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Conflicts when installing RStudio #3886

Closed reid-indeed closed 7 years ago

reid-indeed commented 7 years ago

When attempting to re-install RStudio from my Mac terminal using 'conda install rstudio', I get the following error message:

The following specifications were found to be in conflict:
- csd-python-api
- matplotlib
- pango
Use "conda info " to see the dependencies for each package.

I had uninstalled it because ggplot2 would no longer load without crashing. Does anyone know how I can best resolve this in order to install RStudio smoothly? All system info pasted below this message.

Many thanks,

Marc

Current conda install:

               platform : osx-64
          conda version : 4.3.22
       conda is private : False
      conda-env version : 4.3.22
    conda-build version : not installed
         python version : 2.7.13.final.0
       requests version : 2.12.4
       root environment : /Users/marc/anaconda2  (writable)
    default environment : /Users/marc/anaconda2
       envs directories : /Users/marc/anaconda2/envs
                          /Users/marc/.conda/envs
          package cache : /Users/marc/anaconda2/pkgs
                          /Users/marc/.conda/pkgs
           channel URLs : https://conda.anaconda.org/anaconda-fusion/osx-64
                          https://conda.anaconda.org/anaconda-fusion/noarch
                          https://repo.continuum.io/pkgs/free/osx-64
                          https://repo.continuum.io/pkgs/free/noarch
                          https://repo.continuum.io/pkgs/r/osx-64
                          https://repo.continuum.io/pkgs/r/noarch
                          https://repo.continuum.io/pkgs/pro/osx-64
                          https://repo.continuum.io/pkgs/pro/noarch
            config file : /Users/marc/.condarc
             netrc file : None
           offline mode : False
             user-agent : conda/4.3.22 requests/2.12.4 CPython/2.7.13 Darwin/16.6.0 OSX/10.12.5    
                UID:GID : 501:20
# packages in environment at /Users/marc/anaconda2:
#
_license                  1.1                      py27_1    defaults
alabaster                 0.7.9                    py27_0    defaults
anaconda                  4.3.0               np111py27_0    defaults
anaconda-client           1.6.0                    py27_0    defaults
anaconda-navigator        1.4.3                    py27_0    defaults
appnope                   0.1.0                    py27_0    defaults
appscript                 1.0.1                    py27_0    defaults
argcomplete               1.0.0                    py27_1    defaults
astroid                   1.4.9                    py27_0    defaults
astropy                   1.3                 np111py27_0    defaults
attrs                     15.2.0                   py27_0    defaults
babel                     2.3.4                    py27_0    defaults
backports                 1.0                      py27_0    defaults
backports_abc             0.5                      py27_0    defaults
beautifulsoup4            4.5.3                    py27_0    defaults
bitarray                  0.8.1                    py27_0    defaults
blaze                     0.10.1                   py27_0    defaults
bokeh                     0.12.4                   py27_0    defaults
boost                     1.56.0                   py27_3    rdkit
boto                      2.45.0                   py27_0    defaults
bottleneck                1.2.0               np111py27_0    defaults
bzip2                     1.0.6                         3    defaults
cairo                     1.14.8                        0    defaults
cclib                     1.1                       <pip>
cdecimal                  2.3                      py27_2    defaults
cffi                      1.9.1                    py27_0    defaults
chardet                   2.3.0                    py27_0    defaults
chest                     0.2.3                    py27_0    defaults
click                     6.7                      py27_0    defaults
cloudpickle               0.2.2                    py27_0    defaults
clyent                    1.2.2                    py27_0    defaults
colorama                  0.3.7                    py27_0    defaults
conda                     4.3.22                   py27_0    defaults
conda-env                 2.6.0                         0    defaults
configobj                 5.0.6                    py27_0    defaults
configparser              3.5.0                    py27_0    defaults
constantly                15.1.0                   py27_0    defaults
contextlib2               0.5.4                    py27_0    defaults
cryptography              1.7.1                    py27_0    defaults
csd-python-api            1.3.0                     conda    pkgs
cssselect                 1.0.0                    py27_0    defaults
curl                      7.52.1                        0    defaults
cycler                    0.10.0                   py27_0    defaults
cython                    0.25.2                   py27_0    defaults
cytoolz                   0.8.2                    py27_0    defaults
dask                      0.13.0                   py27_0    defaults
datashape                 0.5.4                    py27_0    defaults
decorator                 4.0.11                   py27_0    defaults
dill                      0.2.5                    py27_0    defaults
docutils                  0.13.1                   py27_0    defaults
dos2unix                  1                         <pip>
dos2unix                  6.0.3                         0    trent
entrypoints               0.2.2                    py27_0    defaults
enum34                    1.1.6                    py27_0    defaults
et_xmlfile                1.0.1                    py27_0    defaults
fastcache                 1.0.2                    py27_1    defaults
flask                     0.12                     py27_0    defaults
flask-cors                3.0.2                    py27_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                2.12.1                        2    defaults
fonts-continuum           1                             0    defaults
freetype                  2.5.5                         2    defaults
funcsigs                  1.0.2                    py27_0    defaults
functools32               3.2.3.2                  py27_0    defaults
futures                   3.0.5                    py27_0    defaults
get_terminal_size         1.0.0                    py27_0    defaults
gettext                   0.19.8                        1    defaults
gevent                    1.2.1                    py27_0    defaults
glib                      2.50.2                        1    defaults
glueviz                   0.9.1                    py27_0    defaults
greenlet                  0.4.11                   py27_0    defaults
grin                      1.2.1                    py27_3    defaults
gsl                       2.2.1                         0    defaults
h5py                      2.6.0               np111py27_2    defaults
harfbuzz                  0.9.39                        2    defaults
hdf5                      1.8.17                        1    defaults
heapdict                  1.0.0                    py27_1    defaults
icu                       54.1                          0    defaults
idisplay                  0.1.2                     <pip>
idna                      2.2                      py27_0    defaults
imagesize                 0.7.1                    py27_0    defaults
incremental               16.10.1                  py27_0    defaults
ipaddress                 1.0.18                   py27_0    defaults
ipykernel                 4.5.2                    py27_0    defaults
ipython                   5.1.0                    py27_1    defaults
ipython_genutils          0.1.0                    py27_0    defaults
ipywidgets                5.2.2                    py27_1    defaults
isodate                   0.5.4                     <pip>
isort                     4.2.5                    py27_0    defaults
itsdangerous              0.24                     py27_0    defaults
jbig                      2.1                           0    defaults
jdcal                     1.3                      py27_0    defaults
jedi                      0.9.0                    py27_1    defaults
jinja2                    2.9.4                    py27_0    defaults
jpeg                      9b                            0    defaults
jsonschema                2.5.1                    py27_0    defaults
jupyter                   1.0.0                    py27_3    defaults
jupyter_client            4.4.0                    py27_0    defaults
jupyter_console           5.0.0                    py27_0    defaults
jupyter_core              4.2.1                    py27_0    defaults
lazy-object-proxy         1.2.2                    py27_0    defaults
libffi                    3.2.1                         1    defaults
libgcc                    4.8.5                         1    defaults
libiconv                  1.14                          0    defaults
libpng                    1.6.27                        0    defaults
libtiff                   4.0.6                         3    defaults
libxml2                   2.9.4                         0    defaults
libxslt                   1.1.29                        0    defaults
llvmlite                  0.15.0                   py27_0    defaults
locket                    0.2.0                    py27_1    defaults
logging                   0.4.9.6                   <pip>
lxml                      3.7.2                    py27_0    defaults
lxml                      3.5.0                     <pip>
markupsafe                0.23                     py27_2    defaults
matplotlib                2.0.0               np111py27_0    defaults
mistune                   0.7.3                    py27_1    defaults
mkl                       2017.0.1                      0    defaults
mkl-service               1.1.2                    py27_3    defaults
Morfessor                 2.0.2a4                   <pip>
mpmath                    0.19                     py27_1    defaults
multipledispatch          0.4.9                    py27_0    defaults
nbconvert                 4.2.0                    py27_0    defaults
nbformat                  4.2.0                    py27_0    defaults
ncurses                   5.9                          10    defaults
networkx                  1.11                     py27_0    defaults
nltk                      3.2.2                    py27_0    defaults
nose                      1.3.7                    py27_1    defaults
notebook                  4.3.1                    py27_0    defaults
numba                     0.30.1              np111py27_0    defaults
numexpr                   2.6.1               np111py27_2    defaults
numpy                     1.11.3                   py27_0    defaults
numpydoc                  0.6.0                    py27_0    defaults
oauthlib                  2.0.2                     <pip>
odo                       0.5.0                    py27_1    defaults
onto2nx                   0.1.0                     <pip>
openbabel                 2.3.2                    py27_1    zachcp
opencv                    1.0.1                     <pip>
openpyxl                  2.4.1                    py27_0    defaults
openssl                   1.0.2k                        0    defaults
pandas                    0.19.2              np111py27_1    defaults
pandoc                    1.19.2.1                      0    defaults
pango                     1.40.3                        1    defaults
parsel                    1.1.0                    py27_0    defaults
partd                     0.3.7                    py27_0    defaults
path.py                   10.0                     py27_0    defaults
pathlib2                  2.2.0                    py27_0    defaults
patsy                     0.4.1                    py27_0    defaults
pcre                      8.39                          1    defaults
pep8                      1.7.0                    py27_0    defaults
pexpect                   4.2.1                    py27_0    defaults
pickleshare               0.7.4                    py27_0    defaults
pillow                    4.0.0                    py27_0    defaults
pip                       9.0.1                    py27_1    defaults
pixman                    0.34.0                        0    defaults
ply                       3.9                      py27_0    defaults
polyglot                  16.7.4                    <pip>
prompt_toolkit            1.0.9                    py27_0    defaults
psutil                    5.0.1                    py27_0    defaults
ptyprocess                0.5.1                    py27_0    defaults
py                        1.4.32                   py27_0    defaults
py2neo                    3.1.2                     <pip>
py3Dmol                   0.6.1                     <pip>
pyasn1                    0.1.9                    py27_0    defaults
pyasn1-modules            0.0.8                    py27_0    defaults
pyaudio                   0.2.7                    py27_0    defaults
PyBEL                     0.3.9                     <pip>
pycld2                    0.31                      <pip>
pycosat                   0.6.1                    py27_1    defaults
pycparser                 2.17                     py27_0    defaults
pycrypto                  2.6.1                    py27_4    defaults
pycurl                    7.43.0                   py27_2    defaults
pydispatcher              2.0.5                    py27_0    defaults
pyfiglet                  0.7.5                     <pip>
pyflakes                  1.5.0                    py27_0    defaults
pygments                  2.1.3                    py27_0    defaults
PyICU                     1.9.6                     <pip>
pylint                    1.6.4                    py27_1    defaults
pyopenssl                 16.2.0                   py27_0    defaults
pyparsing                 2.1.4                    py27_0    defaults
pyqt                      5.6.0                    py27_1    defaults
pyquery                   1.2.10                    <pip>
pytables                  3.3.0               np111py27_0    defaults
pytest                    3.0.5                    py27_0    defaults
python                    2.7.13                        0    defaults
python-dateutil           2.6.0                    py27_0    defaults
python.app                1.2                      py27_4    defaults
pytz                      2016.10                  py27_0    defaults
pyyaml                    3.12                     py27_0    defaults
pyzmq                     16.0.2                   py27_0    defaults
qt                        5.6.2                         0    defaults
qtawesome                 0.4.3                    py27_0    defaults
qtconsole                 4.2.1                    py27_1    defaults
qtpy                      1.2.1                    py27_0    defaults
queuelib                  1.4.2                    py27_0    defaults
r                         3.3.2                  r3.3.2_0    defaults
r-assertthat              0.1                    r3.3.2_4    defaults
r-backports               1.0.4                  r3.3.2_0    defaults
r-base                    3.3.2                         1    defaults
r-base64enc               0.1_3                  r3.3.2_0    defaults
r-bh                      1.62.0_1               r3.3.2_0    defaults
r-bitops                  1.0_6                  r3.3.2_2    defaults
r-boot                    1.3_18                 r3.3.2_0    defaults
r-broom                   0.4.1                  r3.3.2_0    defaults
r-car                     2.1_4                  r3.3.2_0    defaults
r-caret                   6.0_73                 r3.3.2_0    defaults
r-catools                 1.17.1                 r3.3.2_2    defaults
r-class                   7.3_14                 r3.3.2_0    defaults
r-cluster                 2.0.5                  r3.3.2_0    defaults
r-codetools               0.2_15                 r3.3.2_0    defaults
r-colorspace              1.3_1                  r3.3.2_0    defaults
r-crayon                  1.3.2                  r3.3.2_0    defaults
r-curl                    2.3                    r3.3.2_0    defaults
r-data.table              1.10.0                 r3.3.2_0    defaults
r-dbi                     0.5_1                  r3.3.2_0    defaults
r-dichromat               2.0_0                  r3.3.2_2    defaults
r-digest                  0.6.10                 r3.3.2_0    defaults
r-dplyr                   0.5.0                  r3.3.2_0    defaults
r-essentials              1.5.1                         0    defaults
r-evaluate                0.10                   r3.3.2_0    defaults
r-forcats                 0.1.1                  r3.3.2_0    defaults
r-foreach                 1.4.3                  r3.3.2_0    defaults
r-foreign                 0.8_67                 r3.3.2_0    defaults
r-formatr                 1.4                    r3.3.2_0    defaults
r-ggplot2                 2.2.0                  r3.3.2_0    defaults
r-gistr                   0.3.6                  r3.3.2_0    defaults
r-glmnet                  2.0_5                  r3.3.2_0    defaults
r-gtable                  0.2.0                  r3.3.2_0    defaults
r-haven                   1.0.0                  r3.3.2_0    defaults
r-hexbin                  1.27.1                 r3.3.2_0    defaults
r-highr                   0.6                    r3.3.2_0    defaults
r-hms                     0.3                    r3.3.2_0    defaults
r-htmltools               0.3.5                  r3.3.2_0    defaults
r-htmlwidgets             0.8                    r3.3.2_0    defaults
r-httpuv                  1.3.3                  r3.3.2_0    defaults
r-httr                    1.2.1                  r3.3.2_0    defaults
r-irdisplay               0.4.4                  r3.3.2_0    defaults
r-irkernel                0.7.1                  r3.3.2_0    defaults
r-iterators               1.0.8                  r3.3.2_0    defaults
r-jsonlite                1.1                    r3.3.2_0    defaults
r-kernsmooth              2.23_15                r3.3.2_0    defaults
r-knitr                   1.15.1                 r3.3.2_0    defaults
r-labeling                0.3                    r3.3.2_2    defaults
r-lattice                 0.20_34                r3.3.2_0    defaults
r-lazyeval                0.2.0                  r3.3.2_0    defaults
r-leaps                   3.0                    r3.3.2_0    defaults
r-lme4                    1.1_12                 r3.3.2_0    defaults
r-lubridate               1.6.0                  r3.3.2_0    defaults
r-magrittr                1.5                    r3.3.2_2    defaults
r-maps                    3.1.1                  r3.3.2_0    defaults
r-markdown                0.7.7                  r3.3.2_2    defaults
r-mass                    7.3_45                 r3.3.2_0    defaults
r-matrix                  1.2_7.1                r3.3.2_0    defaults
r-matrixmodels            0.4_1                  r3.3.2_0    defaults
r-mgcv                    1.8_16                 r3.3.2_0    defaults
r-mime                    0.5                    r3.3.2_0    defaults
r-minqa                   1.2.4                  r3.3.2_2    defaults
r-mnormt                  1.5_5                  r3.3.2_0    defaults
r-modelmetrics            1.1.0                  r3.3.2_0    defaults
r-modelr                  0.1.0                  r3.3.2_0    defaults
r-munsell                 0.4.3                  r3.3.2_0    defaults
r-nlme                    3.1_128                r3.3.2_0    defaults
r-nloptr                  1.0.4                  r3.3.2_2    defaults
r-nnet                    7.3_12                 r3.3.2_0    defaults
r-openssl                 0.9.5                  r3.3.2_0    defaults
r-packrat                 0.4.8_1                r3.3.2_0    defaults
r-pbdzmq                  0.2_4                  r3.3.2_0    defaults
r-pbkrtest                0.4_6                  r3.3.2_0    defaults
r-pki                     0.1_3                  r3.3.2_0    defaults
r-plyr                    1.8.4                  r3.3.2_0    defaults
r-pryr                    0.1.2                  r3.3.2_0    defaults
r-psych                   1.6.9                  r3.3.2_0    defaults
r-purrr                   0.2.2                  r3.3.2_0    defaults
r-quantmod                0.4_7                  r3.3.2_0    defaults
r-quantreg                5.29                   r3.3.2_0    defaults
r-r6                      2.2.0                  r3.3.2_0    defaults
r-randomforest            4.6_12                 r3.3.2_0    defaults
r-rbokeh                  0.5.0                  r3.3.2_0    defaults
r-rcolorbrewer            1.1_2                  r3.3.2_3    defaults
r-rcpp                    0.12.8                 r3.3.2_0    defaults
r-rcppeigen               0.3.2.9.0              r3.3.2_0    defaults
r-rcurl                   1.95_4.8               r3.3.2_0    defaults
r-readr                   1.0.0                  r3.3.2_0    defaults
r-readxl                  0.1.1                  r3.3.2_0    defaults
r-recommended             3.3.2                  r3.3.2_0    defaults
r-repr                    0.10                   r3.3.2_0    defaults
r-reshape2                1.4.2                  r3.3.2_0    defaults
r-rjsonio                 1.3_0                  r3.3.2_2    defaults
r-rmarkdown               1.2                    r3.3.2_0    defaults
r-rpart                   4.1_10                 r3.3.2_0    defaults
r-rprojroot               1.1                    r3.3.2_0    defaults
r-rsconnect               0.7                    r3.3.2_0    defaults
r-rstudioapi              0.6                    r3.3.2_0    defaults
r-rvest                   0.3.2                  r3.3.2_0    defaults
r-scales                  0.4.1                  r3.3.2_0    defaults
r-selectr                 0.3_0                  r3.3.2_0    defaults
r-shiny                   0.14.2                 r3.3.2_0    defaults
r-sourcetools             0.1.5                  r3.3.2_0    defaults
r-sparsem                 1.74                   r3.3.2_0    defaults
r-spatial                 7.3_11                 r3.3.2_0    defaults
r-stringi                 1.1.2                  r3.3.2_0    defaults
r-stringr                 1.1.0                  r3.3.2_0    defaults
r-survival                2.40_1                 r3.3.2_0    defaults
r-tibble                  1.2                    r3.3.2_0    defaults
r-tidyr                   0.6.0                  r3.3.2_0    defaults
r-tidyverse               1.0.0                  r3.3.2_0    defaults
r-ttr                     0.23_1                 r3.3.2_0    defaults
r-uuid                    0.1_2                  r3.3.2_0    defaults
r-xml2                    1.0.0                  r3.3.2_0    defaults
r-xtable                  1.8_2                  r3.3.2_0    defaults
r-xts                     0.9_7                  r3.3.2_2    defaults
r-yaml                    2.1.14                 r3.3.2_0    defaults
r-zoo                     1.7_13                 r3.3.2_0    defaults
rdflib                    4.2.2                     <pip>
rdflib-jsonld             0.4.0                     <pip>
rdkit                     2016.09.4           np111py27_1    rdkit
readline                  6.2                           2    defaults
redis                     3.2.0                         0    defaults
redis-py                  2.10.5                   py27_0    defaults
requests                  2.12.4                   py27_0    defaults
requests-file             1.4.1                     <pip>
requests-oauthlib         0.8.0                     <pip>
rope                      0.9.4                    py27_1    defaults
rpy2                      2.8.5              py27r3.3.2_2    defaults
ruamel_yaml               0.11.14                  py27_1    defaults
scandir                   1.4                      py27_0    defaults
scikit-image              0.12.3              np111py27_1    defaults
scikit-learn              0.18.1              np111py27_1    defaults
scipy                     0.18.1              np111py27_1    defaults
scrapy                    1.1.1                    py27_0    defaults
seaborn                   0.7.1                    py27_0    defaults
service_identity          16.0.0                   py27_0    defaults
setuptools                27.2.0                   py27_0    defaults
simplegeneric             0.8.1                    py27_1    defaults
singledispatch            3.4.0.3                  py27_0    defaults
sip                       4.18                     py27_0    defaults
six                       1.10.0                   py27_0    defaults
snowballstemmer           1.2.1                    py27_0    defaults
sockjs-tornado            1.0.3                    py27_0    defaults
SPARQLWrapper             1.8.0                     <pip>
sphinx                    1.5.1                    py27_0    defaults
spyder                    3.1.2                    py27_0    defaults
sqlalchemy                1.1.5                    py27_0    defaults
sqlite                    3.13.0                        0    defaults
ssl_match_hostname        3.4.0.2                  py27_1    defaults
statsmodels               0.6.1               np111py27_1    defaults
subprocess32              3.2.7                    py27_0    defaults
sympy                     1.0                      py27_0    defaults
terminado                 0.6                      py27_0    defaults
tk                        8.5.18                        0    defaults
toolz                     0.8.2                    py27_0    defaults
tornado                   4.4.2                    py27_0    defaults
traitlets                 4.3.1                    py27_0    defaults
tweepy                    3.3.0                     <pip>
twisted                   16.6.0                   py27_0    defaults
unicodecsv                0.14.1                   py27_0    defaults
w3lib                     1.16.0                   py27_0    defaults
wcwidth                   0.1.7                    py27_0    defaults
werkzeug                  0.11.15                  py27_0    defaults
wheel                     0.29.0                   py27_0    defaults
widgetsnbextension        1.2.6                    py27_0    defaults
wrapt                     1.10.8                   py27_0    defaults
xlrd                      1.0.0                    py27_0    defaults
xlsxwriter                0.9.6                    py27_0    defaults
xlwings                   0.10.2                   py27_0    defaults
xlwt                      1.2.0                    py27_0    defaults
xz                        5.2.2                         1    defaults
yaml                      0.1.6                         0    defaults
zeromq                    4.1.3                         0    defaults
zlib                      1.2.8                         3    defaults
zope                      1.0                      py27_0    defaults
zope.interface            4.3.3                    py27_0    defaults
mingwandroid commented 7 years ago

Thanks,

Do you know what this package is and how you installed it?

csd-python-api            1.3.0                     conda    pkgs
reid-indeed commented 7 years ago

It's a Python API for the Cambridge Crystal Structure Database:

https://downloads.ccdc.cam.ac.uk/documentation/API/installation_notes.html

mingwandroid commented 7 years ago

Did you install it by following these instructions?

Using conda
Ensure you have installed the CSDS 2017 release, and then:

conda install numpy Pillow six lxml
conda install csd-python-api-1.3.0-<platform>-py2.7-conda.tar.bz2
where <platform> corresponds to the appropriate platform for your system, e.g., “win32”.
reid-indeed commented 7 years ago

As far as I can remember, yes. Is this installation likely to be what's causing issue with the RStudio installation?

mingwandroid commented 7 years ago

Yes

mingwandroid commented 7 years ago

If you need to use that package you'll need to get it updated to use more recent versions of its dependencies.