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Mac OS - No Path to Anaconda bin for applications started in Finder #9830

Open sprague252 opened 5 years ago

sprague252 commented 5 years ago

Actual Behavior

The bug is that Anaconda does not add its bin directory to the path environment variable that is read when an application is opened in the Mac OS Finder. I noticed this when I launched the RStudio application (installed by Anaconda), and RStudio could not find pandoc, which was in the Anaconda bin directory. I have installed Anaconda on my computer in /opt/anaconda so it can be used by all users. The Anaconda installer modifies the user .bash_profile file to add the appropriate bin directory (in my case /opt/anaconda/bin) to the user path. When starting an application such as RStudio from the bash shell, the PATH variable from the shell is passed to the application, but when the application is opened from the Finder (or the Dock), the PATH variable is not determined from .bash_profile, and the application does not know about the Anaconda bin directory. One solution is to add an entry with the path to the Anaconda bin directory in the /etc/paths.d directory. The system reads these entries to set the PATH variable for processes that are not started within a shell. See a discussion of this at https://apple.stackexchange.com/questions/106355/setting-the-system-wide-path-environment-variable-in-mavericks. There may be another place that Anaconda can store the path to its executable directory for Mac OS applications like RStudio, but I am not aware of it.

Expected Behavior

Applications such as RStudio should be able to find the necessary executables when they are launched from the Finder.

Steps to Reproduce

  1. Launch Anaconda-installed RStudio by clicking on the Finder icon anaconda/Applications/RStudio.app.
  2. In the RStudio console run the command rmarkdown:::find_pandoc().
  3. In the console run the command as.list(rmarkdown:::.pandoc).
  4. If $version and $dir are NULL, then pandoc was not found.
  5. In the console run the command Sys.getenv("PATH").
  6. If the Anaconda bin directory is not in the path output, then RStudio cannot locate the executable files in it.
Anaconda or Miniconda version:
conda --version
conda 4.5.8

Anaconda package version: custom, build: py27h2cfa9e9_0

Operating System:

Mac OS 10.13.6

conda info
     active environment : None
       user config file : /Users/mark/.condarc
 populated config files : /Users/mark/.condarc
          conda version : 4.5.8
    conda-build version : not installed
         python version : 2.7.14.final.0
       base environment : /opt/anaconda  (writable)
           channel URLs : https://conda.anaconda.org/r/osx-64
                          https://conda.anaconda.org/r/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/osx-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/osx-64
                          https://repo.anaconda.com/pkgs/pro/noarch
                          https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/vpython/osx-64
                          https://conda.anaconda.org/vpython/noarch
          package cache : /opt/anaconda/pkgs
                          /Users/mark/.conda/pkgs
       envs directories : /opt/anaconda/envs
                          /Users/mark/.conda/envs
               platform : osx-64
             user-agent : conda/4.5.8 requests/2.18.4 CPython/2.7.14 Darwin/17.7.0 OSX/10.13.6
                UID:GID : 502:20
             netrc file : None
           offline mode : False
conda list --show-channel-urls
# packages in environment at /opt/anaconda:
#
# Name                    Version                   Build  Channel
_license                  1.1                      py27_1    defaults
_r-mutex                  1.0.0               anacondar_1    r
acoustics                 0.1.2                     <pip>
alabaster                 0.7.10           py27h9dd7d6e_0    defaults
anaconda                  custom           py27h2cfa9e9_0    defaults
anaconda-client           1.6.9                    py27_0    defaults
anaconda-navigator        1.8.4                    py27_0    defaults
anaconda-project          0.8.2            py27h2dc806c_0    defaults
appnope                   0.1.0            py27hb466136_0    defaults
appscript                 1.0.1            py27h451298e_1    defaults
apptools                  4.4.0                    py27_0    defaults
argcomplete               1.0.0                    py27_1    defaults
asn1crypto                0.24.0                   py27_0    defaults
astroid                   1.6.1                    py27_0    defaults
astropy                   2.0.3            py27h1de35cc_0    defaults
attrs                     17.4.0                   py27_0    defaults
automat                   0.7.0                    py27_0    defaults
babel                     2.5.3                    py27_0    defaults
backports                 1.0              py27hb4f9756_1    defaults
backports.functools_lru_cache 1.4              py27h2aca819_1    defaults
backports.shutil_get_terminal_size 1.0.0            py27hc9115de_2    defaults
backports_abc             0.5              py27h6972548_0    defaults
beautifulsoup4            4.6.0            py27h9416283_1    defaults
bitarray                  0.8.1            py27h1de35cc_1    defaults
bkcharts                  0.2              py27haafc882_0    defaults
blaze                     0.11.3           py27hb49378a_0    defaults
bleach                    2.1.2                    py27_0    defaults
bokeh                     0.12.13          py27h5233db4_0    defaults
boto                      2.48.0           py27hacdd0fd_1    defaults
bwidget                   1.9.11                        0    defaults
bzip2                     1.0.6                hd86a083_4    defaults
ca-certificates           2018.03.07                    0    defaults
cairo                     1.14.12              hab642c4_0    defaults
cctools                   895                  h7512d6f_0    defaults
cdecimal                  2.3              py27h1de35cc_3    defaults
certifi                   2018.4.16                py27_0    defaults
cffi                      1.11.4           py27h342bebf_0    defaults
chardet                   3.0.4            py27h2842e91_1    defaults
chest                     0.2.3                    py27_0    defaults
clang                     4.0.1                h662ec87_0    defaults
clang_osx-64              4.0.1               h1ce6c1d_10    defaults
clangxx                   4.0.1                hc9b4283_0    defaults
clangxx_osx-64            4.0.1               h22b1bf0_10    defaults
click                     6.7              py27h2b86a94_0    defaults
cloudpickle               0.5.2                    py27_1    defaults
clyent                    1.2.2            py27hc0ae608_0    defaults
colorama                  0.3.9            py27hbbe92b6_0    defaults
compiler-rt               4.0.1                h5487866_0    defaults
conda                     4.5.8                    py27_0    defaults
conda-env                 2.6.0                h36134e3_0    defaults
configobj                 5.0.6                    py27_0    defaults
configparser              3.5.0            py27hc7edf1b_0    defaults
constantly                15.1.0           py27h28b3542_0    defaults
contextlib2               0.5.5            py27h9cb85f4_0    defaults
cryptography              2.1.4            py27hdbc5e8f_0    defaults
curl                      7.58.0               ha441bb4_0    defaults
cycler                    0.10.0           py27hfc73c78_0    defaults
cyrus-sasl                2.1.26               ha054001_1    defaults
cython                    0.27.3           py27h6429b90_0    defaults
cytoolz                   0.9.0            py27h1de35cc_0    defaults
dask                      0.16.1                   py27_0    defaults
dask-core                 0.16.1                   py27_0    defaults
datashape                 0.5.4            py27hd6a1745_0    defaults
dbus                      1.12.2               h5243cc1_1    defaults
decorator                 4.2.1                    py27_0    defaults
dill                      0.2.5                    py27_0    defaults
distributed               1.20.2                   py27_0    defaults
docutils                  0.14             py27h0befae3_0    defaults
entrypoints               0.2.3            py27hd680fb1_2    defaults
enum34                    1.1.6            py27hf475452_1    defaults
envisage                  4.6.0            py27h805c201_0    defaults
et_xmlfile                1.0.1            py27hc42f929_0    defaults
expat                     2.2.5                hb8e80ba_0    defaults
fastcache                 1.0.2            py27h1de35cc_2    defaults
filelock                  2.0.13           py27h2c227fa_0    defaults
flask                     0.12.2           py27h3ac5568_0    defaults
flask-cors                3.0.3            py27h13db576_0    defaults
font-ttf-dejavu-sans-mono 2.37                          0    defaults
font-ttf-inconsolata      2.000                         0    defaults
font-ttf-source-code-pro  2.030                         0    defaults
font-ttf-ubuntu           0.83                          0    defaults
fontconfig                2.12.4               hffb9db1_2    defaults
fonts-anaconda            1                    h8fa9717_0    defaults
fonts-continuum           1                             0    defaults
freetype                  2.8                  h143eb01_0    defaults
funcsigs                  1.0.2            py27hb9f6266_0    defaults
functools32               3.2.3.2          py27h8ceab06_1    defaults
futures                   3.2.0            py27h1b80678_0    defaults
geographiclib             1.49                      <pip>
geomag                    0.9.2015                  <pip>
get_terminal_size         1.0.0                h7520d66_0    defaults
gettext                   0.19.8.1             hb0f4f8b_2    defaults
gevent                    1.2.2            py27hc02608c_0    defaults
gfortran_osx-64           4.8.5                h22b1bf0_3    defaults
glib                      2.53.6               ha08cb78_1    defaults
glob2                     0.6              py27h55c9705_0    defaults
gmp                       6.1.2                h4a9834d_0    defaults
gmpy2                     2.0.8            py27h4bc979a_2    defaults
gpxpy                     1.3.1                     <pip>
graphite2                 1.3.10               h233cf8b_0    defaults
greenlet                  0.4.12           py27h081ed54_0    defaults
grin                      1.2.1                    py27_4    defaults
gsl                       2.2.1                         0    defaults
h5py                      2.7.1            py27h75626f5_0    defaults
harfbuzz                  1.5.0                h6db888e_0    defaults
hdf5                      1.10.1               h6090a45_0    defaults
heapdict                  1.0.0                    py27_2    defaults
html5lib                  1.0.1            py27h5233db4_0    defaults
httplib2                  0.10.3                    <pip>
hyperlink                 18.0.0                   py27_0    defaults
icu                       58.2                 h4b95b61_1    defaults
idna                      2.6              py27hedea723_1    defaults
imageio                   2.2.0            py27h37746d9_0    defaults
imagesize                 0.7.1            py27h4f7bcc8_0    defaults
incremental               17.5.0                   py27_0    defaults
intel-openmp              2018.0.0             h8158457_8    defaults
ipaddress                 1.0.19                   py27_0    defaults
ipykernel                 4.8.2                    py27_0    defaults
ipython                   5.4.1                    py27_2    defaults
ipython_genutils          0.2.0            py27h8b9a179_0    defaults
ipywidgets                7.1.1                    py27_0    defaults
isort                     4.2.15           py27h5bf637f_0    defaults
itsdangerous              0.24             py27h3948ded_1    defaults
jbig                      2.1                  h4d881f8_0    defaults
jdcal                     1.3              py27hfeaf94f_0    defaults
jedi                      0.11.1                   py27_0    defaults
jinja2                    2.10             py27h70b8dc5_0    defaults
jpeg                      9b                   he5867d9_2    defaults
jsonschema                2.6.0            py27hd9b497e_0    defaults
jupyter                   1.0.0                    py27_4    defaults
jupyter_client            5.2.2                    py27_0    defaults
jupyter_console           5.2.0            py27h9702a86_1    defaults
jupyter_core              4.4.0            py27h5ea6ba4_0    defaults
jupyterlab                0.31.5                   py27_0    defaults
jupyterlab_launcher       0.10.2                   py27_0    defaults
krb5                      1.14.2               hc0fd8ed_4    defaults
LabJackPython             1.201505                  <pip>
lazy-object-proxy         1.3.1            py27h712ce3f_0    defaults
ld64                      274.2                h7c2db76_0    defaults
libcurl                   7.58.0               hf30b1f0_0    defaults
libcxx                    4.0.1                h579ed51_0    defaults
libcxxabi                 4.0.1                hebd6815_0    defaults
libedit                   3.1                  hb4e282d_0    defaults
libffi                    3.2.1                hd939716_3    defaults
libgcc                    4.8.5                         1    defaults
libgfortran               3.0.1                h93005f0_2    defaults
libiconv                  1.15                 h99df5da_5    defaults
libntlm                   1.4                  h1de35cc_2    defaults
libpng                    1.6.34               he12f830_0    defaults
libsodium                 1.0.15               hd9e47c5_0    defaults
libssh2                   1.8.0                h322a93b_4    defaults
libtiff                   4.0.9                h0dac147_0    defaults
libxml2                   2.9.7                hab757c2_0    defaults
libxslt                   1.1.32               hb819dd2_0    defaults
llvm                      4.0.1                hc748206_0    defaults
llvm-lto-tapi             4.0.1                h6701bc3_0    defaults
llvm-openmp               4.0.1                hda82c8b_0    defaults
llvmlite                  0.21.0           py27hac8ee23_0    defaults
locket                    0.2.0            py27ha10513d_1    defaults
lxml                      4.1.1            py27hef8c89e_1    defaults
lzo                       2.10                 hb6b8854_1    defaults
markupsafe                1.0              py27hd3c86fa_1    defaults
matplotlib                2.1.2            py27h6d6146d_0    defaults
mayavi                    4.5.0                    py27_0    defaults
mccabe                    0.6.1            py27h1f69e8d_0    defaults
mistune                   0.8.3                    py27_0    defaults
mkl                       2018.0.1             hfbd8650_4    defaults
mkl-service               1.1.2            py27hcba3029_4    defaults
mpc                       1.0.3                h7a72875_5    defaults
mpfr                      3.1.5                h711e7fd_2    defaults
mpi                       1.0                       mpich    conda-forge
mpi4py                    3.0.0                   mpich_1    conda-forge
mpich                     3.2.1                         0    conda-forge
mpmath                    1.0.0            py27h6b0eff6_2    defaults
msgpack-python            0.5.1            py27h04f5b5a_0    defaults
multipledispatch          0.4.9            py27h10993aa_0    defaults
nbconvert                 5.3.1            py27h6455e4c_0    defaults
nbformat                  4.4.0            py27hddc86d0_0    defaults
ncurses                   6.0                  ha932d30_1    defaults
networkx                  2.1                      py27_0    defaults
nltk                      3.2.5            py27h2e86947_0    defaults
nose                      1.3.7            py27h2ee3cb8_2    defaults
notebook                  5.6.0                    py27_0    defaults
numba                     0.36.2          np114py27he3a832a_0    defaults
numexpr                   2.6.4            py27hf375000_0    defaults
numpy                     1.14.0           py27h8a80b8c_1    defaults
numpydoc                  0.7.0            py27h022f19e_0    defaults
odo                       0.5.1            py27h992a9f7_0    defaults
olefile                   0.45.1                   py27_0    defaults
openpyxl                  2.4.10                   py27_0    defaults
openssl                   1.0.2o               h26aff7b_0    defaults
packaging                 16.8             py27h24b219a_0    defaults
pandas                    0.22.0           py27h0a44026_0    defaults
pandoc                    2.2.1                h1a437c5_0    defaults
pandocfilters             1.4.2            py27hed78c4e_1    defaults
pango                     1.40.11              h22f5747_0    defaults
parso                     0.1.1            py27he57c4c6_0    defaults
partd                     0.3.8            py27h7560dbf_0    defaults
path.py                   10.5             py27h0d68f8b_0    defaults
pathlib2                  2.3.0            py27he09da1e_0    defaults
patsy                     0.5.0                    py27_0    defaults
pcre                      8.41                 hfb6ab37_1    defaults
pep8                      1.7.1                    py27_0    defaults
pexpect                   4.3.1                    py27_0    defaults
pickleshare               0.7.4            py27h37e3d41_0    defaults
pillow                    5.0.0            py27hfcce615_0    defaults
pip                       9.0.1            py27h1567d89_4    defaults
pip                       10.0.1                    <pip>
pixman                    0.34.0                        0    defaults
pkginfo                   1.4.1            py27ha9221e7_0    defaults
pluggy                    0.6.0            py27had36429_0    defaults
ply                       3.10             py27h6279b8a_0    defaults
portaudio                 19                            0    defaults
prometheus_client         0.2.0                    py27_0    defaults
prompt_toolkit            1.0.15           py27h4a7b9c2_0    defaults
psutil                    5.4.3            py27h1de35cc_0    defaults
ptyprocess                0.5.2            py27h70f6364_0    defaults
py                        1.5.2            py27he6783ac_0    defaults
pyasn1                    0.1.9                    py27_0    defaults
pyaudio                   0.2.7            py27h3777516_1    defaults
pycodestyle               2.3.1            py27h5b634e0_0    defaults
pycosat                   0.6.3            py27h6c51c7e_0    defaults
pycparser                 2.18             py27h0d28d88_1    defaults
pycrypto                  2.6.1            py27h1de35cc_7    defaults
pycurl                    7.43.0.1         py27hdbc3d79_0    defaults
pyface                    5.1.0                    py27_0    defaults
pyflakes                  1.6.0            py27h4446e76_0    defaults
pygments                  2.2.0            py27h1a556bb_0    defaults
pykml                     0.1.3                     <pip>
pylint                    1.8.2                    py27_0    defaults
pyodbc                    4.0.23           py27h0a44026_0    defaults
pyopenssl                 17.5.0           py27hfda213f_0    defaults
pyparsing                 2.2.0            py27h5bb6aaf_0    defaults
pyqt                      4.11.4                   py27_4    defaults
pysocks                   1.6.7            py27h1cff6a6_1    defaults
pytables                  3.4.2            py27ha4551b8_2    defaults
pytest                    3.3.2                    py27_0    defaults
python                    2.7.14              hde5916a_29    defaults
python-dateutil           2.6.1            py27hd56c96b_1    defaults
python.app                2                py27hf2d5e94_7    defaults
pytz                      2017.3           py27h803c07a_0    defaults
pywavelets                0.5.2            py27hd99e88a_0    defaults
pyyaml                    3.12             py27ha7932d0_1    defaults
pyzmq                     17.0.0           py27h1de35cc_0    defaults
qt                        4.8.7                         4    defaults
qtawesome                 0.4.4            py27hdeb2f59_0    defaults
qtconsole                 4.3.1            py27hdc90b4f_0    defaults
qtpy                      1.4.2                    py27_0    defaults
r                         3.4.3                    r343_0    r
r-assertthat              0.2.0            r343h889e2dd_0    r
r-backports               1.1.2            r343h7f474d2_0    r
r-base                    3.4.3                h9b62496_0    r
r-base64enc               0.1_3            r343h7f474d2_4    r
r-bh                      1.65.0_1         r343h889e2dd_0    r
r-bindr                   0.1              r343h889e2dd_0    r
r-bindrcpp                0.2              r343he124285_0    r
r-bit                     1.1_12           r343h7f474d2_0    r
r-bit64                   0.9_7            r343h7f474d2_0    r
r-bitops                  1.0_6            r343h7f474d2_4    r
r-blob                    1.1.0            r343h889e2dd_0    r
r-boot                    1.3_20           r343h889e2dd_0    r
r-broom                   0.4.3            r343h889e2dd_0    r
r-callr                   1.0.0            r343h889e2dd_0    r
r-car                     2.1_6            r343h889e2dd_0    r
r-caret                   6.0_78           r343h7f474d2_0    r
r-catools                 1.17.1           r343he124285_4    r
r-cellranger              1.1.0            r343h889e2dd_0    r
r-class                   7.3_14           r343h7f474d2_4    r
r-cli                     1.0.0            r343h889e2dd_0    r
r-clipr                   0.4.0            r343h889e2dd_0    r
r-cluster                 2.0.6            r343h883f7c5_0    r
r-codetools               0.2_15           r343h889e2dd_0    r
r-colorspace              1.3_2            r343h7f474d2_0    r
r-config                  0.2              r343h889e2dd_0    r
r-crayon                  1.3.4            r343h889e2dd_0    r
r-curl                    3.1              r343h7f474d2_0    r
r-cvst                    0.2_1            r343h889e2dd_0    r
r-data.table              1.10.4_3         r343h7f474d2_0    r
r-dbi                     0.7              r343h889e2dd_0    r
r-dbplyr                  1.1.0            r343h889e2dd_0    r
r-ddalpha                 1.3.1            r343h9f775be_0    r
r-deoptimr                1.0_8            r343h889e2dd_0    r
r-dichromat               2.0_0            r343h889e2dd_4    r
r-digest                  0.6.13           r343h7f474d2_0    r
r-dimred                  0.1.0            r343h889e2dd_0    r
r-dplyr                   0.7.4            r343he124285_0    r
r-drr                     0.0.2            r343h889e2dd_0    r
r-essentials              3.4.3                    r343_0    r
r-evaluate                0.10.1           r343h889e2dd_0    r
r-forcats                 0.2.0            r343h889e2dd_0    r
r-foreach                 1.4.4            r343h889e2dd_0    r
r-foreign                 0.8_69           r343h7f474d2_0    r
r-formatr                 1.5              r343h889e2dd_0    r
r-ggplot2                 2.2.1            r343h889e2dd_0    r
r-gistr                   0.4.0            r343h889e2dd_0    r
r-glmnet                  2.0_13           r343h883f7c5_0    r
r-glue                    1.2.0            r343h7f474d2_0    r
r-gower                   0.1.2            r343h7f474d2_0    r
r-gtable                  0.2.0            r343h889e2dd_0    r
r-haven                   1.1.0            r343he124285_0    r
r-hexbin                  1.27.1           r343h883f7c5_4    r
r-highr                   0.6              r343h889e2dd_0    r
r-hms                     0.4.0            r343h889e2dd_0    r
r-htmltools               0.3.6            r343he124285_0    r
r-htmlwidgets             0.9              r343h889e2dd_0    r
r-httpuv                  1.3.5            r343he124285_0    r
r-httr                    1.3.1            r343h889e2dd_0    r
r-ipred                   0.9_6            r343h7f474d2_0    r
r-irdisplay               0.4.4            r343h889e2dd_0    r
r-irkernel                0.8.11                   r343_0    r
r-iterators               1.0.9            r343h889e2dd_0    r
r-jsonlite                1.5              r343h7f474d2_0    r
r-kernlab                 0.9_25           r343h9f775be_0    r
r-kernsmooth              2.23_15          r343h883f7c5_4    r
r-knitr                   1.18             r343h889e2dd_0    r
r-labeling                0.3              r343h889e2dd_4    r
r-lattice                 0.20_35          r343h7f474d2_0    r
r-lava                    1.5.1            r343h889e2dd_0    r
r-lazyeval                0.2.1            r343h7f474d2_0    r
r-lme4                    1.1_15           r343he124285_0    r
r-lubridate               1.7.1            r343he124285_0    r
r-magrittr                1.5              r343h889e2dd_4    r
r-maps                    3.2.0            r343h7f474d2_0    r
r-markdown                0.8              r343h7f474d2_0    r
r-mass                    7.3_48           r343h7f474d2_0    r
r-matrix                  1.2_12           r343h7f474d2_0    r
r-matrixmodels            0.4_1            r343h889e2dd_4    r
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rope                      0.10.7           py27hffa1879_0    defaults
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mingwandroid commented 5 years ago

These app shortcuts are not really compatible with conda's environments. I am not sure it we should really keep ones like that that cannot work very well.

mingwandroid commented 5 years ago

I'll see what I can do about rmarkdown:::find_pandoc() not looking somewhere relative to the executable path though.

Would you mind testing the R 3.5.0 macOS packages available on rdonnellyr please and let me know if the problem reproduces there? Thanks in advance.

sprague252 commented 5 years ago

No problem. I will test them and let you know.

mingwandroid commented 5 years ago

An update to rstudio is alsso available there, please see if that fixes this (I know if fixes another important bug I introduced to the macOS builds).