libcrispr install error

[11xinqi]

Hi, We think crass is a very cool tool and preparing using it to analysis our data. However, when we install libcripsr, some error occurs. There are there step we should run. I have pasted the message of each step below:

./autogen.sh

Preparing the libcrispr build system...please wait

Found GNU Autoconf version 2.68 Found GNU Automake version 1.9.6 Found GNU Libtool version 2.4

Automatically preparing build ... Warning: autoreconf failed Attempting to run the preparation steps individually

Preparing build ... done

The libcrispr build system is now prepared. To build here, run: ./configure make

./configure

checking for a BSD-compatible install... /usr/bin//install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking how to print strings... printf checking for style of include used by make... GNU checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin//ld checking if the linker (/usr/bin//ld) 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 whether ln -s works... yes checking the maximum length of command line arguments... 98304 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin//ld 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 ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin//nm -B output from gcc object... ok checking for sysroot... no checking for mt... mt checking if mt is a manifest tool... no checking how to run the C preprocessor... gcc -E 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 for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin//ld -m elf_x86_64) supports shared libraries... 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... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin//ld -m elf_x86_64 checking if the linker (/usr/bin//ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin//ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin//ld -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 whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking dependency style of g++... (cached) gcc3 checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking dependency style of gcc... (cached) gcc3 checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... no checking for Xerces C++ Parser headers in /panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include and /panfs/home /jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include/xercesc... found checking for Xerces C++ Parser libraries... found checking for Xerces C++ Parser... yes checking for ANSI C header files... (cached) yes configure: creating ./config.status config.status: creating Makefile config.status: creating libcrispr/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands

make

Making install in libcrispr make[1]: Entering directory /panfs/home/jipfnew/software/ctSkennerton-libcrispr-9efca1a/libcrispr' if /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/panfs/home/jipfnew/software/xerces-c-3.1.1-x8 6_64-linux-gcc-3.4//include -I/panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include/xercesc -Werror -Wall -peda ntic -g -O2 -MT libcrispr_la-base.lo -MD -MP -MF ".deps/libcrispr_la-base.Tpo" -c -o libcrispr_la-base.lotest -f 'base.cpp' || ec ho './'base.cpp; \ then mv -f ".deps/libcrispr_la-base.Tpo" ".deps/libcrispr_la-base.Plo"; else rm -f ".deps/libcrispr_la-base.Tpo"; exit 1; f i libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include -I/ panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include/xercesc -Werror -Wall -pedantic -g -O2 -MT libcrispr_la-ba se.lo -MD -MP -MF .deps/libcrispr_la-base.Tpo -c base.cpp -fPIC -DPIC -o .libs/libcrispr_la-base.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include -I/ panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include/xercesc -Werror -Wall -pedantic -g -O2 -MT libcrispr_la-ba se.lo -MD -MP -MF .deps/libcrispr_la-base.Tpo -c base.cpp -o libcrispr_la-base.o >/dev/null 2>&1 if /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/panfs/home/jipfnew/software/xerces-c-3.1.1-x8 6_64-linux-gcc-3.4//include -I/panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include/xercesc -Werror -Wall -peda ntic -g -O2 -MT libcrispr_la-parser.lo -MD -MP -MF ".deps/libcrispr_la-parser.Tpo" -c -o libcrispr_la-parser.lotest -f 'parser.cp p' || echo './'parser.cpp; \ then mv -f ".deps/libcrispr_la-parser.Tpo" ".deps/libcrispr_la-parser.Plo"; else rm -f ".deps/libcrispr_la-parser.Tpo"; exi t 1; fi libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include -I/ panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include/xercesc -Werror -Wall -pedantic -g -O2 -MT libcrispr_la-pa rser.lo -MD -MP -MF .deps/libcrispr_la-parser.Tpo -c parser.cpp -fPIC -DPIC -o .libs/libcrispr_la-parser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include -I/ panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include/xercesc -Werror -Wall -pedantic -g -O2 -MT libcrispr_la-pa rser.lo -MD -MP -MF .deps/libcrispr_la-parser.Tpo -c parser.cpp -o libcrispr_la-parser.o >/dev/null 2>&1 if /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/panfs/home/jipfnew/software/xerces-c-3.1.1-x8 6_64-linux-gcc-3.4//include -I/panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include/xercesc -Werror -Wall -peda ntic -g -O2 -MT libcrispr_la-reader.lo -MD -MP -MF ".deps/libcrispr_la-reader.Tpo" -c -o libcrispr_la-reader.lotest -f 'reader.cp p' || echo './'reader.cpp; \ then mv -f ".deps/libcrispr_la-reader.Tpo" ".deps/libcrispr_la-reader.Plo"; else rm -f ".deps/libcrispr_la-reader.Tpo"; exi t 1; fi libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include -I/ panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include/xercesc -Werror -Wall -pedantic -g -O2 -MT libcrispr_la-re ader.lo -MD -MP -MF .deps/libcrispr_la-reader.Tpo -c reader.cpp -fPIC -DPIC -o .libs/libcrispr_la-reader.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include -I/ panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include/xercesc -Werror -Wall -pedantic -g -O2 -MT libcrispr_la-re ader.lo -MD -MP -MF .deps/libcrispr_la-reader.Tpo -c reader.cpp -o libcrispr_la-reader.o >/dev/null 2>&1 if /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/panfs/home/jipfnew/software/xerces-c-3.1.1-x8 6_64-linux-gcc-3.4//include -I/panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include/xercesc -Werror -Wall -peda ntic -g -O2 -MT libcrispr_la-writer.lo -MD -MP -MF ".deps/libcrispr_la-writer.Tpo" -c -o libcrispr_la-writer.lotest -f 'writer.cp p' || echo './'writer.cpp; \ then mv -f ".deps/libcrispr_la-writer.Tpo" ".deps/libcrispr_la-writer.Plo"; else rm -f ".deps/libcrispr_la-writer.Tpo"; exi t 1; fi libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include -I/ panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include/xercesc -Werror -Wall -pedantic -g -O2 -MT libcrispr_la-wr iter.lo -MD -MP -MF .deps/libcrispr_la-writer.Tpo -c writer.cpp -fPIC -DPIC -o .libs/libcrispr_la-writer.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include -I/ panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include/xercesc -Werror -Wall -pedantic -g -O2 -MT libcrispr_la-wr iter.lo -MD -MP -MF .deps/libcrispr_la-writer.Tpo -c writer.cpp -o libcrispr_la-writer.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -o libcrispr.la -rpath /usr/local/lib -L/panfs/home/jipfnew/software/xerces- c-3.1.1-x86_64-linux-gcc-3.4//lib -version-info 1:1:0 -lxerces-c libcrispr_la-base.lo libcrispr_la-parser.lo libcrispr_la-reader .lo libcrispr_la-writer.lo make[1]: Leaving directory/panfs/home/jipfnew/software/ctSkennerton-libcrispr-9efca1a/libcrispr' libtool: link: warning: library /panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4//lib/libxerces-c.la' was moved. grep: /usr/local/glibc2/lib/../lib64/libstdc++.la: No such file or directory /bin/sed: can't read /usr/local/glibc2/lib/../lib64/libstdc++.la: No such file or directory libtool: link:/usr/local/glibc2/lib/../lib64/libstdc++.la' is not a valid libtool archive make[1]: * [libcrispr.la] Error 1 make: * [install-recursive] Error 1

It seems happened at the 'make' step. But I don't know how to handle this problem. Can someone tell me what's wrong?

Hope to hear from you soon.

[ctSkennerton]

Can you check your version of g++? From some of this output it look like you are using version 3.4, which is not supported. I've only tested installs with version 4.2 or greater.

[11xinqi]

Hi, ctSkennerton Thank you for you opinion, I have checked my g++ version. The version is 4.5.2. The info as bellow:

 Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-unknown-linux-gnu/4.5.2/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../gcc-4.5.2/configure --with-gmp-lib=/usr/local/lib --with-mpc-lib=/usr/local/lib --with-mpfr-     lib=/usr/local/lib
Thread model: posix
 gcc version 4.5.2 (GCC) 

[ctSkennerton]

Okay so next thing, the error is thrown at this line:

/usr/local/glibc2/lib/../lib64/libstdc++.la: No such file or directory

can you confirm where this file is?

Also, how did you install xerces-c++?

[11xinqi]

Hi,

I have found my libstdc++.la file in the follow dirictories:

cmd: locate libstdc++.la

/usr/local/lib/libstdc++.la
/usr/local/lib64/libstdc++.la

And I have installed the xerces-c++ tool in two ways:

One is downloading the source distributions: Xerces C++ 3.1.1 - tar.gz

and install the software.

The other one is downloading the binary distributions:
Xerces C++ 3.1.1 - x86_64-linux-gcc-3.4.tar.gz

When I install libcrispr, I have give the path to configure command (--with-xerces parameter).

_

On May 13, 2013, at 9:39 AM, "Connor T. Skennerton" notifications@github.com wrote:

Okay so next thing, the error is thrown at this line:

/usr/local/glibc2/lib/../lib64/libstdc++.la: No such file or directory can you confirm where this file is?

Also, how did you install xerces-c++?

— Reply to this email directly or view it on GitHub.

[ctSkennerton]

This is interesting, libstdc++ is in the place where i would expect it, but during install its looking for it in /usr/local/glibc2/lib/../lib64/. During this install are you using the binary distribution of xerces or the one that you compiled from source?

[11xinqi]

Hi, I have compiled the source distribution.

On May 13, 2013, at 10:09 AM, "Connor T. Skennerton" notifications@github.com wrote:

This is interesting, libstdc++ is in the place where i would expect it, but during install its looking for it in /usr/local/glibc2/lib/../lib64/. During this install are you using the binary distribution of xerces or the one that you compiled from source?

— Reply to this email directly or view it on GitHub.

[ctSkennerton]

okay, the only reason I ask is that in the output from configure it is using the name of the binary distribution: xerces-c-3.1.1-x86_64-linux-gcc-3.4

can you show me the exact command that you wrote for configure as well as the path locations to both the binary and source installs of xerces and the command that you used for installing xerces from source?

[11xinqi]

Hi, I have rechecked the xerces tool. Yes, it's binary distribution. For this distribution, i just download the file, and uncompressed the file. Then, I have downloaded the libcripsr file, then ran ./sutogen.sh After that, ran configure file, cmd : ./configure --with-xerces=/panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4 --with-xerces-lib=/panfs/home/jipfnew/software/xerces-c-3.1.1-x86_64-linux-gcc-3.4/lib/ at last, run 'make install'

On May 13, 2013, at 10:34 AM, "Connor T. Skennerton" notifications@github.com wrote:

okay, the only reason I ask is that in the output from configure it is using the name of the binary distribution: xerces-c-3.1.1-x86_64-linux-gcc-3.4

can you show me the exact command that you wrote for configure as well as the path locations to both the binary and source installs of xerces and the command that you used for installing xerces from source?

— Reply to this email directly or view it on GitHub.

[ctSkennerton]

Okay I think that there is a problem with the binary distribution of xerces.

Can you download the source code for xerces off the website, compile and install it (instructions: http://xerces.apache.org/xerces-c/install-3.html#Unix). Then during libcrispr install use the --with-xerces option to point to the directory where you installed xerces (this should be a directory that within it contains lib and include directories for xerces). You don't need to use the --with-xerces-lib option, the library should be automatically detected if you give configure the correct install directory.

[11xinqi]

Hi, Sorry for the late reply. Now, I install the software successfully follow your opinion. I think the problem is xerces. I have downloaded the source code for xerces, installed it. Then everything goes well. I am using it analysis my data. Thank you very much!

On May 13, 2013, at 10:56 AM, Connor T. Skennerton notifications@github.com wrote:

Okay I think that there is a problem with the binary distribution of xerces.

Can you download the source code for xerces off the website, compile and install it (instructions: http://xerces.apache.org/xerces-c/install-3.html#Unix). Then during libcrispr install use the --with-xerces option to point to the directory where you installed xerces (this should be a directory that within it contains lib and include directories for xerces). You don't need to use the --with-xerces-lib option, the library should be automatically detected if you give configure the correct install directory.

— Reply to this email directly or view it on GitHub.

[ctSkennerton]

great to hear