mamba environment fails conda doctor

[gboeing]

Troubleshooting docs

• My problem is not solved in the Troubleshooting docs

Anaconda default channels

• I do NOT use the Anaconda default channels (pkgs/* etc.)

How did you install Mamba?

Mambaforge or latest Miniforge

Search tried in issue tracker

conda doctor

Latest version of Mamba

• My problem is not solved with the latest version

Tried in Conda?

I do not have this problem with Conda, just with Mamba

Describe your issue

If I create a new simple conda environment with one package (and its dependencies), it passes the conda doctor health check without a problem:

conda create -n TEST osmnx
conda activate TEST
conda doctor -v

This new environment passes the health check:

Environment Health Report for: /Users/geoff/miniforge3/envs/TEST

✅ There are no packages with altered files.

✅ The environment is listed in the environments.txt file.

✅ There are no packages with missing files.

But if I create the environment with mamba it fails the health check:

mamba create -n MAMBA osmnx 
conda activate MAMBA
conda doctor -v

It fails the health check with dozens (hundreds?) of "altered files":

Environment Health Report for: /Users/geoff/miniforge3/envs/MAMBA

❌ Altered Files:

blosc-1.21.6-h7dd00d9_1:
lib/pkgconfig/blosc.pc

x265-3.5-hbc6ce65_3:
lib/pkgconfig/x265.pc

openjpeg-2.5.3-h8a3d83b_0:
lib/pkgconfig/libopenjp2.pc

librttopo-1.1.0-ha2cf0f4_17:
lib/pkgconfig/rttopo.pc

zstd-1.5.6-hb46c0d2_0:
lib/pkgconfig/libzstd.pc

krb5-1.21.3-h237132a_0:
bin/compile_et
bin/krb5-config
lib/krb5/plugins/kdb/db2.so
lib/krb5/plugins/preauth/otp.so
lib/libgssapi_krb5.2.2.dylib
lib/libgssapi_krb5.2.dylib
lib/libgssapi_krb5.dylib
lib/libkadm5clnt.dylib
lib/libkadm5clnt_mit.12.0.dylib
lib/libkadm5clnt_mit.12.dylib
lib/libkadm5clnt_mit.dylib
lib/libkadm5srv.dylib
lib/libkadm5srv_mit.12.0.dylib
lib/libkadm5srv_mit.12.dylib
lib/libkadm5srv_mit.dylib
lib/libkdb5.10.0.dylib
lib/libkdb5.10.dylib
lib/libkdb5.dylib
lib/libkrb5.3.3.dylib
lib/libkrb5.3.dylib
lib/libkrb5.dylib
lib/pkgconfig/gssrpc.pc
lib/pkgconfig/kadm-client.pc
lib/pkgconfig/kadm-server.pc
lib/pkgconfig/kdb.pc
lib/pkgconfig/krb5-gssapi.pc
lib/pkgconfig/krb5.pc
lib/pkgconfig/mit-krb5-gssapi.pc
lib/pkgconfig/mit-krb5.pc
sbin/kadmind
sbin/kprop
sbin/kpropd
share/man/man5/kadm5.acl.5
share/man/man5/kdc.conf.5
share/man/man7/kerberos.7
share/man/man8/kadmind.8
share/man/man8/kprop.8
share/man/man8/kpropd.8

freetype-2.12.1-hadb7bae_2:
bin/freetype-config
lib/pkgconfig/freetype2.pc

icu-75.1-hfee45f7_0:
bin/icu-config
lib/icu/75.1/Makefile.inc
lib/icu/75.1/pkgdata.inc
lib/icu/Makefile.inc
lib/icu/pkgdata.inc
lib/pkgconfig/icu-i18n.pc
lib/pkgconfig/icu-io.pc
lib/pkgconfig/icu-uc.pc

xorg-libxdmcp-1.1.5-hd74edd7_0:
lib/pkgconfig/xdmcp.pc

libbrotlidec-1.1.0-hd74edd7_2:
lib/pkgconfig/libbrotlidec.pc

rav1e-0.6.6-h69fbcac_2:
bin/rav1e
lib/pkgconfig/rav1e.pc

c-ares-1.34.4-h5505292_0:
lib/pkgconfig/libcares.pc

svt-av1-2.3.0-hf24288c_0:
lib/pkgconfig/SvtAv1Enc.pc

json-c-0.18-he4178ee_0:
lib/pkgconfig/json-c.pc

pcre2-10.44-h297a79d_2:
bin/pcre2-config
lib/pkgconfig/libpcre2-16.pc
lib/pkgconfig/libpcre2-32.pc
lib/pkgconfig/libpcre2-8.pc
lib/pkgconfig/libpcre2-posix.pc

libwebp-base-1.4.0-h93a5062_0:
lib/pkgconfig/libsharpyuv.pc
lib/pkgconfig/libwebp.pc
lib/pkgconfig/libwebpdecoder.pc
lib/pkgconfig/libwebpdemux.pc
lib/pkgconfig/libwebpmux.pc

lcms2-2.16-ha0e7c42_0:
lib/pkgconfig/lcms2.pc

libdeflate-1.23-hec38601_0:
lib/cmake/libdeflate/libdeflate-targets.cmake
lib/pkgconfig/libdeflate.pc

aom-3.9.1-h7bae524_0:
lib/pkgconfig/aom.pc

libgdal-core-3.10.0-hcf82b6a_9:
bin/gdal-config
include/cpl_config.h
lib/libgdal.36.3.10.0.dylib
lib/libgdal.36.dylib
lib/libgdal.dylib
lib/pkgconfig/gdal.pc

libxml2-2.13.5-h178c5d8_1:
bin/xml2-config
bin/xmlcatalog
bin/xmllint
lib/libxml2.2.dylib
lib/libxml2.dylib
lib/pkgconfig/libxml-2.0.pc

freexl-2.0.0-h3ab3353_2:
lib/pkgconfig/freexl.pc

readline-8.2-h92ec313_1:
lib/pkgconfig/history.pc
lib/pkgconfig/readline.pc

dav1d-1.2.1-hb547adb_0:
lib/pkgconfig/dav1d.pc

lerc-4.0.0-h9a09cb3_0:
lib/pkgconfig/Lerc.pc

uriparser-0.9.8-h00cdb27_0:
lib/pkgconfig/liburiparser.pc

geotiff-1.7.3-h82bf549_3:
lib/pkgconfig/libgeotiff.pc
share/cmake/GeoTIFF/geotiff-depends-release.cmake

libffi-3.4.2-h3422bc3_5:
lib/libffi.8.dylib
lib/libffi.dylib
lib/pkgconfig/libffi.pc

libcblas-3.9.0-26_osxarm64_openblas:
lib/libcblas.3.dylib
lib/libcblas.dylib

geos-3.13.0-hf9b8971_0:
bin/geos-config
lib/pkgconfig/geos.pc

tk-8.6.13-h5083fa2_1:
lib/itcl4.2.3/itclConfig.sh
lib/libtcl8.6.dylib
lib/pkgconfig/tcl.pc
lib/pkgconfig/tk.pc
lib/tclConfig.sh
lib/tdbc1.1.5/tdbcConfig.sh
lib/tkConfig.sh

zlib-1.3.1-h8359307_2:
lib/libz.dylib
lib/pkgconfig/zlib.pc

xorg-libxau-1.0.12-h5505292_0:
lib/pkgconfig/xau.pc

libsqlite-3.47.2-h3f77e49_0:
lib/pkgconfig/sqlite3.pc

scipy-1.14.1-py313hc010ede_2:
lib/python3.13/site-packages/scipy/config.py

ncurses-6.5-h7bae524_1:
bin/ncursesw6-config
lib/libncurses.6.dylib
lib/libncurses.dylib
lib/libncursesw.6.dylib
lib/libncursesw.dylib
lib/libtinfo.6.dylib
lib/libtinfo.dylib
lib/libtinfow.6.dylib
lib/libtinfow.dylib
lib/pkgconfig/form.pc
lib/pkgconfig/formw.pc
lib/pkgconfig/menu.pc
lib/pkgconfig/menuw.pc
lib/pkgconfig/ncurses++.pc
lib/pkgconfig/ncurses++w.pc
lib/pkgconfig/ncurses.pc
lib/pkgconfig/ncursesw.pc
lib/pkgconfig/panel.pc
lib/pkgconfig/panelw.pc
lib/pkgconfig/tinfo.pc
lib/pkgconfig/tinfow.pc
share/terminfo/61/a210
share/terminfo/61/abm85
share/terminfo/61/abm85e
share/terminfo/61/abm85h
share/terminfo/61/abm85h-old
share/terminfo/61/adm36
share/terminfo/61/alt2
share/terminfo/61/alt3
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share/terminfo/63/crt
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share/terminfo/65/emu-220
share/terminfo/65/exec80
share/terminfo/67/go-225
share/terminfo/67/go140
share/terminfo/67/go140w
share/terminfo/67/go225
share/terminfo/68/h29a-kc-bc
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liblapack-3.9.0-26_osxarm64_openblas:
lib/liblapack.3.dylib
lib/liblapack.dylib

openssl-3.4.0-h39f12f2_0:
bin/c_rehash
lib/libcrypto.3.dylib
lib/libcrypto.dylib
lib/pkgconfig/libcrypto.pc
lib/pkgconfig/libssl.pc
lib/pkgconfig/openssl.pc

libspatialite-5.1.0-hf92fc0a_12:
lib/pkgconfig/spatialite.pc

xerces-c-3.2.5-h92fc2f4_2:
lib/pkgconfig/xerces-c.pc

libde265-1.0.15-h2ffa867_0:
lib/pkgconfig/libde265.pc

libcurl-8.11.1-h73640d1_0:
bin/curl-config
lib/libcurl.4.dylib
lib/libcurl.dylib
lib/pkgconfig/libcurl.pc

libarchive-3.7.7-h3b16cec_3:
lib/pkgconfig/libarchive.pc

libjpeg-turbo-3.0.0-hb547adb_1:
lib/cmake/libjpeg-turbo/libjpeg-turboTargets-release.cmake
lib/cmake/libjpeg-turbo/libjpeg-turboTargets.cmake
lib/pkgconfig/libjpeg.pc
lib/pkgconfig/libturbojpeg.pc

libheif-1.18.2-gpl_he913df3_100:
include/libheif/heif_version.h
lib/libheif.1.18.2.dylib
lib/libheif.1.dylib
lib/libheif.dylib
lib/pkgconfig/libheif.pc

pthread-stubs-0.4-hd74edd7_1002:
lib/pkgconfig/pthread-stubs.pc

proj-9.5.1-h1318a7e_0:
bin/projsync
lib/libproj.25.9.5.1.dylib
lib/libproj.25.dylib
lib/libproj.dylib
lib/pkgconfig/proj.pc

python-3.13.1-h4f43103_102_cp313:
bin/idle3
bin/idle3.13
bin/pydoc
bin/pydoc3
bin/pydoc3.13
bin/python
bin/python3
bin/python3-config
bin/python3.1
bin/python3.13
bin/python3.13-config
lib/libpython3.13.dylib
lib/pkgconfig/python-3.13-embed.pc
lib/pkgconfig/python-3.13.pc
lib/pkgconfig/python3-embed.pc
lib/pkgconfig/python3.pc
lib/python3.13/_sysconfigdata__darwin_darwin.py
lib/python3.13/_sysconfigdata__darwin_darwin.py.orig
lib/python3.13/_sysconfigdata_arm64_apple_darwin20_0_0.py
lib/python3.13/config-3.13-darwin/Makefile
lib/python3.13/config-3.13-darwin/python-config.py
lib/python3.13/site-packages/conda-site.pth

libbrotlicommon-1.1.0-hd74edd7_2:
lib/pkgconfig/libbrotlicommon.pc

libtiff-4.7.0-h551f018_3:
lib/pkgconfig/libtiff-4.pc

libedit-3.1.20191231-hc8eb9b7_2:
lib/libedit.0.dylib
lib/libedit.dylib
lib/pkgconfig/libedit.pc

libnghttp2-1.64.0-h6d7220d_0:
bin/nghttpx
lib/pkgconfig/libnghttp2.pc

lz4-c-1.10.0-h286801f_1:
lib/pkgconfig/liblz4.pc

libpng-1.6.44-hc14010f_0:
bin/libpng-config
bin/libpng16-config
lib/pkgconfig/libpng.pc
lib/pkgconfig/libpng16.pc

libgfortran5-13.2.0-hf226fd6_3:
lib/libgomp.1.dylib
lib/libgomp.dylib

libblas-3.9.0-26_osxarm64_openblas:
lib/libblas.3.dylib
lib/libblas.dylib

numpy-2.2.0-py313ha4a2180_0:
bin/f2py
bin/numpy-config
lib/python3.13/site-packages/numpy/config.py

pyproj-3.7.0-py313hef3adbd_0:
bin/pyproj

libbrotlienc-1.1.0-hd74edd7_2:
lib/pkgconfig/libbrotlienc.pc

qhull-2020.2-h420ef59_5:
lib/pkgconfig/qhull_r.pc
lib/pkgconfig/qhullcpp.pc
lib/pkgconfig/qhullstatic.pc
lib/pkgconfig/qhullstatic_r.pc

rasterio-1.4.3-py313h782da51_0:
bin/rio
lib/python3.13/site-packages/rasterio/_filepath.cpython-313-darwin.so
lib/python3.13/site-packages/rasterio/_fill.cpython-313-darwin.so
lib/python3.13/site-packages/rasterio/_warp.cpython-313-darwin.so

kiwisolver-1.4.7-py313hf9c7212_0:
lib/python3.13/site-packages/kiwisolver/_cext.cpython-313-darwin.so

fonttools-4.55.3-py313ha9b7d5b_0:
bin/fonttools
bin/pyftmerge
bin/pyftsubset
bin/ttx

libssh2-1.11.1-h9cc3647_0:
lib/pkgconfig/libssh2.pc

minizip-4.0.7-hff1a8ea_3:
lib/cmake/minizip/minizip.cmake
lib/pkgconfig/minizip.pc

libxcb-1.17.0-hdb1d25a_0:
lib/pkgconfig/xcb-composite.pc
lib/pkgconfig/xcb-damage.pc
lib/pkgconfig/xcb-dbe.pc
lib/pkgconfig/xcb-dpms.pc
lib/pkgconfig/xcb-dri2.pc
lib/pkgconfig/xcb-dri3.pc
lib/pkgconfig/xcb-glx.pc
lib/pkgconfig/xcb-present.pc
lib/pkgconfig/xcb-randr.pc
lib/pkgconfig/xcb-record.pc
lib/pkgconfig/xcb-render.pc
lib/pkgconfig/xcb-res.pc
lib/pkgconfig/xcb-screensaver.pc
lib/pkgconfig/xcb-shape.pc
lib/pkgconfig/xcb-shm.pc
lib/pkgconfig/xcb-sync.pc
lib/pkgconfig/xcb-xf86dri.pc
lib/pkgconfig/xcb-xfixes.pc
lib/pkgconfig/xcb-xinerama.pc
lib/pkgconfig/xcb-xinput.pc
lib/pkgconfig/xcb-xkb.pc
lib/pkgconfig/xcb-xtest.pc
lib/pkgconfig/xcb-xv.pc
lib/pkgconfig/xcb-xvmc.pc
lib/pkgconfig/xcb.pc

✅ The environment is listed in the environments.txt file.

✅ There are no packages with missing files.

Why this inconsistency? Why can't the mamba environment pass the health check?

mamba info / micromamba info

libmamba version : 2.0.5
          mamba version : 2.0.5
           curl version : libcurl/8.11.1 OpenSSL/3.4.0 (SecureTransport) zlib/1.3.1 zstd/1.5.6 libssh2/1.11.1 nghttp2/1.64.0
     libarchive version : libarchive 3.7.7 zlib/1.3.1 liblzma/5.2.6 bz2lib/1.0.8 liblz4/1.9.3 libzstd/1.5.6
       envs directories : /Users/geoff/miniforge3/envs
          package cache : /Users/geoff/miniforge3/pkgs
                          /Users/geoff/.mamba/pkgs
            environment : MAMBA (active)
           env location : /Users/geoff/miniforge3/envs/MAMBA
      user config files : /Users/geoff/.mambarc
 populated config files : /Users/geoff/.condarc
                          /Users/geoff/miniforge3/.condarc
       virtual packages : __unix=0=0
                          __osx=15.1.1=0
                          __archspec=1=arm64
               channels : https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/conda-forge/osx-arm64
       base environment : /Users/geoff/miniforge3
               platform : osx-arm64

Logs

No response

environment.yml

No response

~/.condarc

channels:
  - conda-forge
report_errors: false
show_channel_urls: true
channel_priority: strict