.3.23 openmp_h429af6e_0 conda-forge Cached
+ curl 7.88.1 h6df9250_0 conda-forge 143kB
+ hdf5 1.14.0 mpi_mpich_h18663c6_3 conda-forge Cached
+ libblas 3.9.0 17_osx64_openblas conda-forge Cached
+ libnetcdf 4.9.2 mpi_mpich_h4b56550_5 conda-forge 734kB
+ libcblas 3.9.0 17_osx64_openblas conda-forge Cached
+ liblapack 3.9.0 17_osx64_openblas conda-forge Cached
+ netcdf-fortran 4.6.1 mpi_mpich_h2786e36_0 conda-forge Cached
+ parallelio 2.5.10 mpi_mpich_hda3997c_102 conda-forge Cached
+ numpy 1.25.1 py311hc44ba51_0 conda-forge Cached
+ esmf 8.4.2 mpi_mpich_h39d0f2c_100 conda-forge Cached
+ esmpy 8.4.2 pyhc1e730c_1 conda-forge Cached
Change:
──────────────────────────────────────────────────────────────────────────────────
- zlib 1.2.13 h4dc903c_0 pkgs/main 98kB
+ zlib 1.2.13 h8a1eda9_5 conda-forge Cached
Summary:
Install: 38 packages
Change: 1 packages
Total download: 1MB
──────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] y
Transaction starting
libssh2 227.0kB @ 352.8kB/s 0.6s
libcurl 342.9kB @ 509.9kB/s 0.7s
curl 143.3kB @ 161.0kB/s 0.9s
libnetcdf 734.0kB @ 711.9kB/s 1.0s
Linking libzlib-1.2.13-h8a1eda9_5
warning libmamba [libzlib-1.2.13-h8a1eda9_5] The following files were already present in the environment:
- lib/libz.1.2.13.dylib
- lib/libz.1.dylib
Linking python_abi-3.11-2_cp311
Linking libcxx-16.0.6-hd57cbcb_0
critical libmamba filesystem error: in copy_file: Not a directory ["/Users/mathomp4/installed/Core/GEOSpyD/23.5.2-0_py3.11/2023-07-14/include/c++/v1/__string/char_traits.h"] ["/Users/mathomp4/micromamba/pkgs/libcxx-16.0.6-hd57cbcb_0/include/c++/v1/__string/char_traits.h"]
Troubleshooting docs
How did you install Mamba?
Micromamba
Search tried in issue tracker
Yes
Latest version of Mamba
Tried in Conda?
I do not have this problem with Conda, just with Mamba
Describe your issue
Note 1: I previously reported this at https://github.com/conda-forge/libcxx-feedstock/issues/125 but was told to do so here.
Note 2: I also say above "I do not have this problem with Conda, just with Mamba" only because Conda can't even get far enough to do so. When I try to do
conda install esmpy
(as seen below), it spends about 10 minutes trying to solve dependencies and just spits out hundreds of lines of conflicts.I was trying to install a python stack today and it failed due to an issue with libcxx. To wit, I started with Miniconda3 23.5.2-0 for Intel Mac (Miniconda3-py311_23.5.2-0-MacOSX-x86_64.sh) and installed it. I then grabbed and installed
micromamba
as, for reasons I don't know, it's the only installer that works for me.I then tried
micromamba install esmpy
. One of the things this calls for I guess is an update to libcxx due to an update in conda-forge (see my.condarc
):but:
And this is true, that is a file, not a directory:
And if I look at llvm, in 14.0.6
__string
was a file, but in 16.0.6, it's a directory.Is there perhaps some special command I need to pass to
micromamba
to allow this to work?I can get it to work by using some sort of:
before I know libcxx will be updated, but that seems ... not right to me.
mamba info / micromamba info
Logs
environment.yml
No response
~/.condarc