Install script no longer works for updating installations since `_conda` became a symlink

[LorenzoLeonardini]

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

Starting from version 25.11.0-0, the file _conda inside the prefix directory is no longer a binary file, but a symlink to the micromamba binary.

When running the install script with the -u flag for updating the current installation, the script fails as the symlink target already exists:

PREFIX=/root/miniforge3
Unpacking bootstrapper...
ln: failed to create symbolic link '/root/miniforge3/_conda': File exists

Installed packages

# packages in environment at /root/miniforge3:
#
# Name                     Version          Build                 Channel
_libgcc_mutex              0.1              conda_forge           conda-forge
_openmp_mutex              4.5              2_gnu                 conda-forge
archspec                   0.2.5            pyhd8ed1ab_0          conda-forge
boltons                    25.0.0           pyhd8ed1ab_0          conda-forge
brotli-python              1.2.0            py312hdb49522_1       conda-forge
bzip2                      1.0.8            hda65f42_8            conda-forge
c-ares                     1.34.5           hb9d3cd8_0            conda-forge
ca-certificates            2025.11.12       hbd8a1cb_0            conda-forge
certifi                    2025.11.12       pyhd8ed1ab_0          conda-forge
cffi                       2.0.0            py312h460c074_1       conda-forge
charset-normalizer         3.4.4            pyhd8ed1ab_0          conda-forge
colorama                   0.4.6            pyhd8ed1ab_1          conda-forge
conda                      25.11.0          py312h7900ff3_0       conda-forge
conda-libmamba-solver      25.11.0          pyhd8ed1ab_0          conda-forge
conda-package-handling     2.4.0            pyh7900ff3_2          conda-forge
conda-package-streaming    0.12.0           pyhd8ed1ab_0          conda-forge
cpp-expected               1.3.1            h171cf75_0            conda-forge
distro                     1.9.0            pyhd8ed1ab_1          conda-forge
fmt                        12.0.0           h2b0788b_0            conda-forge
frozendict                 2.4.7            py312h4c3975b_0       conda-forge
h2                         4.3.0            pyhcf101f3_0          conda-forge
hpack                      4.1.0            pyhd8ed1ab_0          conda-forge
hyperframe                 6.1.0            pyhd8ed1ab_0          conda-forge
idna                       3.11             pyhd8ed1ab_0          conda-forge
jsonpatch                  1.33             pyhd8ed1ab_1          conda-forge
jsonpointer                3.0.0            py312h7900ff3_2       conda-forge
keyutils                   1.6.3            hb9d3cd8_0            conda-forge
krb5                       1.21.3           h659f571_0            conda-forge
ld_impl_linux-64           2.45             default_hbd61a6d_104  conda-forge
libarchive                 3.8.2            gpl_h7be2006_100      conda-forge
libcurl                    8.17.0           h4e3cde8_0            conda-forge
libedit                    3.1.20250104     pl5321h7949ede_0      conda-forge
libev                      4.33             hd590300_2            conda-forge
libexpat                   2.7.3            hecca717_0            conda-forge
libffi                     3.5.2            h9ec8514_0            conda-forge
libgcc                     15.2.0           he0feb66_15           conda-forge
libgcc-ng                  15.2.0           h69a702a_15           conda-forge
libgomp                    15.2.0           he0feb66_15           conda-forge
libiconv                   1.18             h3b78370_2            conda-forge
liblzma                    5.8.1            hb9d3cd8_2            conda-forge
libmamba                   2.4.0            hed7d790_1            conda-forge
libmambapy                 2.4.0            py312h17091a9_1       conda-forge
libnghttp2                 1.67.0           had1ee68_0            conda-forge
libnsl                     2.0.1            hb9d3cd8_1            conda-forge
libsolv                    0.7.35           h9463b59_0            conda-forge
libsqlite                  3.51.1           h0c1763c_0            conda-forge
libssh2                    1.11.1           hcf80075_0            conda-forge
libstdcxx                  15.2.0           h934c35e_15           conda-forge
libstdcxx-ng               15.2.0           hdf11a46_15           conda-forge
libuuid                    2.41.2           h5347b49_1            conda-forge
libxcrypt                  4.4.36           hd590300_1            conda-forge
libxml2                    2.15.1           h031cc0b_0            conda-forge
libxml2-16                 2.15.1           hf2a90c1_0            conda-forge
libzlib                    1.3.1            hb9d3cd8_2            conda-forge
lz4-c                      1.10.0           h5888daf_1            conda-forge
lzo                        2.10             h280c20c_1002         conda-forge
mamba                      2.4.0            h7ae174a_1            conda-forge
menuinst                   2.4.1            py312h7900ff3_0       conda-forge
msgpack-python             1.1.2            py312hd9148b4_1       conda-forge
ncurses                    6.5              h2d0b736_3            conda-forge
nlohmann_json-abi          3.12.0           h0f90c79_1            conda-forge
openssl                    3.6.0            h26f9b46_0            conda-forge
packaging                  25.0             pyh29332c3_1          conda-forge
pip                        25.3             pyh8b19718_0          conda-forge
platformdirs               4.5.0            pyhcf101f3_0          conda-forge
pluggy                     1.6.0            pyhf9edf01_1          conda-forge
pybind11-abi               11               hc364b38_1            conda-forge
pycosat                    0.6.6            py312h4c3975b_3       conda-forge
pycparser                  2.22             pyh29332c3_1          conda-forge
pysocks                    1.7.1            pyha55dd90_7          conda-forge
python                     3.12.12          hd63d673_1_cpython    conda-forge
python_abi                 3.12             8_cp312               conda-forge
readline                   8.2              h8c095d6_2            conda-forge
reproc                     14.2.5.post0     hb9d3cd8_0            conda-forge
reproc-cpp                 14.2.5.post0     h5888daf_0            conda-forge
requests                   2.32.5           pyhd8ed1ab_0          conda-forge
ruamel.yaml                0.18.16          py312h4c3975b_0       conda-forge
ruamel.yaml.clib           0.2.14           py312h4c3975b_0       conda-forge
setuptools                 80.9.0           pyhff2d567_0          conda-forge
simdjson                   4.2.2            hb700be7_0            conda-forge
tk                         8.6.13           noxft_ha0e22de_103    conda-forge
tqdm                       4.67.1           pyhd8ed1ab_1          conda-forge
truststore                 0.10.3           pyhe01879c_0          conda-forge
tzdata                     2025b            h78e105d_0            conda-forge
urllib3                    2.5.0            pyhd8ed1ab_0          conda-forge
wheel                      0.45.1           pyhd8ed1ab_1          conda-forge
yaml-cpp                   0.8.0            h3f2d84a_0            conda-forge
zstandard                  0.25.0           py312h5253ce2_1       conda-forge
zstd                       1.5.7            hb78ec9c_6            conda-forge

Environment info

active environment : None
       user config file : /root/.condarc
 populated config files : /root/miniforge3/.condarc
          conda version : 25.11.0
    conda-build version : not installed
         python version : 3.12.12.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=zen2
                          __conda=25.11.0=0
                          __cuda=0=0
                          __glibc=2.39=0
                          __linux=6.8.0=0
                          __unix=0=0
       base environment : /root/miniforge3  (writable)
      conda av data dir : /root/miniforge3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /root/miniforge3/pkgs
                          /root/.conda/pkgs
       envs directories : /root/miniforge3/envs
                          /root/.conda/envs
               platform : linux-64
             user-agent : conda/25.11.0 requests/2.32.5 CPython/3.12.12 Linux/6.8.0-90-generic ubuntu/24.04.3 glibc/2.39 solver/libmamba conda-libmamba-solver/25.11.0 libmambapy/2.4.0
                UID:GID : 0:0
             netrc file : None
           offline mode : False

[hmaarrfk]

I don’t recommend updating that way.

Just use conda to update the base environment.

[LorenzoLeonardini]

It's not the actual way I update conda, but I'm using the install script in an Ansible playbook. Given that every Ansible task should be idempotent, I've always used -b -u to make it work every time the playbook runs

Anyway, if the setup script offers it as a feature, it should work

[hmaarrfk]

That makes sense.

The original issue might be in constructor.

We’ll have to dig a little deeper to resolve it. So I wanted to communicate a workaround to you.

[pirzada-ahmadfaraz]

Hey, I dug into this and traced it back to constructor.

The issue is in constructor/header.sh. When the _conda symlink was introduced in this commit, it used ln -s without the -f flag:

ln -s "$CONDA_EXEC" "$PREFIX"/_conda

This fails on update (-u) because the symlink already exists from the previous installation.

The good news is this was already fixed in constructor PR #1135 (commit, merged Dec 15, 2025), which changed it to:

ln -s -f "$CONDA_EXEC" "$PREFIX"/_conda

The current miniforge releases (25.11.0-0 and 25.11.0-1) were both built before that fix landed. A new release built with the updated constructor should resolve this.

[mballintijn]

Hello,

It does not look like the fix made it into 26.1.0-0, I'm seeing

   381 # In case there are packages that depend on _conda
   382 ln -s "$CONDA_EXEC" "$PREFIX"/_conda
   383

and the script failed with,

"ln: failed to create symbolic link '/opt/conda/_conda': File exists"

as expected

(For Miniforge3-26.1.0-0-Linux-x86_64.sh)

It looks like an older version of "constructor" was used for the release:

#!/bin/sh
#
# Created by constructor 3.14.0
#
# NAME:  Miniforge3
# VER:   26.1.0-0
# PLAT:  linux-64
# MD5:   944fc30bba28352c99c6c10adca616cc

[hmaarrfk]

i'm not sure why you would use the conda installer to update an installation with the -u flag.

It is very "unsafe" for me since it doesn't really "remove" old packages, just adds to them.

Please files a bug to
https://github.com/conda/constructor

[mballintijn]

We're doing something similar to what @LorenzoLeonardini mentioned above, using Ansible to maintain a bunch of nodes.

This used to work fine, until a patch broke constructor. This was then fixed in constructor a while back.

I just saw the constructor release with the fix has not made it into conda-forge yet. following up there too.

[hmaarrfk]

thanks i'll see if i can push it through.