CondaPackError : Files managed by conda were found to have been deleted/overwritten

Hi, I have seen some of conda-pack updates regarding this issues and I have upgraded my conda-pack to the latest version but the problem is still there.

A bit background story: Basically I have two environments which actually if I tried to clone (or move using .yml and spec-list.txt), it throws error because the package probably are obsolete/deprecated/not supported anymore because it was created on Jan 2018. So I try to use conda-pack to see if it can wrap the envs.

_CondaPackError: Files managed by conda were found to have been deleted/overwritten in the following packages:

• pandas=‘0.22.0’
• pip=‘9.0.3’
• util-linux=‘2.21’

This is usually due to pip uninstalling or clobbering conda managed files, resulting in an inconsistent environment. Please check your environment for conda/pip conflicts using conda list, and fix the environment by ensuring only one version of each package is installed (conda preferred)._

When running conda list on those packages: _# Name Version Build Channel geopandas 0.4.0 <pip> pandas 0.22.0 py36_0 conda-for_ge

# Name Version Build Channel pip 9.0.3 py36_0 conda-forge

# Name Version Build Channel util-linux 2.21 0

Anyone could help on these?

PS: updating the package is not an option because it might impact the apps/code that run inside those envs.

[Phillip-M-Feldman]

I’m seeing a similar issue, with messages like the the one shown below. The part of the error message about pip is spurious, because I have learned from hard experience that one should NEVER use pip under any circumstances.

(py38) >conda-pack -n py38 Collecting packages… CondaPackError: Files managed by conda were found to have been deleted/overwritten in the following packages:

• python=‘3.8.5’

This is usually due to pip uninstalling or clobbering conda managed files, resulting in an inconsistent environment. Please check your environment for conda/pip conflicts using conda list, and fix the environment by ensuring only one version of each package is installed (conda preferred).

When I run conda list, I get the output shown below. As far as I can tell, there is only one version of each package. The list shows that two items came from pypi, but I don’t use pip, so I’m unclear as to how these could have gotten installed.

(py38) >conda list

packages in environment at C:\ProgramData\Anaconda3\envs\py38:

Name Version Build Channel

_anaconda_depends 2020.07 py38_0 alabaster 0.7.12 py_0 anaconda custom py38_1 anaconda-client 1.7.2 py38_0 anaconda-project 0.8.4 py_0 argh 0.26.2 py38_0 argon2-cffi 20.1.0 py38he774522_1 asn1crypto 1.4.0 py_0 astroid 2.4.2 py38_0 astropy 4.0.1.post1 py38he774522_1 astroquery 0.4.1 pyh9f0ad1d_0 conda-forge atomicwrites 1.4.0 py_0 attrs 20.2.0 py_0 autopep8 1.5.4 py_0 babel 2.8.0 py_0 backcall 0.2.0 py_0 backports 1.0 py_2 backports.shutil_get_terminal_size 1.0.0 py38_2 bcrypt 3.2.0 py38he774522_0 beautifulsoup4 4.9.1 py38_0 bitarray 1.5.3 py38he774522_0 bkcharts 0.2 py38_0 blas 1.0 mkl bleach 3.2.1 py_0 blosc 1.20.0 h7bd577a_0 bokeh 2.2.1 py38_0 boto 2.49.0 py38_0 bottleneck 1.3.2 py38h2a96729_1 brotlipy 0.7.0 py38he774522_1000 bzip2 1.0.8 he774522_0 ca-certificates 2020.7.22 0 cached-property 1.5.1 py_1 cartopy 0.18.0 py38hd77ba2b_0 certifi 2020.6.20 py38_0 cffi 1.14.2 py38h7a1dbc1_0 cfitsio 3.470 he774522_5 chardet 3.0.4 py38_1003 click 7.1.2 py_0 cloudpickle 1.6.0 py_0 clyent 1.2.2 py38_1 colorama 0.4.3 py_0 comtypes 1.1.7 py38_1001 conda 4.8.4 py38_0 conda-build 3.20.2 py38_0 conda-pack 0.5.0 py_0 conda-package-handling 1.6.1 py38h62dcd97_0 console_shortcut 0.1.1 4 contextlib2 0.6.0.post1 py_0 cryptography 3.1 py38h7a1dbc1_0 curl 7.69.1 h2a8f88b_0 customimporter 2.0.2 py_0 <unknown> cycler 0.10.0 py38_0 cython 0.29.21 py38ha925a31_0 cytoolz 0.10.1 py38he774522_0 dask 2.26.0 py_0 dask-core 2.26.0 py_0 decorator 4.4.2 py_0 defusedxml 0.6.0 py_0 diff-match-patch 20200713 py_0 distributed 2.26.0 py38_0 docutils 0.16 py38_1 entrypoints 0.3 py38_0 et_xmlfile 1.0.1 py_1001 expat 2.2.9 h33f27b4_2 fastcache 1.1.0 py38he774522_0 filelock 3.0.12 py_0 flake8 3.8.3 py_0 flask 1.1.2 py_0 freetype 2.10.2 hd328e21_0 freexl 1.0.5 hfa6e2cd_0 fsspec 0.8.0 py_0 future 0.18.2 py38_1 gdal 3.0.2 py38h2fee047_7 conda-forge geos 3.8.0 h33f27b4_0 geotiff 1.5.1 h5770a2b_1 get_terminal_size 1.0.0 h38e98db_0 gettext 0.19.8.1 hb01d8f6_1002 conda-forge gevent 20.6.2 py38he774522_0 glib 2.65.0 he4de6d7_0 conda-forge glob2 0.7 py_0 gmpy2 2.0.8 py38h7edee0f_3 greenlet 0.4.16 py38he774522_0 h5py 2.10.0 nompi_py38h422b98e_102 conda-forge hdf4 4.2.13 h712560f_2 hdf5 1.10.5 nompi_ha405e13_1104 conda-forge heapdict 1.0.1 py_0 html5lib 1.1 py_0 icc_rt 2019.0.0 h0cc432a_1 icu 64.2 he025d50_1 conda-forge idna 2.10 py_0 imageio 2.9.0 py_0 imagesize 1.2.0 py_0 importlib-metadata 1.7.0 py38_0 importlib_metadata 1.7.0 0 iniconfig 1.0.1 py_0 intel-openmp 2020.1 216 intervaltree 3.1.0 py_0 ipdb 0.13.3 pyh9f0ad1d_0 conda-forge ipykernel 5.3.4 py38h5ca1d4c_0 ipython 7.18.1 py38h5ca1d4c_0 ipython_genutils 0.2.0 py38_0 ipywidgets 7.5.1 py_0 isort 5.4.2 py38_0 itsdangerous 1.1.0 py_0 jdcal 1.4.1 py_0 jedi 0.17.1 py38_0 jinja2 2.11.2 py_0 joblib 0.16.0 py_0 jpeg 9d he774522_0 conda-forge jplephem 2.15 pyh2f6353c_0 conda-forge json5 0.9.5 py_0 jsonschema 3.2.0 py38_0 jupyter 1.0.0 py38_7 jupyter_client 6.1.6 py_0 jupyter_console 6.2.0 py_0 jupyter_core 4.6.3 py38_0 jupyterlab 2.2.6 py_0 jupyterlab_server 1.2.0 py_0 kealib 1.4.13 hd6dc3df_0 conda-forge keyring 21.4.0 py38_0 kiwisolver 1.2.0 py38h74a9793_0 krb5 1.17.1 hc04afaa_0 lazy-object-proxy 1.4.3 py38he774522_0 libarchive 3.4.2 h5e25573_0 libblas 3.8.0 16_mkl conda-forge libboost 1.67.0 hd9e427e_4 libcblas 3.8.0 16_mkl conda-forge libclang 9.0.1 default_hf44288c_0 libcurl 7.69.1 h2a8f88b_0 libffi 3.2.1 ha925a31_1007 conda-forge libflang 5.0.0 h6538335_20180525 conda-forge libgdal 3.0.2 ha9114c6_7 conda-forge libiconv 1.15 h1df5818_7 libkml 1.3.0 he5f2a48_4 liblief 0.10.1 ha925a31_0 libllvm9 9.0.1 h21ff451_0 libnetcdf 4.7.3 nompi_hc957ea6_101 conda-forge libopenblas 0.3.10 pthreads_h1662909_4 conda-forge libpng 1.6.37 h2a8f88b_0 libpq 12.2 h3235a2c_0 libsodium 1.0.18 h62dcd97_0 libspatialindex 1.9.3 h33f27b4_0 libspatialite 4.3.0a h7ffb84d_0 libssh2 1.9.0 h7a1dbc1_1 libtiff 4.1.0 h56a325e_1 libwebp 1.0.2 hfa6e2cd_5 conda-forge libxml2 2.9.10 h464c3ec_1 libxslt 1.1.34 he774522_0 llvm-meta 5.0.0 0 conda-forge llvmlite 0.31.0 py38ha925a31_0 locket 0.2.0 py38_1 lxml 4.5.2 py38h1350720_0 lz4-c 1.9.2 h62dcd97_1 lzo 2.10 he774522_2 m2w64-expat 2.1.1 2 m2w64-gcc-libgfortran 5.3.0 6 m2w64-gcc-libs 5.3.0 7 m2w64-gcc-libs-core 5.3.0 7 m2w64-gettext 0.19.7 2 m2w64-gmp 6.1.0 2 m2w64-libiconv 1.14 6 m2w64-libwinpthread-git 5.0.0.4634.697f757 2 m2w64-xz 5.2.2 2 markupsafe 1.1.1 py38he774522_0 matplotlib 3.3.1 0 matplotlib-base 3.3.1 py38hba9282a_0 mccabe 0.6.1 py38_1 menuinst 1.4.16 py38he774522_1 mistune 0.8.4 py38he774522_1000 mkl 2020.1 216 mkl-service 2.3.0 py38hb782905_0 mkl_fft 1.2.0 py38h45dec08_0 mkl_random 1.1.1 py38h47e9c7a_0 mock 4.0.2 py_0 more-itertools 8.5.0 py_0 mpc 1.1.0 h7edee0f_1 mpfr 4.0.2 h62dcd97_1 mpir 3.0.0 hec2e145_1 mpmath 1.1.0 py38_0 msgpack-python 1.0.0 py38h74a9793_1 msys2-conda-epoch 20160418 1 multipledispatch 0.6.0 py38_0 nbconvert 5.6.1 py38_0 nbformat 5.0.7 py_0 networkx 2.5 py_0 nltk 3.5 py_0 nose 1.3.7 py38_2 notebook 6.1.1 py38_0 numba 0.48.0 py38h47e9c7a_0 numexpr 2.7.1 py38h25d0782_0 numpy 1.19.1 py38h5510c5b_0 numpy-base 1.19.1 py38ha3acd2a_0 numpydoc 1.1.0 py_0 olefile 0.46 py_0 openjpeg 2.3.1 h57dd2e7_3 conda-forge openmp 5.0.0 vc14_1 conda-forge openpyxl 3.0.5 py_0 openssl 1.1.1g he774522_1 owslib 0.20.0 py_0 packaging 20.4 py_0 pandas 1.1.1 py38ha925a31_0 pandoc 2.10.1 0 pandocfilters 1.4.2 py38_1 paramiko 2.7.2 py_0 parso 0.7.0 py_0 partd 1.1.0 py_0 path 15.0.0 py38_0 path.py 12.5.0 0 pathlib2 2.3.5 py38_0 pathtools 0.1.2 py_1 patsy 0.5.1 py38_0 pcre 8.44 ha925a31_0 pep8 1.7.1 py38_0 pexpect 4.8.0 py38_0 pickleshare 0.7.5 py38_1000 pillow 7.2.0 py38hcc1f983_0 pip 20.2.2 py38_0 pkginfo 1.5.0.1 py38_0 plotly 4.10.0 py_0 pluggy 0.13.1 py38_0 ply 3.11 py38_0 poliastro 0.14.0 py_1 conda-forge poppler 0.67.0 h1707e21_8 conda-forge poppler-data 0.4.9 1 conda-forge postgresql 12.2 h3235a2c_0 powershell_shortcut 0.0.1 3 progressbar2 3.37.1 py38_0 proj 6.2.1 h9f7ef89_0 prometheus_client 0.8.0 py_0 prompt-toolkit 3.0.7 py_0 prompt_toolkit 3.0.7 0 psutil 5.7.2 py38he774522_0 py 1.9.0 py_0 py-lief 0.10.1 py38ha925a31_0 pycodestyle 2.6.0 py_0 pycosat 0.6.3 py38he774522_0 pycparser 2.20 py_2 pycurl 7.43.0.5 py38h7a1dbc1_0 pydocstyle 5.1.1 py_0 pyepsg 0.4.0 py_0 pyflakes 2.2.0 py_0 pygments 2.7.0 py_0 pykdtree 1.3.1 py38h8c2d366_1002 pylint 2.6.0 py38_0 pynacl 1.4.0 py38h62dcd97_1 pyodbc 4.0.30 py38ha925a31_0 pyopenssl 19.1.0 py_1 pyparsing 2.4.7 py_0 pyperclip 1.8.0 pyh9f0ad1d_0 conda-forge pyproj 2.6.1.post1 py38hcfa1391_1 pyqt 5.12.3 py38h6538335_1 conda-forge pyqt5-sip 4.19.18 pypi_0 pypi pyqtwebengine 5.12.1 pypi_0 pypi pyreadline 2.1 py38_1 pyrsistent 0.17.3 py38he774522_0 pyshp 2.1.2 py_0 pyside2 5.13.2 py38hfa7ce6d_2 conda-forge pysocks 1.7.1 py38_0 pytables 3.6.1 py38h26f9782_1 conda-forge pytest 6.0.2 py38_0 pytest-runner 5.2 py_0 python 3.8.5 h5fd99cc_1 python-dateutil 2.8.1 py_0 python-docx 0.8.10 py_0 conda-forge python-jsonrpc-server 0.4.0 py_0 python-language-server 0.35.1 py_0 python-libarchive-c 2.9 py_0 python-utils 2.3.0 py38_0 pytz 2020.1 py_0 pywavelets 1.1.1 py38he774522_0 pywin32 227 py38he774522_1 pywin32-ctypes 0.2.0 py38_1000 pywinpty 0.5.7 py38_0 pyyaml 5.3.1 py38he774522_1 pyzmq 19.0.1 py38ha925a31_1 qdarkstyle 2.8.1 py_0 qt 5.12.5 h7ef1ec2_0 conda-forge qtawesome 0.7.2 py_0 qtconsole 4.7.6 py_0 qtpy 1.9.0 py_0 regex 2020.7.14 py38he774522_0 requests 2.24.0 py_0 retrying 1.3.3 py_2 ripgrep 11.0.2 0 rope 0.17.0 py_0 rtree 0.9.4 py38h21ff451_1 ruamel_yaml 0.15.87 py38he774522_1 scikit-image 0.16.2 py38h47e9c7a_0 scikit-learn 0.23.2 py38h47e9c7a_0 scipy 1.5.0 py38h9439919_0 seaborn 0.10.1 py_0 send2trash 1.5.0 py38_0 setuptools 49.6.0 py38_0 shapely 1.7.1 py38h210f175_0 simplegeneric 0.8.1 py38_2 singledispatch 3.4.0.3 py38_0 sip 4.19.24 py38ha925a31_0 six 1.15.0 py_0 snappy 1.1.8 h33f27b4_0 snowballstemmer 2.0.0 py_0 sortedcollections 1.2.1 py_0 sortedcontainers 2.2.2 py_0 soupsieve 2.0.1 py_0 sphinx 3.2.1 py_0 sphinxcontrib 1.0 py38_1 sphinxcontrib-applehelp 1.0.2 py_0 sphinxcontrib-devhelp 1.0.2 py_0 sphinxcontrib-htmlhelp 1.0.3 py_0 sphinxcontrib-jsmath 1.0.1 py_0 sphinxcontrib-qthelp 1.0.3 py_0 sphinxcontrib-serializinghtml 1.1.4 py_0 sphinxcontrib-websupport 1.2.4 py_0 spyder 4.1.5 py38_0 spyder-kernels 1.9.4 py38_0 sqlalchemy 1.3.19 py38he774522_0 sqlite 3.33.0 h2a8f88b_0 statsmodels 0.11.1 py38he774522_0 sympy 1.6.2 py38_0 tbb 2020.2 h74a9793_0 tblib 1.7.0 py_0 terminado 0.8.3 py38_0 testpath 0.4.4 py_0 threadpoolctl 2.1.0 pyh5ca1d4c_0 tiledb 1.7.0 h0b90766_4 conda-forge tk 8.6.10 he774522_0 toml 0.10.1 py_0 toolz 0.10.0 py_0 tornado 6.0.4 py38he774522_1 tqdm 4.48.2 py_0 traitlets 4.3.3 py38_0 typing_extensions 3.7.4.3 py_0 ujson 3.1.0 py38ha925a31_0 unicodecsv 0.14.1 py38_0 urllib3 1.25.10 py_0 vc 14.1 h0510ff6_4 vs2015_runtime 14.16.27012 hf0eaf9b_3 watchdog 0.10.3 py38_0 wcwidth 0.2.5 py_0 webencodings 0.5.1 py38_1 werkzeug 1.0.1 py_0 wheel 0.35.1 py_0 widgetsnbextension 3.5.1 py38_0 win_inet_pton 1.1.0 py38_0 win_unicode_console 0.5 py38_0 wincertstore 0.2 py38_0 winpty 0.4.3 4 wrapt 1.11.2 py38he774522_0 xerces-c 3.2.2 ha925a31_0 xlrd 1.2.0 py_0 xlsxwriter 1.3.3 py_0 xlwings 0.20.5 py38_0 xlwt 1.3.0 py38_0 xz 5.2.5 h62dcd97_0 yaml 0.2.5 he774522_0 yapf 0.30.0 py_0 zeromq 4.3.2 ha925a31_3 zict 2.0.0 py_0 zipp 3.1.0 py_0 zlib 1.2.11 h62dcd97_4 zope 1.0 py38_1 zope.event 4.4 py38_0 zope.interface 5.1.0 py38he774522_0 zstd 1.4.5 h04227a9_0

[mcg1969]

@Phillip-M-Feldman please try the --ignore-missing-files in your case. I’ve noticed this problem with the Python package as well. It’s a duplicate of #145 .

@AaronFaltesek that is, to be frank, way too many Pip packages. Conda-pack is intended to pack environments that were built almost exclusively with conda. In particular, pip packages with binary files have a high probability of failure. You too can try --ignore-missing-files but I would be very concerned that this just will not work for your environment.