Reticulate: how to use reticulate when python package not available on anaconda
I am attempting to work with SMART on FHIR with python FHIR client. It works as expected after installing pip install fhirclient and running the example on python command line.
However, I am stuck with the first step. I get an error ModuleNotFoundError: No module named 'fhirclient'. Anaconda does not have this fhirclient. So, wondering if there is a way I can get this working.
my python test code in a separate file (fhir_test.py). These command run on python command lines without errors and desired output is shown. FYI there is a package called RonFHIR for similar task of pulling fhir data into R, however it seems that python fhirclient is more popular in use, so wanted to try and see if reticulate package helps me to pull data into R
from fhirclient import client
import fhirclient.models.patient as p
settings = {'app_id': 'cerner1',
'api_base': 'https://r3.smarthealthit.org'}
smart = client.FHIRClient(settings=settings)
patient = p.Patient.read('fdb4e56a-145b-4962-8a54-e056757832aa',
smart.server)
The r code
library(reticulate)
use_python(Sys.which("python"))
#py_config()
#py_discover_config()
py_install("fhirclient")
#> Error: Error 1 occurred installing packages into conda environment r-reticulate
py_module_available("fhirclient")
#> [1] FALSE
source_python("fhir_test.py")
#> Error in py_run_file_impl(file, local, convert) :
#> ModuleNotFoundError: No module named 'fhirclient'
#> Detailed traceback: File "<string>", line 1, in <module>
Created on 2019-08-13 by the reprex package (v0.3.0)
devtools::session_info()
#> - Session info ----------------------------------------------------------
#> setting value
#> version R version 3.5.3 (2019-03-11)
#> os Windows 10 x64
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_United States.1252
#> ctype English_United States.1252
#> tz America/New_York
#> date 2019-08-13
#>
#> - Packages --------------------------------------------------------------
#> package * version date lib source
#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.5.3)
#> backports 1.1.4 2019-04-10 [1] CRAN (R 3.5.3)
#> callr 3.3.1 2019-07-18 [1] CRAN (R 3.5.3)
#> cli 1.1.0 2019-03-19 [1] CRAN (R 3.5.3)
#> crayon 1.3.4 2017-09-16 [1] CRAN (R 3.5.3)
#> desc 1.2.0 2018-05-01 [1] CRAN (R 3.5.3)
#> devtools 2.1.0 2019-07-06 [1] CRAN (R 3.5.3)
#> digest 0.6.20 2019-07-04 [1] CRAN (R 3.5.3)
#> evaluate 0.14 2019-05-28 [1] CRAN (R 3.5.3)
#> fs 1.3.1 2019-05-06 [1] CRAN (R 3.5.3)
#> glue 1.3.1 2019-03-12 [1] CRAN (R 3.5.3)
#> highr 0.8 2019-03-20 [1] CRAN (R 3.5.3)
#> htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.5.3)
#> jsonlite 1.6 2018-12-07 [1] CRAN (R 3.5.3)
#> knitr 1.23 2019-05-18 [1] CRAN (R 3.5.3)
#> lattice 0.20-38 2018-11-04 [1] CRAN (R 3.5.3)
#> magrittr 1.5 2014-11-22 [1] CRAN (R 3.5.3)
#> Matrix 1.2-17 2019-03-22 [1] CRAN (R 3.5.3)
#> memoise 1.1.0 2017-04-21 [1] CRAN (R 3.5.3)
#> pkgbuild 1.0.3 2019-03-20 [1] CRAN (R 3.5.3)
#> pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.5.3)
#> prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.5.3)
#> processx 3.4.1 2019-07-18 [1] CRAN (R 3.5.3)
#> ps 1.3.0 2018-12-21 [1] CRAN (R 3.5.3)
#> R6 2.4.0 2019-02-14 [1] CRAN (R 3.5.3)
#> Rcpp 1.0.2 2019-07-25 [1] CRAN (R 3.5.3)
#> remotes 2.1.0 2019-06-24 [1] CRAN (R 3.5.3)
#> reticulate * 1.13 2019-07-24 [1] CRAN (R 3.5.3)
#> rlang 0.4.0 2019-06-25 [1] CRAN (R 3.5.3)
#> rmarkdown 1.14 2019-07-12 [1] CRAN (R 3.5.3)
#> rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.5.3)
#> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.5.3)
#> stringi 1.4.3 2019-03-12 [1] CRAN (R 3.5.3)
#> stringr 1.4.0 2019-02-10 [1] CRAN (R 3.5.3)
#> testthat 2.2.1 2019-07-25 [1] CRAN (R 3.5.3)
#> usethis 1.5.1 2019-07-04 [1] CRAN (R 3.5.3)
#> withr 2.1.2 2018-03-15 [1] CRAN (R 3.5.3)
#> xfun 0.8 2019-06-25 [1] CRAN (R 3.5.3)
#> yaml 2.2.0 2018-07-25 [1] CRAN (R 3.5.3)
#>
#> [1] C:/Users/gade04/Documents/R/R-3.5.3/library
gadepallivs
All 8 comments
You can use py_install("fhirclient", pip = TRUE) to force installation with pip as opposed to conda.
kevinushey
on 14 Aug 2019
It throws the following error. and the method is auto, options are virtulaenv or conda. I guess, it is picking conda by default here.
py_install("numpy", pip = TRUE)
Error: Conda installation not found (failed to locate conda binary)
Please install Anaconda for Windows (https://www.anaconda.com/download/#windows)
before proceeding.
However, if I sidestep by directly opening windows powershell and then install the package pip install fhirclient it works
py_module_available("fhirclient")
[1] TRUE
Do you have Anaconda installed? On Windows, py_install() is mainly tooled for working with Python environments (conda on Windows; virtualenvs on other platforms)
kevinushey
on 14 Aug 2019
Yes, I have Anaconda installed. If I try py_install with pip = TRUE & with anaconda installed on the computer. The pip = TRUE parameter does force install fhirclient without errors ( could not locate the directories the modules were installed) . However, It still throws the error ModuleNotFoundError: No module named fhirclient. And, when I check py_module_available("fhirclient") it outputs FALSE. May be the directories path needs to be set for python to access modules installed using py_install ?. Uninstalling anaconda and installing fhirclient on command line, I was able to load the fhirclinet module and run within reticulate package.
gadepallivs
on 19 Aug 2019
When selecting a working condaenv, this works as expected
library(reticulate)
use_condaenv("r-reticulate")
py_install("fhirclient", pip = TRUE)
py_module_available("fhirclient")
fh <- import("fhirclient")
cderv
on 22 Sep 2019
When selecting a working condaenv, this works as expected
library(reticulate) use_condaenv("r-reticulate") py_install("fhirclient", pip = TRUE) py_module_available("fhirclient") fh <- import("fhirclient")
This worked
absognety
on 23 Jun 2020
When selecting a working condaenv, this works as expected
library(reticulate) use_condaenv("r-reticulate") py_install("fhirclient", pip = TRUE) py_module_available("fhirclient") fh <- import("fhirclient")This worked
This didn't work. Everything seems to install, but when I get to py_module_available('fhirclient'), I get FALSE.
Prometheus77
on 12 Aug 2020
When selecting a working condaenv, this works as expected
library(reticulate) use_condaenv("r-reticulate") py_install("fhirclient", pip = TRUE) py_module_available("fhirclient") fh <- import("fhirclient")This worked
This didn't work. Everything seems to install, but when I get to
py_module_available('fhirclient'), I getFALSE.
@Prometheus77, python you are using must have been from different environment from the environment in which r-reticulate is installed.
Do:
conda_list()to see all available conda envsuse_python("/home/vikas/.local/share/r-miniconda/envs/r-reticulate/bin/python")to change the python to correct one in which r-reticulate is setupSys.which("python")to see if it is changed properly
Then proceed to installing package you want with py_install("fhirclient", pip = TRUE) and see py_module_available("fhirclient"). everything is illustrated below:
> library(reticulate)
> use_condaenv("r-reticulate")
> py_install("fhirclient", pip = TRUE)
EnvironmentLocationNotFound: Not a conda environment: /home/vikas/anaconda3/envs/r-reticulate
Error: installation of 'python' into environment 'r-reticulate' failed [error code 1]
> Sys.which("python")
python
"/home/vikas/anaconda3/bin/python"
> py_module_available("fhirclient")
[1] FALSE
> conda_list()
name
1 r-miniconda
2 r-reticulate
3 anaconda3
python
1 /home/vikas/.local/share/r-miniconda/bin/python
2 /home/vikas/.local/share/r-miniconda/envs/r-reticulate/bin/python
3 /home/vikas/anaconda3/bin/python
> use_python
function (python, required = FALSE)
{
if (required && !file_test("-f", python) && !file_test("-d",
python))
stop("Specified version of python '", python, "' does not exist.")
if (required && is_python_initialized()) {
if (!file_same(py_config()$python, python)) {
fmt <- paste("ERROR: The requested version of Python ('%s') cannot be used, as",
"another version of Python ('%s') has already been initialized.",
"Please restart the R session if you need to attach reticulate",
"to a different version of Python.")
msg <- sprintf(fmt, python, py_config()$python)
writeLines(strwrap(msg), con = stderr())
stop("failed to initialize requested version of Python")
}
}
if (required)
.globals$required_python_version <- python
.globals$use_python_versions <- unique(c(.globals$use_python_versions,
python))
}
<bytecode: 0x56000d7a7090>
<environment: namespace:reticulate>
> use_python("/home/vikas/.local/share/r-miniconda/envs/r-reticulate/bin/python")
> Sys.which("python")
python
"/home/vikas/.local/share/r-miniconda/envs/r-reticulate/bin/python"
> py_module_available("fhirclient")
[1] FALSE
> py_install("fhirclient", pip = TRUE)
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.8.3
latest version: 4.8.4
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/vikas/.local/share/r-miniconda/envs/r-reticulate
added / updated specs:
- python
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2020.6.24 | 0 125 KB
------------------------------------------------------------
Total: 125 KB
The following packages will be UPDATED:
ca-certificates 2020.1.1-0 --> 2020.6.24-0
Downloading and Extracting Packages
ca-certificates-2020 | 125 KB | ################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Collecting fhirclient
Downloading fhirclient-3.2.0-py2.py3-none-any.whl (550 kB)
|鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅| 550 kB 98 kB/s
Collecting isodate
Using cached isodate-0.6.0-py2.py3-none-any.whl (45 kB)
Collecting requests
Using cached requests-2.24.0-py2.py3-none-any.whl (61 kB)
Requirement already satisfied, skipping upgrade: six in /home/vikas/.local/lib/python3.6/site-packages (from isodate->fhirclient) (1.14.0)
Collecting idna<3,>=2.5
Using cached idna-2.10-py2.py3-none-any.whl (58 kB)
Collecting chardet<4,>=3.0.2
Using cached chardet-3.0.4-py2.py3-none-any.whl (133 kB)
Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/vikas/.local/share/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages (from requests->fhirclient) (2020.6.20)
Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/vikas/.local/share/r-miniconda/envs/r-reticulate/lib/python3.6/site-packages (from requests->fhirclient) (1.25.9)
Installing collected packages: isodate, idna, chardet, requests, fhirclient
Successfully installed chardet-3.0.4 fhirclient-3.2.0 idna-2.10 isodate-0.6.0 requests-2.24.0
> pip_list()
Error in pip_list() : could not find function "pip_list"
> py_module_available("fhirclient")
[1] TRUE
> Sys.which("python")
python
"/home/vikas/.local/share/r-miniconda/envs/r-reticulate/bin/python"
> pd
Error: object 'pd' not found
> pd <- import("pandas")
> pd
Module(pandas)
> fclient <- import("fhirclient")
> fclient
Module(fhirclient)
Related issues
Seito-N
路
4Comments
myoung3
路
7Comments
lbocken
路
3Comments
berkorbay
路
4Comments
herboratory
路
6Comments
Most helpful comment
You can use
py_install("fhirclient", pip = TRUE)to force installation withpipas opposed to conda.