How can I use Octave from R 4.1? - r

Question

I've installed Octave in Linux machine (Ubuntu 20.04) using this code:
sudo apt-add-repository -y ppa:octave/stable;
sudo apt install -y software-properties-common;
sudo apt-get update;
sudo apt-get install -y octave liboctave-dev
The program works perfectly using his interface.
I now wanted to use it through R via the library RcppOctave but I'm not even able to install it.
Using the default installation doesn't work because of the R version:
> install.packages('RcppOctave')
Installing package into ‘/home/cesarkero/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘RcppOctave’ is not available for this version of R
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
> install.packages("RcppOctave", repos="http://R-Forge.R-project.org")
Installing package into ‘/home/cesarkero/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘RcppOctave’ is not available for this version of R
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
Then I tried to installed it from github (install_github('https://github.com/renozao/RcppOctave')) or directly from the tar.gz latest release, but this is the error I get:
> file <- '../../05_Software/R/RcppOctave_0.8.5.tar.gz'
> install.packages(pkgs=file, type="source", repos=NULL)
Installing package into ‘/home/cesarkero/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
* installing *source* package ‘RcppOctave’ ...
** package ‘RcppOctave’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether R is a shared library... yes
Using R LDFLAGS: -Wl,--export-dynamic -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre2-8 -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n
Using R CPPFLAGS: -I/usr/share/R/include
checking for octave-config... /usr/bin/octave-config
checking for mkoctfile... /usr/bin/mkoctfile
checking Octave include directory... /usr/include/octave-5.2.0/octave
checking Octave library directory... /usr/lib/x86_64-linux-gnu/octave/5.2.0
checking Octave version... 5.2.0
checking whether to infer output names for Octave function (>= 3.4.3)... yes
configure: creating ./config.status
config.status: creating src/Makevars
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/modules/Makefile
** libs
cd modules;\
make; \
mkdir -p "/home/cesarkero/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-RcppOctave/00new/RcppOctave/modules"; \
echo "Moving Octave modules to '"/home/cesarkero/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-RcppOctave/00new/RcppOctave/modules"'"; \
cp -f PKG_ADD *.oct "/home/cesarkero/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-RcppOctave/00new/RcppOctave/modules";
make[1]: se entra en el directorio '/tmp/RtmpJjatgt/R.INSTALL144cc3d8bf8b1/RcppOctave/src/modules'
/usr/bin/mkoctfile -v -c -I/usr/share/R/include Rrng.cc
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/octave-5.2.0/octave/.. -I/usr/include/octave-5.2.0/octave -pthread -fopenmp -g -O2 -fdebug-prefix-map=/build/octave-rvRilm/octave-5.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/R/include Rrng.cc -o Rrng.o
Rrng.cc:32:10: fatal error: octave/config.h: No existe el archivo o el directorio
32 | #include <octave/config.h>
| ^~~~~~~~~~~~~~~~~
compilation terminated.
make[1]: *** [Makefile:25: Rrng.oct] Error 1
make[1]: se sale del directorio '/tmp/RtmpJjatgt/R.INSTALL144cc3d8bf8b1/RcppOctave/src/modules'
Moving Octave modules to '/home/cesarkero/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-RcppOctave/00new/RcppOctave/modules'
cp: no se puede efectuar `stat' sobre '*.oct': No existe el archivo o el directorio
make: *** [Makevars:18: OctaveModule] Error 1
ERROR: compilation failed for package ‘RcppOctave’
* removing ‘/home/cesarkero/R/x86_64-pc-linux-gnu-library/4.1/RcppOctave’
Warning in install.packages :
installation of package ‘../../05_Software/R/RcppOctave_0.8.5.tar.gz’ had non-zero exit status
The goal es clear: How can I install this library in R 4.1 (Ubuntu machine 20.04)?
UPDATE (20/10/21)
I've used this comand as #Gorka sujested:
sudo ln -s /usr/include/octave-5.2.0/octave/octave-config.h /usr/include/octave-5.2.0/octave/config.h
...but this is the new error:
> install_github('https://github.com/renozao/RcppOctave')
Downloading GitHub repo renozao/RcppOctave#HEAD
✓ checking for file ‘/tmp/Rtmp2OpHDN/remotes23297a629ef/renozao-RcppOctave-fcf4d02/DESCRIPTION’ ...
─ preparing ‘RcppOctave’:
✓ checking DESCRIPTION meta-information ...
─ cleaning src
─ running ‘cleanup’
─ installing the package to process help pages
-----------------------------------
─ installing *source* package ‘RcppOctave’ ...
** using staged installation
checking R architecture... none
checking for R... /usr/lib/R/bin/R
checking for Rscript... /usr/lib/R/bin/Rscript
checking whether loading Rprofile writes to stdout... no
checking R version... R version 4.1.1 (2021-08-10)
checking R platform... x86_64-pc-linux-gnu
checking R CC... gcc -std=gnu99
checking R CFLAGS... -g -O2 -fdebug-prefix-map=/build/r-base-QwogzP/r-base-4.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -pedantic -fdiagnostics-color=always
checking R CPPFLAGS...
checking R CXXFLAGS... -g -O2 -fdebug-prefix-map=/build/r-base-QwogzP/r-base-4.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -pedantic -fdiagnostics-color=always
checking for gcc... /usr/bin/gcc
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for g++... /usr/bin/g++
configure: Original R_LDFLAGS: -Wl,--export-dynamic -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre2-8 -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n
configure: Original R_CPPFLAGS: -I/usr/share/R/include
checking whether R is a shared library... yes
checking type of Operating System... Linux
checking whether OS is Mac OS (Darwin)... no
configure: Using mkoctfile with R_LDFLAGS: -Wl,--export-dynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre2-8 -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n
configure: Using mkoctfile with R_CPPFLAGS: -I/usr/share/R/include
checking Octave custom binary path specification... none
configure: using Octave binary path from $PATH
checking for octave-config... /usr/bin/octave-config
checking for mkoctfile... /usr/bin/mkoctfile
checking Octave Octave bin directory... /usr/bin
checking Octave Octave libraries directory... /usr/lib/x86_64-linux-gnu/octave/5.2.0
checking for octave... /usr/bin/octave
checking PATH changes... none
checking Octave module make target... all
checking mkoctfile command... /usr/bin/mkoctfile
checking Octave cpp flags... -Wdate-time -D_FORTIFY_SOURCE=2
checking Octave include flags... -I/usr/include/octave-5.2.0/octave/.. -I/usr/include/octave-5.2.0/octave
checking Octave -L flags... warning: LFLAGS is deprecated and will be removed in a future version of Octave, use LDFLAGS instead
-L/usr/lib/x86_64-linux-gnu
checking Octave libraries... -loctinterp -loctave
checking Octave C compiler... gcc
checking Octave Fortran compiler... gfortran
checking Octave platform... x86_64-pc-linux-gnu
checking Octave API version... api-v53
checking Octave version... 5.2.0
checking whether to infer output names for Octave function (>= 3.4.3)... yes
configure: Using Octave LDFLAGS: -L/usr/lib/x86_64-linux-gnu -loctinterp -loctave
configure: Using Octave CPPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/octave-5.2.0/octave/.. -I/usr/include/octave-5.2.0/octave -DOCT_POST_3_4_0=1
checking RcppOctave Octave module directory... /tmp/Rtmprp7Rn4/Rinst241a34c4f6ea/00LOCK-RcppOctave/00new/RcppOctave/modules
configure: creating ./config.status
config.status: creating R/config-vars.R
configure: creating ./config.status
config.status: creating R/config-vars.R
config.status: creating src/Makevars
configure: creating ./config.status
config.status: creating R/config-vars.R
config.status: creating src/Makevars
config.status: creating src/modules/Makefile
** libs
# Making Octave module [r_arch: all]
make[1]: se entra en el directorio '/tmp/Rtmprp7Rn4/Rbuild241a5f538b08/RcppOctave/src/modules'
*** Building octave module: utils.oct
/usr/bin/mkoctfile -v utils.cc
g++ -std=gnu++11 -c -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/octave-5.2.0/octave/.. -I/usr/include/octave-5.2.0/octave -pthread -fopenmp -g -O2 -fdebug-prefix-map=/build/octave-rvRilm/octave-5.2.0=. -fstack-protector-strong -Wformat -Werror=format-security utils.cc -o /tmp/oct-XxPJKC.o
g++ -I/usr/include/octave-5.2.0/octave/.. -I/usr/include/octave-5.2.0/octave -pthread -fopenmp -g -O2 -fdebug-prefix-map=/build/octave-rvRilm/octave-5.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -shared -Wl,-Bsymbolic -Wl,-Bsymbolic-functions -Wl,-z,relro -o utils.oct /tmp/oct-XxPJKC.o -L/usr/lib/x86_64-linux-gnu -Wl,-Bsymbolic-functions -Wl,-z,relro
*** Building octave module: Rrng.oct
/usr/bin/mkoctfile -v -I/usr/share/R/include -Wl,--export-dynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre2-8 -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n Rrng.cc
g++ -std=gnu++11 -c -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/octave-5.2.0/octave/.. -I/usr/include/octave-5.2.0/octave -pthread -fopenmp -g -O2 -fdebug-prefix-map=/build/octave-rvRilm/octave-5.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/share/R/include Rrng.cc -o /tmp/oct-zr4Boo.o
Rrng.cc: In function ‘octave_value_list Frand(const octave_value_list&, int)’:
Rrng.cc:163:54: warning: ‘bool octave_value::is_empty() const’ is deprecated: [4.4]: use 'isempty' instead [-Wdeprecated-declarations]
163 | k = ( nargs > iarg_col && !args(iarg_col).is_empty() ? long(args(iarg_col).double_value()) : n);\
| ^
Rrng.cc:181:1: note: in expansion of macro ‘RAND_ARGS’
181 | RAND_ARGS(octave_fun, 0, 2, 0, 1) \
| ^~~~~~~~~
Rrng.cc:196:3: note: in expansion of macro ‘RAND_FUNCTION’
196 | RAND_FUNCTION(unif_rand, "rand")
| ^~~~~~~~~~~~~
In file included from /usr/include/octave-5.2.0/octave/../octave/ovl.h:36,
from /usr/include/octave-5.2.0/octave/../octave/ov-fcn.h:33,
from /usr/include/octave-5.2.0/octave/../octave/ov-builtin.h:32,
from /usr/include/octave-5.2.0/octave/../octave/defun-int.h:30,
from /usr/include/octave-5.2.0/octave/../octave/defun-dld.h:32,
from /usr/include/octave-5.2.0/octave/../octave/oct.h:32,
from Rrng.cc:33:
/usr/include/octave-5.2.0/octave/../octave/ov.h:534:8: note: declared here
534 | bool is_empty (void) const
| ^~~~~~~~
Rrng.cc: In function ‘octave_value_list Frandn(const octave_value_list&, int)’:
Rrng.cc:163:54: warning: ‘bool octave_value::is_empty() const’ is deprecated: [4.4]: use 'isempty' instead [-Wdeprecated-declarations]
163 | k = ( nargs > iarg_col && !args(iarg_col).is_empty() ? long(args(iarg_col).double_value()) : n);\
| ^
Rrng.cc:181:1: note: in expansion of macro ‘RAND_ARGS’
181 | RAND_ARGS(octave_fun, 0, 2, 0, 1) \
| ^~~~~~~~~
Rrng.cc:207:2: note: in expansion of macro ‘RAND_FUNCTION’
207 | RAND_FUNCTION(norm_rand, "randn")
| ^~~~~~~~~~~~~
In file included from /usr/include/octave-5.2.0/octave/../octave/ovl.h:36,
from /usr/include/octave-5.2.0/octave/../octave/ov-fcn.h:33,
from /usr/include/octave-5.2.0/octave/../octave/ov-builtin.h:32,
from /usr/include/octave-5.2.0/octave/../octave/defun-int.h:30,
from /usr/include/octave-5.2.0/octave/../octave/defun-dld.h:32,
from /usr/include/octave-5.2.0/octave/../octave/oct.h:32,
from Rrng.cc:33:
/usr/include/octave-5.2.0/octave/../octave/ov.h:534:8: note: declared here
534 | bool is_empty (void) const
| ^~~~~~~~
Rrng.cc: In function ‘octave_value_list Frande(const octave_value_list&, int)’:
Rrng.cc:163:54: warning: ‘bool octave_value::is_empty() const’ is deprecated: [4.4]: use 'isempty' instead [-Wdeprecated-declarations]
163 | k = ( nargs > iarg_col && !args(iarg_col).is_empty() ? long(args(iarg_col).double_value()) : n);\
| ^
Rrng.cc:181:1: note: in expansion of macro ‘RAND_ARGS’
181 | RAND_ARGS(octave_fun, 0, 2, 0, 1) \
| ^~~~~~~~~
Rrng.cc:218:2: note: in expansion of macro ‘RAND_FUNCTION’
218 | RAND_FUNCTION(exp_rand, "rande")
| ^~~~~~~~~~~~~
In file included from /usr/include/octave-5.2.0/octave/../octave/ovl.h:36,
from /usr/include/octave-5.2.0/octave/../octave/ov-fcn.h:33,
from /usr/include/octave-5.2.0/octave/../octave/ov-builtin.h:32,
from /usr/include/octave-5.2.0/octave/../octave/defun-int.h:30,
from /usr/include/octave-5.2.0/octave/../octave/defun-dld.h:32,
from /usr/include/octave-5.2.0/octave/../octave/oct.h:32,
from Rrng.cc:33:
/usr/include/octave-5.2.0/octave/../octave/ov.h:534:8: note: declared here
534 | bool is_empty (void) const
| ^~~~~~~~
Rrng.cc: In function ‘octave_value_list Frandg(const octave_value_list&, int)’:
Rrng.cc:163:54: warning: ‘bool octave_value::is_empty() const’ is deprecated: [4.4]: use 'isempty' instead [-Wdeprecated-declarations]
163 | k = ( nargs > iarg_col && !args(iarg_col).is_empty() ? long(args(iarg_col).double_value()) : n);\
| ^
Rrng.cc:232:3: note: in expansion of macro ‘RAND_ARGS’
232 | RAND_ARGS("randg", 1, 4, 1, 2)
| ^~~~~~~~~
In file included from /usr/include/octave-5.2.0/octave/../octave/ovl.h:36,
from /usr/include/octave-5.2.0/octave/../octave/ov-fcn.h:33,
from /usr/include/octave-5.2.0/octave/../octave/ov-builtin.h:32,
from /usr/include/octave-5.2.0/octave/../octave/defun-int.h:30,
from /usr/include/octave-5.2.0/octave/../octave/defun-dld.h:32,
from /usr/include/octave-5.2.0/octave/../octave/oct.h:32,
from Rrng.cc:33:
/usr/include/octave-5.2.0/octave/../octave/ov.h:534:8: note: declared here
534 | bool is_empty (void) const
| ^~~~~~~~
Rrng.cc:238:48: warning: ‘bool octave_value::is_empty() const’ is deprecated: [4.4]: use 'isempty' instead [-Wdeprecated-declarations]
238 | double scale(nArgs >= 4 && !args(3).is_empty() ? args(3).double_value() : 1);
| ^
In file included from /usr/include/octave-5.2.0/octave/../octave/ovl.h:36,
from /usr/include/octave-5.2.0/octave/../octave/ov-fcn.h:33,
from /usr/include/octave-5.2.0/octave/../octave/ov-builtin.h:32,
from /usr/include/octave-5.2.0/octave/../octave/defun-int.h:30,
from /usr/include/octave-5.2.0/octave/../octave/defun-dld.h:32,
from /usr/include/octave-5.2.0/octave/../octave/oct.h:32,
from Rrng.cc:33:
/usr/include/octave-5.2.0/octave/../octave/ov.h:534:8: note: declared here
534 | bool is_empty (void) const
| ^~~~~~~~
Rrng.cc: In function ‘octave_value_list Frandp(const octave_value_list&, int)’:
Rrng.cc:163:54: warning: ‘bool octave_value::is_empty() const’ is deprecated: [4.4]: use 'isempty' instead [-Wdeprecated-declarations]
163 | k = ( nargs > iarg_col && !args(iarg_col).is_empty() ? long(args(iarg_col).double_value()) : n);\
| ^
Rrng.cc:256:3: note: in expansion of macro ‘RAND_ARGS’
256 | RAND_ARGS("randp", 2, 3, 1, 2)
| ^~~~~~~~~
In file included from /usr/include/octave-5.2.0/octave/../octave/ovl.h:36,
from /usr/include/octave-5.2.0/octave/../octave/ov-fcn.h:33,
from /usr/include/octave-5.2.0/octave/../octave/ov-builtin.h:32,
from /usr/include/octave-5.2.0/octave/../octave/defun-int.h:30,
from /usr/include/octave-5.2.0/octave/../octave/defun-dld.h:32,
from /usr/include/octave-5.2.0/octave/../octave/oct.h:32,
from Rrng.cc:33:
/usr/include/octave-5.2.0/octave/../octave/ov.h:534:8: note: declared here
534 | bool is_empty (void) const
| ^~~~~~~~
g++ -I/usr/include/octave-5.2.0/octave/.. -I/usr/include/octave-5.2.0/octave -pthread -fopenmp -g -O2 -fdebug-prefix-map=/build/octave-rvRilm/octave-5.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -shared -Wl,-Bsymbolic -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rrng.oct /tmp/oct-zr4Boo.o -Wl,--export-dynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre2-8 -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n -L/usr/lib/x86_64-linux-gnu -Wl,-Bsymbolic-functions -Wl,-z,relro
make[1]: se sale del directorio '/tmp/Rtmprp7Rn4/Rbuild241a5f538b08/RcppOctave/src/modules'
# Copying Octave modules to directory '/tmp/Rtmprp7Rn4/Rinst241a34c4f6ea/00LOCK-RcppOctave/00new/RcppOctave/modules'
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG `"/usr/lib/R/bin/Rscript" -e "Rcpp:::CxxFlags()"` -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/octave-5.2.0/octave/.. -I/usr/include/octave-5.2.0/octave -DOCT_POST_3_4_0=1 -I'/home/cesarkero/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-QwogzP/r-base-4.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -pedantic -fdiagnostics-color=always -c conversion.cpp -o conversion.o
In file included from /usr/include/octave-5.2.0/octave/../octave/lo-utils.h:35
from /usr/include/octave-5.2.0/octave/../octave/Array.h:41
from /usr/include/octave-5.2.0/octave/../octave/str-vec.h:32
from /usr/include/octave-5.2.0/octave/../octave/ovl.h:33
from rcpp_octave.h:32
from conversion.cpp:5
/usr/include/octave-5.2.0/octave/../octave/quit.h:178:2:warning: tra ‘;-Wpedantic
178 | };
| ^
In file included from /usr/include/octave-5.2.0/octave/../octave/boolMatrix.h:30
from /usr/include/octave-5.2.0/octave/../octave/mx-base.h:34
from /usr/include/octave-5.2.0/octave/../octave/ov.h:40
from /usr/include/octave-5.2.0/octave/../octave/ovl.h:36
from rcpp_octave.h:32
from conversion.cpp:5
/usr/include/octave-5.2.0/octave/../octave/boolNDArray.h:121:46:warning: tra ‘;-Wpedantic
121 | BSXFUN_OP_DECL (and, boolNDArray, OCTAVE_API);
| ^
/usr/include/octave-5.2.0/octave/../octave/boolNDArray.h:122:45:warning: tra ‘;-Wpedantic
122 | BSXFUN_OP_DECL (or, boolNDArray, OCTAVE_API);
| ^
conversion.cpp:n function ‘SEXPREC* wrap(const Cell&, bool)
conversion.cpp:134:9:error: const class Cellhas no member named ‘is_cellstr did you mean ‘iscellstr
134 | if( x.is_cellstr
| ^~~~~~~~~~
| iscellstr
conversion.cpp:n function ‘SEXPREC* Rcpp::wrap(const T&) [with T = octave_value; SEXP = SEXPREC*]
conversion.cpp:180:24:warning: bool octave_value::is_null_value() constdeprecated: [4.4]: use 'isnull' instead [-Wdeprecated-declarations
180 | if( val.is_null_value()
| ^
In file included from /usr/include/octave-5.2.0/octave/../octave/ovl.h:36
from rcpp_octave.h:32
from conversion.cpp:5
/usr/include/octave-5.2.0/octave/../octave/ov.h:633:8:note: red here
633 | bool is_null_valued) const
| ^~~~~~~~~~~~~
conversion.cpp:214:30:warning: bool octave_value::is_bool_type() constdeprecated: [4.4]: use 'islogical' instead [-Wdeprecated-declarations
214 | else if ( val.is_bool_type()
| ^
In file included from /usr/include/octave-5.2.0/octave/../octave/ovl.h:36
from rcpp_octave.h:32
from conversion.cpp:5
/usr/include/octave-5.2.0/octave/../octave/ov.h:701:8:note: red here
701 | bool is_bool_typed) const
| ^~~~~~~~~~~~
conversion.cpp:219:102:warning: bool octave_value::is_integer_type() constdeprecated: [4.4]: use 'isinteger' instead [-Wdeprecated-declarations
219 | }else if( val.is_int32_type() || val.is_int64_type() || val.is_int16_type() || val.is_integer_type()
| ^
In file included from /usr/include/octave-5.2.0/octave/../octave/ovl.h:36
from rcpp_octave.h:32
from conversion.cpp:5
/usr/include/octave-5.2.0/octave/../octave/ov.h:692:8:note: red here
692 | bool is_integer_typed) const
| ^~~~~~~~~~~~~~~
conversion.cpp:223:30:warning: bool octave_value::is_real_type() constdeprecated: [4.4]: use 'isreal' instead [-Wdeprecated-declarations
223 | }else if( val.is_real_type()
| ^
In file included from /usr/include/octave-5.2.0/octave/../octave/ovl.h:36
from rcpp_octave.h:32
from conversion.cpp:5
/usr/include/octave-5.2.0/octave/../octave/ov.h:708:8:note: red here
708 | bool is_real_typed) const
| ^~~~~~~~~~~~
conversion.cpp:250:33:warning: bool octave_value::is_integer_type() constdeprecated: [4.4]: use 'isinteger' instead [-Wdeprecated-declarations
250 | else if ( val.is_integer_type()
| ^
In file included from /usr/include/octave-5.2.0/octave/../octave/ovl.h:36
from rcpp_octave.h:32
from conversion.cpp:5
/usr/include/octave-5.2.0/octave/../octave/ov.h:692:8:note: red here
692 | bool is_integer_typed) const
| ^~~~~~~~~~~~~~~
conversion.cpp:255:30:warning: bool octave_value::is_real_type() constdeprecated: [4.4]: use 'isreal' instead [-Wdeprecated-declarations
255 | }else if( val.is_real_type()
| ^
In file included from /usr/include/octave-5.2.0/octave/../octave/ovl.h:36
from rcpp_octave.h:32
from conversion.cpp:5
/usr/include/octave-5.2.0/octave/../octave/ov.h:708:8:note: red here
708 | bool is_real_typed) const
| ^~~~~~~~~~~~
conversion.cpp:270:24:warning: bool octave_value::is_map() constdeprecated: [4.4]: use 'isstruct' instead [-Wdeprecated-declarations
270 | } else if( val.is_map()/ Maps are converted into lists
| ^
In file included from /usr/include/octave-5.2.0/octave/../octave/ovl.h:36
from rcpp_octave.h:32
from conversion.cpp:5
/usr/include/octave-5.2.0/octave/../octave/ov.h:594:8:note: red here
594 | bool is_mapd) const
| ^~~~~~
conversion.cpp:307:25:warning: bool octave_value::is_cell() constdeprecated: [4.4]: use 'iscell' instead [-Wdeprecated-declarations
307 | } else if( val.is_cell() Cell objects are used for character vectors
| ^
In file included from /usr/include/octave-5.2.0/octave/../octave/ovl.h:36
from rcpp_octave.h:32
from conversion.cpp:5
/usr/include/octave-5.2.0/octave/../octave/ov.h:541:8:note: red here
541 | bool is_celld) const
| ^~~~~~~
conversion.cpp:n function ‘T Rcpp::as(SEXP) [with T = octave_value; SEXP = SEXPREC*]
conversion.cpp:471:50:error: valid initialization of reference of type ‘const octave_value&from expression of type ‘octave_value_list
471 | const octave_value& ol = as<octave_value_list>(x)
| ~~~~~~~~~~~~~~~~~~~~~^~~
make: *** [/usr/lib/R/etc/Makeconf:177: conversion.o] Error 1
ERROR: compilation failed for package ‘RcppOctave’
─ removing ‘/tmp/Rtmprp7Rn4/Rinst241a34c4f6ea/RcppOctave’
-----------------------------------
ERROR: package installation failed
Error: Failed to install 'RcppOctave' from GitHub:
System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines):
E> | ^~~~~~~
E> conversion.cpp:n function ‘T Rcpp::as(SEXP) [with T = octave_value; SEXP = SEXPREC*]
E> conversion.cpp:471:50:error: valid initialization of reference of type ‘const octave_value&from expression of type ‘octave_value_list
E> 471 | const octave_value& ol = as<octave_value_list>(x)
E> | ~~~~~~~~~~~~~~~~~~~~~^~~
E> make: *** [/usr/lib/R/etc/Makeconf:177: conversion.o] Error 1
E> ERROR: compilation failed for package ‘RcppOctave’
E> * removing ‘/tmp/Rtmprp7Rn4/Rinst241a34c4f6ea/RcppOctave’
E> -----------------------------------
E> ERROR: package installation failed

Answer 1

Sometimes just downloading and installing/building the package on your own is enough, when the package ... is not available for this version of R error message appears.
In this case obviously not ... and Gorka is probably right, when he says it could be the Octave version.
In general I would rather try to get the latest CRAN version RcppOctave_0.18.1 running instead of the GitHub version (whose latest updates were also years ago).
Since the package seems to be temporary or permanently discontinued you never know, if they stopped their Github version in the middle of some changes that didn't work out.
Whereas for the latest CRAN version it is more likely that it was a staple build, that worked at the time it was being uploaded (2015-10-06).
So probably if you replicate the environment from this time (R version, Version of package dependencies, Ubuntu version, Octave version) you have a pretty high chance to get this package running.
But just bringing the Octave version to the current version at the time of RcppOctave_0.18.1 release might also already do the job.
Looking at https://wiki.octave.org/Release_History indicates that version 4.0.0 or 3.8.2 could be a good fit.
I am not really a linux/ubuntu user, but I'd guess just
apt-get install octave=4.0.0
won't do the job of installing the package, since the package must be present in the repository/ package manager. Probably you have to get the old package version from somewhere / add a repository that includes the package version (which you also did in your code with apt-add-repository -y ppa ...).
For Ubuntu you can find old packages at launchpad
https://launchpad.net/ubuntu/trusty/+source/octave
https://launchpad.net/ubuntu/+source/octave/3.8.2-4.1
For Debian you can find old packages at
https://snapshot.debian.org/
Would be interesting to see if building the package works with Octave 4.0.0 or 3.8.2 (and if it is possible to install these).
If you get it running this way and you anyway don't need functionality from newer Octave versions - perfect.
If not ... I don't know of any other R - Octave interface package, which would probably rule out the solution of just using another R package.
A solution (depending on your plans) could be using system() / system2() for invoking system commands.
system invokes the OS command specified by command.
Since (as far as I know) you can also run Octave scripts from the shell, this could be a possible workaround.

Answer 2

I also failed to install RcppOctave in R 4.1.2.
Instead I found a way to run Octave script in R Markdown file. Take a look at this example:
```{octave, engine.path='/usr/local/opt/octave/bin/octave', warning=F}
addpath('/Applications/freesurfer/matlab')
[vertex_coords_sp, faces] = read_surf("/Applications/freesurfer/subjects/fsaverage5/surf/lh.sphere")
save('~/RAS_coord_fs_sphere.mat','-v6')
```
You can refer to this page for more details on Octave code in R Markdown.
Hope this could help someone who also have trouble dealing with split environments :D