在RedHat上安装RSPerl时出现问题_Perl_R_Redhat

在RedHat上安装RSPerl时出现问题

perl r

在RedHat上安装RSPerl时出现问题,perl,r,redhat,Perl,R,Redhat,我想在RedHat Linux中从Perl运行R（统计包）。我在网上发现有一个名为的包可以完成这项工作，但我很难在RedHat中安装它。此软件要求R作为一个组件安装。我按照说明进行了操作，但在（毫无问题地安装R之后）尝试安装RSPerl时，我遇到了以下问题 [root@xxx opt]# R CMD INSTALL -c -l ./ RSPerl_0.92-1.tar.gz * installing *source* package âRSPerlâ ... checking for perl

我想在RedHat Linux中从Perl运行R（统计包）。我在网上发现有一个名为的包可以完成这项工作，但我很难在RedHat中安装它。此软件要求R作为一个组件安装。我按照说明进行了操作，但在（毫无问题地安装R之后）尝试安装RSPerl时，我遇到了以下问题

[root@xxx opt]#  R CMD INSTALL -c -l ./ RSPerl_0.92-1.tar.gz
* installing *source* package âRSPerlâ ...
checking for perl... /usr/bin/perl
No support for any of the Perl modules from calling Perl from R.
*****************************************************

       Set PERL5LIB to /opt/RSPerl/perl

*****************************************************
Testing: -L/usr/local/lib64/R/lib -lR
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
gcc -std=gnu99 -I/usr/local/lib64/R/include -I.  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/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
gcc -std=gnu99 -I/usr/local/lib64/R/include -I.  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/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 Reflectance.c -o Reflectance.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I.  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/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 ForeignReference.c -o ForeignReference.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I.  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/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 UserConverters.c -o UserConverters.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I.  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/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 GeneralConverters.c -o GeneralConverters.o
making libPerlConverter.so
/usr/local/lib64/R/bin/R CMD SHLIB -o libPerlConverter.so Converters.c Reflectance.c ForeignReference.c UserConverters.o GeneralConverters.o
make[1]: Entering directory `/tmp/RtmpSqebDp/R.INSTALL68be5031/RSPerl/src'
gcc -std=gnu99 -shared -L/usr/local/lib64 -o libPerlConverter.so Converters.o Reflectance.o ForeignReference.o UserConverters.o GeneralConverters.o -Wl,-E -Wl,-rpath,/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/auto/DynaLoader/DynaLoader.a -L/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -lperl -lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc -L/usr/local/lib64/R/lib -lR
make[1]: Leaving directory `/tmp/RtmpSqebDp/R.INSTALL68be5031/RSPerl/src'
if test ! -d /opt/RSPerl/libs ; then mkdir /opt/RSPerl/libs ; fi
cp libPerlConverter.so /opt/RSPerl/libs
Makefile.PL PREFIX=/opt/RSPerl LIB=/opt/RSPerl/perl
make: Makefile.PL: Command not found
make: *** [Makefile.perl] Error 127
calling make -f Makefile.perl install
make: Makefile.perl: No such file or directory
make: *** No rule to make target `Makefile.perl'.  Stop.
chmod: cannot access `blib/lib/R.pm': No such file or directory
Finished configuration
** libs
gcc -std=gnu99 -I/usr/local/lib64/R/include -I.  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/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 RPerlElements.c -o RPerlElements.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I.  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/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 RPerlEval.c -o RPerlEval.o
RPerlEval.c: In function âRS_PerlEvalStringâ:
RPerlEval.c:20: warning: ISO C90 forbids mixed declarations and code
RPerlEval.c: In function âRS_PerlGetâ:
RPerlEval.c:128: warning: ISO C90 forbids mixed declarations and code
RPerlEval.c: In function âRS_PerlCallModifiedâ:
RPerlEval.c:208: warning: ISO C90 forbids mixed declarations and code
RPerlEval.c: In function âRS_PerlCallâ:
RPerlEval.c:377: warning: ISO C90 forbids mixed declarations and code
gcc -std=gnu99 -I/usr/local/lib64/R/include -I.  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/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 RPerlInit.c -o RPerlInit.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I.  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/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 RPerlNew.c -o RPerlNew.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I.  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/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 RPerlReference.c -o RPerlReference.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I.  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/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 RPerlVars.c -o RPerlVars.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I.  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/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 Utils.c -o Utils.o
Utils.c: In function âcharacterVectorToNullTerminatedArrayâ:
Utils.c:35: warning: assignment discards qualifiers from pointer target type
Utils.c: In function âcharacterVectorToArrayâ:
Utils.c:78: warning: assignment discards qualifiers from pointer target type
gcc -std=gnu99 -I/usr/local/lib64/R/include -I.  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/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 xsinit.c -o xsinit.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o RSPerl.so Converters.o ForeignReference.o GeneralConverters.o RPerlElements.o RPerlEval.o RPerlInit.o RPerlNew.o RPerlReference.o RPerlVars.o Reflectance.o UserConverters.o Utils.o xsinit.o -Wl,-E -Wl,-rpath,/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/auto/DynaLoader/DynaLoader.a -L/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -lperl -lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc -L/usr/local/lib64/R/lib -lR
installing to /opt/RSPerl/libs
** R
** inst
** preparing package for lazy loading
** help
Warning: /tmp/RtmpSqebDp/R.INSTALL68be5031/RSPerl/man/PerlReferenceObjects.Rd:32: unknown macro '\textit'
*** installing help indices
** building package indices ...
Removing additional files
rm: cannot remove `src/Makefile.perl': No such file or directory
rm: cannot remove `src/pm_to_blib': No such file or directory
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/opt/RSPerl/libs/RSPerl.so':
  /opt/RSPerl/libs/RSPerl.so: undefined symbol: boot_R
Error: loading failed
Execution halted
ERROR: loading failed
* removing â/opt/RSPerlâ
* restoring previous â/opt/RSPerlâ
[root@xxx opt]#

我的系统信息如下：

Linux version 2.6.18-194.el5 (mockbuild@x86-005.build.bos.redhat.com) (gcc version 4.1.2 20080704 (Red Hat 4.1.2-48)) #1 SMP Tue Mar 16 21:52:39 EDT 2010

它运行在64位Xeon服务器上

你知道发生了什么事吗

提前感谢。

RSPerl是R（或S）和Perl之间的接口。看起来您需要做更多的研究，找到一个适合您的安装的Perl包，或者如果您确实有一个兼容的版本，那么使用一个编译器标志或一个环境变量来告诉R在哪里可以找到它。然后安装RSPerl

您可能想看看这个从R-2.12中设置环境变量的示例。它们删除了对perl的要求，因此lib/R/etc/Renviron中的perl（env变量）将不再设置

一个快速修复方法是手动设置PERL，如下所示：

PERL=`which perl` R --vanilla CMD INSTALL -c -l ~/library/ RSPerl_0.92-1.tar.gz

通过设置环境变量$perl指向正确的perl目录（即export perl=/usr/bin/perl），确保您得到了perl dev，而不仅仅是perl（例如，在ubuntu下，apt get install libperl dev，如果您自己编译perl，这将不会是一个问题）

谢谢！