I'm trying to install rpy2 inside a Watson Studio 'environment':
!pip install rpy2
However, the environments don't appear to have R available:
Collecting rpy2
Downloading https://files.pythonhosted.org/packages/f1/98/c7652cc9d7fc0afce74d2c30a52b9c9ac391713a63d037e4ab8feb56c530/rpy2-2.9.4.tar.gz (194kB)
100% |████████████████████████████████| 204kB 4.4MB/s eta 0:00:01
Complete output from command python setup.py egg_info:
Error: Tried to guess R's HOME but no command 'R' in the PATH.
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /home/dsxuser/.tmp/pip-build-t7_r6q8e/rpy2/
How can I install rpy2 inside a Watson Studio Python 'Enviroment'? Is this possble?
Note: Watson Studio Environments are custom containers, so an answer should only be provided if the answer is known to work on Watson Studio Environments.
Use conda instead of pip. It knows how to install the R runtime. But beware, there are many packages that need to be installed...
!conda install rpy2
Fetching package metadata ...........
Solving package specifications: .
Package plan for installation in environment /opt/conda/envs/DSX-Python35:
The following NEW packages will be INSTALLED:
_r-mutex: 1.0.0-mro_2
binutils_impl_linux-64: 2.31.1-h6176602_1
binutils_linux-64: 2.31.1-h6176602_3
fribidi: 1.0.5-h7b6447c_0
gcc_impl_linux-64: 7.3.0-habb00fd_1
gcc_linux-64: 7.3.0-h553295d_3
gfortran_impl_linux-64: 7.3.0-hdf63c60_1
gfortran_linux-64: 7.3.0-h553295d_3
gxx_impl_linux-64: 7.3.0-hdf63c60_1
gxx_linux-64: 7.3.0-h553295d_3
kiwisolver: 1.0.1-py35hf484d3e_0
libcurl: 7.61.1-heec0ca6_0
libuuid: 1.0.3-h1bed415_2
make: 4.2.1-h1bed415_1
mro-base: 3.5.1-3
mro-base_impl: 3.5.1-h9a62091_0
r-assertthat: 0.2.0-mro351hf348343_0
r-bh: 1.66.0_1-mro351hf348343_0
r-bindr: 0.1.1-mro351hf348343_0
r-bindrcpp: 0.2.2-mro351hebc1506_0
r-bit: 1.1_14-mro351hd10c6a6_0
r-bit64: 0.9_7-mro351hd10c6a6_0
r-blob: 1.1.1-mro351hf348343_0
r-cli: 1.0.0-mro351hf348343_0
r-crayon: 1.3.4-mro351hf348343_0
r-dbi: 1.0.0-mro351hf348343_0
r-dbplyr: 1.2.2-mro351hf348343_0
r-digest: 0.6.15-mro351hd10c6a6_0
r-dplyr: 0.7.6-mro351hebc1506_0
r-fansi: 0.2.3-mro351hd10c6a6_0
r-glue: 1.3.0-mro351hd10c6a6_0
r-magrittr: 1.5-mro351hf348343_0
r-memoise: 1.1.0-mro351hf348343_0
r-pillar: 1.3.0-mro351hf348343_0
r-pkgconfig: 2.0.1-mro351hf348343_0
r-plogr: 0.2.0-mro351hf348343_0
r-prettyunits: 1.0.2-mro351hf348343_0
r-purrr: 0.2.5-mro351hd10c6a6_0
r-r6: 2.2.2-mro351hf348343_0
r-rcpp: 0.12.18-mro351hebc1506_0
r-revoutils: 11.0.0-mro351_0
r-revoutilsmath: 11.0.0-mro351_0
r-rlang: 0.2.1-mro351hd10c6a6_0
r-rsqlite: 2.1.1-mro351hebc1506_0
r-tibble: 1.4.2-mro351hd10c6a6_0
r-tidyselect: 0.2.4-mro351hebc1506_0
r-utf8: 1.1.4-mro351hd10c6a6_0
rpy2: 2.9.4-py35mro351h6853232_0
The following packages will be UPDATED:
cairo: 1.14.12-h77bcde2_0 --> 1.14.12-h8948797_3
curl: 7.55.1-h78862de_4 --> 7.61.1-hbc83047_0
dbus: 1.10.22-h3b5a359_0 --> 1.13.2-h714fa37_1
fontconfig: 2.12.4-h88586e7_1 --> 2.13.0-h9420a91_0
freetype: 2.8-hab7d2ae_1 --> 2.9.1-h8a8886c_1
glib: 2.53.6-h5d9569c_2 --> 2.56.2-hd408876_0
graphite2: 1.3.10-hf63cedd_1 --> 1.3.12-h23475e2_2
graphviz: 2.40.1-h25d223c_0 --> 2.40.1-h21bd128_2
gst-plugins-base: 1.12.2-he3457e5_0 --> 1.14.0-hbbd80ab_1
gstreamer: 1.12.2-h4f93127_0 --> 1.14.0-hb453b48_1
harfbuzz: 1.7.4-hc5b324e_0 --> 1.8.8-hffaf4a1_0
libgcc-ng: 7.2.0-h7cc24e2_2 --> 8.2.0-hdf63c60_1
libgfortran-ng: 7.2.0-h9f7466a_2 --> 7.3.0-hdf63c60_0
libstdcxx-ng: 7.2.0-h7a57d05_2 --> 8.2.0-hdf63c60_1
libxcb: 1.12-hcd93eb1_4 --> 1.13-h1bed415_1
libxml2: 2.9.4-h6b072ca_5 --> 2.9.8-h26e45fe_1
matplotlib: 2.1.0-py35h2cbf27e_0 --> 2.2.3-py35hb69df0a_0
pango: 1.41.0-hd475d92_0 --> 1.42.4-h049681c_0
pcre: 8.41-hc27e229_1 --> 8.42-h439df22_0
pillow: 4.2.1-py35h03abc04_0 --> 5.2.0-py35heded4f4_0
pycurl: 7.43.0-py35h7a9665c_3 --> 7.43.0.2-py35hb7f436b_0
pyqt: 5.6.0-py35h0e41ada_5 --> 5.9.2-py35h05f1152_2
qt: 5.6.2-h974d657_12 --> 5.9.6-h8703b6f_2
sip: 4.18.1-py35h9eaea60_2 --> 4.19.8-py35hf484d3e_0
xz: 5.2.3-h55aa19d_2 --> 5.2.4-h14c3975_4
