search

gagolews / stringi

Fast and portable character string processing in R (with the Unicode ICU)
https://stringi.gagolewski.com/
Other
304 stars 44 forks source link

Failure to compile on Debian container #441

Closed offbynull closed 3 years ago

offbynull commented 3 years ago

I'm getting an error during installation. I'm assuming it's complaining about a missing feature in my C++ compiler (long long support), but AFAIK my compiler isn't missing that feature. Any tips on how I can debug this further?

Here's my C++ compiler:

c++ (crosstool-NG 1.24.0.133_b0863d8_dirty) 9.3.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

g++ (crosstool-NG 1.24.0.133_b0863d8_dirty) 9.3.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Here's the error that keeps displaying:

* installing *source* package ‘stringi’ ...
** package ‘stringi’ successfully unpacked and MD5 sums checked
** using staged installation
checking for R_HOME... /opt/conda/envs/netrias/lib/R
checking for R... /opt/conda/envs/netrias/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... icu69/data
checking for x86_64-conda-linux-gnu-gcc... x86_64-conda-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-linux-gnu-cc accepts -g... yes
checking for x86_64-conda-linux-gnu-cc option to accept ISO C89... none needed
checking how to run the C preprocessor... /opt/conda/envs/netrias/bin/x86_64-conda-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-linux-gnu-c++ -std=gnu++11 accepts -g... yes
checking whether the C++ compiler supports the long long type... no
*** Trying with C++11 compiler disabled.
checking for local ICUDT_DIR... icu55/data
checking for x86_64-conda-linux-gnu-gcc... x86_64-conda-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-linux-gnu-cc accepts -g... yes
checking for x86_64-conda-linux-gnu-cc option to accept ISO C89... none needed
checking how to run the C preprocessor... /opt/conda/envs/netrias/bin/x86_64-conda-linux-gnu-cpp
checking for grep that handles long lines and -e... (cached) /bin/grep
checking for egrep... (cached) /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for memory.h... (cached) yes
checking for strings.h... (cached) yes
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for unistd.h... (cached) yes
checking for elf.h... (cached) yes
checking whether we are using the GNU C++ compiler... yes
checking whether x86_64-conda-linux-gnu-c++ -std=gnu++11 accepts -g... yes
checking whether the C++ compiler supports the long long type... no

*** *********************************************************************
*** stringi cannot be built with these settings in place.
*** See the INSTALL file for the solutions to the most common problems.
*** Moreover, explore the list of open and closed issues at
*** https://github.com/gagolews/stringi/issues/
*** *********************************************************************
gagolews commented 3 years ago

The test here is very simple: either what follows can be compiled or not:

#include <iostream>
using namespace std;
int main() {
    long long x = 1;
    cout << x << endl;
    cout << 1LL << 1ULL << endl;
    cout << 9223372036854775807LL << 18446744073709551615ULL << endl;
    return 0;
}

This is not the case with your configuration.

I suggest you update your configuration in <R_inst_dir>/etc/Makeconf see also https://cran.r-project.org/doc/manuals/r-release/R-admin.html

offbynull commented 3 years ago

Below is the output of the test C++ code you posted above, the C++ compiler being referenced by Makeconf, and Makeconf itself. I'm not seeing anything out of the ordinary here?

(base) root@d7f466414776:/source# conda run -n netrias x86_64-conda-linux-gnu-c++ -c ~/test.cpp
(base) root@d7f466414776:/source# ls -al
total 16
drwxr-xr-x 3 root root 4096 Jun 21 16:03 .
drwxr-xr-x 1 root root 4096 Jun 21 15:01 ..
drwxr-xr-x 2 root root 4096 Jun 21 15:03 .empty
-rw-r--r-- 1 root root 3096 Jun 21 16:03 test.o
(base) root@d7f466414776:/source# conda run -n netrias x86_64-conda-linux-gnu-c++ --version
x86_64-conda-linux-gnu-c++ (crosstool-NG 1.24.0.133_b0863d8_dirty) 9.3.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
(base) root@d7f466414776:/source# cat /opt/conda/envs/netrias/lib/R/etc/Makeconf
R_HOME=/opt/conda/envs/netrias/lib/R
# 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=/opt/conda/envs/netrias' '--host=x86_64-conda-linux-gnu' '--build=x86_64-conda-linux-gnu' '--enable-shared' '--enable-R-shlib' '--with-blas=-lblas' '--with-lapack=-llapack' '--disable-prebuilt-html' '--enable-memory-profiling' '--with-tk-config=/opt/conda/envs/netrias/lib/tkConfig.sh' '--with-tcl-config=/opt/conda/envs/netrias/lib/tclConfig.sh' '--with-x' '--with-pic' '--with-cairo' '--with-readline' '--with-recommended-packages=no' '--without-libintl-prefix' 'LIBnn=lib' 'build_alias=x86_64-conda-linux-gnu' 'host_alias=x86_64-conda-linux-gnu' 'PKG_CONFIG_PATH=/opt/conda/envs/netrias/lib/pkgconfig' 'CC=x86_64-conda-linux-gnu-cc' 'CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/envs/netrias/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1607284869564/work=/usr/local/src/conda/r-base-4.0.3 -fdebug-prefix-map=/opt/conda/envs/netrias=/usr/local/src/conda-prefix' 'LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/opt/conda/envs/netrias/lib -Wl,-rpath-link,/opt/conda/envs/netrias/lib -L/opt/conda/envs/netrias/lib -Wl,-rpath-link,/opt/conda/envs/netrias/lib' 'CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/envs/netrias/include -I/opt/conda/envs/netrias/include -Wl,-rpath-link,/opt/conda/envs/netrias/lib' 'CPP=/home/conda/feedstock_root/build_artifacts/r-base-split_1607284869564/_build_env/bin/x86_64-conda-linux-gnu-cpp' 'FC=x86_64-conda-linux-gnu-gfortran' 'CXX=x86_64-conda-linux-gnu-c++' 'CXXFLAGS=-fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/envs/netrias/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1607284869564/work=/usr/local/src/conda/r-base-4.0.3 -fdebug-prefix-map=/opt/conda/envs/netrias=/usr/local/src/conda-prefix' 'OBJC=x86_64-conda-linux-gnu-cc'

## This fails if it contains spaces, or if it is quoted
include $(R_SHARE_DIR)/make/vars.mk

AR = x86_64-conda-linux-gnu-ar
BLAS_LIBS = -lblas
C_VISIBILITY = -fvisibility=hidden
CC = x86_64-conda-linux-gnu-cc
CFLAGS = -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/envs/netrias/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1607284869564/work=/usr/local/src/conda/r-base-4.0.3 -fdebug-prefix-map=/opt/conda/envs/netrias=/usr/local/src/conda-prefix $(LTO)
CPICFLAGS = -fpic
CPPFLAGS = -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/envs/netrias/include -I/opt/conda/envs/netrias/include -Wl,-rpath-link,/opt/conda/envs/netrias/lib
CXX = x86_64-conda-linux-gnu-c++ -std=gnu++11
## Not used by anything in R, in particular not for the .cc.d rule
## but used via R CMD config by several packages
CXXCPP = $(CXX) -E
CXXFLAGS = -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/envs/netrias/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1607284869564/work=/usr/local/src/conda/r-base-4.0.3 -fdebug-prefix-map=/opt/conda/envs/netrias=/usr/local/src/conda-prefix $(LTO)
CXXPICFLAGS = -fpic
CXX11 = x86_64-conda-linux-gnu-c++
CXX11FLAGS = -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/envs/netrias/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1607284869564/work=/usr/local/src/conda/r-base-4.0.3 -fdebug-prefix-map=/opt/conda/envs/netrias=/usr/local/src/conda-prefix $(LTO)
CXX11PICFLAGS = -fpic
CXX11STD = -std=gnu++11
CXX14 = x86_64-conda-linux-gnu-c++
CXX14FLAGS = -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/envs/netrias/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1607284869564/work=/usr/local/src/conda/r-base-4.0.3 -fdebug-prefix-map=/opt/conda/envs/netrias=/usr/local/src/conda-prefix $(LTO)
CXX14PICFLAGS = -fpic
CXX14STD = -std=gnu++14
CXX17 = x86_64-conda-linux-gnu-c++
CXX17FLAGS = -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/envs/netrias/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1607284869564/work=/usr/local/src/conda/r-base-4.0.3 -fdebug-prefix-map=/opt/conda/envs/netrias=/usr/local/src/conda-prefix $(LTO)
CXX17PICFLAGS = -fpic
CXX17STD = -std=gnu++17
CXX20 = x86_64-conda-linux-gnu-c++
CXX20FLAGS = -fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/envs/netrias/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1607284869564/work=/usr/local/src/conda/r-base-4.0.3 -fdebug-prefix-map=/opt/conda/envs/netrias=/usr/local/src/conda-prefix $(LTO)
CXX20PICFLAGS = -fpic
CXX20STD = -std=gnu++2a
CXX_VISIBILITY = -fvisibility=hidden
DYLIB_EXT = .so
DYLIB_LD = $(CC)
DYLIB_LDFLAGS = -shared -fopenmp# $(CFLAGS) $(CPICFLAGS) 
## should be used by packges for dylibs, but at the time of writing was not
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 = x86_64-conda-linux-gnu-gfortran
FCFLAGS = -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/envs/netrias/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1607284869564/work=/usr/local/src/conda/r-base-4.0.3 -fdebug-prefix-map=/opt/conda/envs/netrias=/usr/local/src/conda-prefix $(LTO_FC)
## additional libs needed when linking with $(FC), e.g. on some Oracle compilers
FCLIBS_XTRA = 
FFLAGS = -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/envs/netrias/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1607284869564/work=/usr/local/src/conda/r-base-4.0.3 -fdebug-prefix-map=/opt/conda/envs/netrias=/usr/local/src/conda-prefix $(LTO_FC)
FLIBS =  -lgfortran -lm -lgomp -lquadmath -lpthread
FPICFLAGS = -fpic
FOUNDATION_CPPFLAGS = 
FOUNDATION_LIBS = 
JAR = /home/conda/feedstock_root/build_artifacts/r-base-split_1607284869564/_build_env/bin/jar
JAVA = /home/conda/feedstock_root/build_artifacts/r-base-split_1607284869564/_build_env/bin/java
JAVAC = /home/conda/feedstock_root/build_artifacts/r-base-split_1607284869564/_build_env/bin/javac
JAVAH = 
## JAVA_HOME might be used in the next three.  
## They are for packages 'JavaGD' and 'rJava'
JAVA_HOME = /home/conda/feedstock_root/build_artifacts/r-base-split_1607284869564/_build_env
JAVA_CPPFLAGS = -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JAVA_LIBS = -L$(JAVA_HOME)/lib/server -ljvm
JAVA_LD_LIBRARY_PATH = /home/conda/feedstock_root/build_artifacts/r-base-split_1607284869564/_build_env/lib/server
LAPACK_LIBS = -llapack
LDFLAGS = -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/opt/conda/envs/netrias/lib -Wl,-rpath-link,/opt/conda/envs/netrias/lib -L/opt/conda/envs/netrias/lib -Wl,-rpath-link,/opt/conda/envs/netrias/lib
## 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 = -L/opt/conda/envs/netrias/lib -lpcre2-8 -llzma -lbz2 -lz -lrt -ldl -lm -liconv -licuuc -licui18n
## needed by R CMD config
LIBnn = lib
LIBTOOL = $(SHELL) "$(R_HOME)/bin/libtool"
## set for --enable-lto, --enable-lto=check
LTO = 
LTO_FC = 
LTO_LD = 
## needed to build applications linking to static libR
MAIN_LD = $(CC)
MAIN_LDFLAGS = -Wl,--export-dynamic -fopenmp
RPATH_LDFLAGS = -Wl,-rpath,$(abs_top_builddir)/lib -Wl,-rpath,/opt/conda/envs/netrias/lib
MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS) $(RPATH_LDFLAGS)
MKINSTALLDIRS = "$(R_HOME)/bin/mkinstalldirs"
NM = /home/conda/feedstock_root/build_artifacts/r-base-split_1607284869564/_build_env/bin/x86_64-conda-linux-gnu-nm
OBJC = x86_64-conda-linux-gnu-cc
OBJCFLAGS = -g -O2 -fobjc-exceptions $(LTO)
OBJC_LIBS =  
OBJCXX = 
R_ARCH = 
RANLIB = x86_64-conda-linux-gnu-ranlib
SAFE_FFLAGS = -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/envs/netrias/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1607284869564/work=/usr/local/src/conda/r-base-4.0.3 -fdebug-prefix-map=/opt/conda/envs/netrias=/usr/local/src/conda-prefix -msse2 -mfpmath=sse
SED = /opt/conda/envs/netrias/bin/sed
SHELL = /bin/sh
SHLIB_CFLAGS = 
SHLIB_CXXFLAGS = 
SHLIB_CXXLD = $(CXX)
SHLIB_CXXLDFLAGS = -shared# $(CXXFLAGS) $(CXXPICFLAGS) $(LTO_LD)
SHLIB_CXX11LD = $(CXX11) $(CXX11STD)
SHLIB_CXX11LDFLAGS = -shared# $(CXX11FLAGS) $(CXX11PICFLAGS) $(LTO_LD)
SHLIB_CXX14LD = $(CXX14) $(CXX14STD)
SHLIB_CXX14LDFLAGS = -shared# $(CXX14FLAGS) $(CXX14PICFLAGS) $(LTO_LD)
SHLIB_CXX17LD = $(CXX17) $(CXX17STD)
SHLIB_CXX17LDFLAGS = -shared# $(CXX17FLAGS) $(CXX17PICFLAGS) $(LTO_LD)
SHLIB_CXX20LD = $(CXX20) $(CXX20STD)
SHLIB_CXX20LDFLAGS = -shared# $(CXX20FLAGS) $(CXX20PICFLAGS) $(LTO_LD)
SHLIB_EXT = .so
SHLIB_FCLD = $(FC)
SHLIB_FCLDFLAGS = -shared# $(FCFLAGS) $(FPICFLAGS)
SHLIB_FFLAGS = 
SHLIB_LD = $(CC)
## used for add-on packages linked by C
SHLIB_LDFLAGS = -shared# $(CFLAGS) $(CPICFLAGS) $(LTO_LD)
## used for standard packages
SHLIB_LDFLAGS_R = -shared# $(CFLAGS) $(CPICFLAGS) $(LTO_LD)
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 = 
STRIP_STATIC_LIB = x86_64-conda-linux-gnu-strip --strip-debug
STRIP_SHARED_LIB = x86_64-conda-linux-gnu-strip --strip-unneeded
TCLTK_CPPFLAGS = -I/opt/conda/envs/netrias/include -I/opt/conda/envs/netrias/include 
TCLTK_LIBS = -L/opt/conda/envs/netrias/lib -ltcl8.6 -L/opt/conda/envs/netrias/lib -ltk8.6 -lX11
YACC = yacc

## 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

## CXX98 is no longer supported, but packages may use it.
SHLIB_CXX98LD = @SHLIB_CXX98LD@
SHLIB_CXX98LDFLAGS = @SHLIB_CXX98LDFLAGS@

## 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) $< > $@
.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 $@
.m.d:
    @echo "making $@ from $<"
    @$(OBJC) -MM $(ALL_CPPFLAGS) $< > $@
.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 $@
offbynull commented 3 years ago

Here's what I see in the INSTALL file:

Overall, your build chain may be misconfigured, check out,
amongst others, `<R_inst_dir>/etc/Makeconf`
(e.g., are you using `--std=gnu++11` instead of `--std=c++11`?). Refer to
https://cran.r-project.org/doc/manuals/r-release/R-admin.html for more details.

It looks like Makeconf is using gnu++11. Is the workaround here to use install.packages("stringi", configure.args = "--with-extra-cxxflags='--std=c++11'") as suggested by the document? It doesn't seem to do anything.

EDIT: Changing all gnu++ references to c++ in Makeconf doesn't produce different results.

offbynull commented 3 years ago

It looks like it's the linking that might be causing the check to crap out. It looks like some library / library configs might be misconfigured on my end.

(base) root@d7f466414776:/source# conda run -n netrias x86_64-conda-linux-gnu-c++ ~/test.cpp
ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['x86_64-conda-linux-gnu-c++', '/root/test.cpp']' command failed.  (See above for error)
/opt/conda/envs/netrias/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/conda/envs/netrias/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/lib/../lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/opt/conda/envs/netrias/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/conda/envs/netrias/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/lib/../lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
offbynull commented 3 years ago

I got it sorted out. I'll leave an answer here for anyone else having problems: If you're installing R through conda and referencing against multiple channels, there's a chance that dependencies will get mixed up across channels.

Here's what I was originally doing: conda install -n netrias -c defaults -c r -c conda-forge r-base==4.0.3

Here's what I ended up changing that to: conda install -n netrias -c conda-forge r-base==4.0.3

gagolews commented 3 years ago

Thanks for posting the solution.