I am having trouble trying to install perl Tk on my system(fedora,perl v5.8.8).I downloaded the tarred module from http://search.cpan.org/~srezic/Tk-804.029/pod/gencmd, untarred it.In the terminal,I gave "perl Makefile.PL" which worked fine and then "make" which could not complete.Here is what it gave:
"make[1]: Entering directory `/work/harikal/Tk-804.029/pTk'
gcc -c -I.. -I. -Ibitmaps -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 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -DVERSION=\"804.029\" -DXS_VERSION=\"804.029\" -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE" -Wall -Wno-implicit-int -Wno-comment -Wno-unused -D__USE_FIXED_PROTOTYPES__ tkImgPhoto.c
tkImgPhoto.c: In function ‘AllocateColors’:
tkImgPhoto.c:3584: warning: implicit declaration of function ‘sazeof’
tkImgPhoto.c:3584: error: expected expression before ‘XColor’
make[1]: *** [tkImgPhoto.o] Error 1
make[1]: Leaving directory `/work/harikal/Tk-804.029/pTk'
make: *** [pTk/libpTk.a] Error 2"
and then it exits. What am I supposed to do??
Please Help
Thanks.
If you're using the system-installed Perl, then why not use the Fedora project's pre-built package for the module.
$ sudo yum install perl-Tk
I looked at http://cpansearch.perl.org/src/SREZIC/Tk-804.029/pTk/mTk/generic/tkImgPhoto.c - line 3584 and here says "sizeof" not "sazeof". Doublecheck your source/download.
Related
I want to perform pg_repack in remote postgres server. pg_repack is used to remove bloat from PostgreSQL.
I am following this for reference: https://reorg.github.io/pg_repack/#installation
After installing pgxn, we need to install pg_repack. It's done by
sudo pgxn install pg_repack
And it's resulting in this
INFO: best version: pg_repack 1.4.8
INFO: saving /tmp/tmp3dyb4e3e/pg_repack-1.4.8.zip
INFO: unpacking: /tmp/tmp3dyb4e3e/pg_repack-1.4.8.zip
INFO: building extension
gmake[1]: Entering directory '/tmp/tmp3dyb4e3e/pg_repack-1.4.8/bin'
gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-omit-frame-pointer -I/usr/include/postgresql -DREPACK_VERSION=1.4.8 -I. -I./ -I/usr/include/postgresql/14/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -c -o pg_repack.o pg_repack.c
gmake[1]: gcc: No such file or directory
gmake[1]: *** [<builtin>: pg_repack.o] Error 127
gmake[1]: Leaving directory '/tmp/tmp3dyb4e3e/pg_repack-1.4.8/bin'
gmake: *** [Makefile:35: all] Error 2
ERROR: command returned 2: gmake PG_CONFIG=/usr/bin/pg_config all`
I tried to clone this repo and perform gmake on it directly
gmake PG_CONFIG=/pg_config all
but still I'm getting
gmake: *** No rule to make target 'all'. Stop.
When I install B::C with cpanm, it hangs
$ sudo cpanm B::C
--> Working on B::C
Fetching http://www.cpan.org/authors/id/R/RU/RURBAN/B-C-1.57.tar.gz ... OK
Configuring B-C-1.57 ... OK
Building and testing B-C-1.57 ... ^C
First you'll want to try to check the install by using the verbose flag cpanm -v B::C, after which you should see a lot of looping like
x86_64-linux-gnu-gcc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib/x86_64-linux-gnu/perl/5.28/CORE -o cccode1_o1 cccode1_o1.c -Wl,-E -fstack-protector-strong -L/usr/local/lib -L/usr/lib/x86_64-linux-gnu/perl/5.28/CORE -lperl -ldl -lm -lpthread -lc -lcrypt 2>/dev/null 2>&1
# /usr/bin/ld: cannot find -lperl
collect2: error: ld returned 1 exit status
This is because ld can't find libperl.so. If you're on Debian you'll need to run,
sudo apt install libperl-dev
I am having trouble with ImageMagik on CentOS.
The error is:
Error: identify: no decode delegate for this image format `PNG' #
error/constitute.c/ReadImage/501.
convert -list configure
Path: /usr/lib64/ImageMagick-6.5.4/config/configure.xml
Name Value
-------------------------------------------------------------------------------
CC gcc -std=gnu99
CFLAGS -fopenmp -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -Wall -W -pthread
CONFIGURE ./configure '--build=x86_64-redhat-linux-gnu' '--host=x86_64-redhat-linux-gnu' '--target=x86_64-redhat-linux-gnu' '--program-prefix=' '--prefix=/usr' '--exec-prefix=/usr' '--bindir=/usr/bin' '--sbindir=/usr/sbin' '--sysconfdir=/etc' '--datadir=/usr/share' '--includedir=/usr/include' '--libdir=/usr/lib64' '--libexecdir=/usr/libexec' '--localstatedir=/var' '--sharedstatedir=/var/lib' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--enable-shared' '--disable-static' '--with-modules' '--with-perl' '--with-x' '--with-threads' '--with-magick_plus_plus' '--with-gslib' '--with-wmf' '--with-lcms' '--with-rsvg' '--with-xml' '--with-perl-options=INSTALLDIRS=vendor CC='\''gcc -L/builddir/build/BUILD/ImageMagick-6.5.4-7/magick/.libs'\'' LDDLFLAGS='\''-shared -L/builddir/build/BUILD/ImageMagick-6.5.4-7/magick/.libs'\''' '--without-dps' '--without-included-ltdl' '--with-ltdl-include=/usr/include' '--with-ltdl-lib=/usr/lib64' 'build_alias=x86_64-redhat-linux-gnu' 'host_alias=x86_64-redhat-linux-gnu' 'target_alias=x86_64-redhat-linux-gnu' 'CFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic' 'CXXFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic'
COPYRIGHT Copyright (C) 1999-2009 ImageMagick Studio LLC
CPPFLAGS -I/usr/include/ImageMagick
CXX g++
CXXFLAGS -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -Wall -W -pthread
DEFS -DHAVE_CONFIG_H
DELEGATES bzlib fontconfig freetype gs jpeg jng jp2 lcms openexr png rsvg tiff x11 xml wmf zlib
DISTCHECK_CONFIG_FLAGS 'CFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic' --disable-deprecated --with-quantum-depth=16 --with-umem=no --with-autotrace=no --with-dps=no --with-fontpath=
EXEC-PREFIX /usr
HOST x86_64-redhat-linux-gnu
LDFLAGS -L/usr/lib64 -lfreetype
LIB_VERSION 0x654
LIB_VERSION_NUMBER 6,5,4,7
LIBS -lMagickCore -llcms -ltiff -lfreetype -ljpeg -lfontconfig -lXext -lSM -lICE -lX11 -lXt -lbz2 -lz -lm -lgomp -lpthread -lltdl
NAME ImageMagick
PCFLAGS -fopenmp
PREFIX /usr
QuantumDepth 16
RELEASE_DATE 2014-02-10
VERSION 6.5.4
WEBSITE http://www.imagemagick.org
I can see "PNG" in the list of DELEGATES but there doesn't seem to be anything in the LIBS section (see above).
I have tried installing libpng, which is already installed and I've have re-installed ImageMagik from source but it still isn't working.
Any ideas?
configure attempts to configure with every available image delegate, so when you're building from source, you'll need to have the libpng-devel package installed. If for some reason it didn't detect it, you may want to try forcing it with --with-png=yes in your options to configure to get some feedback.
See http://www.imagemagick.org/script/advanced-unix-installation.php
i tried installing the perl module XML::LibXSLT but it fails. googled for it for hours now but nothing help so i am posting this. Maybe someone can help!
Thanks in advance!
cpan XML::LibXSLT
CPAN: Storable loaded ok (v2.20)
Going to read '/root/.cpan/Metadata'
Database was generated on Mon, 28 Oct 2013 11:08:37 GMT
Running install for module 'XML::LibXSLT'
CPAN: YAML loaded ok (v0.84)
Running make for S/SH/SHLOMIF/XML-LibXSLT-1.81.tar.gz
CPAN: Digest::SHA loaded ok (v5.47)
CPAN: Compress::Zlib loaded ok (v2.062)
Checksum for /root/.cpan/sources/authors/id/S/SH/SHLOMIF/XML-LibXSLT-1.81.tar.gz ok
CPAN: Archive::Tar loaded ok (v1.58)
XML-LibXSLT-1.81/
XML-LibXSLT-1.81/perl-libxml-mm.h
XML-LibXSLT-1.81/benchmark/
XML-LibXSLT-1.81/benchmark/Driver/
XML-LibXSLT-1.81/benchmark/Driver/Sablotron.pm
XML-LibXSLT-1.81/benchmark/Driver/LibXSLT.pm
XML-LibXSLT-1.81/benchmark/Driver/BaseClass.pm
XML-LibXSLT-1.81/benchmark/benchmark.pl
XML-LibXSLT-1.81/Changes
XML-LibXSLT-1.81/LibXSLT.pm
XML-LibXSLT-1.81/MANIFEST
XML-LibXSLT-1.81/testcases/
XML-LibXSLT-1.81/testcases/default.conf
XML-LibXSLT-1.81/example/
XML-LibXSLT-1.81/example/fatal.xsl
XML-LibXSLT-1.81/example/2.xml
XML-LibXSLT-1.81/example/bad3.xsl
XML-LibXSLT-1.81/example/nonfatal.xsl
XML-LibXSLT-1.81/example/1.xml
XML-LibXSLT-1.81/example/bad2.xsl
XML-LibXSLT-1.81/example/1.xsl
XML-LibXSLT-1.81/example/2.xsl
XML-LibXSLT-1.81/example/bad1.xsl
XML-LibXSLT-1.81/Makefile.PL
XML-LibXSLT-1.81/META.yml
XML-LibXSLT-1.81/META.json
XML-LibXSLT-1.81/README
XML-LibXSLT-1.81/t/
XML-LibXSLT-1.81/t/04params.t
XML-LibXSLT-1.81/t/rt71345_a.t
XML-LibXSLT-1.81/t/09exslt.t
XML-LibXSLT-1.81/t/06output.t
XML-LibXSLT-1.81/t/03input.t
XML-LibXSLT-1.81/t/08literal.t
XML-LibXSLT-1.81/t/02dromeds.t
XML-LibXSLT-1.81/t/06entities.t
XML-LibXSLT-1.81/t/11utf8.t
XML-LibXSLT-1.81/t/10functions.t
XML-LibXSLT-1.81/t/05quick.t
XML-LibXSLT-1.81/t/07blankdoc.t
XML-LibXSLT-1.81/t/13error.t
XML-LibXSLT-1.81/t/01basic.t
XML-LibXSLT-1.81/t/14security.t
XML-LibXSLT-1.81/t/12import.t
XML-LibXSLT-1.81/t/15misc.t
XML-LibXSLT-1.81/t/rt71345_b.t
XML-LibXSLT-1.81/typemap
XML-LibXSLT-1.81/LibXSLT.xs
XML-LibXSLT-1.81/ppport.h
XML-LibXSLT-1.81/perl-libxml-mm.c
CPAN: File::Temp loaded ok (v0.22)
CPAN.pm: Going to build S/SH/SHLOMIF/XML-LibXSLT-1.81.tar.gz
running xslt-config... failed
using fallback values for LIBS and INC
options:
LIBS='-L/usr/local/lib -L/usr/lib -lxslt -lxml2 -lz -lm'
INC='-I/usr/local/include -I/usr/include'
If this is wrong, Re-run as:
$ /usr/bin/perl Makefile.PL LIBS='-L/path/to/lib' INC='-I/path/to/include'
looking for -lxslt... yes
looking for -lexslt... yes
running pkg-config libexslt... ok
Checking if your kit is complete...
Looks good
Generating a GNU-style Makefile
Writing Makefile for XML::LibXSLT
Writing MYMETA.yml and MYMETA.json
cp LibXSLT.pm blib/lib/XML/LibXSLT.pm
/usr/bin/perl /usr/share/perl5/ExtUtils/xsubpp -typemap /usr/share/perl5/ExtUtils/typemap -typemap typemap LibXSLT.xs > LibXSLT.xsc && mv LibXSLT.xsc LibXSLT.c
gcc -c -I/usr/local/include -I/usr/include -I/usr/include/libxml2 -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DVERSION=\"1.81\" -DXS_VERSION=\"1.81\" -fPIC "-I/usr/lib64/perl5/CORE" -DHAVE_BLANK -DHAVE_BLANK -DHAVE_EXSLT LibXSLT.c
LibXSLT.xs: In function ‘LibXSLT__function’:
LibXSLT.xs:252: warning: pointer targets in passing argument 1 of ‘xmlNewDoc’ differ in signedness
/usr/include/libxml2/libxml/tree.h:735: note: expected ‘const xmlChar *’ but argument is of type ‘char *’
LibXSLT.xs: In function ‘LibXSLT_context_element’:
LibXSLT.xs:518: warning: unused variable ‘ent’
LibXSLT.xs: In function ‘LibXSLT_init_functions’:
LibXSLT.xs:916: warning: suggest parentheses around assignment used as truth value
LibXSLT.xs: In function ‘LibXSLT_init_elements’:
LibXSLT.xs:948: warning: suggest parentheses around assignment used as truth value
gcc -c -I/usr/local/include -I/usr/include -I/usr/include/libxml2 -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DVERSION=\"1.81\" -DXS_VERSION=\"1.81\" -fPIC "-I/usr/lib64/perl5/CORE" -DHAVE_BLANK -DHAVE_BLANK -DHAVE_EXSLT perl-libxml-mm.c
rm -f blib/arch/auto/XML/LibXSLT/LibXSLT.so
LD_RUN_PATH="/usr/lib64:/lib64" gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic LibXSLT.o perl-libxml-mm.o -o blib/arch/auto/XML/LibXSLT/LibXSLT.so \
-L/usr/local/lib -L/usr/lib -lxslt -lxml2 -lz -lm -lexslt -lgcrypt -ldl -lgpg-error -lresolv -lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lpthread -lc \
/usr/bin/ld: cannot find -lgdbm
collect2: ld returned 1 exit status
make: *** [blib/arch/auto/XML/LibXSLT/LibXSLT.so] Error 1
SHLOMIF/XML-LibXSLT-1.81.tar.gz
/usr/bin/make -- NOT OK
Running make test
Can't test without successful make
Running make install
Make had returned bad status, install seems impossible
'
Any help is highly appreciated!
The error is /usr/bin/ld: cannot find -lgdbm. do you find gdbm library on your system?
run:
# updatedb
# locate gdbm
The output of locate command should list libgdbm.so. If it is not then try installing the same using your Distro's package manager:
Here is output on my ubuntu:
# locate gdbm
/usr/lib/libgdbm.so.3
/usr/lib/libgdbm.so.3.0.0
/usr/lib/libgdbm_compat.so.3
/usr/lib/libgdbm_compat.so.3.0.0
and here is the output from my RHEL 6.4:
# locate gdbm
/usr/lib64/libgdbm.so.2
/usr/lib64/libgdbm.so.2.0.0
To install gdbm, run these commands:
on ubuntu: apt-get install libgdbm3
On centos/RHEL: yum install gdbm
hope this helps.
/usr/bin/ld: cannot find -lgdbm
Looks like you don't have the gdbm library installed. I can't see which Linux (or, perhaps, Unix) distribution you're using, but gdbm is almost certainly per-packaged for it, so you just need to work out what the package is called and use apt or yum (or whatever is appropriate) to install it.
I want to run R (the statistical package) from Perl in RedHat Linux. I found online that there is a package called RSPerl that does this job but I have hard time installing it in RedHat. This software requires R to be installed as a shared library. I followed the instructions but I am facing the following problem when (after installing R without problem) I try to install RSPerl.
[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]#
My system information is the following:
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
and it runs on a 64 bit Xeon server.
Do you have any idea what's going on?
Thank you in advance.
From R-2.12 they remove requirement on perl, hence the PERL (env variable) in lib/R/etc/Renviron will not be set anymore.
One quick fix is to manually set PERL, as following:
PERL=`which perl` R --vanilla CMD INSTALL -c -l ~/library/ RSPerl_0.92-1.tar.gz
make sure you get perl-dev, not only perl (e.g. under ubuntu, apt-get install libperl-dev, if you compiled perl yourself, this won't be a problem)
RSPerl is an interface between R (or S) and Perl. It looks like you need to do some more research and find a Perl package that fits your installation or if you do have a compatible version use a compiler flag or an environment variable that tells R where to find it. Then install RSPerl.
You might want to look at this example of setting environment variables from an admittedly old posting from Duncan Temple Lang.