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
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.
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
I want to compile the units package in Renjin, which currently does not work in the online repository, see http://packages.renjin.org/package/org.renjin.cran/units/0.6-3/build/5
I created a pom.xml for the current release of udunits, see https://github.com/nuest/renjin-docker/blob/master/geospatial-packages/units/pom.xml
I built a Dockerfile for compiling packages and having the required compilers, see https://github.com/nuest/renjin-docker/blob/master/0.9.2726/Dockerfile.builder
Within a container created from an image built from that Dockerfile, I can run library('org.renjin.cran:Rcpp') in an R session, but when I run mvn clean install on units I get the following error:
[...]
Downloaded: https://nexus.bedatadriven.com/content/groups/public/org/sonatype/aether/aether-impl/1.13.1/aether-impl-1.13.1.jar (128 KB at 7.4 KB/sec)
EXECUTING: -print-file-name=plugin
EXECUTING: -shared -xc++ -I/usr/lib/gcc/x86_64-linux-gnu/4.7/plugin/include -fPIC -fno-rtti -O2 plugin.c -lstdc++ -shared-libgcc -o /packages/units/units/target/bridge.so
configure: units: 0.6-4
Warning: unsupported configuration variable CFLAGS
Warning: unsupported configuration variable CPPFLAGS
Warning: unsupported configuration variable LDFLAGS
Warning: unsupported configuration variable CXXFLAGS
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 g++-4.7 accepts -g... yes
checking how to run the C++ preprocessor... g++-4.7 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... no
checking for error_at_line... yes
checking for gcc... gcc-4.7
checking whether we are using the GNU C compiler... yes
checking whether gcc-4.7 accepts -g... yes
checking for gcc-4.7 option to accept ISO C89... none needed
checking for XML_ParserCreate in -lexpat... no
checking udunits2.h usability... yes
checking udunits2.h presence... yes
checking for udunits2.h... yes
checking for ut_read_xml in -ludunits2... yes
configure: creating ./config.status
config.status: creating src/Makevars
Checking wether in Makevars CXX_STD is set to CXX11... no
g++-4.7 -I/packages/units/units/target/gnur/include -DNDEBUG -DUDUNITS2_DIR=0 -I"/packages/units/units/target/include" -fpic -m32 -fplugin=/packages/units/units/target/bridge.so -DRENJIN -fno-inline-functions -fdisable-tree-einline -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c udunits.cpp -o udunits.o
cc1plus: note: disable pass tree-einline for functions in the range of [0, 4294967295]
udunits.cpp:11:18: fatal error: Rcpp.h: No such file or directory
compilation terminated.
/packages/units/units/target/gnur/etc/Makeconf:202: recipe for target 'udunits.o' failed
make: *** [udunits.o] Error 1
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 02:20 min
[INFO] Finished at: 2019-11-15T15:27:52+00:00
[INFO] Final Memory: 17M/445M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.renjin:renjin-maven-plugin:0.9.2726:gnur-compile (gnur-compile) on project units: Compilation of GNU R sources failed: Failed to execute Makefile -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
root#987c61d45fbf:/packages/units/units# exit
Anyone an idea how to tell Renjin where to find Rcpp.h ?
More details on the resources I consulted are in this GitHub issue: https://github.com/nuest/renjin-docker/issues/4
If you're using Maven to build the package, you also need to add Rcpp headers as a dependency:
<dependency>
<groupId>org.renjin.cran</groupId>
<artifactId>Rcpp</artifactId>
<version>0.12.13-renjin-15</version>
<classifier>headers</classifier>
<scope>provided</scope>
</dependency>
You can use the pom file for plyr as an example.
Note that if you just want to build a package for use with Renjin, the command line tool is far simpler:
renjin build units
This will take care of downloading the required dependencies and producing a jar file.
Do note that Renjin does not support packages which depend on external native libraries. You can see from the automated build logs that the units package will fail because of a dependency on udunits2.
That is the reason that the units packages is labeled as incompatible in our package site.
I am trying to install R from source code in my Ubuntu 14.04. I ran ./configure but that shows some warning-
..........................................
.........................................
config.status: creating tests/Examples/Makefile
config.status: creating tools/Makefile
config.status: creating src/include/config.h
config.status: executing libtool commands
config.status: executing stamp-h commands
R is now configured for x86_64-pc-linux-gnu
Source directory: .
Installation directory: /usr/local
C compiler: gcc -std=gnu99 -g -O2
Fortran 77 compiler: gfortran -g -O2
Default C++ compiler: g++ -g -O2
C++98 compiler: g++ -g -O2
C++11 compiler: g++ -std=gnu++11 -g -O2
C++14 compiler:
C++17 compiler:
Fortran 90/95 compiler: gfortran -g -O2
Obj-C compiler:
Interfaces supported: X11
External libraries: readline, curl
Additional capabilities: PNG, JPEG, NLS
Options enabled: shared BLAS, R profiling
Capabilities skipped: TIFF, cairo, ICU
Options not enabled: memory profiling
Recommended packages: yes
configure: WARNING: pcre < 8.32 is deprecated
configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: WARNING: you cannot build PDF versions of vignettes and help pages
configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally
Texlive 2017 is also installed in my system. I want to full featured R. Now, what can I do for fixing the warnings?
I have followed all the instructions mentioned in the Apache thrift wiki. I downloaded the thrift source code, then installed the dependencies
sudo yum install automake libtool flex bison pkgconfig gcc-c++ boost-devel libevent-devel zlib-devel python-devel ruby-devel
Then ran
./configure
(didn't run bootstrap.sh because there is no bootstrap.sh in the thrift-0.9.0 codebase). Finally, I get this error. Any idea why this is happening?
libtool: link: ( cd ".libs" && rm -f "libthriftz.la" && ln -s "../libthriftz.la" "libthriftz.la" )
/bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/include -I./src -I./src/thrift -DQT_SHARED -I/usr/include/QtCore -I/usr/include/QtNetwork -Wall -g -O2 -MT libthriftqt_la-moc_TQTcpServer.lo -MD -MP -MF .deps/libthriftqt_la-moc_TQTcpServer.Tpo -c -o libthriftqt_la-moc_TQTcpServer.lo `test -f 'src/thrift/qt/moc_TQTcpServer.cpp' || echo './'`src/thrift/qt/moc_TQTcpServer.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/include -I./src -I./src/thrift -DQT_SHARED -I/usr/include/QtCore -I/usr/include/QtNetwork -Wall -g -O2 -MT libthriftqt_la-moc_TQTcpServer.lo -MD -MP -MF .deps/libthriftqt_la-moc_TQTcpServer.Tpo -c src/thrift/qt/moc_TQTcpServer.cpp -fPIC -DPIC -o .libs/libthriftqt_la-moc_TQTcpServer.o
src/thrift/qt/moc_TQTcpServer.cpp:14:2: error: #error "This file was generated using the moc from 4.8.1. It"
src/thrift/qt/moc_TQTcpServer.cpp:15:2: error: #error "cannot be used with the include files from this version of Qt."
src/thrift/qt/moc_TQTcpServer.cpp:16:2: error: #error "(The moc has changed too much.)"
src/thrift/qt/moc_TQTcpServer.cpp:47: error: no 'void apache::thrift::async::TQTcpServer::qt_static_metacall(QObject*, QMetaObject::Call, int, void**)' member function declared in class 'apache::thrift::async::TQTcpServer'
src/thrift/qt/moc_TQTcpServer.cpp:62: error: 'const QMetaObjectExtraData apache::thrift::async::TQTcpServer::staticMetaObjectExtraData' is not a static member of 'class apache::thrift::async::TQTcpServer'
src/thrift/qt/moc_TQTcpServer.cpp:63: error: 'qt_static_metacall' was not declared in this scope
src/thrift/qt/moc_TQTcpServer.cpp:64: error: too many initializers for 'const QMetaObjectExtraData'
src/thrift/qt/moc_TQTcpServer.cpp:68: error: 'staticMetaObjectExtraData' was not declared in this scope
src/thrift/qt/moc_TQTcpServer.cpp:69: error: too many initializers for 'QMetaObject::<anonymous struct>'
src/thrift/qt/moc_TQTcpServer.cpp: In member function 'virtual int apache::thrift::async::TQTcpServer::qt_metacall(QMetaObject::Call, int, void**)':
src/thrift/qt/moc_TQTcpServer.cpp:95: error: 'qt_static_metacall' was not declared in this scope
make[4]: *** [libthriftqt_la-moc_TQTcpServer.lo] Error 1
make[4]: Leaving directory `/home/rjain/Downloads/thrift-0.9.0/lib/cpp'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/rjain/Downloads/thrift-0.9.0/lib/cpp'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/rjain/Downloads/thrift-0.9.0/lib'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/rjain/Downloads/thrift-0.9.0'
make: *** [all] Error 2
I download the source from: http://www.apache.org/dyn/closer.cgi?path=/thrift/0.9.0/thrift-0.9.0.tar.gz
Your qt-devel is out of date for thrift. Just remove the qt-devel rpm and rerun the configure script which will skip this part. It works for me.
First of all, check your qt related rpms by executing the following command
rpm -qa | grep qt-devel
If you find qt-devel is installed version below 4.6, please remove this package by executing command
rpm -qa | grep qt-devel | xargs rpm -e
If this is done, the qt part of thrift will be skipped.
It looks like the version of Qt that is on your system is older than what this program expects. Can you try updating Qt to a later version?
sudo yum install qt4-devel
I am trying to build 'lcms2' static library which is dependent on libtiff. libtiff has again dependency on libjbig. I have successfully configured libtest with the following parameters:
CFLAGS="-fPIC" CXXFLAGS="-fPIC" LIBS="-ljbig" ./configure --prefix=/usr/local --enable-static=yes --enable-shared=no --with-zlib=yes --with-jpeg=yes --with-tiff=yes --with-pic=PIC
The configure reports no error:
checking for TIFF support ...
checking tiff.h usability... yes
checking tiff.h presence... yes
checking for tiff.h... yes
checking tiffio.h usability... yes
checking tiffio.h presence... yes
checking for tiffio.h... yes
checking for TIFFOpen in -ltiff... yes
checking for TIFFClientOpen in -ltiff... yes
checking for TIFFIsByteSwapped in -ltiff... yes
checking if TIFF package is complete... yes
checking tiffconf.h usability... yes
checking tiffconf.h presence... yes
checking for tiffconf.h... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating lcms2.pc
config.status: creating include/Makefile
config.status: creating src/Makefile
config.status: creating utils/tificc/Makefile
config.status: creating utils/transicc/Makefile
config.status: creating utils/linkicc/Makefile
config.status: creating utils/jpgicc/Makefile
config.status: creating utils/psicc/Makefile
config.status: creating testbed/Makefile
config.status: executing depfiles commands
config.status: executing libtool commands
The when I make the library it throws the following error:
/bin/sh ../../libtool --tag=CC --mode=link gcc -std=gnu99 -fPIC -o tificc tificc.o xgetopt.o vprf.o ../../src/liblcms2.la -ltiff -ljpeg -lz -lm
libtool: link: gcc -std=gnu99 -fPIC -o tificc tificc.o xgetopt.o vprf.o ../../src/.libs/liblcms2.a -ltiff -ljpeg -lz -lm
/usr/local/lib/libtiff.a(tif_jbig.o): In function `JBIGDecode':
tif_jbig.c:(.text+0xc4): undefined reference to `jbg_dec_init'
tif_jbig.c:(.text+0xe4): undefined reference to `jbg_newlen'
tif_jbig.c:(.text+0x116): undefined reference to `jbg_dec_in'
tif_jbig.c:(.text+0x12a): undefined reference to `jbg_strerror'
tif_jbig.c:(.text+0x177): undefined reference to `jbg_dec_getimage'
tif_jbig.c:(.text+0x188): undefined reference to `jbg_dec_getsize'
tif_jbig.c:(.text+0x1ac): undefined reference to `jbg_dec_free'
/usr/local/lib/libtiff.a(tif_jbig.o): In function `JBIGEncode':
tif_jbig.c:(.text+0x402): undefined reference to `jbg_enc_init'
tif_jbig.c:(.text+0x40d): undefined reference to `jbg_enc_out'
tif_jbig.c:(.text+0x418): undefined reference to `jbg_enc_free'
collect2: ld returned 1 exit status
make[1]: *** [tificc] Error 1
libtool: link: gcc -std=gnu99 -fPIC -o tificc tificc.o xgetopt.o vprf.o ../../src/.libs/liblcms2.a -ltiff -ljpeg -lz -lm
There is no reference to JBIG library in the linking command (I don't remember if it should go before or after - some libraries require both - the reference to libtiff, -ltiff), so jbg_* references can't be resolved. Having LCMS linked does not help you, since JBIG is not linked in, but only referred to, by JBIG.
Add -ljbig to the link command.
Or, manually edit the Makefile and add -ljbig to LIBS (eg. LIBS = -ljbig).