Problem installing ARACHNEof Broad Institute

[aurora.labastida]

Hi everyone,

I have been trying to install Arachne in Ubuntu 13.04 with no succes. I have gcc version 4.7.3 and this is what I did:

+I downloaded and extracted the binary distribution of XERCES (xerces-c-3.1.1-x86_64-linux-gcc-3.4.tar.gz)
+I downloaded and extracted the ARACHNE (arachne-46233.tar.gz)
:::From now on I will refer to xerces-c-3.1.1-x86_64-linux-gcc-3.4/ and to arachne-46233/ as XERCES/ and ARACHNE/:::
+I copied the the following files from XERCES/bin to ARACHNE/src

CreateDOMDocument
DOMCount
DOMPrint
EnumVal
MemParse
PParse
PSVIWriter
Redirect
SAX2Count
SAX2Print
SAXCount
SAXPrint
SCMPrint
SEnumVal
StdInParse
XInclude

+ I also copied the XERCES/include/ and XERCES/lib/ to ARACHNE/src

+ I ran: sudo ./configure --with-xerces=XERCES/ with apparently no errors.

+I ran sudo make with the following errors at the end:

g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=3.8.0-19-generic -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -I/opt/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include -I/opt/xerces-c-3.1.1-x86_64-linux-gcc-3.4//include/xercesc -fopenmp -g -O2 -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -ggdb -DNDEBUG -MT ReadTemplate.o -MD -MP -MF .deps/ReadTemplate.Tpo -c -o ReadTemplate.o `test -f 'simulation/ReadTemplate.cc' || echo './'`simulation/ReadTemplate.cc
In file included from ./random/SerRand.h:13:0,
from simulation/ReadTemplate.cc:6:
./random/GnuRandom.h:52:5: error: ‘_G_uint32_t’ does not name a type
./random/GnuRandom.h:57:5: error: ‘_G_uint32_t’ does not name a type
./random/GnuRandom.h:71:13: error: ‘_G_uint32_t’ does not name a type
./random/GnuRandom.h:157:5: error: ‘_G_int32_t’ does not name a type
./random/GnuRandom.h:158:5: error: ‘_G_int32_t’ does not name a type
./random/GnuRandom.h:159:5: error: ‘_G_int32_t’ does not name a type
./random/GnuRandom.h:160:5: error: ‘_G_int32_t’ does not name a type
./random/GnuRandom.h:165:21: error: expected ‘)’ before ‘seed1’
./random/GnuRandom.h:170:13: error: ‘_G_uint32_t’ does not name a type
./random/GnuRandom.h:172:5: error: ‘_G_int32_t’ does not name a type
./random/GnuRandom.h:173:16: error: ‘_G_int32_t’ has not been declared
./random/GnuRandom.h:174:5: error: ‘_G_int32_t’ does not name a type
./random/GnuRandom.h:175:16: error: ‘_G_int32_t’ has not been declared
./random/GnuRandom.h:176:17: error: ‘_G_int32_t’ has not been declared
./random/GnuRandom.h:176:29: error: ‘_G_int32_t’ has not been declared
./random/GnuRandom.h:179:8: error: ‘_G_int32_t’ does not name a type
./random/GnuRandom.h:184:13: error: variable or field ‘seed1’ declared void
./random/GnuRandom.h:184:13: error: ‘_G_int32_t’ was not declared in this scope
./random/GnuRandom.h:188:8: error: ‘_G_int32_t’ does not name a type
./random/GnuRandom.h:193:13: error: variable or field ‘seed2’ declared void
./random/GnuRandom.h:193:13: error: ‘_G_int32_t’ was not declared in this scope
./random/GnuRandom.h:198:14: error: variable or field ‘reseed’ declared void
./random/GnuRandom.h:198:14: error: ‘_G_int32_t’ was not declared in this scope
./random/GnuRandom.h:198:29: error: ‘_G_int32_t’ was not declared in this scope
make[2]: *** [ReadTemplate.o] Error 1
make[2]: Leaving directory `/opt/arachne-46233/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/opt/arachne-46233/src'
make: *** [all-recursive] Error 1

No ARACHNE/bin directory has been generated, Does anyone knows how to solve it?

Thank you in advance for your help
AURORA

[ddenny]

One fix

I had the exact same problem. It seems that a header file is missing in a couple of places. I hacked it in by hand and it rebuilt okay.

The file missing is src/random/GnuTypes.h.
The files I patched up (by hand) are:
src/ueberal/MiniSuperizer.cc
src/simulator/ReadTemplate.cc
src/random/SerRand.cc
src/random/GnuRandom.cc

I placed a line:
#include "random/GnuTypes.h"
above all the includes in each offending file and restarted make process.

This is an example from GnuRandom:
"
#ifdef __GNUG__
#pragma implementation
#include "random/GnuTypes.h"
#include "random/GnuRandom.h"

// DiscUnif.cc
"

I'm sure there is a more elegant way, but this was expedient and trivial (once the problem was identified.)

[bram]

Dear users,

I am trying to install Arachne on an osx 10.6.8, but cannot seem to install ARACHNE correctly. Following the instructions on their wiki, I installed xerces-c-3.1.1 from source simply by following the instructions for UNIX systems, and added the following lines (as indicated) to my .bash_profile:

export PATH="/Applications/xerces-c-3.1.1-x86_64-linux-gcc-3.4/bin:$PATH"
export DYLD_LIBRARY_PATH="/Applications/xerces-c-3.1.1-x86_64-linux-gcc-3.4/lib:$DYLD_LIBRARY_PATH"

After that, I copied the contents of the entire xerces directory to ARACHNE/src to be sure I did't miss a required file [but did not overwrite files with the same name].

What's weird is that, when I configure, I always fail...

Below the output of the configure and make messages. Is there someone that can point me to what I,m doing wrong?

$ ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... i386-apple-darwin10.8.0
checking host system type... i386-apple-darwin10.8.0
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... /opt/local/bin/gsed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /opt/local/bin/ld
checking if the linker (/opt/local/bin/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /opt/local/bin/nm
checking the name lister (/opt/local/bin/nm) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /opt/local/bin/ld option to reload object files... -r
checking for objdump... no
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /opt/local/bin/nm output from gcc object... ok
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
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... -fno-common -DPIC
checking if gcc PIC flag -fno-common -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/opt/local/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin10.8.0 dyld
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... no
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 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 how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /opt/local/bin/ld
checking if the linker (/opt/local/bin/ld) is GNU ld... no
checking whether the g++ linker (/opt/local/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fno-common -DPIC
checking if g++ PIC flag -fno-common -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/opt/local/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin10.8.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether byte ordering is bigendian... no
g++ version is >= 4.7... yes
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... -D_THREAD_SAFE
checking for gcc option to support OpenMP... -fopenmp
checking validity of OpenMP configuation.... checking for Xerces C++ Parser headers in /usr/local/include and /usr/local/include/xercesc... found
checking for Xerces C++ Parser libraries... found
checking for Xerces C++ Parser... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
config.status: executing libtool commands

and after $ make
Making all in src
make all-am
g++ -DHAVE_CONFIG_H -I. -DRELEASE=3.0 -DMAKE_OS_RELEASE=10.8.0 -DMAKE_RELEASE=3.0 -DSVN_VERSION=46233 -I/usr/local/include -I/usr/local/include/xercesc -fopenmp -g -O2 -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -ggdb -DNDEBUG -MT ErrNo.o -MD -MP -MF .deps/ErrNo.Tpo -c -o ErrNo.o `test -f 'system/ErrNo.cc' || echo './'`system/ErrNo.cc
In file included from ./feudal/BinaryStream.h:26:0,
from ./feudal/FeudalString.h:21,
from ./feudal/CharString.h:19,
from ./string.h:13,
from /opt/local/include/gcc47/c++/cstring:44,
from system/ErrNo.cc:17:
/opt/local/include/gcc47/c++/cstring:77:11: error: '::memchr' has not been declared
/opt/local/include/gcc47/c++/cstring:78:11: error: '::memcmp' has not been declared
/opt/local/include/gcc47/c++/cstring:79:11: error: '::memcpy' has not been declared
/opt/local/include/gcc47/c++/cstring:80:11: error: '::memmove' has not been declared
/opt/local/include/gcc47/c++/cstring:81:11: error: '::memset' has not been declared
/opt/local/include/gcc47/c++/cstring:82:11: error: '::strcat' has not been declared
/opt/local/include/gcc47/c++/cstring:83:11: error: '::strcmp' has not been declared
/opt/local/include/gcc47/c++/cstring:84:11: error: '::strcoll' has not been declared
/opt/local/include/gcc47/c++/cstring:85:11: error: '::strcpy' has not been declared
/opt/local/include/gcc47/c++/cstring:86:11: error: '::strcspn' has not been declared
/opt/local/include/gcc47/c++/cstring:87:11: error: '::strerror' has not been declared
/opt/local/include/gcc47/c++/cstring:88:11: error: '::strlen' has not been declared
/opt/local/include/gcc47/c++/cstring:89:11: error: '::strncat' has not been declared
/opt/local/include/gcc47/c++/cstring:90:11: error: '::strncmp' has not been declared
/opt/local/include/gcc47/c++/cstring:91:11: error: '::strncpy' has not been declared
/opt/local/include/gcc47/c++/cstring:92:11: error: '::strspn' has not been declared
/opt/local/include/gcc47/c++/cstring:93:11: error: '::strtok' has not been declared
/opt/local/include/gcc47/c++/cstring:94:11: error: '::strxfrm' has not been declared
/opt/local/include/gcc47/c++/cstring:95:11: error: '::strchr' has not been declared
/opt/local/include/gcc47/c++/cstring:96:11: error: '::strpbrk' has not been declared
/opt/local/include/gcc47/c++/cstring:97:11: error: '::strrchr' has not been declared
/opt/local/include/gcc47/c++/cstring:98:11: error: '::strstr' has not been declared
In file included from ./feudal/FeudalString.h:21:0,
from ./feudal/CharString.h:19,
from ./string.h:13,
from /opt/local/include/gcc47/c++/cstring:44,
from system/ErrNo.cc:17:
./feudal/BinaryStream.h: In constructor 'MagicToken::MagicToken()':
./feudal/BinaryStream.h:37:46: error: 'memcpy' was not declared in this scope
./feudal/BinaryStream.h: In member function 'bool MagicToken::isValid()':
./feudal/BinaryStream.h:42:54: error: 'memcmp' was not declared in this scope
./feudal/BinaryStream.h: In member function 'void BinaryWriter::writeBuf(const void*, size_t)':
./feudal/BinaryStream.h:148:30: error: 'memcpy' was not declared in this scope
./feudal/BinaryStream.h:150:33: error: 'memcpy' was not declared in this scope
./feudal/BinaryStream.h: In member function 'void BinaryReader::read(void*, size_t)':
./feudal/BinaryStream.h:272:30: error: 'memcpy' was not declared in this scope
./feudal/BinaryStream.h:275:35: error: 'memcpy' was not declared in this scope
system/ErrNo.cc: In member function 'std::string ErrNo::text() const':
system/ErrNo.cc:30:55: error: 'strerror_r' was not declared in this scope
make[2]: *** [ErrNo.o] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1

Already many thanks!

Bram

[GenoMax]

Are you using the newest version of Xcode available for OS X (10.6.x, which is old BTW)?

Based on the errors you are seeing you may need to check (and optionally add) the order of two header lines suggested in this post: http://stackoverflow.com/questions/9...mpiling-c-code

[bram]

Dear GenoMax,

Thanks for the hint to this post, but this unfortunately does not seem to work.
I tried several options by replacements in all the *.h files:
a) replaced all occurrences of "#include <string>" with
#include <string>
#include <cstring>
b) replaced all occurrences of "#include <string>" with
#include <cstring>
#include <string>
c) replaced all occurrences of "#include <cstring>" with
#include <cstring>
#include <string>
d) replaced all occurrences of "#include <cstring>" with
#include <string>
#include <cstring>

Each time, I re-configured from a freshly extracted arachne.tar.gz, but the error message at the make-step keeps being the same as above.

Any more hints?

Thanks again!

Bram

[offspring]

Dear users,

I am trying to install Arachne on an osx 10.6.8, but cannot seem to install ARACHNE correctly. Following the instructions on their wiki, I installed xerces-c-3.1.1 from source simply by following the instructions for UNIX systems, and added the following lines (as indicated) to my .bash_profile:

export PATH="/Applications/xerces-c-3.1.1-x86_64-linux-gcc-3.4/bin:$PATH"
export DYLD_LIBRARY_PATH="/Applications/xerces-c-3.1.1-x86_64-linux-gcc-3.4/lib:$DYLD_LIBRARY_PATH"

After that, I copied the contents of the entire xerces directory to ARACHNE/src to be sure I did't miss a required file [but did not overwrite files with the same name].

Hi Bram,

you said you built xerces from source, but the export lines above point to directories from the xerces Linux distribution. Are you sure you're using the correct xerces?

[bram]

Dear offspring,

Thx for pointing that out. I rebuilt from source and set the correct path to /bin and /lib, but unfortunately that too doesn't do the trick.