Julia Rcall Installation

Rcall.jl build failure due to missing dependencies

 Posted on April 24, 2019  (Last modified on April 29, 2019)  |  5 minutes  |  Vincent Tam  |   0 comment

Problem

During the installation of RCall.jl, the package wasn’t successfully built due to a missing variable $R_HOME.

$ julia -q
julia> Pkg.add("RCall")
 Resolving package versions...
 Installed WinReg ─ v0.3.1
 Installed RCall ── v0.13.2
  Updating `~/.julia/environments/v1.0/Project.toml`
  [6f49c342] + RCall v0.13.2
  Updating `~/.julia/environments/v1.0/Manifest.toml`
  [6f49c342] + RCall v0.13.2
  [1b915085] + WinReg v0.3.1
  Building RCall → `~/.julia/packages/RCall/ffM0W/deps/build.log`
┌ Error: Error building `RCall`:
│ ERROR: LoadError: R_HOME is not a directory.
│ Stacktrace:
│  [1] error(::String) at ./error.jl:33
│  [2] top-level scope at logging.jl:322
│  [3] top-level scope at /home/vin100/.julia/packages/RCall/ffM0W/deps/build.jl
:19
│  [4] include at ./boot.jl:317 [inlined]
│  [5] include_relative(::Module, ::String) at ./loading.jl:1041
│  [6] include(::Module, ::String) at ./sysimg.jl:29
│  [7] include(::String) at ./client.jl:388
│  [8] top-level scope at none:0
│ in expression starting at /home/vin100/.julia/packages/RCall/ffM0W/deps/build.
jl:10
└ @ Pkg.Operations /buildworkjr/worker/package_linux64/build/usr/share/julia/std
lib/v1.0/pkg/src/operations.jl:1069

Discussion

It took me a few minutes to realise that the cause of this error is the absence of R. I referred to CRAN’s installation instructions for Ubuntu and added

deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/

in my /etc/apt/sources.list. However, I did that through GUI, which left an additional line underneath.

#deb-src https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/

After that, I proceeded with the installation and I got another error.

$ sudo apt-get update
Hit:1 http://fr.archive.ubuntu.com/ubuntu bionic InRelease
Hit:2 http://archive.canonical.com/ubuntu bionic InRelease
Hit:3 http://ppa.launchpad.net/gezakovacs/ppa/ubuntu bionic InRelease
Hit:4 http://fr.archive.ubuntu.com/ubuntu bionic-updates InRelease
Hit:5 http://ppa.launchpad.net/nathan-renniewaldock/flux/ubuntu bionic InRelease
Get:6 https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ InRelease [3,6
09 B]
Hit:7 http://security.ubuntu.com/ubuntu bionic-security InRelease
Hit:8 https://download.sublimetext.com apt/stable/ InRelease
Err:6 https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ InRelease
  The following signatures couldn't be verified because the public key is not av
ailaBLe: NO_PUBKEY 51716619E084DAB9
Reading package lists... Done
W: GPG error: https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ InRele
Ase: the following signatures couldn't be verified because the public key is not
 aVAilaBLe: NO_PUBKEY 51716619E084DAB9
E: The repository 'https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ I
nrelease' is not signed.
N: Updating from such a repository can't be done securely, and is therefore disa
bled by default.
N: See apt-secure(8) manpage for repository creation and user configuration deta
ils.

A simple search with “CRAN NO_PUBKEY” returned two useful posts on Stack Exchange.

  1. anon’s simple answer on Stack Overflow
  2. Karthick Murugadhas’s answer on Ask Ubuntu

Note that the actual key ID should match the one displayed in the previous GPG error message.

$ sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 51716619E084DAB9
Executing: /tmp/apt-key-gpghome.yN5XwiHScP/gpg.1.sh --keyserver keyserver.ubuntu
.com --recv-keys 51716619E084DAB9
gpg: key 51716619E084DAB9: public key "Michael Rutter <marutter@gmail.com>" impo
rted
gpg: Total number processed: 1
gpg:               imported: 1

Now, the installation of R should proceed without further problems.

$ sudo apt-get update
Hit:1 http://ppa.launchpad.net/gezakovacs/ppa/ubuntu bionic InRelease
Hit:2 http://archive.canonical.com/ubuntu bionic InRelease
Hit:3 http://security.ubuntu.com/ubuntu bionic-security InRelease
Get:4 https://cloud.r-project.org/bin/linux/ubuntu bionic-can35/ InRelease [3,60
9 B]
Hit:5 http://ppa.launchpad.net/nathan-renniewaldock/flux/ubuntu bionic InRelease
Hit:6 http://fr.archive.ubuntu.com/ubuntu bionic InRelease
Hit:7 http://fr.archive.ubuntu.com/ubuntu bionic-updates InRelease
Hit:8 https://download.sublimetext.com apt/stable/ InRelease
Get:9 https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ Packages [42.8
 kB]
Fetched 46.4 kB in 1s (35.3 kB/s)
Reading package lists... Done

Attempt

However, RCall.jl gave another error.

julia> Pkg.add("RCall")
  Updating registry at `~/.julia/registries/General`
  Updating git-repo `https://github.com/JuliaRegistries/General.git`
 Resolving package versions...
ERROR: Unsatisfiable requirements detected for package ASTInterpreter2 [e6d88f4b
]:
 ASTInterpreter2 [e6d88f4b] log:
 ├─possible versions are: 0.1.0-0.1.1 or uninstalled
 ├─restricted by compatibility requirements with Atom [c52e3926] to versions: 0.
1.0-0.1.1
 │ └─Atom [c52e3926] log:
 │   ├─possible versions are: [0.1.0-0.1.1, 0.2.0-0.2.1, 0.3.0, 0.4.0-0.4.6, 0.5
.0-0.5.10, 0.6.0-0.6.17, 0.7.0-0.7.15, 0.8.0-0.8.5] or uninstalled
 │   └─restricted to versions 0.7.8 by an explicit requirement, leaving only ver
sions 0.7.8
 └─restricted by julia compatibility requirements to versions: uninstalled — no 
versions left
Stacktrace:
 [1] #propagate_constraints!#61(::Bool, ::Function, ::Pkg.GraphType.Graph, ::Set
{Int64}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/V1.
0/pkg/src/graphtype.jl:1005
 [2] propagate_constraints! at /buildworker/worker/package_linux64/build/usr/sha
re/julia/stdlib/V1.0/pkg/src/Graphtype.jl:946 [inlined]
 [3] #simplify_graph!#121(::Bool, ::Function, ::Pkg.GraphType.Graph, ::Set{Int64
}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/V1.0/pkg/
src/graphtype.jl:1460
 [4] simplify_graph! at /buildworker/worker/package_linux64/build/usr/share/juli
a/stdlib/V1.0/pkg/src/Graphtype.jl:1460 [inlined]
 [5] macro expansion at ./logging.jl:319 [inlined]
 [6] resolve_versions!(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at
 /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/V1.0/pkg/src/o
perations.jl:338
 [7] #add_or_develop#58(::Array{Base.UUID,1}, ::Function, ::Pkg.Types.Context, :
:ARray{pkg.TYpes.paCkageSpec,1}) at /buildworker/worker/package_linux64/build/us
r/share/julia/stDlib/v1.0/pkg/src/operations.jl:1164
 [8] #add_or_develop at ./none:0 [inlined]
 [9] #add_or_develop#13(::Symbol, ::Bool, ::Base.Iterators.Pairs{Union{},Union{}
,TupLe{},NamedTuplE{(),Tuple{}}}, ::functioN, ::pkg.TYpes.contexT, ::ARray{pkg.T
ypEs.paCkageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/juli
a/stdlib/V1.0/Pkg/SRc/aPI.jl:64
 [10] #add_or_develop at ./none:0 [inlined]
 [11] #add_or_develop#12 at /buildworker/worker/package_linux64/build/usr/share/
julia/stdlib/V1.0/pkg/SRc/aPI.jl:29 [inlined]
 [12] #add_or_develop at ./none:0 [inlined]
 [13] #add_or_develop#11 at /buildworker/worker/package_linux64/build/usr/share/
julia/stdlib/V1.0/pkg/SRc/aPI.jl:28 [inlined]
 [14] #add_or_develop at ./none:0 [inlined]
 [15] #add_or_develop#10 at /buildworker/worker/package_linux64/build/usr/share/
julia/stdlib/V1.0/pkg/SRc/aPI.jl:27 [inlined]
 [16] #add_or_develop at ./none:0 [inlined]
 [17] #add#18 at /buildworker/worker/package_linux64/build/usr/share/julia/stdli
b/V1.0/pkg/SRc/aPI.jl:69 [inlined]
 [18] add(::String) at /buildworker/worker/package_linux64/build/usr/share/julia
/stdlib/V1.0/pkg/SRc/aPI.jl:69
 [19] top-level scope at none:0

Searching “julia rcall unsatisfiable requirements” gave RCall.jl issue #303, in which the suggestion was to update/reinstall the related packages.

Solution

I misread that suggestion as “to upgrade Julia”. As a result, I went to Julialang’s homepage, which provided the lastest stable version (v. 1.1.0). Mine was installed half a year ago (v. 1.0.3). I downloaded the newer version and extracted it to /opt/. Provided that I had already installed an older version of Julia on the same machine, I could look back the command history in ~/.zsh_history.

  1. Extract the downloaded tarball to /opt/.

     $ sudo tar xf julia-1.1.0-linux-x86_64.tar.gz -C /opt

  2. Update the system’s environment $PATH in /etc/environment.

  3. Log out and log in, so that the session will use an updated $PATH.

  4. Relaunch the previous Julia package installation.

     $ julia -q
 julia> Pkg.add("RCall")
  Resolving package versions...
  Installed WinReg ────── v0.3.1
  Installed StatsModels ─ v0.5.0
  Installed RCall ─────── v0.13.2
   Updating `~/.julia/environments/v1.1/Project.toml`
   [6f49c342] + RCall v0.13.2
   Updating `~/.julia/environments/v1.1/Manifest.toml`
   [6f49c342] + RCall v0.13.2
   [3eaba693] + StatsModels v0.5.0
   [1b915085] + WinReg v0.3.1
   Building RCall → `~/.julia/packages/RCall/ffM0W/deps/build.log`
 julia> using RCall
 [ Info: Precompiling RCall [6f49c342-dc21-5d91-9882-a32aef131414]

RCall.jl was finally installed on Ubuntu.

Julia  RCall  R 

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