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#1 2017-05-23 09:54:34

meccanus
Member
Registered: 2013-04-23
Posts: 14

cannot compile r-mkl 3.4 from AUR

I am trying to compile r-mkl 3.4 rev3 from AUR (with intel-mkl 2017.17.0.4.4.196-1) but compilation fails.

I tried to:

  • google parts of the error message (below) for hints, with no success

  • use the _cc variable in PKGBUILD to toggle from ICC to ICC --> both fail with the same error message

  • comment out all flags in makepkg.conf before compiling r-mkl (i took care of sourcing the new file) -> no effect and the error message is the same

  • to compile regular r -> compilation was successful

The error message is:

make[4]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/extra/tre'
make[4]: 'libtre.a' is up to date.
make[4]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/extra/tre'
make[3]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/extra/tre'
make[2]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/extra'
make[2]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/appl'
make[3]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/appl'
icc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -O3 -xHost -m64 -qopenmp -fp-model precise -fp-model source -diag-disable=188,308 -I/opt/intel/composerxe/linux/mkl/include  -c interv.c -o interv.o
In file included from ../../src/include/R_ext/RS.h(39),
                 from ../../src/include/R_ext/Applic.h(40),
                 from interv.c(26):
../../src/include/Rconfig.h(7): error: identifier "Binary" is undefined
  Binary file config.h matches
  ^

In file included from ../../src/include/R_ext/RS.h(39),
                 from ../../src/include/R_ext/Applic.h(40),
                 from interv.c(26):
../../src/include/Rconfig.h(7): error: expected a ";"
  Binary file config.h matches
              ^

In file included from ../../src/include/R_ext/RS.h(47),
                 from ../../src/include/R_ext/Applic.h(40),
                 from interv.c(26):
../../src/include/R_ext/Error.h(39): warning #12: parsing restarts here after previous syntax error
  void NORET Rf_error(const char *, ...);
                                        ^

compilation aborted for interv.c (code 2)
make[3]: *** [../../Makeconf:119: interv.o] Error 2
make[3]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/appl'
make[2]: *** [Makefile:47: R] Error 2
make[2]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/appl'
make[1]: *** [Makefile:28: R] Error 1
make[1]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src'
make: *** [Makefile:61: R] Error 1

Any hints?

Last edited by meccanus (2017-05-23 09:55:20)

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#2 2017-05-23 10:34:29

WorMzy
Forum Moderator
From: Scotland
Registered: 2010-06-16
Posts: 11,868
Website

Re: cannot compile r-mkl 3.4 from AUR

Mod note: moving to AUR issues

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#3 2017-05-28 14:20:24

Lone_Wolf
Forum Moderator
From: Netherlands, Europe
Registered: 2005-10-04
Posts: 11,922

Re: cannot compile r-mkl 3.4 from AUR

Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/extra/tre'

are you using an aur helper ? if so, does building with makepkg also fail ?

please post full build output.

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(A works at time B)  && (time C > time B ) ≠  (A works at time C)

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#4 2017-05-28 15:15:30

meccanus
Member
Registered: 2013-04-23
Posts: 14

Re: cannot compile r-mkl 3.4 from AUR

All checks described above were done using makepkg, which fails.

Full output is below, but as you can see it fails immediately after all checks are performed.

==> Making package: r-mkl 3.4.0-3 (dom 28 mag 2017, 17.11.13, CEST)
==> Checking runtime dependencies...
==> Checking buildtime dependencies...
==> Retrieving sources...
  -> Found R-3.4.0.tar.gz
  -> Found r.desktop
  -> Found r.png
  -> Found R.conf
==> Validating source files with md5sums...
    R-3.4.0.tar.gz ... Passed
    r.desktop ... Passed
    r.png ... Passed
    R.conf ... Passed
==> Validating source files with sha512sums...
    R-3.4.0.tar.gz ... Passed
    r.desktop ... Passed
    r.png ... Passed
    R.conf ... Passed
==> Extracting sources...
  -> Extracting R-3.4.0.tar.gz with bsdtar
==> Starting prepare()...
==> Removing existing $pkgdir/ directory...
==> Starting build()...
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /usr/bin/pwd
checking whether builddir is srcdir... yes
checking for working aclocal... found
checking for working autoconf... found                                                                                                                                             
checking for working automake... found                                                                                                                                             
checking for working autoheader... found                                                                                                                                           
checking whether ln -s works... yes                                                                                                                                                
checking for bison... bison -y                                                                                                                                                     
checking for xiar... xiar                                                                                                                                                          
checking for a BSD-compatible install... /usr/bin/install -c                                                                                                                       
checking for sed... /usr/bin/sed                                                                                                                                                   
checking for which... /usr/bin/which                                                                                                                                               
checking for less... /usr/bin/less                                                                                                                                                 
checking for gtar... no                                                                                                                                                            
checking for gnutar... no                                                                                                                                                          
checking for tar... /usr/bin/tar                                                                                                                                                   
checking for tex... /usr/bin/tex                                                                                                                                                   
checking for pdftex... /usr/bin/pdftex                                                                                                                                             
checking for pdflatex... /usr/bin/pdflatex                                                                                                                                         
checking for makeindex... /usr/bin/makeindex                                                                                                                                       
checking for texi2any... /usr/bin/texi2any                                                                                                                                         
checking whether texi2any version is at least 5.1... yes                                                                                                                           
checking for ginstall-info... no                                                                                                                                                   
checking for install-info... /usr/bin/install-info                                                                                                                                 
checking for texi2dvi... /usr/bin/texi2dvi                                                                                                                                         
checking for kpsewhich... /usr/bin/kpsewhich                                                                                                                                       
checking for latex inconsolata package... found zi4.sty                                                                                                                            
checking for unzip... /usr/bin/unzip                                                                                                                                               
checking for zip... /usr/bin/zip                                                                                                                                                   
checking for gzip... /usr/bin/gzip                                                                                                                                                 
checking for bzip2... /usr/bin/bzip2                                                                                                                                               
checking for firefox... /usr/bin/firefox                                                                                                                                           
using default browser ... /usr/bin/firefox                                                                                                                                         
checking for acroread... no                                                                                                                                                        
checking for acroread4... no                                                                                                                                                       
checking for xdg-open... /home/roberto/bin/xdg-open                                                                                                                                
checking for notangle... false                                                                                                                                                     
checking for realpath... /usr/bin/realpath                                                                                                                                         
checking for pkg-config... /usr/bin/pkg-config                                                                                                                                     
checking for gcc... icc                                                                                                                                                            
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 icc accepts -g... yes                                                                                                                                             
checking for icc option to accept ISO C89... none needed                                                                                                                           
checking how to run the C preprocessor... icc -E                                                                                                                                   
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking whether icc needs -traditional... no
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 minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking how to run the C preprocessor... icc -E
defining F77 to be ifort
checking whether we are using the GNU Fortran 77 compiler... no
checking whether ifort accepts -g... yes
checking whether we are using the GNU C++ compiler... yes
checking whether icpc accepts -g... yes
checking whether icpc  -O3 -xHost -m64 -qopenmp -fp-model precise -fp-model source -diag-disable=188,308 -I/opt/intel/composerxe/linux/mkl/include can compile C++ code... yes
checking how to run the C++ preprocessor... icpc -E
checking whether __attribute__((visibility())) is supported... yes
checking whether icc accepts -fvisibility... yes
checking whether ifort accepts -fvisibility... yes
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... yes
checking whether gcc accepts -g... yes
checking for Objective C++ compiler... trying some possibilities
checking whether icpc can compile ObjC++... yes
icpc
checking how to print strings... printf
checking for a sed that does not truncate output... (cached) /usr/bin/sed
checking for fgrep... /usr/bin/grep -F
checking for ld used by icc... xild
checking if the linker (xild) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for xild option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking for gawk... gawk
checking command to parse /usr/bin/nm -B output from icc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if icc supports -fno-rtti -fno-exceptions... yes
checking for icc option to produce PIC... -fPIC -DPIC
checking if icc PIC flag -fPIC -DPIC works... yes
checking if icc static flag -static works... yes
checking if icc supports -c -o file.o... yes
checking if icc supports -c -o file.o... (cached) yes
checking whether the icc linker (xild -m elf_x86_64) supports shared libraries... xild: warning #10013: no objects specified for multi-file optimization
xild: executing 'ld'
yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... icpc -E
checking for ld used by icpc... xild -m elf_x86_64
checking if the linker (xild -m elf_x86_64) is GNU ld... yes
checking whether the icpc linker (xild -m elf_x86_64) supports shared libraries... yes
checking for icpc option to produce PIC... -fPIC -DPIC
checking if icpc PIC flag -fPIC -DPIC works... yes
checking if icpc static flag -static works... yes
checking if icpc supports -c -o file.o... yes
checking if icpc supports -c -o file.o... (cached) yes
checking whether the icpc linker (xild -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for ifort option to produce PIC... -fPIC
checking if ifort PIC flag -fPIC works... yes
checking if ifort static flag -static works... yes
checking if ifort supports -c -o file.o... yes
checking if ifort supports -c -o file.o... (cached) yes
checking whether the ifort linker (xild -m elf_x86_64) supports shared libraries... xild: warning #10013: no objects specified for multi-file optimization
xild: executing 'ld'
yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking readline/history.h usability... yes
checking readline/history.h presence... yes
checking for readline/history.h... yes
checking readline/readline.h usability... yes
checking readline/readline.h presence... yes
checking for readline/readline.h... yes
checking for rl_callback_read_char in -lreadline... yes
checking for history_truncate_file... yes
checking whether rl_callback_sigcleanup exists and is declared... yes
checking whether rl_completion_matches exists and is declared... yes
checking whether rl_resize_terminal exists and is declared... yes
checking whether rl_sort_completion_matches exists and is declared... yes
checking for ANSI C header files... (cached) yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for dlfcn.h... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
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checking glob.h usability... yes
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checking sched.h usability... yes
checking sched.h presence... yes
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checking for strings.h... (cached) yes
checking sys/resource.h usability... yes
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checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for sys/stat.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking sys/utsname.h usability... yes
checking sys/utsname.h presence... yes
checking for sys/utsname.h... yes
checking for unistd.h... (cached) yes
checking utime.h usability... yes
checking utime.h presence... yes
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checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking dl.h usability... no
checking dl.h presence... no
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checking elf.h usability... yes
checking elf.h presence... yes
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checking features.h usability... yes
checking features.h presence... yes
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checking floatingpoint.h usability... no
checking floatingpoint.h presence... no
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checking langinfo.h usability... yes
checking langinfo.h presence... yes
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checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking netinet/in.h usability... ^[[1;5Byes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking stdalign.h usability... yes
checking stdalign.h presence... yes
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checking errno.h usability... yes
checking errno.h presence... yes
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checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
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checking locale.h usability... yes
checking locale.h presence... ^[[Ayes
checking for locale.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
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checking stdbool.h usability... yes
checking stdbool.h presence... yes
checking for stdbool.h... yes
checking for stdint.h... (cached) yes
checking for string.h... (cached) yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking for GNU C library with version >= 2... yes
checking return type of signal handlers... void
checking for uint64_t... yes
checking for int64_t... yes
checking for int_fast64_t... yes
checking for pid_t... yes
checking for size_t... yes
checking whether SIZE_MAX is declared... yes
checking for blkcnt_t... yes
checking for type of socket length... ^[[5;5~socklen_t *
checking for stack_t... yes
checking for intptr_t... ^[[5;5~yes
checking for uintptr_t... yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for icc option to accept ISO C99... none needed
checking for icc option to accept ISO Standard C... (cached) none needed
checking for inline... inline
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of double... 8
checking size of size_t... 8
checking size of long double... 16
checking whether we can compute C Make dependencies... yes, using $(CC) -MM
checking whether icc supports -c -o FILE.lo... yes
checking for icc option to support OpenMP... none needed
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
checking whether ifort appends underscores to external names... yes
checking whether ifort appends extra underscores to external names... no
checking whether mixed C/Fortran code can be run... yes
checking whether ifort and icc agree on int and double... yes
checking whether ifort and icc agree on double complex... yes
checking for ifort option to support OpenMP... none needed
checking whether icpc accepts -M for generating dependencies... yes
checking for icpc option to support OpenMP... none needed
checking whether we can compute ObjC Make dependencies... yes, using gcc -MM
checking for ObjC runtime library... -lobjc
checking for ObjC runtime style... unknown
checking whether gcc accepts -fobjc-exceptions... yes
checking whether C runtime needs -D__NO_MATH_INLINES... no
checking for xmkmf... no
checking whether icpc  supports C++98 features by default... no
checking whether icpc  supports C++98 features with -std=gnu++98... yes
checking whether icpc  supports C++11 features by default... no
checking whether icpc  supports C++11 features with -std=gnu++11... yes
checking whether icpc  supports C++14 features by default... yes
checking whether icpc  supports C++17 features by default... no
checking whether icpc  supports C++17 features with -std=gnu++17... no
checking whether icpc  supports C++17 features with -std=gnu++1z... no
checking whether icpc  supports C++17 features with -std=c++17... no
checking whether icpc  supports C++17 features with -std=c++1z... no
configure: No compiler with C++17 support was found
checking for off_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking whether alloca is declared... yes
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checking whether hypot exists and is declared... yes
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checking whether fcntl exists and is declared... yes
checking whether getgrgid exists and is declared... yes
checking whether getpwuid exists and is declared... yes
checking whether kill exists and is declared... yes
checking whether sigaction exists and is declared... yes
checking whether sigaltstack exists and is declared... yes
checking whether sigemptyset exists and is declared... yes
checking whether fdopen exists and is declared... yes
checking whether popen exists and is declared... yes
checking whether getline exists and is declared... yes
checking whether select exists and is declared... yes
checking whether setenv exists and is declared... yes
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checking whether getrlimit exists and is declared... yes
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checking whether getpriority exists and is declared... yes
checking whether chmod exists and is declared... yes
checking whether mkfifo exists and is declared... yes
checking whether stat exists and is declared... yes
checking whether umask exists and is declared... yes
checking whether gettimeofday exists and is declared... yes
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checking whether times exists and is declared... yes
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checking whether access exists and is declared... yes
checking whether chdir exists and is declared... yes
checking whether execv exists and is declared... yes
checking whether ftruncate exists and is declared... yes
checking whether getcwd exists and is declared... yes
checking whether geteuid exists and is declared... yes
checking whether getuid exists and is declared... yes
checking whether link exists and is declared... yes
checking whether readlink exists and is declared... yes
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checking whether sysconf exists and is declared... yes
checking whether sched_setaffinity exists and is declared... yes
checking whether sched_getaffinity exists and is declared... yes
checking whether utime exists and is declared... yes
checking whether utimensat exists and is declared... yes
checking for clock_gettime in -lrt... yes
checking whether clock_gettime exists and is declared... yes
checking whether timespec_get exists and is declared... yes
checking for putenv... yes
checking whether putenv is declared... yes
checking for vasprintf... yes
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checking whether dlsym is declared... yes
checking whether RTLD_DEFAULT is declared... yes
checking whether RTLD_NEXT is declared... yes
checking for isnan... yes
checking whether isfinite is declared... yes
checking whether isnan is declared... yes
checking whether you have IEEE 754 floating-point arithmetic... yes
checking whether putenv("FOO") can unset an environment variable... yes
checking whether putenv("FOO=") can unset an environment variable... no
checking for nl_langinfo and CODESET... yes
checking for mkdtemp... yes
checking for strdup... yes
checking for strncasecmp... yes
checking whether mkdtemp is declared... yes
checking whether strdup is declared... yes
checking whether strncasecmp is declared... yes
checking for library containing connect... none required
checking for library containing gethostbyname... none required
checking for library containing xdr_string... none required
checking for working calloc... yes
checking for working isfinite... yes
checking for working log1p... yes
checking whether ftell works correctly on files opened for append... yes
checking for working sigaction... yes
checking whether mktime sets errno... no
checking whether mktime works correctly outside 1902-2037... yes
checking complex.h usability... yes
checking complex.h presence... yes
checking for complex.h... yes
checking for double complex... yes
checking whether C99 double complex is supported... yes
checking whether cabs exists and is declared... yes
checking whether carg exists and is declared... yes
checking whether cexp exists and is declared... yes
checking whether clog exists and is declared... yes
checking whether csqrt exists and is declared... yes
checking whether cpow exists and is declared... yes
checking whether ccos exists and is declared... yes
checking whether csin exists and is declared... yes
checking whether ctan exists and is declared... yes
checking whether cacos exists and is declared... yes
checking whether casin exists and is declared... yes
checking whether catan exists and is declared... yes
checking whether ccosh exists and is declared... yes
checking whether csinh exists and is declared... yes
checking whether ctanh exists and is declared... yes
checking whether 'struct tm' includes tm_zone... yes
checking whether 'struct tm' includes tm_gmtoff... yes
checking for dgemm_ in  -L/opt/intel/composerxe/linux/mkl/lib/intel64       -lmkl_intel_lp64       -lmkl_intel_thread       -lmkl_core       -liomp5       -lpthread       -lm       -ldl... yes
checking whether double complex BLAS can be used... yes
checking whether the BLAS is complete... yes
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checking iconv.h usability... yes
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checking whether iconv accepts "UTF-8", "latin1", "ASCII" and "UCS-*"... yes
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         extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
checking wchar.h usability... yes
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checking whether mbrtowc exists and is declared... yes
checking whether wcrtomb exists and is declared... yes
checking whether wcscoll exists and is declared... yes
checking whether wcsftime exists and is declared... yes
checking whether wcstod exists and is declared... yes
checking whether mbstowcs exists and is declared... yes
checking whether wcstombs exists and is declared... yes
checking whether wctrans exists and is declared... yes
checking whether iswblank exists and is declared... yes
checking whether wctype exists and is declared... yes
checking whether iswctype exists and is declared... yes
checking for wctrans_t... yes
checking for mbstate_t... yes
checking for ICU... yes
checking for X... libraries , headers 
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking X11/Intrinsic.h usability... yes
checking X11/Intrinsic.h presence... yes
checking for X11/Intrinsic.h... yes
checking for XtToolkitInitialize in -lXt... yes
using X11 ... yes
checking for KeySym... yes
checking X11/Xmu/Atoms.h usability... yes
checking X11/Xmu/Atoms.h presence... yes
checking for X11/Xmu/Atoms.h... yes
checking for XmuInternAtom in -lXmu... yes
checking whether pkg-config knows about cairo and pango... yes
checking whether cairo including pango is >= 1.2 and works... yes
checking for tclConfig.sh... no
checking for tclConfig.sh in library (sub)directories... /usr/lib/tclConfig.sh
checking for tkConfig.sh... no
checking for tkConfig.sh in library (sub)directories... /usr/lib/tkConfig.sh
checking tcl.h usability... yes
checking tcl.h presence... yes
checking for tcl.h... yes
checking tk.h usability... yes
checking tk.h presence... yes
checking for tk.h... yes
checking whether compiling/linking Tcl/Tk code works... yes
checking for BSD networking... yes
checking rpc/types.h usability... yes
checking rpc/types.h presence... yes
checking for rpc/types.h... yes
checking for rpc/xdr.h... yes
checking for XDR support... yes
checking for inflateInit2_ in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking if zlib version >= 1.2.5... yes
checking whether zlib support suffices... yes
checking mmap support for zlib... yes
checking for BZ2_bzlibVersion in -lbz2... yes
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking if bzip2 version >= 1.0.6... yes
checking whether bzip2 support suffices... yes
checking for lzma_version_number in -llzma... yes
checking lzma.h usability... yes
checking lzma.h presence... yes
checking for lzma.h... yes
checking if lzma version >= 5.0.3... yes
checking for pcre_fullinfo in -lpcre... yes
checking pcre.h usability... yes
checking pcre.h presence... yes
checking for pcre.h... yes
checking pcre/pcre.h usability... no
checking pcre/pcre.h presence... no
checking for pcre/pcre.h... no
checking if PCRE version >= 8.10, < 10.0 and has UTF-8 support... yes
checking if PCRE version >= 8.32... yes
checking whether PCRE support suffices... yes
checking for curl-config... /usr/bin/curl-config
checking libcurl version ... 7.54.0
checking curl/curl.h usability... yes
checking curl/curl.h presence... yes
checking for curl/curl.h... yes
checking if libcurl is version 7 and >= 7.22.0... yes
checking if libcurl supports https... yes
checking if jpeglib version >= 6b... yes
checking for jpeg_destroy_compress in -ljpeg... yes
checking if libpng version >= 1.2.7... yes
checking for png_create_write_struct in -lpng... yes
checking tiffio.h usability... yes
checking tiffio.h presence... yes
checking for tiffio.h... yes
checking for TIFFOpen in -ltiff... yes
checking whether leap seconds are treated according to POSIX... yes
checking for inline... inline
checking for sys/time.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for struct stat.st_atim.tv_nsec... yes
checking whether struct stat.st_atim is of type struct timespec... yes
checking for setitimer... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking whether KERN_USRSTACK sysctl is supported... no
checking for visible __lib_stack_end... yes
checking for lpr... lpr
checking for paperconf... /usr/bin/paperconf
checking whether we are using the GNU Fortran compiler... no
checking whether ifort accepts -g... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for ifort option to produce PIC... -fPIC
checking if ifort PIC flag -fPIC works... yes
checking if ifort static flag -static works... no
checking if ifort supports -c -o file.o... yes
checking if ifort supports -c -o file.o... (cached) yes
checking whether the ifort linker (xild -m elf_x86_64) supports shared libraries... xild: warning #10013: no objects specified for multi-file optimization
xild: executing 'ld'
yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for Fortran flag to compile .f90 files... none
checking for Fortran flag to compile .f95 files... -Tf
checking for ifort option to support OpenMP... none needed
checking for recommended packages... yes
checking whether NLS is requested... yes

Configuring src/extra/intl directory
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking whether we are using the GNU C Library 2 or newer... yes
checking for ranlib... (cached) ranlib
checking for simple visibility declarations... yes
checking for stdint.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking whether integer division by zero raises SIGFPE... yes
checking for inttypes.h... yes
checking for unsigned long long int... yes
checking for inttypes.h... (cached) yes
checking whether the inttypes.h PRIxNN macros are broken... no
checking for ld used by icc... xild -m elf_x86_64
checking if the linker (xild -m elf_x86_64) is GNU ld... yes
checking for shared library run path origin... done
checking whether imported symbols can be declared weak... yes
checking for multithread API to use... none
checking argz.h usability... yes
checking argz.h presence... yes
checking for argz.h... yes
checking for inttypes.h... (cached) yes
checking for limits.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for getcwd... yes
checking for getegid... yes
checking for geteuid... yes
checking for getgid... yes
checking for getuid... yes
checking for mempcpy... (cached) yes
checking for munmap... yes
checking for stpcpy... yes
checking for strcasecmp... yes
checking for strdup... (cached) yes
checking for strtoul... yes
checking for tsearch... yes
checking for argz_count... yes
checking for argz_stringify... yes
checking for argz_next... yes
checking for __fsetlocking... yes
checking whether feof_unlocked is declared... yes
checking whether fgets_unlocked is declared... yes
checking for iconv... (cached) yes
checking for iconv declaration... (cached) 
         extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
checking for NL_LOCALE_NAME macro... yes
checking for bison... bison
checking version of bison... 3.0.4, ok
checking for long long int... yes
checking for long double... yes
checking for wchar_t... yes
checking for wint_t... yes
checking for intmax_t... yes
checking whether printf() supports POSIX/XSI format strings... yes
checking whether we are using the GNU C Library 2.1 or newer... yes
checking for stdint.h... (cached) yes
checking for SIZE_MAX... yes
checking for stdint.h... (cached) yes
checking for CFPreferencesCopyAppValue... no
checking for CFLocaleCopyCurrent... no
checking for ptrdiff_t... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for asprintf... yes
checking for fwprintf... yes
checking for putenv... (cached) yes
checking for setenv... yes
checking for setlocale... yes
checking for snprintf... yes
checking for wcslen... yes
checking whether _snprintf is declared... no
checking whether _snwprintf is declared... no
checking whether getc_unlocked is declared... yes
checking for nl_langinfo and CODESET... (cached) yes
checking for LC_MESSAGES... yes
checking for CFPreferencesCopyAppValue... (cached) no
checking for CFLocaleCopyCurrent... (cached) no
checking whether included gettext is requested... no
checking for GNU gettext in libc... yes
checking whether to use NLS... yes
checking where the gettext function comes from... libc
Finished configuring src/extra/intl directory

checking whether OpenMP SIMD reduction is supported... yes
using as R_SHELL for scripts ... /bin/sh
configure: creating ./config.status
config.status: creating Makeconf
config.status: creating Makefile
config.status: creating doc/Makefile
config.status: creating doc/html/Makefile
config.status: creating doc/manual/Makefile
config.status: creating etc/Makefile
config.status: creating etc/Makeconf
config.status: creating etc/Renviron
config.status: creating etc/javaconf
config.status: creating etc/ldpaths
config.status: creating m4/Makefile
config.status: creating po/Makefile
config.status: creating share/Makefile
config.status: creating src/Makefile
config.status: creating src/appl/Makefile
config.status: creating src/extra/Makefile
config.status: creating src/extra/blas/Makefile
config.status: creating src/extra/intl/Makefile
config.status: creating src/extra/tre/Makefile
config.status: creating src/extra/tzone/Makefile
config.status: creating src/extra/xdr/Makefile
config.status: creating src/include/Makefile
config.status: creating src/include/Rmath.h0
config.status: creating src/include/R_ext/Makefile
config.status: creating src/library/Recommended/Makefile
config.status: creating src/library/Makefile
config.status: creating src/library/base/DESCRIPTION
config.status: creating src/library/base/Makefile
config.status: creating src/library/compiler/DESCRIPTION
config.status: creating src/library/compiler/Makefile
config.status: creating src/library/datasets/DESCRIPTION
config.status: creating src/library/datasets/Makefile
config.status: creating src/library/graphics/DESCRIPTION
config.status: creating src/library/graphics/Makefile
config.status: creating src/library/graphics/src/Makefile
config.status: creating src/library/grDevices/DESCRIPTION
config.status: creating src/library/grDevices/Makefile
config.status: creating src/library/grDevices/src/Makefile
config.status: creating src/library/grDevices/src/cairo/Makefile
config.status: creating src/library/grid/DESCRIPTION
config.status: creating src/library/grid/Makefile
config.status: creating src/library/grid/src/Makefile
config.status: creating src/library/methods/DESCRIPTION
config.status: creating src/library/methods/Makefile
config.status: creating src/library/methods/src/Makefile
config.status: creating src/library/parallel/DESCRIPTION
config.status: creating src/library/parallel/Makefile
config.status: creating src/library/parallel/src/Makefile
config.status: creating src/library/profile/Makefile
config.status: creating src/library/stats/DESCRIPTION
config.status: creating src/library/stats/Makefile
config.status: creating src/library/stats/src/Makefile
config.status: creating src/library/stats4/DESCRIPTION
config.status: creating src/library/stats4/Makefile
config.status: creating src/library/splines/DESCRIPTION
config.status: creating src/library/splines/Makefile
config.status: creating src/library/splines/src/Makefile
config.status: creating src/library/tcltk/DESCRIPTION
config.status: creating src/library/tcltk/Makefile
config.status: creating src/library/tcltk/src/Makefile
config.status: creating src/library/tools/DESCRIPTION
config.status: creating src/library/tools/Makefile
config.status: creating src/library/tools/src/Makefile
config.status: creating src/library/translations/DESCRIPTION
config.status: creating src/library/translations/Makefile
config.status: creating src/library/utils/DESCRIPTION
config.status: creating src/library/utils/Makefile
config.status: creating src/library/utils/src/Makefile
config.status: creating src/main/Makefile
config.status: creating src/modules/Makefile
config.status: creating src/modules/X11/Makefile
config.status: creating src/modules/internet/Makefile
config.status: creating src/modules/lapack/Makefile
config.status: creating src/nmath/Makefile
config.status: creating src/nmath/standalone/Makefile
config.status: creating src/scripts/Makefile
config.status: creating src/scripts/R.sh
config.status: creating src/scripts/Rcmd
config.status: creating src/scripts/f77_f2c
config.status: creating src/scripts/javareconf
config.status: creating src/scripts/mkinstalldirs
config.status: creating src/scripts/pager
config.status: creating src/scripts/rtags
config.status: creating src/unix/Makefile
config.status: creating tests/Makefile
config.status: creating tests/Embedding/Makefile
config.status: creating tests/Examples/Makefile
config.status: creating tools/Makefile
config.status: creating src/include/config.h
config.status: src/include/config.h is unchanged
config.status: executing libtool commands
config.status: executing stamp-h commands

R is now configured for x86_64-pc-linux-gnu

  Source directory:          .
  Installation directory:    /usr

  C compiler:                icc   -O3 -xHost -m64 -qopenmp -fp-model precise -fp-model source -diag-disable=188,308 -I/opt/intel/composerxe/linux/mkl/include
  Fortran 77 compiler:       ifort   -O3 -xHost -m64 -qopenmp -fp-model precise -fp-model source -diag-disable=188,308 -I/opt/intel/composerxe/linux/mkl/include

  Default C++ compiler:      icpc    -O3 -xHost -m64 -qopenmp -fp-model precise -fp-model source -diag-disable=188,308 -I/opt/intel/composerxe/linux/mkl/include
  C++98 compiler:            icpc -std=gnu++98  -O3 -xHost -m64 -qopenmp -fp-model precise -fp-model source -diag-disable=188,308 -I/opt/intel/composerxe/linux/mkl/include
  C++11 compiler:            icpc -std=gnu++11  -O3 -xHost -m64 -qopenmp -fp-model precise -fp-model source -diag-disable=188,308 -I/opt/intel/composerxe/linux/mkl/include
  C++14 compiler:            icpc   -O3 -xHost -m64 -qopenmp -fp-model precise -fp-model source -diag-disable=188,308 -I/opt/intel/composerxe/linux/mkl/include
  C++17 compiler:              
  Fortran 90/95 compiler:    ifort  -O3 -xHost -m64 -qopenmp -fp-model precise -fp-model source -diag-disable=188,308 -I/opt/intel/composerxe/linux/mkl/include
  Obj-C compiler:            gcc -g -O2 -fobjc-exceptions

  Interfaces supported:      X11, tcltk
  External libraries:        readline, BLAS(MKL), LAPACK(in blas), curl
  Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo, ICU
  Options enabled:           shared R library, R profiling

  Capabilities skipped:      
  Options not enabled:       shared BLAS, memory profiling

  Recommended packages:      yes

make[1]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/m4'
make[1]: Nothing to be done for 'R'.
make[1]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/m4'
make[1]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/tools'
make[1]: Nothing to be done for 'R'.
make[1]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/tools'
make[1]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/doc'
make[2]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/doc/html'
make[2]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/doc/html'
make[2]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/doc/manual'
make[2]: Nothing to be done for 'R'.
make[2]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/doc/manual'
make[1]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/doc'
make[1]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/etc'
make[1]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/etc'
make[1]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/share'
make[1]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/share'
make[1]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src'
make[2]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/scripts'
creating src/scripts/R.fe
make[3]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/scripts'
make[3]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/scripts'
make[2]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/scripts'
make[2]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/include'
config.status: creating src/include/config.h
config.status: src/include/config.h is unchanged
Rmath.h is unchanged
make[3]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/include/R_ext'
make[3]: Nothing to be done for 'R'.
make[3]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/include/R_ext'
make[2]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/include'
make[2]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/extra'
make[3]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/extra/tre'
make[4]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/extra/tre'
make[4]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/extra/tre'
make[4]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/extra/tre'
make[4]: 'libtre.a' is up to date.
make[4]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/extra/tre'
make[3]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/extra/tre'
make[2]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/extra'
make[2]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/appl'
make[3]: Entering directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/appl'
icc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H    -fpic  -O3 -xHost -m64 -qopenmp -fp-model precise -fp-model source -diag-disable=188,308 -I/opt/intel/composerxe/linux/mkl/include  -c interv.c -o interv.o
In file included from ../../src/include/R_ext/RS.h(39),
                 from ../../src/include/R_ext/Applic.h(40),
                 from interv.c(26):
../../src/include/Rconfig.h(7): error: identifier "Binary" is undefined
  Binary file config.h matches
  ^

In file included from ../../src/include/R_ext/RS.h(39),
                 from ../../src/include/R_ext/Applic.h(40),
                 from interv.c(26):
../../src/include/Rconfig.h(7): error: expected a ";"
  Binary file config.h matches
              ^

In file included from ../../src/include/R_ext/RS.h(47),
                 from ../../src/include/R_ext/Applic.h(40),
                 from interv.c(26):
../../src/include/R_ext/Error.h(39): warning #12: parsing restarts here after previous syntax error
  void NORET Rf_error(const char *, ...);
                                        ^

compilation aborted for interv.c (code 2)
make[3]: *** [../../Makeconf:119: interv.o] Error 2
make[3]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/appl'
make[2]: *** [Makefile:47: R] Error 2
make[2]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src/appl'
make[1]: *** [Makefile:28: R] Error 1
make[1]: Leaving directory '/var/tmp/makepkg/r-mkl/src/R-3.4.0/src'
make: *** [Makefile:61: R] Error 1
==> ERROR: A failure occurred in build().

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