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gagolews / stringi

Fast and portable character string processing in R (with the Unicode ICU)
https://stringi.gagolewski.com/
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Cannot install stringi after upgrading to R 3.5.0, Mac OS Sierra #297

Closed SevaVigg closed 6 years ago

SevaVigg commented 6 years ago

tried both install.packages('stringi', configure.args='--disable-cxx11') and install.package('stringi') Here is the outcome

I have gcc installed as /usr/local/gcc-8.1/bin/gcc

I also tried wget https://github.com/gagolews/stringi/archive/master.zip and R CMD INSTALL stringi-master

but keep obtaining the same error from configure. It appears some problem with clang (I'm running the updated Xcode 9.3), but I failed to explain ./configure that it must use gcc instead of clang. The config.log file is below

This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake.

It was created by stringi configure 1.2, which was generated by GNU Autoconf 2.69. Invocation command line was

$ ./configure

---------

Platform.

---------

hostname = SevaFlamingo.local uname -m = x86_64 uname -r = 16.7.0 uname -s = Darwin uname -v = Darwin Kernel Version 16.7.0: Tue Jan 30 11:27:06 PST 2018; root:xnu-3789.73.11~1/RELEASE_X86_64

/usr/bin/uname -p = i386 /bin/uname -X = unknown

/bin/arch = unknown /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = Mach kernel version: Darwin Kernel Version 16.7.0: Tue Jan 30 11:27:06 PST 2018; root:xnu-3789.73.11~1/RELEASE_X86_64 Kernel configured for up to 4 processors. 2 processors are physically available. 4 processors are logically available. Processor type: i486 (Intel 80486) Processors active: 0 1 2 3 Primary memory available: 16.00 gigabytes Default processor set: 328 tasks, 1366 threads, 4 processors Load average: 2.24, Mach factor: 1.86 /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown

PATH: /usr/local/gcc-8.1/bin PATH: /usr/local/gcc-8.1/bin PATH: /usr/local/gcc-8.1/bin PATH: /Users/vsevolodmakeev/Local/lib/Samtools/tabix-0.2.6 PATH: /Users/vsevolodmakeev/Local/lib/Samtools/samtools-0.1.19/misc/ PATH: /Users/vsevolodmakeev/Local/lib/Samtools/samtools-0.1.19/bcftools/ PATH: /Users/vsevolodmakeev/Local/lib/Samtools/samtools-0.1.19 PATH: /usr/local/bin PATH: /usr/bin PATH: /bin PATH: /usr/sbin PATH: /sbin PATH: /opt/X11/bin PATH: /Library/TeX/texbin PATH: /Users/vsevolodmakeev/Local/lib/vcftools/vcftools_0.1.12b/bin/

-----------

Core tests.

-----------

configure:2347: checking for R_HOME configure:2358: result: /Library/Frameworks/R.framework/Resources configure:2364: checking for R configure:2374: result: /Library/Frameworks/R.framework/Resources/bin/R configure:2377: checking for endianness configure:2386: result: little configure:2390: checking for R >= 3.1.0 for C++11 use configure:2394: result: yes configure:2406: checking for R < 3.4.0 for CXX1X flag use configure:2410: result: no configure:2422: checking for local ICUDT_DIR configure:2428: result: icu61/data configure:2437: checking for cat configure:2455: found /bin/cat configure:2467: result: /bin/cat configure:2583: checking for gcc configure:2610: result: /usr/local/opt/llvm/bin/clang -fopenmp configure:2839: checking for C compiler version configure:2848: /usr/local/opt/llvm/bin/clang -fopenmp --version >&5 clang version 3.9.1 (tags/RELEASE_391/final) Target: x86_64-apple-darwin16.7.0 Thread model: posix InstalledDir: /usr/local/opt/llvm/bin configure:2859: $? = 0 configure:2848: /usr/local/opt/llvm/bin/clang -fopenmp -v >&5 clang version 3.9.1 (tags/RELEASE_391/final) Target: x86_64-apple-darwin16.7.0 Thread model: posix InstalledDir: /usr/local/opt/llvm/bin configure:2859: $? = 0 configure:2848: /usr/local/opt/llvm/bin/clang -fopenmp -V >&5 clang-3.9: error: argument to '-V' is missing (expected 1 value) clang-3.9: error: no input files configure:2859: $? = 1 configure:2848: /usr/local/opt/llvm/bin/clang -fopenmp -qversion >&5 clang-3.9: error: unknown argument: '-qversion' clang-3.9: error: no input files configure:2859: $? = 1 configure:2879: checking whether the C compiler works configure:2901: /usr/local/opt/llvm/bin/clang -fopenmp -Wall -g -O2 -fPIC -DU_CHARSET_IS_UTF8=0 -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -DU_CHARSET_IS_UTF8=0 -UDEBUG -DNDEBUG conftest.c >&5 ld: library not found for -lomp clang-3.9: error: linker command failed with exit code 1 (use -v to see invocation) configure:2905: $? = 1 configure:2943: result: no configure: failed program was: / confdefs.h / #define PACKAGE_NAME "stringi" #define PACKAGE_TARNAME "stringi" #define PACKAGE_VERSION "1.2" #define PACKAGE_STRING "stringi 1.2" #define PACKAGE_BUGREPORT "gagolews@rexamine.com" #define PACKAGE_URL "" / end confdefs.h. /
int
main ()
{
;
return 0;
}

configure:2948: error: in /Users/vsevolodmakeev/Lenovo/Work/Projects/Single_cell/Seurat/stringi-master': configure:2950: error: C compiler cannot create executables Seeconfig.log' for more details

----------------

Cache variables.

----------------

ac_cv_env_CAT_set= ac_cv_env_CAT_value= ac_cv_env_CCC_set= ac_cv_env_CCC_value= ac_cv_env_CC_set= ac_cv_env_CC_value= ac_cv_env_CFLAGS_set= ac_cv_env_CFLAGS_value= ac_cv_env_CPPFLAGS_set= ac_cv_env_CPPFLAGS_value= ac_cv_env_CPP_set= ac_cv_env_CPP_value= ac_cv_env_CXXCPP_set= ac_cv_env_CXXCPP_value= ac_cv_env_CXXFLAGS_set= ac_cv_env_CXXFLAGS_value= ac_cv_env_CXX_set= ac_cv_env_CXX_value= ac_cv_env_ICUDT_DIR_set= ac_cv_env_ICUDT_DIR_value= ac_cv_env_LDFLAGS_set= ac_cv_env_LDFLAGS_value= ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_PKG_CONFIG_PATH_set= ac_cv_env_PKG_CONFIG_PATH_value= ac_cv_env_PKG_CONFIG_set= ac_cv_env_PKG_CONFIG_value= ac_cv_env_R_HOME_set= ac_cv_env_R_HOME_value= ac_cv_env_STRINGI_CFLAGS_set= ac_cv_env_STRINGI_CFLAGS_value= ac_cv_env_STRINGI_CPPFLAGS_set= ac_cv_env_STRINGI_CPPFLAGS_value= ac_cv_env_STRINGI_CXXFLAGS_set= ac_cv_env_STRINGI_CXXFLAGS_value= ac_cv_env_STRINGI_DISABLE_CXX11_set= ac_cv_env_STRINGI_DISABLE_CXX11_value= ac_cv_env_STRINGI_DISABLE_ICU_BUNDLE_set= ac_cv_env_STRINGI_DISABLE_ICU_BUNDLE_value= ac_cv_env_STRINGI_DISABLE_PKG_CONFIG_set= ac_cv_env_STRINGI_DISABLE_PKG_CONFIG_value= ac_cv_env_STRINGI_LDFLAGS_set= ac_cv_env_STRINGI_LDFLAGS_value= ac_cv_env_STRINGI_LIBS_set= ac_cv_env_STRINGI_LIBS_value= ac_cv_env_build_alias_set= ac_cv_env_build_alias_value= ac_cv_env_host_alias_set= ac_cv_env_host_alias_value= ac_cv_env_target_alias_set= ac_cv_env_target_alias_value= ac_cv_path_CAT=/bin/cat ac_cv_prog_ac_ct_CC='/usr/local/opt/llvm/bin/clang -fopenmp'

-----------------

Output variables.

-----------------

CAT='/bin/cat' CC='/usr/local/opt/llvm/bin/clang -fopenmp' CFLAGS='-Wall -g -O2 -fPIC -DU_CHARSET_IS_UTF8=0' CPP='/usr/local/opt/llvm/bin/clang++ -E' CPPFLAGS='-I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -DU_CHARSET_IS_UTF8=0 -UDEBUG -DNDEBUG' CXX='gcc++ -std=gnu++11' CXXCPP='' CXXFLAGS='-Wall -g -O2 -fPIC -DU_CHARSET_IS_UTF8=0' DEFS='' ECHO_C='\c' ECHO_N='' ECHO_T='' EGREP='' EXEEXT='' GREP='' ICUDT_DIR='icu61/data' ICUDT_ENDIANNESS='little' ICU_BUNDLE_VERSION='61' ICU_FOUND='' LDFLAGS=' ' LIBOBJS='' LIBS=' ' LTLIBOBJS='' OBJEXT='' PACKAGE_BUGREPORT='gagolews@rexamine.com' PACKAGE_NAME='stringi' PACKAGE_STRING='stringi 1.2' PACKAGE_TARNAME='stringi' PACKAGE_URL='' PACKAGE_VERSION='1.2' PATH_SEPARATOR=':' PKG_CONFIG='' PKG_CONFIG_PATH='' R_HOME='/Library/Frameworks/R.framework/Resources' SHELL='/bin/sh' STRINGI_CFLAGS='' STRINGI_CPPFLAGS='' STRINGI_CXXFLAGS='' STRINGI_CXXSTD='CXX_STD=CXX11' STRINGI_DISABLE_CXX11='' STRINGI_DISABLE_ICU_BUNDLE='' STRINGI_DISABLE_PKG_CONFIG='' STRINGI_ICU_COMMON_SOURCES_C='' STRINGI_ICU_COMMON_SOURCES_CPP='' STRINGI_ICU_I18N_SOURCES_C='' STRINGI_ICU_I18N_SOURCES_CPP='' STRINGI_ICU_STUBDATA_SOURCES_C='' STRINGI_ICU_STUBDATA_SOURCES_CPP='' STRINGI_LDFLAGS='' STRINGI_LIBS='' STRINGI_OBJECTS='' STRINGI_SOURCES_CPP='' ac_ct_CC='/usr/local/opt/llvm/bin/clang -fopenmp' ac_ct_CXX='' bindir='${exec_prefix}/bin' build_alias='' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' exec_prefix='NONE' host_alias='' htmldir='${docdir}' includedir='${prefix}/include' infodir='${datarootdir}/info' libdir='${exec_prefix}/lib' libexecdir='${exec_prefix}/libexec' localedir='${datarootdir}/locale' localstatedir='${prefix}/var' mandir='${datarootdir}/man' oldincludedir='/usr/include' pdfdir='${docdir}' prefix='NONE' program_transform_name='s,x,x,' psdir='${docdir}' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' sysconfdir='${prefix}/etc' target_alias=''

-----------

confdefs.h.

-----------

/ confdefs.h /

define PACKAGE_NAME "stringi"

define PACKAGE_TARNAME "stringi"

define PACKAGE_VERSION "1.2"

define PACKAGE_STRING "stringi 1.2"

define PACKAGE_BUGREPORT "gagolews@rexamine.com"

define PACKAGE_URL ""

configure: exit 77

SevaVigg commented 6 years ago

UPDATE: Resolved by removing -fopenmp in ~/.R/Makevars CC=/usr/local/opt/llvm/bin/clang -fopenmp and then running install.packages('stringi', configure.args='--disable-cxx11')