Installing harp in R

I’m trying to use the harp package for R. I’ve downloaded it using Conda and I can see that it’s saved in my anaconda packages folder like the following:
r-harp-1.17-py311h4489670_1
r-harp-1.17-py311h4489670_1.conda

However, I’m still getting an error when I try to import it into my R environment:

> library(harp)
Error in library(harp) : there is no package called ‘harp’

How do I fix this?

I don’t see the same problem.
The following works for me:

$ conda create -n harp-r
...
$ conda activate harp-r
$ conda install r-harp
...
$ R
> library(harp)
> harp::version()
[1] "1.20.2"
>

Are you doing anything different?

I just tried the same thing as you, step by step, and I got the same error. When I use conda install r-harp I see this:

PackagesNotFoundError: The following packages are not available from current channels:

  - r-harp

I was using miniforge, which already had the conda channel set to conda-forge by default. If you use anaconda, you should use:

$ conda install -c conda-forge r-harp

Hi Sander - that was the first thing I tried, it also didn’t work, after which I posted a question on this forum and used your second method. This is the output from that attempt:

(base) priyapatel@Priyas-MacBook-Air ~ % conda install -c conda-forge r-harp
Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 23.9.0
  latest version: 24.1.2

Please update conda by running

    $ conda update -n base -c defaults conda

Or to minimize the number of packages updated during conda update use

     conda install conda=24.1.2


Collecting package metadata (repodata.json): | WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.9.0.*, but conda is ignoring the .* and treating it as 1.9.0
WARNING conda.models.version:get_matcher(556): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.8.0.*, but conda is ignoring the .* and treating it as 1.8.0
done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 23.9.0
  latest version: 24.1.2

Please update conda by running

    $ conda update -n base -c defaults conda

Or to minimize the number of packages updated during conda update use

     conda install conda=24.1.2



## Package Plan ##

  environment location: /Users/priyapatel/anaconda3

  added / updated specs:
    - r-harp


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    archspec-0.2.3             |     pyhd8ed1ab_0          48 KB  conda-forge
    conda-23.9.0               |  py311h267d04e_2         1.2 MB  conda-forge
    r-harp-1.17                |  py311h4489670_1           8 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         1.3 MB

The following NEW packages will be INSTALLED:

  archspec           conda-forge/noarch::archspec-0.2.3-pyhd8ed1ab_0 
  r-harp             conda-forge/osx-arm64::r-harp-1.17-py311h4489670_1 

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2023.12.12~ --> conda-forge::ca-certificates-2024.2.2-hf0a4a13_0 
  conda              pkgs/main::conda-23.9.0-py311hca03da5~ --> conda-forge::conda-23.9.0-py311h267d04e_2 

The following packages will be SUPERSEDED by a higher-priority channel:

  certifi            pkgs/main/osx-arm64::certifi-2024.2.2~ --> conda-forge/noarch::certifi-2024.2.2-pyhd8ed1ab_0 
  openssl              pkgs/main::openssl-1.1.1w-h1a28f6b_0 --> conda-forge::openssl-1.1.1w-h53f4e23_0 


Proceed ([y]/n)? y


Downloading and Extracting Packages:
                                                                                                
Preparing transaction: done                                                                     
Verifying transaction: done                                                                     
Executing transaction: done
(base) priyapatel@Priyas-MacBook-Air ~ % R

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Previously saved workspace restored]

> library(harp_
+ )
Error in library(harp_) : there is no package called ‘harp_’
> library(harp)
Error in library(harp) : there is no package called ‘harp’

Don’t try to install harp in the base anaconda environment. Mixing conda-forge packages and anaconda default channel packages will usually not work correctly.
Create a separate conda environment as I showed. You should then also end up with harp 1.20.2 instead of 1.17.

I create a new environment and used Conda-forge to install - same error. Could it be that it’s not using the correct path to pull the package? I’m very confused at this point.

(harp-r) priyapatel@Priyas-MacBook-Air ~ % conda install -c conda-forge r-harp
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 23.9.0
  latest version: 24.1.2

Please update conda by running

    $ conda update -n base -c conda-forge conda

Or to minimize the number of packages updated during conda update use

     conda install conda=24.1.2



## Package Plan ##

  environment location: /Users/priyapatel/anaconda3/envs/harp-r

  added / updated specs:
    - r-harp


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-arm64::bzip2-1.0.8-h93a5062_5 
  c-ares             conda-forge/osx-arm64::c-ares-1.27.0-h93a5062_0 
  ca-certificates    conda-forge/osx-arm64::ca-certificates-2024.2.2-hf0a4a13_0 
  cffi               conda-forge/osx-arm64::cffi-1.16.0-py311h4a08483_0 
  coda               conda-forge/osx-arm64::coda-2.25.1-py311he72ca09_1 
  harp               conda-forge/osx-arm64::harp-1.20.2-py311ha597b10_1 
  hdf4               conda-forge/osx-arm64::hdf4-4.2.15-h2ee6834_7 
  hdf5               conda-forge/osx-arm64::hdf5-1.14.3-nompi_h5bb55e9_100 
  krb5               conda-forge/osx-arm64::krb5-1.21.2-h92f50d5_0 
  libaec             conda-forge/osx-arm64::libaec-1.1.2-h13dd4ca_1 
  libblas            conda-forge/osx-arm64::libblas-3.9.0-21_osxarm64_openblas 
  libcblas           conda-forge/osx-arm64::libcblas-3.9.0-21_osxarm64_openblas 
  libcurl            conda-forge/osx-arm64::libcurl-8.5.0-h2d989ff_0 
  libcxx             conda-forge/osx-arm64::libcxx-16.0.6-h4653b0c_0 
  libedit            conda-forge/osx-arm64::libedit-3.1.20191231-hc8eb9b7_2 
  libev              conda-forge/osx-arm64::libev-4.33-h93a5062_2 
  libexpat           conda-forge/osx-arm64::libexpat-2.5.0-hb7217d7_1 
  libffi             conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5 
  libgfortran        conda-forge/osx-arm64::libgfortran-5.0.0-13_2_0_hd922786_3 
  libgfortran5       conda-forge/osx-arm64::libgfortran5-13.2.0-hf226fd6_3 
  libjpeg-turbo      conda-forge/osx-arm64::libjpeg-turbo-3.0.0-hb547adb_1 
  liblapack          conda-forge/osx-arm64::liblapack-3.9.0-21_osxarm64_openblas 
  libnghttp2         conda-forge/osx-arm64::libnghttp2-1.58.0-ha4dd798_1 
  libopenblas        conda-forge/osx-arm64::libopenblas-0.3.26-openmp_h6c19121_0 
  libsqlite          conda-forge/osx-arm64::libsqlite-3.45.1-h091b4b1_0 
  libssh2            conda-forge/osx-arm64::libssh2-1.11.0-h7a5bd25_0 
  libzlib            conda-forge/osx-arm64::libzlib-1.2.13-h53f4e23_5 
  llvm-openmp        conda-forge/osx-arm64::llvm-openmp-17.0.6-hcd81f8e_0 
  ncurses            conda-forge/osx-arm64::ncurses-6.4-h463b476_2 
  numpy              conda-forge/osx-arm64::numpy-1.26.4-py311h7125741_0 
  openssl            conda-forge/osx-arm64::openssl-3.2.1-h0d3ecfb_0 
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 
  pycparser          conda-forge/noarch::pycparser-2.21-pyhd8ed1ab_0 
  python             conda-forge/osx-arm64::python-3.11.8-hdf0ec26_0_cpython 
  python_abi         conda-forge/osx-arm64::python_abi-3.11-4_cp311 
  r-harp             conda-forge/osx-arm64::r-harp-1.20.2-py311he72ca09_1 
  readline           conda-forge/osx-arm64::readline-8.2-h92ec313_1 
  setuptools         conda-forge/noarch::setuptools-69.1.1-pyhd8ed1ab_0 
  tk                 conda-forge/osx-arm64::tk-8.6.13-h5083fa2_1 
  tzdata             conda-forge/noarch::tzdata-2024a-h0c530f3_0 
  wheel              conda-forge/noarch::wheel-0.42.0-pyhd8ed1ab_0 
  xz                 conda-forge/osx-arm64::xz-5.2.6-h57fd34a_0 
  zstd               conda-forge/osx-arm64::zstd-1.5.5-h4f39d0f_0 


Proceed ([y]/n)? y


Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(harp-r) priyapatel@Priyas-MacBook-Air ~ % R

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Previously saved workspace restored]

> library(harp)
Error in library(harp) : there is no package called ‘harp’

Perhaps your library path is wrong.
What does this give you in R?:

> .libPaths()
[1] "/Users/sander/mambaforge/envs/harp-r/lib/R/site-library"
[2] "/Users/sander/mambaforge/envs/harp-r/lib/R/library"     

This should include the site-library directory of your conda environment, which should contain the harp R extension.

I get the path where all my R libraries are saved, but r-harp isn’t there.

> .libPaths()
[1] "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library"

I redirected to this directory and could not find harp-r. I found all my other R packages. When I look for the r-harp, I see that it’s being saved here:

/Users/priyapatel/anaconda3/envs/harp-r/conda-meta/r-harp-1.20.2-py311he72ca09_1.json

Then, I tried to install the r-harp library directly in the folder where the rest of my R packages are saved and this is what I got.

(harp-r) priyapatel@Priyas-MacBook-Air harp-r % conda install -c conda-forge r-harp --prefix /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library

DirectoryNotACondaEnvironmentError: The target directory exists, but it is not a conda environment.
Use 'conda create' to convert the directory to a conda environment.
  target directory: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library

Should I convert it into a conda environment? Not sure if there are any ramifications for this.

One more comment, I think the r-harp package is still being saved here:

/Users/priyapatel/anaconda3/pkgs

Because all I see in the harp-r environment folder is an r-harp json file, which isn’t the actual package.
/Users/priyapatel/anaconda3/envs/harp-r/conda-meta/r-harp-1.20.2-py311he72ca09_1.json

In the /Users/priyapatel/anaconda3/pkgs folder, I see the r-harp files:

r-harp-1.17-py311h4489670_1
r-harp-1.17-py311h4489670_1.conda
r-harp-1.20.2-py311he72ca09_1
r-harp-1.20.2-py311he72ca09_1.conda

I can directory download the file into my R library path but I need to turn it into a conda environment.

The conda installation of r-harp only works with an R installation within that same conda environment. Not with a system installed version of R. I think this is your problem.

  • I create a new conda environment.
  • I installed R.
  • I also install mamba.
  • I then install r-harp successfully (I think).
(renv) priyapatel@ envs % conda install -c conda-forge r-harp
Channels:
 - conda-forge
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/priyapatel/anaconda3/envs/renv

  added / updated specs:
    - r-harp


The following NEW packages will be INSTALLED:

  cffi               conda-forge/osx-arm64::cffi-1.16.0-py311h4a08483_0 
  coda               conda-forge/osx-arm64::coda-2.25.1-py311he72ca09_1 
  harp               conda-forge/osx-arm64::harp-1.20.2-py311ha597b10_1 
  hdf4               conda-forge/osx-arm64::hdf4-4.2.15-h2ee6834_7 
  hdf5               conda-forge/osx-arm64::hdf5-1.14.3-nompi_h5bb55e9_100 
  libaec             conda-forge/osx-arm64::libaec-1.1.2-h13dd4ca_1 
  libcblas           conda-forge/osx-arm64::libcblas-3.9.0-21_osxarm64_openblas 
  libsqlite          conda-forge/osx-arm64::libsqlite-3.45.1-h091b4b1_0 
  numpy              conda-forge/osx-arm64::numpy-1.26.4-py311h7125741_0 
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 
  pycparser          conda-forge/noarch::pycparser-2.21-pyhd8ed1ab_0 
  python             conda-forge/osx-arm64::python-3.11.8-hdf0ec26_0_cpython 
  python_abi         conda-forge/osx-arm64::python_abi-3.11-4_cp311 
  r-harp             conda-forge/osx-arm64::r-harp-1.20.2-py311he72ca09_1 
  setuptools         conda-forge/noarch::setuptools-69.1.1-pyhd8ed1ab_0 
  tzdata             conda-forge/noarch::tzdata-2024a-h0c530f3_0 
  wheel              conda-forge/noarch::wheel-0.42.0-pyhd8ed1ab_0 


Proceed ([y]/n)? y


Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Then, I again try to install harp and it can’t find it.

(renv) priyapatel@ envs % R

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20.0.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(harp)
Error in library(harp) : there is no package called ‘harp’

I also checked the lib path:

> .libPaths()
[1] "/Users/priyapatel/anaconda3/envs/renv/lib/R/library"

Which points to the correct environment. However, when I check the path for r-harp, I don’t see it.

(renv) priyapatel@ renv % cd /Users/priyapatel/anaconda3/envs/renv/lib/R/library
(renv) priyapatel@ library % ls
base		datasets	graphics	methods		splines		stats4		tools		utils
compiler	grDevices	grid		parallel	stats		tcltk		translations

What am I doing wrong?

I seem to have the site-library as well in my R library path:

> .libPaths()    
[1] "/Users/sander/mambaforge/envs/harp-r/lib/R/site-library"
[2] "/Users/sander/mambaforge/envs/harp-r/lib/R/library"     

This is also where the HARP extension is installed.

Does your R-harp install look like this:

r-harp-1.20.2-py311he72ca09_1

Hi @sander.niemeijer - this continues to be an issue for me. can you provide some additional advice?