Compilation errors Ubuntu 16.04 R3.6

[slagtermaarten]

Hi, thanks for developing this package! I've tried all the installation commands listed here: #296, but to no avail. Am I missing something?

install.packages('stringi') trying URL 'https://cran.rstudio.com/src/contrib/stringi_1.4.6.tar.gz' Content type 'application/x-gzip' length 7284354 bytes (6.9 MB)

downloaded 6.9 MB

• installing source package ‘stringi’ ... package ‘stringi’ successfully unpacked and MD5 sums checked using staged installation checking for R_HOME... /home/m.slagter/conda/envs/r36/lib/R checking for R... /home/m.slagter/conda/envs/r36/lib/R/bin/R checking for endianness... little checking for R >= 3.1.0 for C++11 use... yes checking for R < 3.4.0 for CXX1X flag use... no checking for cat... /bin/cat checking for local ICUDT_DIR... icu61/data checking for gcc... x86_64-conda_cos6-linux-gnu-cc 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 x86_64-conda_cos6-linux-gnu-cc accepts -g... yes checking for x86_64-conda_cos6-linux-gnu-cc option to accept ISO C89... none needed checking how to run the C preprocessor... x86_64-conda_cos6-linux-gnu-cc -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 elf.h usability... yes checking elf.h presence... yes checking for elf.h... yes checking whether we are using the GNU C++ compiler... yes checking whether x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 accepts -g... yes checking whether the C++ compiler supports the long long type... yes checking whether the compiler implements namespaces... yes checking whether the compiler supports Standard Template Library... yes checking whether std::map is available... yes checking for pkg-config... /usr/bin/pkg-config checking with pkg-config for the system ICU4C... 55.1 checking for ICU4C >= 55... yes checking for additional required CPPFLAGS, LDFLAGS, and LIBS... done checking whether we may build an ICU4C-based project... yes checking programmatically for sufficient U_ICU_VERSION_MAJOR_NUM... yes checking programmatically if U_CHARSET_IS_UTF8 is defined and set... no checking for available ICU data library (ucnv, uloc, utrans)... yes checking for available ICU data library (ucol)... yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/uconfig_local.h config.status: creating src/install.libs.R

*** stringi configure summary: ICU_FOUND=1 STRINGI_CXXSTD=CXX_STD=CXX11 STRINGI_CFLAGS= -fpic STRINGI_CPPFLAGS=-I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H STRINGI_CXXFLAGS= -fpic STRINGI_LDFLAGS=-L/usr/lib/x86_64-linux-gnu STRINGI_LIBS=-licui18n -licuuc -licudata

*** compiler settings used: CC=x86_64-conda_cos6-linux-gnu-cc LD=x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/m.slagter/conda/envs/r36/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1580939145230/work=/usr/local/src/conda/r-base-3.6.2 -fdebug-prefix-map=/home/m.slagter/conda/envs/r36=/usr/local/src/conda-prefix -fpic CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/m.slagter/conda/envs/r36/include -I/home/m.slagter/conda/envs/r36/include -Wl,-rpath-link,/home/m.slagter/conda/envs/r36/lib -UDEBUG -DNDEBUG CXX=x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/m.slagter/conda/envs/r36/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1580939145230/work=/usr/local/src/conda/r-base-3.6.2 -fdebug-prefix-map=/home/m.slagter/conda/envs/r36=/usr/local/src/conda-prefix -fpic LDFLAGS= LIBS=

* libs x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I"/home/m.slagter/conda/envs/r36/lib/R/include" -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/m.slagter/conda/envs/r36/include -I/home/m.slagter/conda/envs/r36/include -Wl,-rpath-link,/home/m.slagter/conda/envs/r36/lib -fpic -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/m.slagter/conda/envs/r36/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1580939145230/work=/usr/local/src/conda/r-base-3.6.2 -fdebug-prefix-map=/home/m.slagter/conda/envs/r36=/usr/local/src/conda-prefix -c stri_brkiter.cpp -o stri_brkiter.o In file included from /DATA/users/m.slagter/conda.bu/envs/r36/x86_64-conda_cos6-linux-gnu/sysroot/usr/include/math.h:71:0, from /DATA/users/m.slagter/conda.bu/envs/r36/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:45, from /home/m.slagter/conda/envs/r36/lib/R/include/R.h:50, from stri_external.h:67, from stri_stringi.h:36, from stri_brkiter.cpp:32: /usr/include/x86_64-linux-gnu/bits/mathcalls.h:63:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (cos,, (Mdouble __x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:65:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (sin,, (Mdouble __x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:81:22: error: 'sincos' has not been declared MATHDECL_VEC (void,sincos,, ^~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:81:29: error: expected identifier before ',' token MATHDECL_VEC (void,sincos,, ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:82:3: error: expected identifier before '(' token (Mdouble __x, Mdouble sinx, Mdouble *cosx)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:82:57: error: expected constructor, destructor, or type conversion before ';' token (Mdouble x, Mdouble *sinx, Mdouble cosx)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:100:16: error: expected constructor, destructor, or type conversion before '(' token __MATHCALL_VEC (exp,, (Mdouble x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:109:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (log,, (Mdouble __x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:153:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (pow,, (Mdouble x, Mdouble y)); ^ In file included from /DATA/users/m.slagter/conda.bu/envs/r36/x86_64-conda_cos6-linux-gnu/sysroot/usr/include/math.h:94:0, from /DATA/users/m.slagter/conda.bu/envs/r36/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:45, from /home/m.slagter/conda/envs/r36/lib/R/include/R.h:50, from stri_external.h:67, from stri_stringi.h:36, from stri_brkiter.cpp:32: /usr/include/x86_64-linux-gnu/bits/mathcalls.h:63:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (cos,, (Mdouble __x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:65:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (sin,, (Mdouble __x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:81:22: error: 'sincos' has not been declared MATHDECL_VEC (void,sincos,, ^~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:81:29: error: expected identifier before ',' token MATHDECL_VEC (void,sincos,, ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:82:3: error: expected identifier before '(' token (Mdouble __x, Mdouble sinx, Mdouble *cosx)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:82:57: error: expected constructor, destructor, or type conversion before ';' token (Mdouble x, Mdouble *sinx, Mdouble cosx)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:100:16: error: expected constructor, destructor, or type conversion before '(' token __MATHCALL_VEC (exp,, (Mdouble x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:109:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (log,, (Mdouble __x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:153:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (pow,, (Mdouble x, Mdouble y)); ^ In file included from /DATA/users/m.slagter/conda.bu/envs/r36/x86_64-conda_cos6-linux-gnu/sysroot/usr/include/math.h:141:0, from /DATA/users/m.slagter/conda.bu/envs/r36/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:45, from /home/m.slagter/conda/envs/r36/lib/R/include/R.h:50, from stri_external.h:67, from stri_stringi.h:36, from stri_brkiter.cpp:32: /usr/include/x86_64-linux-gnu/bits/mathcalls.h:63:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (cos,, (Mdouble __x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:65:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (sin,, (Mdouble __x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:81:22: error: 'sincos' has not been declared MATHDECL_VEC (void,sincos,, ^~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:81:29: error: expected identifier before ',' token MATHDECL_VEC (void,sincos,, ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:82:3: error: expected identifier before '(' token (Mdouble __x, Mdouble sinx, Mdouble *cosx)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:82:57: error: expected constructor, destructor, or type conversion before ';' token (Mdouble x, Mdouble *sinx, Mdouble *cosx)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:100:16: error: expected constructor, destructor, or type conversion before '(' token __MATHCALL_VEC (exp,, (Mdouble x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:109:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (log,, (Mdouble __x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:153:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (pow,, (Mdouble x, Mdouble y)); ^ In file included from /home/m.slagter/conda/envs/r36/lib/R/include/R.h:50:0, from stri_external.h:67, from stri_stringi.h:36, from stri_brkiter.cpp:32: /DATA/users/m.slagter/conda.bu/envs/r36/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:180:11: error: '::cos' has not been declared using ::cos; ^~~ /DATA/users/m.slagter/conda.bu/envs/r36/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:218:11: error: '::exp' has not been declared using ::exp; ^~~ /DATA/users/m.slagter/conda.bu/envs/r36/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:334:11: error: '::log' has not been declared using ::log; ^~~ /DATA/users/m.slagter/conda.bu/envs/r36/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:384:11: error: '::pow' has not been declared using ::pow; ^~~ /DATA/users/m.slagter/conda.bu/envs/r36/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:421:11: error: '::sin' has not been declared using ::sin; ^~~ make: *** [/home/m.slagter/conda/envs/r36/lib/R/etc/Makeconf:176: stri_brkiter.o] Error 1 ERROR: compilation failed for package ‘stringi’

• removing ‘/DATA/users/m.slagter/conda.bu/envs/r36/lib/R/library/stringi’
• restoring previous ‘/DATA/users/m.slagter/conda.bu/envs/r36/lib/R/library/stringi’

The downloaded source packages are in ‘/tmp/RtmpIaXvdM/downloaded_packages’ Warning message: In install.packages("stringi") : installation of package ‘stringi’ had non-zero exit status

[gagolews]

Most likely, your build chain is broken. Anaconda seems to be ill-configured. I reckon you are unable to build other packages too (e.g., Rcpp), so this is not stringi-related issues

I recommend you edit the Makeconf file /path_to_anaconda/lib/R/etc/Makeconf, e.g., /opt/anaconda3/lib/R/etc/Makeconf and replace all occurrences of x86_64-conda_cos6-linux-gnu-cc with gcc as well as x86_64-conda_cos6-linux-gnu-c++ with g++

[slagtermaarten]

Thanks for your help!

I checked the Makeconf file and it didn't list x86_64-conda_cos6-linux-gnu-cc nor x86_64-conda_cos6-linux-gnu-c++. I reinstalled conda, made a new environment with R3.6 in it and tried to install Rcpp, which went fine. But stringi once again gave problems:

install.packages('stringi') trying URL 'https://cran.rstudio.com/src/contrib/stringi_1.4.6.tar.gz' Content type 'application/x-gzip' length 7284354 bytes (6.9 MB)

downloaded 6.9 MB

• installing source package ‘stringi’ ... package ‘stringi’ successfully unpacked and MD5 sums checked using staged installation checking for R_HOME... /DATA/users/m.slagter/miniconda3/envs/r36/lib/R checking for R... /DATA/users/m.slagter/miniconda3/envs/r36/lib/R/bin/R checking for endianness... little checking for R >= 3.1.0 for C++11 use... yes checking for R < 3.4.0 for CXX1X flag use... no checking for cat... /bin/cat checking for local ICUDT_DIR... icu61/data checking for gcc... x86_64-conda_cos6-linux-gnu-cc 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 x86_64-conda_cos6-linux-gnu-cc accepts -g... yes checking for x86_64-conda_cos6-linux-gnu-cc option to accept ISO C89... none needed checking how to run the C preprocessor... /DATA/users/m.slagter/miniconda3/envs/r36/bin/x86_64-conda_cos6-linux-gnu-cpp 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 elf.h usability... yes checking elf.h presence... yes checking for elf.h... yes checking whether we are using the GNU C++ compiler... yes checking whether x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 accepts -g... yes checking whether the C++ compiler supports the long long type... yes checking whether the compiler implements namespaces... yes checking whether the compiler supports Standard Template Library... yes checking whether std::map is available... yes checking for pkg-config... /usr/bin/pkg-config checking with pkg-config for the system ICU4C... 55.1 checking for ICU4C >= 55... yes checking for additional required CPPFLAGS, LDFLAGS, and LIBS... done checking whether we may build an ICU4C-based project... yes checking programmatically for sufficient U_ICU_VERSION_MAJOR_NUM... yes checking programmatically if U_CHARSET_IS_UTF8 is defined and set... no checking for available ICU data library (ucnv, uloc, utrans)... yes checking for available ICU data library (ucol)... yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/uconfig_local.h config.status: creating src/install.libs.R

*** stringi configure summary: ICU_FOUND=1 STRINGI_CXXSTD=CXX_STD=CXX11 STRINGI_CFLAGS= -fpic STRINGI_CPPFLAGS=-I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H STRINGI_CXXFLAGS= -fpic STRINGI_LDFLAGS=-L/usr/lib/x86_64-linux-gnu STRINGI_LIBS=-licui18n -licuuc -licudata

*** compiler settings used: CC=x86_64-conda_cos6-linux-gnu-cc LD=x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /DATA/users/m.slagter/miniconda3/envs/r36/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1587480512619/work=/usr/local/src/conda/r-base-3.6.3 -fdebug-prefix-map=/DATA/users/m.slagter/miniconda3/envs/r36=/usr/local/src/conda-prefix -fpic CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /DATA/users/m.slagter/miniconda3/envs/r36/include -I/DATA/users/m.slagter/miniconda3/envs/r36/include -Wl,-rpath-link,/DATA/users/m.slagter/miniconda3/envs/r36/lib -UDEBUG -DNDEBUG CXX=x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /DATA/users/m.slagter/miniconda3/envs/r36/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1587480512619/work=/usr/local/src/conda/r-base-3.6.3 -fdebug-prefix-map=/DATA/users/m.slagter/miniconda3/envs/r36=/usr/local/src/conda-prefix -fpic LDFLAGS= LIBS=

* libs x86_64-conda_cos6-linux-gnu-c++ -std=gnu++11 -I"/DATA/users/m.slagter/miniconda3/envs/r36/lib/R/include" -DNDEBUG -I. -I/usr/include/x86_64-linux-gnu -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /DATA/users/m.slagter/miniconda3/envs/r36/include -I/DATA/users/m.slagter/miniconda3/envs/r36/include -Wl,-rpath-link,/DATA/users/m.slagter/miniconda3/envs/r36/lib -fpic -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /DATA/users/m.slagter/miniconda3/envs/r36/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1587480512619/work=/usr/local/src/conda/r-base-3.6.3 -fdebug-prefix-map=/DATA/users/m.slagter/miniconda3/envs/r36=/usr/local/src/conda-prefix -c stri_brkiter.cpp -o stri_brkiter.o In file included from /DATA/users/m.slagter/miniconda3/envs/r36/x86_64-conda_cos6-linux-gnu/sysroot/usr/include/math.h:71:0, from /DATA/users/m.slagter/miniconda3/envs/r36/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:45, from /DATA/users/m.slagter/miniconda3/envs/r36/lib/R/include/R.h:50, from stri_external.h:67, from stri_stringi.h:36, from stri_brkiter.cpp:32: /usr/include/x86_64-linux-gnu/bits/mathcalls.h:63:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (cos,, (Mdouble __x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:65:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (sin,, (Mdouble __x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:81:22: error: 'sincos' has not been declared MATHDECL_VEC (void,sincos,, ^~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:81:29: error: expected identifier before ',' token MATHDECL_VEC (void,sincos,, ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:82:3: error: expected identifier before '(' token (Mdouble __x, Mdouble sinx, Mdouble *cosx)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:82:57: error: expected constructor, destructor, or type conversion before ';' token (Mdouble x, Mdouble *sinx, Mdouble cosx)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:100:16: error: expected constructor, destructor, or type conversion before '(' token __MATHCALL_VEC (exp,, (Mdouble x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:109:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (log,, (Mdouble __x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:153:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (pow,, (Mdouble x, Mdouble y)); ^ In file included from /DATA/users/m.slagter/miniconda3/envs/r36/x86_64-conda_cos6-linux-gnu/sysroot/usr/include/math.h:94:0, from /DATA/users/m.slagter/miniconda3/envs/r36/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:45, from /DATA/users/m.slagter/miniconda3/envs/r36/lib/R/include/R.h:50, from stri_external.h:67, from stri_stringi.h:36, from stri_brkiter.cpp:32: /usr/include/x86_64-linux-gnu/bits/mathcalls.h:63:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (cos,, (Mdouble __x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:65:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (sin,, (Mdouble __x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:81:22: error: 'sincos' has not been declared MATHDECL_VEC (void,sincos,, ^~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:81:29: error: expected identifier before ',' token MATHDECL_VEC (void,sincos,, ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:82:3: error: expected identifier before '(' token (Mdouble __x, Mdouble sinx, Mdouble *cosx)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:82:57: error: expected constructor, destructor, or type conversion before ';' token (Mdouble x, Mdouble *sinx, Mdouble cosx)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:100:16: error: expected constructor, destructor, or type conversion before '(' token __MATHCALL_VEC (exp,, (Mdouble x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:109:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (log,, (Mdouble __x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:153:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (pow,, (Mdouble x, Mdouble y)); ^ In file included from /DATA/users/m.slagter/miniconda3/envs/r36/x86_64-conda_cos6-linux-gnu/sysroot/usr/include/math.h:141:0, from /DATA/users/m.slagter/miniconda3/envs/r36/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:45, from /DATA/users/m.slagter/miniconda3/envs/r36/lib/R/include/R.h:50, from stri_external.h:67, from stri_stringi.h:36, from stri_brkiter.cpp:32: /usr/include/x86_64-linux-gnu/bits/mathcalls.h:63:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (cos,, (Mdouble __x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:65:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (sin,, (Mdouble __x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:81:22: error: 'sincos' has not been declared MATHDECL_VEC (void,sincos,, ^~ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:81:29: error: expected identifier before ',' token MATHDECL_VEC (void,sincos,, ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:82:3: error: expected identifier before '(' token (Mdouble __x, Mdouble sinx, Mdouble *cosx)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:82:57: error: expected constructor, destructor, or type conversion before ';' token (Mdouble x, Mdouble *sinx, Mdouble *cosx)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:100:16: error: expected constructor, destructor, or type conversion before '(' token __MATHCALL_VEC (exp,, (Mdouble x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:109:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (log,, (Mdouble __x)); ^ /usr/include/x86_64-linux-gnu/bits/mathcalls.h:153:16: error: expected constructor, destructor, or type conversion before '(' token MATHCALL_VEC (pow,, (Mdouble x, Mdouble y)); ^ In file included from /DATA/users/m.slagter/miniconda3/envs/r36/lib/R/include/R.h:50:0, from stri_external.h:67, from stri_stringi.h:36, from stri_brkiter.cpp:32: /DATA/users/m.slagter/miniconda3/envs/r36/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:180:11: error: '::cos' has not been declared using ::cos; ^~~ /DATA/users/m.slagter/miniconda3/envs/r36/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:218:11: error: '::exp' has not been declared using ::exp; ^~~ /DATA/users/m.slagter/miniconda3/envs/r36/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:334:11: error: '::log' has not been declared using ::log; ^~~ /DATA/users/m.slagter/miniconda3/envs/r36/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:384:11: error: '::pow' has not been declared using ::pow; ^~~ /DATA/users/m.slagter/miniconda3/envs/r36/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/cmath:421:11: error: '::sin' has not been declared using ::sin; ^~~ make: *** [/DATA/users/m.slagter/miniconda3/envs/r36/lib/R/etc/Makeconf:176: stri_brkiter.o] Error 1 ERROR: compilation failed for package ‘stringi’

• removing ‘/DATA/users/m.slagter/miniconda3/envs/r36/lib/R/library/stringi’
• restoring previous ‘/DATA/users/m.slagter/miniconda3/envs/r36/lib/R/library/stringi’

The downloaded source packages are in ‘/tmp/RtmpVkqaTi/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning message: In install.packages("stringi") : installation of package ‘stringi’ had non-zero exit status

[slagtermaarten]

Luckily, I can use the precompiled stringi as well.

[gagolews]

How about /DATA/users/m.slagter/miniconda3/envs/r36/lib/R/etc/Makeconf ?

[slagtermaarten]

Yes! Once again, thanks for your help.

After having changed the file, I now get this in R 3.6

install.packages('stringi') trying URL 'https://cran.rstudio.com/src/contrib/stringi_1.4.6.tar.gz' Content type 'application/x-gzip' length 7284354 bytes (6.9 MB)

downloaded 6.9 MB

• installing source package ‘stringi’ ... package ‘stringi’ successfully unpacked and MD5 sums checked using staged installation checking for R_HOME... /DATA/users/m.slagter/miniconda3/envs/r36/lib/R checking for R... /DATA/users/m.slagter/miniconda3/envs/r36/lib/R/bin/R checking for endianness... little checking for R >= 3.1.0 for C++11 use... yes checking for R < 3.4.0 for CXX1X flag use... no checking for cat... /bin/cat checking for local ICUDT_DIR... icu61/data checking for gcc... gcc checking whether the C compiler works... no configure: error: in /tmp/Rtmp9BPDT3/R.INSTALL6d731fbee20d/stringi': configure: error: C compiler cannot create executables Seeconfig.log' for more details ERROR: configuration failed for package ‘stringi’
• removing ‘/DATA/users/m.slagter/miniconda3/envs/r36/lib/R/library/stringi’
• restoring previous ‘/DATA/users/m.slagter/miniconda3/envs/r36/lib/R/library/stringi’

The downloaded source packages are in ‘/tmp/Rtmp7HGSf7/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning message: In install.packages("stringi") : installation of package ‘stringi’ had non-zero exit status

[gagolews]

The next question is whether you have gcc/g++ installed, and so on, and so forth...

Anyway, this is not really related to stringi, but your local system config...