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conda / conda

A system-level, binary package and environment manager running on all major operating systems and platforms.
https://docs.conda.io/projects/conda/
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Activating a custom conda environment breaks standard bash commands #9232

Closed StevenCHowell closed 2 years ago

StevenCHowell commented 5 years ago

Current Behavior

After activating a custom conda environment, several tools from /usr/bin/ no longer function. It seem that the $PATH variable was changed so these tools are now being used from .../<the environment>/Library/usr/bin/ directory instead.

Steps to Reproduce

Expected Behavior

Activating a conda environment should not change other parts of my path variable making basic tool unavailable.

Environment Information

`conda info`

``` (my_env) steven.howell@desktop MINGW64 ~/Favorites $ conda info /usr/bin/dirname: missing operand Try '/usr/bin/dirname --help' for more information. /usr/bin/dirname: missing operand Try '/usr/bin/dirname --help' for more information. active environment : my_env active env location : C:\Users\steven.howell\AppData\Local\Continuum\anaconda3\envs\my_env shell level : 2 user config file : C:\Users\steven.howell\.condarc populated config files : C:\Users\steven.howell\.condarc conda version : 4.7.11 conda-build version : 3.18.8 python version : 3.7.3.final.0 virtual packages : __cuda=10.1 base environment : C:\Users\steven.howell\AppData\Local\Continuum\anaconda3 (writable) channel URLs : https://repo.anaconda.com/pkgs/main/win-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/win-64 https://repo.anaconda.com/pkgs/r/noarch https://repo.anaconda.com/pkgs/msys2/win-64 https://repo.anaconda.com/pkgs/msys2/noarch package cache : C:\Users\steven.howell\AppData\Local\Continuum\anaconda3\pkgs C:\Users\steven.howell\.conda\pkgs C:\Users\steven.howell\AppData\Local\conda\conda\pkgs envs directories : C:\Users\steven.howell\AppData\Local\Continuum\anaconda3\envs C:\Users\steven.howell\.conda\envs C:\Users\steven.howell\AppData\Local\conda\conda\envs platform : win-64 user-agent : conda/4.7.11 requests/2.22.0 CPython/3.7.3 Windows/10 Windows/10.0.17763 administrator : False netrc file : None offline mode : False ```

`conda config --show-sources`

``` (my_env) steven.howell@desktop MINGW64 ~/Favorites $ conda config --show-sources /usr/bin/dirname: missing operand Try '/usr/bin/dirname --help' for more information. /usr/bin/dirname: missing operand Try '/usr/bin/dirname --help' for more information. ==> C:\Users\steven.howell\.condarc <== ssl_verify: True channels: - defaults ```

`conda list --show-channel-urls`

``` (my_env) steven.howell@2001-R-NGJCDE46 MINGW64 ~/Favorites $ conda list --show-channel-urls /usr/bin/dirname: missing operand Try '/usr/bin/dirname --help' for more information. /usr/bin/dirname: missing operand Try '/usr/bin/dirname --help' for more information. # packages in environment at C:\Users\steven.howell\AppData\Local\Continuum\anaconda3\envs\my_env: # # Name Version Build Channel _pytorch_select 1.1.0 cpu defaults _r-mutex 1.0.0 anacondar_1 defaults _tflow_select 2.1.0 gpu defaults absl-py 0.7.1 py37_0 defaults alabaster 0.7.12 py37_0 defaults asn1crypto 0.24.0 py37_0 defaults astor 0.8.0 py37_0 defaults astroid 2.2.5 py37_0 defaults atomicwrites 1.3.0 py37_1 defaults attrs 19.1.0 py37_1 defaults babel 2.7.0 py_0 defaults backcall 0.1.0 py37_0 defaults beautifulsoup4 4.8.0 py37_0 defaults blas 1.0 mkl defaults bleach 3.1.0 py37_0 defaults blosc 1.15.0 h7bd577a_0 defaults bokeh 1.3.4 py37_0 defaults bzip2 1.0.8 he774522_0 defaults ca-certificates 2019.5.15 1 defaults certifi 2019.6.16 py37_1 defaults cffi 1.12.3 py37h7a1dbc1_0 defaults chardet 3.0.4 py37_1003 defaults click 7.0 py37_0 defaults cloudpickle 1.2.1 py_0 defaults colorama 0.4.1 py37_0 defaults colorcet 2.0.1 py_0 defaults conda 4.7.11 py37_0 defaults conda-build 3.18.9 py37_3 defaults conda-package-handling 1.3.11 py37_0 defaults coverage 4.5.3 py37he774522_0 defaults cryptography 2.3.1 py37h74b6da3_0 defaults cudatoolkit 10.0.130 0 defaults cudnn 7.6.0 cuda10.0_0 defaults cupy 6.0.0 py37h230ac6f_0 defaults cycler 0.10.0 py37_0 defaults cython 0.29.13 py37ha925a31_0 defaults cytoolz 0.10.0 py37he774522_0 defaults dask 2.3.0 py_0 defaults dask-core 2.3.0 py_0 defaults dask-glm 0.2.0 py37_0 defaults dask-ml 1.0.0 py_0 defaults datashader 0.7.0 py_0 defaults datashape 0.5.4 py37_1 defaults decorator 4.4.0 py37_1 defaults defusedxml 0.6.0 py_0 defaults distributed 2.3.2 py_1 defaults docutils 0.15.2 py37_0 defaults entrypoints 0.3 py37_0 defaults fastcache 1.1.0 py37he774522_0 defaults fastrlock 0.4 py37h6538335_0 defaults filelock 3.0.12 py_0 defaults flake8 3.7.7 py37_0 defaults font-ttf-dejavu-sans-mono 2.37 h6964260_0 defaults font-ttf-inconsolata 2.001 hcb22688_0 defaults font-ttf-source-code-pro 2.030 h7457263_0 defaults font-ttf-ubuntu 0.83 h8b1ccd4_0 defaults fonts-anaconda 1 h8fa9717_0 defaults freetype 2.9.1 ha9979f8_1 defaults fsspec 0.4.0 py_0 defaults gast 0.2.2 py37_0 defaults glob2 0.7 py_0 defaults graphviz 2.38 hfd603c8_2 defaults grpcio 1.14.1 py37h5c4b210_0 defaults h5py 2.9.0 py37h5e291fa_0 defaults hdf5 1.10.4 h7ebc959_0 defaults heapdict 1.0.0 py37_2 defaults icc_rt 2019.0.0 h0cc432a_1 defaults icu 58.2 ha66f8fd_1 defaults idna 2.8 py37_0 defaults imageio 2.5.0 py37_0 defaults imagesize 1.1.0 py37_0 defaults importlib_metadata 0.19 py37_0 defaults intel-openmp 2019.4 245 defaults ipykernel 5.1.2 py37h39e3cac_0 defaults ipython 7.8.0 py37h39e3cac_0 defaults ipython_genutils 0.2.0 py37_0 defaults ipywidgets 7.5.1 py_0 defaults isort 4.3.21 py37_0 defaults jedi 0.15.1 py37_0 defaults jinja2 2.10.1 py37_0 defaults joblib 0.12.5 py37_0 defaults jpeg 9b hb83a4c4_2 defaults json5 0.8.5 py_0 defaults jsonschema 3.0.2 py37_0 defaults jupyter 1.0.0 py37_7 defaults jupyter_client 5.3.1 py_0 defaults jupyter_console 6.0.0 py37_0 defaults jupyter_core 4.5.0 py_0 defaults jupyterlab 1.0.2 py37hf63ae98_0 defaults jupyterlab_server 1.0.0 py_1 defaults keras-applications 1.0.8 py_0 defaults keras-preprocessing 1.1.0 py_1 defaults keyring 18.0.0 py37_0 defaults kiwisolver 1.1.0 py37ha925a31_0 defaults lazy-object-proxy 1.4.2 py37he774522_0 defaults libarchive 3.3.3 h798a506_1 defaults libgpuarray 0.7.6 hfa6e2cd_0 defaults libiconv 1.15 h1df5818_7 defaults liblief 0.9.0 ha925a31_2 defaults libpng 1.6.37 h2a8f88b_0 defaults libprotobuf 3.8.0 h7bd577a_0 defaults libpython 2.1 py37_0 defaults libsodium 1.0.16 h9d3ae62_0 defaults libtiff 4.0.9 h36446d0_2 defaults libxml2 2.9.9 h464c3ec_0 defaults libxslt 1.1.33 h579f668_0 defaults line_profiler 2.1.2 py37hfa6e2cd_0 defaults llvmlite 0.29.0 py37ha925a31_0 defaults locket 0.2.0 py37_1 defaults luigi 2.8.7 py37_0 defaults lxml 4.4.1 py37h1350720_0 defaults lz4-c 1.8.1.2 h2fa13f4_0 defaults lzo 2.10 h6df0209_2 defaults m2-bash 4.3.042 5 defaults m2-coreutils 8.25 102 defaults m2-findutils 4.6.0 2 defaults m2-gcc-libs 5.3.0 4 defaults m2-gmp 6.1.0 3 defaults m2-heimdal 1.5.3 10 defaults m2-heimdal-libs 1.5.3 10 defaults m2-icu 56.1 2 defaults m2-libcrypt 1.3 2 defaults m2-libdb 5.3.28 3 defaults m2-libedit 3.1 20150326 defaults m2-libiconv 1.14 3 defaults m2-libintl 0.19.7 4 defaults m2-libopenssl 1.0.2.g 2 defaults m2-libreadline 6.3.008 8 defaults m2-libsqlite 3.10.0.0 2 defaults m2-msys2-runtime 2.5.0.17080.65c939c 3 defaults m2-ncurses 6.0.20160220 2 defaults m2-openssh 7.1p2 2 defaults m2-openssl 1.0.2.g 2 defaults m2-zlib 1.2.8 4 defaults m2w64-binutils 2.25.1 5 defaults m2w64-bwidget 1.9.10 2 defaults m2w64-bzip2 1.0.6 6 defaults m2w64-c-ares 1.11.0 2 defaults m2w64-ca-certificates 20150426 104 defaults m2w64-crt-git 5.0.0.4636.2595836 2 defaults m2w64-curl 7.48.0 2 defaults m2w64-diffutils 3.3.2 2 defaults m2w64-expat 2.1.1 2 defaults m2w64-fftw 3.3.4 6 defaults m2w64-flac 1.3.1 3 defaults m2w64-gcc 5.3.0 6 defaults m2w64-gcc-ada 5.3.0 6 defaults m2w64-gcc-fortran 5.3.0 6 defaults m2w64-gcc-libgfortran 5.3.0 6 defaults m2w64-gcc-libs 5.3.0 7 defaults m2w64-gcc-libs-core 5.3.0 7 defaults m2w64-gcc-objc 5.3.0 6 defaults m2w64-gettext 0.19.7 2 defaults m2w64-gmp 6.1.0 2 defaults m2w64-gnutls 3.4.11 2 defaults m2w64-grep 2.24 2 defaults m2w64-gsl 2.1 2 defaults m2w64-headers-git 5.0.0.4636.c0ad18a 2 defaults m2w64-isl 0.16.1 2 defaults m2w64-jansson 2.7 3 defaults m2w64-libffi 3.2.1 4 defaults m2w64-libiconv 1.14 6 defaults m2w64-libidn 1.32 4 defaults m2w64-libjpeg-turbo 1.4.2 3 defaults m2w64-libmangle-git 5.0.0.4509.2e5a9a2 2 defaults m2w64-libmetalink 0.1.3 2 defaults m2w64-libogg 1.3.2 3 defaults m2w64-libpng 1.6.21 2 defaults m2w64-libsndfile 1.0.26 2 defaults m2w64-libsodium 1.0.10 2 defaults m2w64-libssh2 1.7.0 2 defaults m2w64-libsystre 1.0.1 3 defaults m2w64-libtasn1 4.7 2 defaults m2w64-libtiff 4.0.6 2 defaults m2w64-libtre-git 122.c2f5d13 5 defaults m2w64-libvorbis 1.3.5 2 defaults m2w64-libwinpthread-git 5.0.0.4634.697f757 2 defaults m2w64-libxml2 2.9.3 4 defaults m2w64-make 4.1.2351.a80a8b8 2 defaults m2w64-mpc 1.0.3 3 defaults m2w64-mpfr 3.1.4 4 defaults m2w64-nettle 3.1.1 4 defaults m2w64-nghttp2 1.9.2 2 defaults m2w64-nlopt 2.4.2 3 defaults m2w64-openblas 0.2.19 1 defaults m2w64-openssl 1.0.2.g 2 defaults m2w64-p11-kit 0.23.2 3 defaults m2w64-pcre 8.38 2 defaults m2w64-pkg-config 0.29.1 2 defaults m2w64-rtmpdump-git 499.a107cef 4 defaults m2w64-speex 1.2rc2 3 defaults m2w64-speexdsp 1.2rc3 3 defaults m2w64-tcl 8.6.5 3 defaults m2w64-tk 8.6.5 3 defaults m2w64-tktable 2.10 5 defaults m2w64-toolchain 5.3.0 7 defaults m2w64-tools-git 5.0.0.4592.90b8472 2 defaults m2w64-windows-default-manifest 6.4 3 defaults m2w64-wineditline 2.101 5 defaults m2w64-winpthreads-git 5.0.0.4634.697f757 2 defaults m2w64-xz 5.2.2 2 defaults m2w64-zeromq 4.1.4 2 defaults m2w64-zlib 1.2.8 10 defaults mako 1.0.10 py_0 defaults markdown 3.1.1 py37_0 defaults markupsafe 1.1.1 py37he774522_0 defaults matplotlib 2.2.2 py37had4c4a9_2 defaults mccabe 0.6.1 py37_1 defaults menuinst 1.4.16 py37he774522_0 defaults mistune 0.8.4 py37he774522_0 defaults mkl 2019.4 245 defaults mkl-service 2.3.0 py37hb782905_0 defaults mkl_fft 1.0.14 py37h14836fe_0 defaults mkl_random 1.0.2 py37h343c172_0 defaults more-itertools 7.2.0 py37_0 defaults mpmath 1.1.0 py37_0 defaults msgpack-python 0.6.1 py37h74a9793_1 defaults msys2-conda-epoch 20160418 1 defaults multipledispatch 0.6.0 py37_0 defaults mypy 0.701 py_1 defaults mypy_extensions 0.4.1 py37_0 defaults nb_conda_kernels 2.2.2 py37_0 defaults nbconvert 5.5.0 py_0 defaults nbformat 4.4.0 py37_0 defaults networkx 2.3 py_0 defaults ninja 1.9.0 py37h74a9793_0 defaults nltk 3.4.5 py37_0 defaults notebook 6.0.1 py37_0 defaults numba 0.45.1 py37hf9181ef_0 defaults numexpr 2.7.0 py37hdce8814_0 defaults numpy 1.16.4 py37h19fb1c0_0 defaults numpy-base 1.16.4 py37hc3f5095_0 defaults numpydoc 0.9.1 py_0 defaults olefile 0.46 py37_0 defaults openssl 1.0.2s he774522_0 defaults packaging 19.1 py37_0 defaults pandas 0.25.1 py37ha925a31_0 defaults pandoc 2.2.3.2 0 defaults pandocfilters 1.4.2 py37_1 defaults param 1.9.1 py_0 defaults parso 0.5.1 py_0 defaults partd 1.0.0 py_0 defaults patsy 0.5.1 py37_0 defaults pep8 1.7.1 py37_0 defaults pickleshare 0.7.5 py37_0 defaults pillow 5.4.1 py37hdc69c19_0 defaults pip 19.2.2 py37_0 defaults pkginfo 1.5.0.1 py37_0 defaults pluggy 0.12.0 py_0 defaults prometheus_client 0.5.0 py37_0 defaults prompt_toolkit 2.0.9 py37_0 defaults protobuf 3.8.0 py37h33f27b4_0 defaults psutil 5.4.8 py37he774522_0 defaults py 1.8.0 py37_0 defaults py-lief 0.9.0 py37ha925a31_2 defaults pycodestyle 2.5.0 py37_0 defaults pycosat 0.6.3 py37hfa6e2cd_0 defaults pycparser 2.19 py37_0 defaults pyct 0.4.6 py37_0 defaults pyflakes 2.1.1 py37_0 defaults pygments 2.4.2 py_0 defaults pygpu 0.7.6 py37h452e1ab_0 defaults pylint 2.3.1 py37_0 defaults pymc3 3.6 py37_0 defaults pymongo 3.8.0 py37ha925a31_1 defaults pyopenssl 19.0.0 py37_0 defaults pyparsing 2.4.2 py_0 defaults pyqt 5.6.0 py37ha878b3d_6 defaults pyreadline 2.1 py37_1 defaults pyrsistent 0.14.11 py37he774522_0 defaults pysocks 1.7.0 py37_0 defaults pytables 3.5.1 py37h1da0976_0 defaults pytest 5.0.1 py37_0 defaults pytest-cov 2.7.1 py_0 defaults python 3.7.1 h33f27b4_4 defaults python-dateutil 2.8.0 py37_0 defaults python-libarchive-c 2.8 py37_13 defaults pytorch 1.0.1 cpu_py37h39a92a0_0 defaults pytz 2019.2 py_0 defaults pywavelets 1.0.3 py37h8c2d366_1 defaults pywin32 223 py37hfa6e2cd_1 defaults pywinpty 0.5.5 py37_1000 defaults pyyaml 5.1.2 py37he774522_0 defaults pyzmq 18.1.0 py37ha925a31_0 defaults qt 5.6.2 vc14h6f8c307_12 defaults qtawesome 0.5.7 py37_1 defaults qtconsole 4.5.5 py_0 defaults qtpy 1.9.0 py_0 defaults r-abind 1.4_5 r351h6f4ce42_0 defaults r-argparse 1.1.1 r351h6f4ce42_0 defaults r-assertthat 0.2.0 r351hf348343_0 defaults r-backports 1.1.2 r351hf348343_0 defaults r-base 3.5.1 hac0af64_1 defaults r-base64enc 0.1_3 r351hf348343_4 defaults r-bh 1.66.0_1 r351hf348343_0 defaults r-bindr 0.1.1 r351hf348343_0 defaults r-bindrcpp 0.2.2 r351hf348343_0 defaults r-bit 1.1_14 r351h6f4ce42_0 defaults r-bit64 0.9_7 r351h6f4ce42_0 defaults r-bitops 1.0_6 r351h6f4ce42_4 defaults r-blob 1.1.1 r351h6f4ce42_0 defaults r-boot 1.3_20 r351h6f4ce42_0 defaults r-broom 0.5.0 r351h6f4ce42_0 defaults r-callr 2.0.4 r351hf348343_0 defaults r-car 3.0_0 r351h6f4ce42_0 defaults r-cardata 3.0_1 r351hf348343_0 defaults r-caret 6.0_80 r351h6f4ce42_0 defaults r-catools 1.17.1.1 r351h6f4ce42_0 defaults r-cellranger 1.1.0 r351h6f4ce42_0 defaults r-class 7.3_14 r351h6f4ce42_4 defaults r-cli 1.0.0 r351hf348343_0 defaults r-clipr 0.4.1 r351h6f4ce42_0 defaults r-cluster 2.0.7_1 r351h6f4ce42_0 defaults r-codetools 0.2_15 r351hf348343_0 defaults r-colorspace 1.3_2 r351hf348343_0 defaults r-config 0.3 r351h6f4ce42_0 defaults r-crayon 1.3.4 r351hf348343_0 defaults r-crosstalk 1.0.0 r351h6f4ce42_0 defaults r-curl 3.2 r351hf348343_0 defaults r-cvst 0.2_2 r351h6f4ce42_0 defaults r-data.table 1.11.4 r351h6f4ce42_0 defaults r-dbi 1.0.0 r351h6f4ce42_0 defaults r-dbplyr 1.2.2 r351h6f4ce42_0 defaults r-ddalpha 1.3.4 r351h6f4ce42_0 defaults r-deoptimr 1.0_8 r351h6f4ce42_0 defaults r-devtools 1.13.6 r351h6f4ce42_0 defaults r-dichromat 2.0_0 r351hf348343_4 defaults r-digest 0.6.15 r351hf348343_0 defaults r-dimred 0.1.0 r351h6f4ce42_0 defaults r-dplyr 0.7.6 r351hf348343_0 defaults r-drr 0.0.3 r351h6f4ce42_0 defaults r-e1071 1.7_0 r351h6f4ce42_0 defaults r-essentials 3.5.1 r351_0 defaults r-evaluate 0.11 r351hf348343_0 defaults r-fansi 0.2.3 r351hf348343_0 defaults r-findpython 1.0.3 r351h6f4ce42_0 defaults r-forcats 0.3.0 r351h6f4ce42_0 defaults r-foreach 1.4.4 r351hf348343_0 defaults r-foreign 0.8_71 r351h6f4ce42_0 defaults r-formatr 1.5 r351h6f4ce42_0 defaults r-gdata 2.18.0 r351h6f4ce42_0 defaults r-geometry 0.3_6 r351h6f4ce42_0 defaults r-getopt 1.20.2 r351h6f4ce42_0 defaults r-ggplot2 3.0.0 r351hf348343_0 defaults r-git2r 0.23.0 r351h6f4ce42_0 defaults r-glmnet 2.0_16 r351h6f4ce42_0 defaults r-glue 1.3.0 r351hf348343_0 defaults r-gower 0.1.2 r351h6f4ce42_0 defaults r-gtable 0.2.0 r351hf348343_0 defaults r-gtools 3.8.1 r351h6f4ce42_0 defaults r-haven 1.1.2 r351h6f4ce42_0 defaults r-hexbin 1.27.2 r351h6f4ce42_0 defaults r-highr 0.7 r351hf348343_0 defaults r-hms 0.4.2 r351hf348343_0 defaults r-htmltools 0.3.6 r351hf348343_0 defaults r-htmlwidgets 1.2 r351hf348343_0 defaults r-httpuv 1.4.5 r351h6f4ce42_0 defaults r-httr 1.3.1 r351hf348343_0 defaults r-ipred 0.9_6 r351h6f4ce42_0 defaults r-irdisplay 0.5.0 r351h6f4ce42_0 defaults r-irkernel 0.8.12 r351_0 defaults r-iterators 1.0.10 r351hf348343_0 defaults r-jsonlite 1.5 r351hf348343_0 defaults r-kernlab 0.9_26 r351h6f4ce42_0 defaults r-kernsmooth 2.23_15 r351h6f4ce42_4 defaults r-knitr 1.20 r351hf348343_0 defaults r-labeling 0.3 r351hf348343_4 defaults r-later 0.7.3 r351h6f4ce42_0 defaults r-lattice 0.20_35 r351hf348343_0 defaults r-lava 1.6.2 r351h6f4ce42_0 defaults r-lazyeval 0.2.1 r351hf348343_0 defaults r-leaps 3.0 r351h6f4ce42_0 defaults r-lme4 1.1_17 r351h6f4ce42_0 defaults r-lmtest 0.9_36 r351h6f4ce42_0 defaults r-lubridate 1.7.4 r351h6f4ce42_0 defaults r-magic 1.5_8 r351h6f4ce42_0 defaults r-magrittr 1.5 r351hf348343_4 defaults r-manipulatewidget 0.10.0 r351h6f4ce42_0 defaults r-maps 3.3.0 r351h6f4ce42_0 defaults r-maptools 0.9_3 r351h6f4ce42_0 defaults r-markdown 0.8 r351hf348343_0 defaults r-mass 7.3_50 r351hf348343_0 defaults r-matrix 1.2_14 r351hf348343_0 defaults r-matrixmodels 0.4_1 r351hf348343_4 defaults r-memoise 1.1.0 r351h6f4ce42_0 defaults r-mgcv 1.8_24 r351hf348343_0 defaults r-mime 0.5 r351hf348343_0 defaults r-miniui 0.1.1.1 r351h6f4ce42_0 defaults r-minqa 1.2.4 r351hf348343_4 defaults r-modelmetrics 1.1.0 r351h6f4ce42_0 defaults r-modelr 0.1.2 r351h6f4ce42_0 defaults r-mongolite 1.6 r351h6f4ce42_0 defaults r-munsell 0.5.0 r351hf348343_0 defaults r-mvtnorm 1.0_8 r351hf348343_0 defaults r-nlme 3.1_137 r351hf348343_0 defaults r-nloptr 1.0.4 r351h6f4ce42_4 defaults r-nnet 7.3_12 r351h6f4ce42_0 defaults r-numderiv 2016.8_1 r351h6f4ce42_0 defaults r-odbc 1.1.5 r351_0 defaults r-openssl 1.0.2 r351hf348343_0 defaults r-openxlsx 4.1.0 r351h6f4ce42_0 defaults r-packrat 0.4.9_3 r351h6f4ce42_0 defaults r-pbdzmq 0.3_3 r351h6f4ce42_0 defaults r-pbkrtest 0.4_7 r351h6f4ce42_0 defaults r-pillar 1.3.0 r351hf348343_0 defaults r-pkgconfig 2.0.1 r351hf348343_0 defaults r-pki 0.1_5.1 r351h6f4ce42_0 defaults r-plogr 0.2.0 r351hf348343_0 defaults r-pls 2.6_0 r351h6f4ce42_0 defaults r-plyr 1.8.4 r351hf348343_0 defaults r-praise 1.0.0 r351hf348343_4 defaults r-prettyunits 1.0.2 r351h6f4ce42_0 defaults r-processx 3.1.0 r351hf348343_0 defaults r-prodlim 2018.04.18 r351h6f4ce42_0 defaults r-profvis 0.3.5 r351h6f4ce42_0 defaults r-promises 1.0.1 r351h6f4ce42_0 defaults r-proto 1.0.0 r351h6f4ce42_0 defaults r-purrr 0.2.5 r351hf348343_0 defaults r-quantmod 0.4_13 r351h6f4ce42_0 defaults r-quantreg 5.36 r351hf348343_0 defaults r-r6 2.2.2 r351hf348343_0 defaults r-randomforest 4.6_14 r351h6f4ce42_0 defaults r-rappdirs 0.3.1 r351h6f4ce42_0 defaults r-rbokeh 0.6.3 r351_0 defaults r-rcolorbrewer 1.1_2 r351hf348343_0 defaults r-rcpp 0.12.18 r351hf348343_0 defaults r-rcppeigen 0.3.3.4.0 r351hf348343_0 defaults r-rcpproll 0.3.0 r351h6f4ce42_0 defaults r-rcurl 1.95_4.11 r351h6f4ce42_0 defaults r-readr 1.1.1 r351hf348343_0 defaults r-readxl 1.1.0 r351h6f4ce42_0 defaults r-recipes 0.1.3 r351h6f4ce42_0 defaults r-recommended 3.5.1 r351_0 defaults r-rematch 1.0.1 r351h6f4ce42_0 defaults r-repr 0.15.0 r351h6f4ce42_0 defaults r-reprex 0.2.0 r351h6f4ce42_0 defaults r-reshape2 1.4.3 r351hf348343_0 defaults r-rgl 0.99.16 r351h6f4ce42_0 defaults r-rio 0.5.10 r351h6f4ce42_0 defaults r-rjava 0.9_10 r351h6f4ce42_0 defaults r-rjdbc 0.2_7.1 r351h6f4ce42_0 defaults r-rjsonio 1.3_0 r351h6f4ce42_4 defaults r-rlang 0.2.1 r351hf348343_0 defaults r-rmarkdown 1.10 r351hf348343_0 defaults r-robustbase 0.93_2 r351h6f4ce42_0 defaults r-rpart 4.1_13 r351h6f4ce42_0 defaults r-rprojroot 1.3_2 r351hf348343_0 defaults r-rsconnect 0.8.8 r351h6f4ce42_0 defaults r-rsqlite 2.1.1 r351h6f4ce42_0 defaults r-rstudioapi 0.7 r351hf348343_0 defaults r-rvest 0.3.2 r351h6f4ce42_0 defaults r-sandwich 2.4_0 r351h6f4ce42_0 defaults r-scales 0.5.0 r351hf348343_0 defaults r-selectr 0.4_1 r351h6f4ce42_0 defaults r-sfsmisc 1.1_2 r351h6f4ce42_0 defaults r-shiny 1.1.0 r351h6f4ce42_0 defaults r-shinythemes 1.1.1 r351h6f4ce42_0 defaults r-sourcetools 0.1.7 r351h6f4ce42_0 defaults r-sp 1.3_1 r351h6f4ce42_0 defaults r-sparklyr 0.8.4 r351h6f4ce42_0 defaults r-sparsem 1.77 r351hf348343_0 defaults r-spatial 7.3_11 r351h6f4ce42_4 defaults r-squarem 2017.10_1 r351h6f4ce42_0 defaults r-stringi 1.2.4 r351hf348343_0 defaults r-stringr 1.3.1 r351hf348343_0 defaults r-survival 2.42_6 r351h6f4ce42_0 defaults r-testthat 2.0.0 r351hf348343_0 defaults r-th.data 1.0_9 r351h6f4ce42_0 defaults r-tibble 1.4.2 r351hf348343_0 defaults r-tidyr 0.8.1 r351hf348343_0 defaults r-tidyselect 0.2.4 r351hf348343_0 defaults r-tidyverse 1.2.1 r351h6f4ce42_0 defaults r-timedate 3043.102 r351h6f4ce42_0 defaults r-tinytex 0.6 r351hf348343_0 defaults r-ttr 0.23_3 r351h6f4ce42_0 defaults r-utf8 1.1.4 r351hf348343_0 defaults r-uuid 0.1_2 r351h6f4ce42_4 defaults r-viridislite 0.3.0 r351hf348343_0 defaults r-webshot 0.5.0 r351h6f4ce42_0 defaults r-whisker 0.3_2 r351h6f4ce42_4 defaults r-withr 2.1.2 r351hf348343_0 defaults r-xfun 0.3 r351hf348343_0 defaults r-xml2 1.2.0 r351hf348343_0 defaults r-xtable 1.8_2 r351hf348343_0 defaults r-xts 0.11_0 r351h6f4ce42_0 defaults r-yaml 2.2.0 r351hf348343_0 defaults r-zip 1.0.0 r351h6f4ce42_0 defaults r-zoo 1.8_3 r351h6f4ce42_0 defaults requests 2.22.0 py37_0 defaults rope 0.14.0 py_0 defaults rstudio 1.1.456 vc14h1ad3211_1 [vc14] defaults rtools 3.4.0 0 defaults ruamel_yaml 0.15.46 py37hfa6e2cd_0 defaults scikit-image 0.15.0 py37ha925a31_0 defaults scikit-learn 0.21.2 py37h6288b17_0 defaults scipy 1.3.1 py37h29ff71c_0 defaults seaborn 0.9.0 py37_0 defaults send2trash 1.5.0 py37_0 defaults setuptools 41.0.1 py37_0 defaults sip 4.18.1 py37h6538335_2 defaults six 1.12.0 py37_0 defaults snappy 1.1.7 h777316e_3 defaults snowballstemmer 1.9.0 py_0 defaults sortedcontainers 2.1.0 py37_0 defaults soupsieve 1.9.2 py37_0 defaults sphinx 2.1.2 py_0 defaults sphinxcontrib-applehelp 1.0.1 py_0 defaults sphinxcontrib-devhelp 1.0.1 py_0 defaults sphinxcontrib-htmlhelp 1.0.2 py_0 defaults sphinxcontrib-jsmath 1.0.1 py_0 defaults sphinxcontrib-qthelp 1.0.2 py_0 defaults sphinxcontrib-serializinghtml 1.1.3 py_0 defaults spyder 3.3.6 py37_0 defaults spyder-kernels 0.5.1 py37_0 defaults sqlalchemy 1.3.7 py37he774522_0 defaults sqlite 3.29.0 he774522_0 defaults statsmodels 0.10.1 py37h8c2d366_0 defaults sympy 1.4 py37_0 defaults tbb 2019.4 h74a9793_0 defaults tblib 1.4.0 py_0 defaults tensorboard 1.14.0 py37he3c9ec2_0 defaults tensorflow 1.14.0 gpu_py37h5512b17_0 defaults tensorflow-base 1.14.0 gpu_py37h55fc52a_0 defaults tensorflow-estimator 1.14.0 py_0 defaults tensorflow-gpu 1.14.0 h0d30ee6_0 defaults termcolor 1.1.0 py37_1 defaults terminado 0.8.2 py37_0 defaults testpath 0.4.2 py37_0 defaults theano 1.0.3 py37_0 defaults tk 8.6.8 hfa6e2cd_0 defaults toolz 0.10.0 py_0 defaults tornado 5.1.1 py37hfa6e2cd_0 defaults tqdm 4.32.1 py_0 defaults traitlets 4.3.2 py37_0 defaults typed-ast 1.3.4 py37he774522_0 defaults urllib3 1.24.2 py37_0 defaults vc 14.1 h0510ff6_4 defaults vs2015_runtime 14.16.27012 hf0eaf9b_0 defaults wcwidth 0.1.7 py37_0 defaults webencodings 0.5.1 py37_1 defaults werkzeug 0.15.5 py_0 defaults wheel 0.33.4 py37_0 defaults widgetsnbextension 3.5.1 py37_0 defaults win_inet_pton 1.1.0 py37_0 defaults wincertstore 0.2 py37_0 defaults winpty 0.4.3 4 defaults wrapt 1.11.2 py37he774522_0 defaults xarray 0.12.1 py_0 defaults xlrd 1.2.0 py37_0 defaults xlsxwriter 1.1.8 py_0 defaults xlwt 1.3.0 py37_0 defaults xz 5.2.4 h2fa13f4_4 defaults yaml 0.1.7 hc54c509_2 defaults zeromq 4.3.1 h33f27b4_3 defaults zict 1.0.0 py_0 defaults zipp 0.5.2 py_0 defaults zlib 1.2.11 h62dcd97_3 defaults zstd 1.3.3 hfe6a214_0 defaults ```

mingwandroid commented 5 years ago

Thanks for the report. I've seen this on one of my own Windows installs, but not consistently (probably env dependent) so I sort of ignored it and hoped it was just down to some misconfiguration. I think I was grasping at straws though really.

As you say, we are shadowing your 'system' (Git for Windows/MSYS2/Cygwin/WSL/whatever it may be) tools with similar ones used by conda's R eco-system. Unfortunately, due to the way that the MSYS2 runtime works (which is very much the Cygwin runtime with a few patches) only one can be loaded at once (it is like a Linux kernel in this regard).

I think the only easy thing we can really do here is to have an option to put conda's PATH entries later in PATH instead of at the front, but if we do that, then I suspect some bits of R will not work for you.

For the record, this also affects me so I'm invested in having it work. However, I am also flexible as to which Unix shell I use. If making WSL work as my Unix shell to drive conda on Windows proves to be an easier task (I feel having choice here would be a good thing and making WSL work could offer that), that might be the best course of action.

I'll bring it up with the Anaconda Distribution team though and perform some tests when I boot into Windows next.

C0nrado commented 4 years ago

I am having the same issue. I have Miniconda Installed (WINDOWS) and 2 envs. The root (base) and a pure R env (r-env). The issue will occur every time I activate r-env. if I change to the root env, it doesn't occur. However, If I comeback to the r-env it doesn't happen anymore. It's only on the first activation (weather it be directly into r-env, or first the root env, and then the r-env

The solution has been the back and forth activation of my r-env

The first time I though it was hapnning due to r-essentials packages, as it install python and jupyter, I though they together in the same env were causing the issue, but that's not true

mszefler commented 4 years ago

I am having the same problem. It occurs for me when I activate a conda environment containing msys2/posix from git-bash: 

C:\>conda create -n posix -c msys2 posix
...
C:\>conda activate posix
(posix) C:\>bash
[username@host c]$ dirname $(pwd) # (1) this works fine
/
[username@hostname c] $ exit
(posix) C:\> conda deactivate
C:\> C:\....\Programs\Git\bin\bash.exe
[username@host c]$ source activate posix
(posix) [username@host c]$ dirname $(pwd) # (2) this fails 
/usr/bin/dirname: missing operand
Try '/usr/bin/dirname --help' for more information.
(posix) [username@host c]$ /usr/bin/dirname $(pwd) # (3) this  works, though!
/

This happens for all the standard programs in /bin and /usr/bin: the program gets invoked, but the command line arguments are lost. It seems that the msys2/posix version of dirname is getting invoked:

(posix) [username@hostname c]$ /bin/which dirname
/c/Users/username/AppData/Local/Continuum/anaconda3/envs/posix/Library/usr/bin/dirname
(posix) [username@hostname c]$ /c/Users/username/AppData/Local/Continuum/anaconda3/envs/posix/Library/usr/bin/dirname $(pwd)
/usr/bin/dirname: missing operand
Try '/usr/bin/dirname --help' for more information.

It seems that there is some problem in argument passing between git-bash and msys2/posix. In addition there is a problem of the mounts for /bin and /usr/bin not getting remapped, even though they appear to be remapped:

(posix) [username@hostname c]$ mount
C:/WINDOWS on /tmp type ntfs (binary,posix=0,usertemp)
C:/Users/username/AppData/Local/Continuum/anaconda3/envs/posix/Library on / type ntfs (binary,noacl,auto)
C:/Users/username/AppData/Local/Continuum/anaconda3/envs/posix/Library/usr/bin on /bin type ntfs (binary,noacl,auto)
C: on /c type ntfs (binary,noacl,posix=0,user,noumount,auto)

Despite the above output /bin is still pointing to git's version of /bin:

C:\>\Users\username\AppData\Local\Programs\Git\bin\bash.exe
[username@hostname c]$ mount
C:/Users/username/AppData/Local/Temp/1 on /tmp type ntfs (binary,noacl,posix=0,usertemp)
C:/Users/username/AppData/Local/Programs/Git on / type ntfs (binary,noacl,auto)
C:/Users/username/AppData/Local/Programs/Git/usr/bin on /bin type ntfs (binary,noacl,auto)
C: on /c type ntfs (binary,noacl,posix=0,user,noumount,auto)
.
.
.
[username@hostname c]$ /bin/ls /bin | /bin/wc -l
438
[username@hostname c]$ source activate posix
(posix) [username@hostname c]$ /bin/ls /bin | /bin/wc -l
438
(posix) [username@hostname c]$ mount
C:/WINDOWS on /tmp type ntfs (binary,posix=0,usertemp)
C:/Users/username/AppData/Local/Continuum/anaconda3/envs/posix/Library on / type ntfs (binary,noacl,auto)
C:/Users/username/AppData/Local/Continuum/anaconda3/envs/posix/Library/usr/bin on /bin type ntfs (binary,noacl,auto)
C: on /c type ntfs (binary,noacl,posix=0,user,noumount,auto)
F: on /f type cifs (binary,noacl,posix=0,user,noumount,auto)
J: on /j type cifs (binary,noacl,posix=0,user,noumount,auto)
K: on /k type cifs (binary,noacl,posix=0,user,noumount,auto)
L: on /l type cifs (binary,noacl,posix=0,user,noumount,auto)
O: on /o type cifs (binary,noacl,posix=0,user,noumount,auto)
X: on /x type cifs (binary,noacl,posix=0,user,noumount,auto)
(posix) [username@hostname c]$

My posix environment looks like this:

C:\>conda list -n posix
# packages in environment at C:\Users\username\AppData\Local\Continuum\anaconda3\envs\posix:
#
# Name                    Version                   Build  Channel
m2-base                   1.0.0                         3    msys2
m2-bash                   4.3.042                       5    msys2
m2-bash-completion        2.3                           2    msys2
m2-catgets                1.1                           3    msys2
m2-coreutils              8.25                        102    msys2
m2-dash                   0.5.8                         2    msys2
m2-diffutils              3.3                           4    msys2
m2-file                   5.25                          2    msys2
m2-filesystem             2016.04                       4    msys2
m2-findutils              4.6.0                         2    msys2
m2-gawk                   4.1.3                         2    msys2
m2-gcc-libs               5.3.0                         4    msys2
m2-gettext                0.19.7                        4    msys2
m2-gmp                    6.1.0                         3    msys2
m2-grep                   2.22                          4    msys2
m2-gzip                   1.7                           2    msys2
m2-inetutils              1.9.2                         2    msys2
m2-info                   6.0                           2    msys2
m2-less                   481                           2    msys2
m2-libasprintf            0.19.7                        4    msys2
m2-libbz2                 1.0.6                         3    msys2
m2-libcatgets             1.1                           3    msys2
m2-libcrypt               1.3                           2    msys2
m2-libgettextpo           0.19.7                        4    msys2
m2-libiconv               1.14                          3    msys2
m2-libintl                0.19.7                        4    msys2
m2-liblzma                5.2.2                         2    msys2
m2-libpcre                8.38                          2    msys2
m2-libreadline            6.3.008                       8    msys2
m2-libutil-linux          2.26.2                        2    msys2
m2-libxml2                2.9.2                         3    msys2
m2-make                   4.1                           5    msys2
m2-mintty                 1!2.2.3                       2    msys2
m2-mpfr                   3.1.4                         2    msys2
m2-msys2-launcher-git     0.3.28.860c495                2    msys2
m2-msys2-runtime          2.5.0.17080.65c939c               3    msys2
m2-ncurses                6.0.20160220                  2    msys2
m2-sed                    4.2.2                         3    msys2
m2-tar                    1.28                          4    msys2
m2-tftp-hpa               5.2                           2    msys2
m2-time                   1.7                           2    msys2
m2-ttyrec                 1.0.8                         2    msys2
m2-tzcode                 2015.e                        2    msys2
m2-unzip                  6.0                           3    msys2
m2-util-linux             2.26.2                        2    msys2
m2-which                  2.21                          3    msys2
m2-zip                    3.0                           2    msys2
m2-zlib                   1.2.8                         4    msys2
msys2-conda-epoch         20160418                      1    msys2
posix                     1.0.0                         2    msys2

C:\> conda info

     active environment : None
            shell level : 0
       user config file : C:\Users\username\.condarc
 populated config files : C:\Users\username\AppData\Local\Continuum\anaconda3\.condarc
                          C:\Users\username\.condarc
          conda version : 4.8.5
    conda-build version : 3.18.11
         python version : 3.7.7.final.0
       virtual packages :
       base environment : C:\Users\username\AppData\Local\Continuum\anaconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/win-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/win-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/msys2/win-64
                          https://repo.anaconda.com/pkgs/msys2/noarch
          package cache : C:\Users\username\AppData\Local\Continuum\anaconda3\pkgs
                          C:\Users\username\.conda\pkgs
                          C:\Users\username\AppData\Local\conda\conda\pkgs
       envs directories : C:\Users\username\AppData\Local\Continuum\anaconda3\envs
                          C:\Users\username\.conda\envs
                          C:\Users\username\AppData\Local\conda\conda\envs
               platform : win-64
             user-agent : conda/4.8.5 requests/2.24.0 CPython/3.7.7 Windows/10 Windows/10.0.17763
          administrator : False
             netrc file : None
           offline mode : False

C:\>git --version
git version 2.28.0.windows.1
github-actions[bot] commented 2 years ago

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