Hi I am having an issue installing Rcpp package:
I tried install.packages("Rcpp",dependecies=F) also tried with T but same error:
- installing source package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -include /usr/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp -I /usr/lib/R/site-library/StanHeaders/include -I /home/biostat_laptop/R/x86_64-pc-linux-gnu-library/3.6/RcppEigen/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api.cpp -o api.o
In file included from :
/usr/lib/R/site-library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:10: fatal error: Eigen/Dense: No such file or directory
13 | #include <Eigen/Dense>
| ^~~~~~~~~~~~~
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:177: api.o] Error 1
ERROR: compilation failed for package ‘Rcpp’ - removing ‘/home/biostat_laptop/R/x86_64-pc-linux-gnu-library/3.6/Rcpp’
Warning in install.packages :
installation of package ‘Rcpp’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmpove0nY/downloaded_packages’
I navigated to the Makeconf file BUT NOT SURE what to change there. The contents are as follows:
etc/Makeconf. Generated from Makeconf.in by configure.
${R_HOME}/etc/Makeconf
R was configured using the following call
(not including env. vars and site configuration)
configure '--prefix=/usr' '--with-cairo' '--with-jpeglib' '--with-readline' '--with-tcltk' '--with-system-bzlib' '--with-system-pcre' '--with-system-zlib' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share/R/share' '--includedir=/usr/share/R/include' '--with-blas' '--with-lapack' '--enable-R-profiling' '--enable-R-shlib' '--enable-memory-profiling' '--without-recommended-packages' '--build' 'x86_64-linux-gnu' 'build_alias=x86_64-linux-gnu' 'R_PRINTCMD=/usr/bin/lpr' 'R_PAPERSIZE=letter' 'TAR=/bin/tar' 'R_BROWSER=xdg-open' 'LIBnn=lib' 'JAVA_HOME=/usr/lib/jvm/default-java' 'R_SHELL=/bin/bash' 'CC=gcc -std=gnu99' 'CFLAGS=-g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g' 'LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro' 'CPPFLAGS=' 'FC=gfortran' 'FCFLAGS=-g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong' 'CXX=g++' 'CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g'
This fails if it contains spaces, or if it is quoted
include $(R_SHARE_DIR)/make/vars.mk
AR = ar
BLAS_LIBS = -lblas
C_VISIBILITY = -fvisibility=hidden
CC = gcc -std=gnu99
CFLAGS = -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g $(LTO)
CPICFLAGS = -fpic
CPPFLAGS =
CXX = g++ -std=gnu++11
Not used by anything in R, in particular not for the .cc.d rule
CXXCPP = (CXX) -E
CXXFLAGS = -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g (LTO)
CXXPICFLAGS = -fpic
CXX98 = g++
CXX98FLAGS = -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g (LTO)
CXX98PICFLAGS = -fpic
CXX98STD = -std=gnu++98
CXX11 = g++
CXX11FLAGS = -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g (LTO)
CXX11PICFLAGS = -fpic
CXX11STD = -std=gnu++11
CXX14 = g++
CXX14FLAGS = -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g (LTO)
CXX14PICFLAGS = -fpic
CXX14STD = -std=gnu++14
CXX17 = g++
CXX17FLAGS = -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g (LTO)
CXX17PICFLAGS = -fpic
CXX17STD = -std=gnu++17
CXX_VISIBILITY = -fvisibility=hidden
DYLIB_EXT = .so
DYLIB_LD = (CC)
DYLIB_LDFLAGS = -shared -fopenmp# (CFLAGS) (CPICFLAGS)
DYLIB_LINK = (DYLIB_LD) (DYLIB_LDFLAGS) (LDFLAGS)
ECHO = echo
ECHO_C =
ECHO_N = -n
ECHO_T =
F_VISIBILITY = -fvisibility=hidden
FC is the compiler used for all Fortran as from R 3.6.0
FC = gfortran
FCFLAGS = -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong $(LTO)
additional libs needed when linking with $(FC), e.g. on some Oracle compilers
FCLIBS_XTRA =
FFLAGS = -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong $(LTO)
FLIBS = -lgfortran -lm -lquadmath
FPICFLAGS = -fpic
FOUNDATION_CPPFLAGS =
FOUNDATION_LIBS =
JAR = /usr/lib/jvm/default-java/bin/jar
JAVA = /usr/lib/jvm/default-java/bin/java
JAVAC = /usr/lib/jvm/default-java/bin/javac
JAVAH =
JAVA_HOME might be used in the next three.
They are for packages 'JavaGD' and 'rJava'
JAVA_HOME = /usr/lib/jvm/default-java
JAVA_CPPFLAGS = -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JAVA_LIBS = -L$(JAVA_HOME)/lib/server -ljvm
JAVA_LD_LIBRARY_PATH = $(JAVA_HOME)/lib/server
LAPACK_LIBS = -llapack
LDFLAGS = -Wl,-Bsymbolic-functions -Wl,-z,relro
we only need this is if it is external, as otherwise link to R
LIBINTL=
LIBM = -lm
LIBR0 = -L"(R_HOME)/lib(R_ARCH)"
LIBR1 = -lR
LIBR = -L"(R_HOME)/lib(R_ARCH)" -lR
LIBS = -lpcre2-8 -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -licuuc -licui18n
needed by R CMD config
LIBnn = lib
LIBTOOL = (SHELL) "(R_HOME)/bin/libtool"
LTO =
needed to build applications linking to static libR
MAIN_LD = (CC)
MAIN_LDFLAGS = -Wl,--export-dynamic -fopenmp
MAIN_LINK = (MAIN_LD) (MAIN_LDFLAGS) (LDFLAGS)
MKINSTALLDIRS = "(R_HOME)/bin/mkinstalldirs"
OBJC =
OBJCFLAGS = (LTO)
OBJC_LIBS =
OBJCXX =
R_ARCH =
RANLIB = ranlib
SAFE_FFLAGS = -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -msse2 -mfpmath=sse
SED = /bin/sed
SHELL = /bin/bash
SHLIB_CFLAGS =
SHLIB_CXXFLAGS =
SHLIB_CXXLD = (CXX)
SHLIB_CXXLDFLAGS = -shared
SHLIB_CXX98LD = (CXX98) (CXX98STD)
SHLIB_CXX98LDFLAGS = -shared
SHLIB_CXX11LD = (CXX11) (CXX11STD)
SHLIB_CXX11LDFLAGS = -shared
SHLIB_CXX14LD = (CXX14) (CXX14STD)
SHLIB_CXX14LDFLAGS = -shared
SHLIB_CXX17LD = (CXX17) (CXX17STD)
SHLIB_CXX17LDFLAGS = -shared
SHLIB_EXT = .so
SHLIB_FFLAGS =
SHLIB_LD = (CC)
SHLIB_LDFLAGS = -shared# (CFLAGS) (CPICFLAGS)
SHLIB_LIBADD =
We want to ensure libR is picked up from $(R_HOME)/lib
before e.g. /usr/local/lib if a version is already installed.
SHLIB_LINK = (SHLIB_LD) (SHLIB_LDFLAGS) (LIBR0) (LDFLAGS)
SHLIB_OPENMP_CFLAGS = -fopenmp
SHLIB_OPENMP_CXXFLAGS = -fopenmp
SHLIB_OPENMP_FFLAGS = -fopenmp
STRIP_STATIC_LIB = strip --strip-debug
STRIP_SHARED_LIB = strip --strip-unneeded
TCLTK_CPPFLAGS = -I/usr/include/tcl8.6 -I/usr/include/tcl8.6
TCLTK_LIBS = -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -L/usr/lib/x86_64-linux-gnu -ltk8.6 -lX11 -lXss -lXext
YACC = bison -y
Legacy settings: no longer used by R as of 3.6.0
Setting FC often sets F77 (on Solaris make even if set)
so must follow FC in this file.
F77 = gfortran
FCPICFLAGS = -fpic
F77_VISIBILITY = -fvisibility=hidden
SHLIB_FCLD = $(FC)
SHLIB_FCLDFLAGS = -shared
SHLIB_OPENMP_FCFLAGS = -fopenmp
for linking to libR.a
STATIC_LIBR = # -Wl,--whole-archive "(R_HOME)/lib(R_ARCH)/libR.a" -Wl,--no-whole-archive (BLAS_LIBS) (FLIBS) (LIBINTL) -lreadline (LIBS)
These are recorded as macros for legacy use in packages
set on AIX, formerly for old glibc (-D__NO_MATH_INLINES)
R_XTRA_CFLAGS =
was formerly set on HP-UX
R_XTRA_CPPFLAGS = -I"$(R_INCLUDE_DIR)" -DNDEBUG
currently unset
R_XTRA_CXXFLAGS =
used for gfortran in R > 3.6.0
R_XTRA_FFLAGS = -fno-optimize-sibling-calls
SHLIB_CFLAGS SHLIB_CXXFLAGS SHLIB_FFLAGS are apparently currently unused
SHLIB_CXXFLAGS is undocumented, there is no SHLIB_FCFLAGS
ALL_CFLAGS = (PKG_CFLAGS) (CPICFLAGS) (SHLIB_CFLAGS) (CFLAGS)
ALL_CPPFLAGS = -I"(R_INCLUDE_DIR)" -DNDEBUG (PKG_CPPFLAGS) (CLINK_CPPFLAGS) (CPPFLAGS)
ALL_CXXFLAGS = (PKG_CXXFLAGS) (CXXPICFLAGS) (SHLIB_CXXFLAGS) (CXXFLAGS)
ALL_OBJCFLAGS = (PKG_OBJCFLAGS) (CPICFLAGS) (SHLIB_CFLAGS) (OBJCFLAGS)
ALL_OBJCXXFLAGS = (PKG_OBJCXXFLAGS) (CXXPICFLAGS) (SHLIB_CXXFLAGS) (OBJCXXFLAGS)
ALL_FFLAGS = -fno-optimize-sibling-calls (PKG_FFLAGS) (FPICFLAGS) (SHLIB_FFLAGS) (FFLAGS)
can be overridden by R CMD SHLIB
P_FCFLAGS = (PKG_FFLAGS) ALL_FCFLAGS = -fno-optimize-sibling-calls (P_FCFLAGS) (FPICFLAGS) (SHLIB_FFLAGS) $(FCFLAGS)
LIBR here as a couple of packages use this without SHLIB_LINK
ALL_LIBS = (PKG_LIBS) (SHLIB_LIBADD) (LIBR)# (LIBINTL)
.SUFFIXES:
.SUFFIXES: .c .cc .cpp .d .f .f90 .f95 .m .mm .M .o
.c.o:
(CC) (ALL_CPPFLAGS) (ALL_CFLAGS) -c < -o @
.c.d:
@echo "making @ from <"
@(CC) -MM (ALL_CPPFLAGS) < > @
.m.d:
@echo > @
.cc.o:
(CXX) (ALL_CPPFLAGS) (ALL_CXXFLAGS) -c < -o @
.cpp.o:
(CXX) (ALL_CPPFLAGS) (ALL_CXXFLAGS) -c < -o @
.cc.d:
@echo "making @ from <"
@(CXX) -M (ALL_CPPFLAGS) < > @
.cpp.d:
@echo "making @ from <"
@(CXX) -M (ALL_CPPFLAGS) < > @
.m.o:
(OBJC) (ALL_CPPFLAGS) (ALL_OBJCFLAGS) -c < -o @
.mm.o:
(OBJCXX) (ALL_CPPFLAGS) (ALL_OBJCXXFLAGS) -c < -o @
.M.o:
(OBJCXX) (ALL_CPPFLAGS) (ALL_OBJCXXFLAGS) -c < -o @
.f.o:
(FC) (ALL_FFLAGS) -c < -o $@
@FCFLAGS_f9x@ are flags needed to recognise the extensions
.f95.o:
(FC) (ALL_FCFLAGS) -c < -o @
.f90.o:
(FC) (ALL_FCFLAGS) -c < -o @