Я хочу установить модуль R-Perl для использования R из Perl, но у меня нет успеха при выполнении команды sudo R CMD INSTALL --configure-args='--with-in-perl' RSPerl/, как описано здесь: http://www.omegahat.org/RSPerl/RFromPerl.html. Я писал ранее об этой проблеме и определил, что У меня были проблемы с новым GCC 4.2. Тем не менее, я сейчас использую GCC 4.0.1 и у меня другие проблемы. Вот вывод команды выше:
* installing to library ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library’
* installing *source* package ‘RSPerl’ ...
checking for perl... /usr/bin/perl
No support for any of the Perl modules from calling Perl from R.
*****************************************************
Set PERL5LIB to /Library/Frameworks/R.framework/Versions/2.13/Resources/library/RSPerl/perl
*****************************************************
Testing: -F/Library/Frameworks/R.framework/.. -framework R
Using '/usr/bin/perl' as the perl executable
Perl modules (no):
Adding R package to list of Perl modules to enable callbacks to R from Perl
Creating the C code for dynamically loading modules with native code for Perl: R
modules: R; linking:
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
Support R in Perl: yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating inst/scripts/RSPerl.csh
config.status: creating inst/scripts/RSPerl.bsh
config.status: creating src/RinPerlMakefile
config.status: creating src/Makefile.PL
config.status: creating cleanup
config.status: creating src/R.pm
config.status: creating R/perl5lib.R
making target all in RinPerlMakefile
RinPerlMakefile:5: /Library/Frameworks/R.framework/Resources/etc/Makeconf: No such file or directory
make: *** No rule to make target `/Library/Frameworks/R.framework/Resources/etc/Makeconf'. Stop.
calling make -f Makefile.perl install
make: Makefile.perl: No such file or directory
make: *** No rule to make target `Makefile.perl'. Stop.
chmod: blib/lib/R.pm: No such file or directory
Finished configuration
** libs
*** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I. -arch x86_64 -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -I/usr/local/include -I/System/Library/Perl/5.10.0/darwin-thread-multi-2level/CORE -DPERL_POLLUTE -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -I/usr/local/include -fPIC -g -O2 -c Converters.c -o Converters.o
In file included from /Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:27,
from /Library/Frameworks/R.framework/Resources/include/Rdefines.h:26,
from RSCommon.h:55,
from RSPerl.h:8,
from Converters.h:4,
from Converters.c:1:
/Library/Frameworks/R.framework/Resources/include/Rconfig.h:5:25: error: ppc/Rconfig.h: No such file or directory
In file included from RSCommon.h:72,
from RSPerl.h:8,
from Converters.h:4,
from Converters.c:1:
/Library/Frameworks/R.framework/Resources/include/Rversion.h:5:26: error: ppc/Rversion.h: No such file or directory
In file included from RSPerl.h:8,
from Converters.h:4,
from Converters.c:1:
RSCommon.h:73:28: error: missing binary operator before token "("
lipo: can't open input file: /var/tmp//ccd76npm.out (No such file or directory)
make: *** [Converters.o] Error 1
ERROR: compilation failed for package ‘RSPerl’
* removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/RSPerl’
А вот содержимое config.log:
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by configure, which was
generated by GNU Autoconf 2.60. Invocation command line was
$ ./configure --with-in-perl
## --------- ##
## Platform. ##
## --------- ##
hostname = N01-0006-_MBP.local
uname -m = x86_64
uname -r = 10.8.0
uname -s = Darwin
uname -v = Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/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 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/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: 4.00 gigabytes
Default processor set: 79 tasks, 365 threads, 4 processors
Load average: 0.52, Mach factor: 3.46
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /usr/local/bin
PATH: /usr/local/sbin
PATH: /usr/local/mysql/bin
PATH: /opt/local/bin
PATH: /opt/local/sbin
PATH: /opt/local/bin
PATH: /opt/local/sbin
PATH: /usr/bin
PATH: /bin
PATH: /usr/sbin
PATH: /sbin
PATH: /usr/local/bin
PATH: /usr/X11/bin
## ----------- ##
## Core tests. ##
## ----------- ##
configure:1645: checking for perl
configure:1663: found /usr/bin/perl
configure:1675: result: /usr/bin/perl
configure:2013: checking for gcc
configure:2029: found /usr/bin/gcc
configure:2040: result: gcc
configure:2278: checking for C compiler version
configure:2285: gcc --version >&5
i686-apple-darwin10-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5494)
Copyright (C) 2005 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.
configure:2288: $? = 0
configure:2295: gcc -v >&5
Using built-in specs.
Target: i686-apple-darwin10
Configured with: /var/tmp/gcc_40/gcc_40-5494~315/src/configure --disable-checking -enable-werror --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/$/-4.0/ --with-gxx-include-dir=/include/c++/4.0.0 --with-slibdir=/usr/lib --build=i686-apple-darwin10 --with-arch=apple --with-tune=generic --host=i686-apple-darwin10 --target=i686-apple-darwin10
Thread model: posix
gcc version 4.0.1 (Apple Inc. build 5494)
configure:2298: $? = 0
configure:2305: gcc -V >&5
gcc-4.0: argument to `-V' is missing
configure:2308: $? = 1
configure:2331: checking for C compiler default output file name
configure:2358: gcc -arch x86_64 -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -I/usr/local/include -I/System/Library/Perl/5.10.0/darwin-thread-multi-2level/CORE -DPERL_POLLUTE conftest.c >&5
configure:2361: $? = 0
configure:2407: result: a.out
configure:2412: checking whether the C compiler works
configure:2422: ./a.out
configure:2425: $? = 0
configure:2442: result: yes
configure:2449: checking whether we are cross compiling
configure:2451: result: no
configure:2454: checking for suffix of executables
configure:2461: gcc -o conftest -arch x86_64 -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -I/usr/local/include -I/System/Library/Perl/5.10.0/darwin-thread-multi-2level/CORE -DPERL_POLLUTE conftest.c >&5
configure:2464: $? = 0
configure:2488: result:
configure:2494: checking for suffix of object files
configure:2520: gcc -c -arch x86_64 -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -I/usr/local/include -I/System/Library/Perl/5.10.0/darwin-thread-multi-2level/CORE -DPERL_POLLUTE conftest.c >&5
configure:2523: $? = 0
configure:2546: result: o
configure:2550: checking whether we are using the GNU C compiler
configure:2579: gcc -c -arch x86_64 -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -I/usr/local/include -I/System/Library/Perl/5.10.0/darwin-thread-multi-2level/CORE -DPERL_POLLUTE conftest.c >&5
configure:2585: $? = 0
configure:2592: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:2595: $? = 0
configure:2602: test -s conftest.o
configure:2605: $? = 0
configure:2619: result: yes
configure:2624: checking whether gcc accepts -g
configure:2654: gcc -c -g conftest.c >&5
configure:2660: $? = 0
configure:2667: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:2670: $? = 0
configure:2677: test -s conftest.o
configure:2680: $? = 0
configure:2810: result: yes
configure:2827: checking for gcc option to accept ISO C89
configure:2901: gcc -c -arch x86_64 -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -I/usr/local/include -I/System/Library/Perl/5.10.0/darwin-thread-multi-2level/CORE -DPERL_POLLUTE conftest.c >&5
configure:2907: $? = 0
configure:2914: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:2917: $? = 0
configure:2924: test -s conftest.o
configure:2927: $? = 0
configure:2947: result: none needed
configure:2988: gcc -c -arch x86_64 -arch i386 -arch ppc -g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -I/usr/local/include -I/System/Library/Perl/5.10.0/darwin-thread-multi-2level/CORE -DPERL_POLLUTE conftest.c >&5
configure:2994: $? = 0
configure:3001: test -z "$ac_c_werror_flag" || test ! -s conftest.err
configure:3004: $? = 0
configure:3011: test -s conftest.o
configure:3014: $? = 0
configure:3211: creating ./config.status
## ---------------------- ##
## Running config.status. ##
## ---------------------- ##
This file was extended by config.status, which was
generated by GNU Autoconf 2.60. Invocation command line was
CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status
on N01-0006-_MBP.local
config.status:584: creating src/Makevars
config.status:584: creating inst/scripts/RSPerl.csh
config.status:584: creating inst/scripts/RSPerl.bsh
config.status:584: creating src/RinPerlMakefile
config.status:584: creating src/Makefile.PL
config.status:584: creating cleanup
config.status:584: creating src/R.pm
config.status:584: creating R/perl5lib.R
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_c_compiler_gnu=yes
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_LDFLAGS_set=
ac_cv_env_LDFLAGS_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_objext=o
ac_cv_path_PERL=/usr/bin/perl
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
## ----------------- ##
## Output variables. ##
## ----------------- ##
CC='gcc'
CFLAGS=''
CPPFLAGS=''
DEFS='-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"'
ECHO_C='ECHO_N=''
ECHO_T=''
EXEEXT=''
LANGUAGE_DEFS=' -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1'
LDFLAGS=''
LD_PATH='/Library/Frameworks/R.framework/Versions/2.13/Resources/library/RSPerl/libs'
LD_PATH_VAR='DYLD_LIBRARY_PATH'
LIBOBJS=''
LIBS=''
LTLIBOBJS=''
NO_SUPPORT_R_IN_PERL='0'
OBJEXT='o'
OTHERLDFLAGS='-F/Library/Frameworks/R.framework/.. -framework R'
PACKAGE_BUGREPORT=''
PACKAGE_NAME=''
PACKAGE_STRING=''
PACKAGE_TARNAME=''
PACKAGE_VERSION=''
PATH_SEPARATOR=':'
PERL5_PATH='/Library/Frameworks/R.framework/Versions/2.13/Resources/library/RSPerl/perl'
PERL='/usr/bin/perl'
PERL_INSTALL_PREFIX='PREFIX=/Library/Frameworks/R.framework/Versions/2.13/Resources/library/RSPerl LIB=/Library/Frameworks/R.framework/Versions/2.13/Resources/library/RSPerl/perl'
PERL_LD_MAKE_ARG='LD=/usr/bin/gcc'
PERL_MODULE_SO_DIRS=''
R_HOME='/Library/Frameworks/R.framework/Resources'
R_IN_PERL_DEFINES='-DWITH_R_IN_PERL=1'
R_IN_PERL_LIBRARY='RinPerl'
R_LIBRARY_DIR='/Library/Frameworks/R.framework/Versions/2.13/Resources/library'
R_PACKAGE_DIR='/Library/Frameworks/R.framework/Versions/2.13/Resources/library/RSPerl'
R_PERL_MODULES='c("R")'
R_SHLIB_CPPFLAGS='-I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64'
R_SHLIB_LDFLAGS='-F/Library/Frameworks/R.framework/.. -framework R'
R_SO_DIR='-F/Library/Frameworks/R.framework/.. -framework R'
SHELL='/bin/sh'
ac_ct_CC='gcc'
bindir='${exec_prefix}/bin'
build_alias=''
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host_alias=''
htmldir='${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='/usr/local'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
configure: exit 0
Основываясь на некоторой информации, которую я прочитал http://passingcuriosity.com/2009/installing-pil-on-mac-os-x-leopard/, Я удалил флаги -arch ppc и -arch i386 из вызова gcc, и это сработало без ошибок. Однако я не уверен, как отредактировать исходный код R-Perl, чтобы убедиться, что при выполнении этого вызова GCC он запускается без ненужных флагов. Я попытался sudo R --arch=x86_64 CMD INSTALL ..., однако это все равно не удаляет другие архитектуры из этого вызова GCC.
Буду весьма признателен за понимание тех, у кого больше опыта, чем у меня. Спасибо!