Installation issue: R 3.6.0 on Ubuntu 16.04

[biodan25]

I just tried to install RcppOctave from R 3.6.0 (via RStudio)

install.packages("RcppOctave", repos="http://R-Forge.R-project.org")

And got the error: "RcppOctave" is not available (for R version 3.6.0)

Is there any ETA for when it might become available? On a machine with R 3.5.1, it downloaded but i ran into other issues (which might resolved if i create a VM or make a docker image).

[biodan25]

On my older Ubuntu 16.04 box with R-3.5.1, i just installed Octave 5.1 from source and tried to install RcppOctave on it. If this was successful, i was going to use the same process for a docker image with 3.5.1 on the 1st Ubuntu16.04 box (which is running R-3.6 on bare metal). But i just ran into a problem on the older 16.04 box:
(BTW, the 4 packages are already installed but the installation gives "not available")

devtools::install_github("renozao/RcppOctave",ref="develop",quick=TRUE)
Downloading GitHub repo renozao/RcppOctave@develop
Skipping 4 packages not available: digest, pkgmaker, Rcpp, stringr
✔ checking for file ‘/tmp/RtmpoFrL48/remotes3bb6f48e43/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’ ...
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 3.5.1 (2018-07-02)
checking R platform... x86_64-pc-linux-gnu
checking R CC... gcc -std=gnu99
checking R CFLAGS... -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
checking R CPPFLAGS...
checking R CXXFLAGS... -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
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 -lpcre -llzma -lbz2 -lz -lrt -ldl -lm
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 -lpcre -llzma -lbz2 -lz -lrt -ldl -lm
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/local/bin/octave-config
checking for mkoctfile... /usr/local/bin/mkoctfile
checking Octave Octave bin directory... /usr/local/bin
checking Octave Octave libraries directory... /usr/local/lib/octave/5.1.0
checking for octave... /usr/local/bin/octave
checking PATH changes... none
checking Octave module make target... all
checking mkoctfile command... /usr/local/bin/mkoctfile
checking Octave cpp flags...
checking Octave include flags... -I/usr/local/include/octave-5.1.0/octave/.. -I/usr/local/include/octave-5.1.0/octave -I/usr/local/include
checking Octave -L flags... warning: LFLAGS is deprecated and will be removed in a future version of Octave, use LDFLAGS instead
-L/usr/local/lib
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... 5.1.0
checking whether to infer output names for Octave function (>= 3.4.3)... yes
configure: Using Octave LDFLAGS: -L/usr/local/lib -loctinterp -loctave
configure: Using Octave CPPFLAGS: -I/usr/local/include/octave-5.1.0/octave/.. -I/usr/local/include/octave-5.1.0/octave -I/usr/local/include -DOCT_POST_3_4_0=1
checking RcppOctave Octave module directory... /tmp/RtmpGFexmb/Rinst61567e75864/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]: Entering directory '/tmp/RtmpGFexmb/Rbuild61566452bc14/RcppOctave/src/modules'
*** Building octave module: utils.oct
/usr/local/bin/mkoctfile -v utils.cc
g++ -std=gnu++11 -c -fPIC -I/usr/local/include/octave-5.1.0/octave/.. -I/usr/local/include/octave-5.1.0/octave -I/usr/local/include -pthread -fopenmp -g -O2 utils.cc -o /tmp/oct-JnYru3.o
g++ -std=gnu++11 -I/usr/local/include/octave-5.1.0/octave/.. -I/usr/local/include/octave-5.1.0/octave -I/usr/local/include -pthread -fopenmp -g -O2 -shared -Wl,-Bsymbolic -o utils.oct /tmp/oct-JnYru3.o -L/usr/local/lib
*** Building octave module: Rrng.oct
/usr/local/bin/mkoctfile -v -I/usr/share/R/include -Wl,--export-dynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre -llzma -lbz2 -lz -lrt -ldl -lm Rrng.cc
g++ -std=gnu++11 -c -fPIC -I/usr/local/include/octave-5.1.0/octave/.. -I/usr/local/include/octave-5.1.0/octave -I/usr/local/include -pthread -fopenmp -g -O2 -I/usr/share/R/include Rrng.cc -o /tmp/oct-xhA2tJ.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]
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’
RAND_ARGS(octave_fun, 0, 2, 0, 1)
^
Rrng.cc:196:3: note: in expansion of macro ‘RAND_FUNCTION’
RAND_FUNCTION(unif_rand, "rand")
^
In file included from /usr/local/include/octave-5.1.0/octave/../octave/ovl.h:36:0,
from /usr/local/include/octave-5.1.0/octave/../octave/ov-fcn.h:33,
from /usr/local/include/octave-5.1.0/octave/../octave/ov-builtin.h:32,
from /usr/local/include/octave-5.1.0/octave/../octave/defun-int.h:30,
from /usr/local/include/octave-5.1.0/octave/../octave/defun-dld.h:32,
from /usr/local/include/octave-5.1.0/octave/../octave/oct.h:32,
from Rrng.cc:33:
/usr/local/include/octave-5.1.0/octave/../octave/ov.h:534:8: note: declared here
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]
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’
RAND_ARGS(octave_fun, 0, 2, 0, 1)
^
Rrng.cc:207:2: note: in expansion of macro ‘RAND_FUNCTION’
RAND_FUNCTION(norm_rand, "randn")
^
In file included from /usr/local/include/octave-5.1.0/octave/../octave/ovl.h:36:0,
from /usr/local/include/octave-5.1.0/octave/../octave/ov-fcn.h:33,
from /usr/local/include/octave-5.1.0/octave/../octave/ov-builtin.h:32,
from /usr/local/include/octave-5.1.0/octave/../octave/defun-int.h:30,
from /usr/local/include/octave-5.1.0/octave/../octave/defun-dld.h:32,
from /usr/local/include/octave-5.1.0/octave/../octave/oct.h:32,
from Rrng.cc:33:
/usr/local/include/octave-5.1.0/octave/../octave/ov.h:534:8: note: declared here
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]
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’
RAND_ARGS(octave_fun, 0, 2, 0, 1)
^
Rrng.cc:218:2: note: in expansion of macro ‘RAND_FUNCTION’
RAND_FUNCTION(exp_rand, "rande")
^
In file included from /usr/local/include/octave-5.1.0/octave/../octave/ovl.h:36:0,
from /usr/local/include/octave-5.1.0/octave/../octave/ov-fcn.h:33,
from /usr/local/include/octave-5.1.0/octave/../octave/ov-builtin.h:32,
from /usr/local/include/octave-5.1.0/octave/../octave/defun-int.h:30,
from /usr/local/include/octave-5.1.0/octave/../octave/defun-dld.h:32,
from /usr/local/include/octave-5.1.0/octave/../octave/oct.h:32,
from Rrng.cc:33:
/usr/local/include/octave-5.1.0/octave/../octave/ov.h:534:8: note: declared here
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]
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’
RAND_ARGS("randg", 1, 4, 1, 2)
^
In file included from /usr/local/include/octave-5.1.0/octave/../octave/ovl.h:36:0,
from /usr/local/include/octave-5.1.0/octave/../octave/ov-fcn.h:33,
from /usr/local/include/octave-5.1.0/octave/../octave/ov-builtin.h:32,
from /usr/local/include/octave-5.1.0/octave/../octave/defun-int.h:30,
from /usr/local/include/octave-5.1.0/octave/../octave/defun-dld.h:32,
from /usr/local/include/octave-5.1.0/octave/../octave/oct.h:32,
from Rrng.cc:33:
/usr/local/include/octave-5.1.0/octave/../octave/ov.h:534:8: note: declared here
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]
double scale(nArgs >= 4 && !args(3).is_empty() ? args(3).double_value() : 1);
^
In file included from /usr/local/include/octave-5.1.0/octave/../octave/ovl.h:36:0,
from /usr/local/include/octave-5.1.0/octave/../octave/ov-fcn.h:33,
from /usr/local/include/octave-5.1.0/octave/../octave/ov-builtin.h:32,
from /usr/local/include/octave-5.1.0/octave/../octave/defun-int.h:30,
from /usr/local/include/octave-5.1.0/octave/../octave/defun-dld.h:32,
from /usr/local/include/octave-5.1.0/octave/../octave/oct.h:32,
from Rrng.cc:33:
/usr/local/include/octave-5.1.0/octave/../octave/ov.h:534:8: note: declared here
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]
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’
RAND_ARGS("randp", 2, 3, 1, 2)
^
In file included from /usr/local/include/octave-5.1.0/octave/../octave/ovl.h:36:0,
from /usr/local/include/octave-5.1.0/octave/../octave/ov-fcn.h:33,
from /usr/local/include/octave-5.1.0/octave/../octave/ov-builtin.h:32,
from /usr/local/include/octave-5.1.0/octave/../octave/defun-int.h:30,
from /usr/local/include/octave-5.1.0/octave/../octave/defun-dld.h:32,
from /usr/local/include/octave-5.1.0/octave/../octave/oct.h:32,
from Rrng.cc:33:
/usr/local/include/octave-5.1.0/octave/../octave/ov.h:534:8: note: declared here
bool is_empty (void) const
^
g++ -std=gnu++11 -I/usr/local/include/octave-5.1.0/octave/.. -I/usr/local/include/octave-5.1.0/octave -I/usr/local/include -pthread -fopenmp -g -O2 -shared -Wl,-Bsymbolic -o Rrng.oct /tmp/oct-xhA2tJ.o -Wl,--export-dynamic -Wl,-Bsymbolic-functions -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -L/usr/local/lib
make[1]: Leaving directory '/tmp/RtmpGFexmb/Rbuild61566452bc14/RcppOctave/src/modules'

Copying Octave modules to directory '/tmp/RtmpGFexmb/Rinst61567e75864/RcppOctave/modules'

g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG "/usr/lib/R/bin/Rscript" -e "Rcpp:::CxxFlags()" -I/usr/local/include/octave-5.1.0/octave/.. -I/usr/local/include/octave-5.1.0/octave -I/usr/local/include -DOCT_POST_3_4_0=1 -I"/home/dchin/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c conversion.cpp -o conversion.o
conversion.cpp: In function ‘SEXPREC* wrap(const Cell&, bool)’:
conversion.cpp:134:9: error: ‘const class Cell’ has no member named ‘is_cellstr’
if( x.is_cellstr() ){
^
conversion.cpp: In function ‘SEXPREC* Rcpp::wrap(const T&) [with T = octave_value; SEXP = SEXPREC*]’:
conversion.cpp:180:24: warning: ‘bool octave_value::is_null_value() const’ is deprecated: [4.4]: use 'isnull' instead [-Wdeprecated-declarations]
if( val.is_null_value() ){
^
In file included from /usr/local/include/octave-5.1.0/octave/../octave/ovl.h:36:0,
from rcpp_octave.h:32,
from conversion.cpp:5:
/usr/local/include/octave-5.1.0/octave/../octave/ov.h:633:8: note: declared here
bool is_null_value (void) const
^
conversion.cpp:214:30: warning: ‘bool octave_value::is_bool_type() const’ is deprecated: [4.4]: use 'islogical' instead [-Wdeprecated-declarations]
else if ( val.is_bool_type() ){
^
In file included from /usr/local/include/octave-5.1.0/octave/../octave/ovl.h:36:0,
from rcpp_octave.h:32,
from conversion.cpp:5:
/usr/local/include/octave-5.1.0/octave/../octave/ov.h:701:8: note: declared here
bool is_bool_type (void) const
^
conversion.cpp:219:102: warning: ‘bool octave_value::is_integer_type() const’ is deprecated: [4.4]: use 'isinteger' instead [-Wdeprecated-declarations]
}else if( val.is_int32_type() || val.is_int64_type() || val.is_int16_type() || val.is_integer_type() ){
^
In file included from /usr/local/include/octave-5.1.0/octave/../octave/ovl.h:36:0,
from rcpp_octave.h:32,
from conversion.cpp:5:
/usr/local/include/octave-5.1.0/octave/../octave/ov.h:692:8: note: declared here
bool is_integer_type (void) const
^
conversion.cpp:223:30: warning: ‘bool octave_value::is_real_type() const’ is deprecated: [4.4]: use 'isreal' instead [-Wdeprecated-declarations]
}else if( val.is_real_type() ){
^
In file included from /usr/local/include/octave-5.1.0/octave/../octave/ovl.h:36:0,
from rcpp_octave.h:32,
from conversion.cpp:5:
/usr/local/include/octave-5.1.0/octave/../octave/ov.h:708:8: note: declared here
bool is_real_type (void) const
^
conversion.cpp:250:33: warning: ‘bool octave_value::is_integer_type() const’ is deprecated: [4.4]: use 'isinteger' instead [-Wdeprecated-declarations]
else if ( val.is_integer_type() ){
^
In file included from /usr/local/include/octave-5.1.0/octave/../octave/ovl.h:36:0,
from rcpp_octave.h:32,
from conversion.cpp:5:
/usr/local/include/octave-5.1.0/octave/../octave/ov.h:692:8: note: declared here
bool is_integer_type (void) const
^
conversion.cpp:255:30: warning: ‘bool octave_value::is_real_type() const’ is deprecated: [4.4]: use 'isreal' instead [-Wdeprecated-declarations]
}else if( val.is_real_type() ){
^
In file included from /usr/local/include/octave-5.1.0/octave/../octave/ovl.h:36:0,
from rcpp_octave.h:32,
from conversion.cpp:5:
/usr/local/include/octave-5.1.0/octave/../octave/ov.h:708:8: note: declared here
bool is_real_type (void) const
^
conversion.cpp:270:24: warning: ‘bool octave_value::is_map() const’ is deprecated: [4.4]: use 'isstruct' instead [-Wdeprecated-declarations]
} else if( val.is_map() ){ // Maps are converted into lists
^
In file included from /usr/local/include/octave-5.1.0/octave/../octave/ovl.h:36:0,
from rcpp_octave.h:32,
from conversion.cpp:5:
/usr/local/include/octave-5.1.0/octave/../octave/ov.h:594:8: note: declared here
bool is_map (void) const
^
conversion.cpp:307:25: warning: ‘bool octave_value::is_cell() const’ is deprecated: [4.4]: use 'iscell' instead [-Wdeprecated-declarations]
} else if( val.is_cell() ){// Cell objects are used for character vectors
^
In file included from /usr/local/include/octave-5.1.0/octave/../octave/ovl.h:36:0,
from rcpp_octave.h:32,
from conversion.cpp:5:
/usr/local/include/octave-5.1.0/octave/../octave/ov.h:541:8: note: declared here
bool is_cell (void) const
^
conversion.cpp: In function ‘T Rcpp::as(SEXP) [with T = octave_value; SEXP = SEXPREC*]’:
conversion.cpp:471:50: error: invalid initialization of reference of type ‘const octave_value&’ from expression of type ‘octave_value_list’
const octave_value& ol = as<octave_value_list>(x);
^
/usr/lib/R/etc/Makeconf:168: recipe for target 'conversion.o' failed
make: *** [conversion.o] Error 1
ERROR: compilation failed for package ‘RcppOctave’
─ removing ‘/tmp/RtmpGFexmb/Rinst61567e75864/RcppOctave’
-----------------------------------
ERROR: package installation failed
Error in processx::run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout), :
System command error