Yep, I just found that also and it works.
I only have survival skills in C++ so thanks for you quick responses.
With the xtandem build from the xtandem site I had to define GCC4_3 in
the Makefile and then change the if GCC4_3 block in stdafx.h from:
#include <stdio>
#include <stdlib>
#include <cstring>
to:
#include <stdio.h>
#include <stdlib.h>
#include <cstring>
I have no idea why it worked but it did not work with the TPP xtandem
source.
this is the error if I set it up the way it worked with the Xtandem
site version:
g++ -O2 -DGCC4 -DPLUGGABLE_SCORING -D__LINUX__ -
DDEFAULT_TPP_INSTALL_ROOT=\"/usr/local/labkey/bin/\" -
D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DREAD_GZIP -I ../../
gzstream -DHAVE_PWIZ_MZML_LIB -iprefix /root/trans_proteomic_pipeline/
src/../extern/pwiz/ -iwithprefix pwiz/data/msdata -iwithprefix pwiz/
data -I/root/trans_proteomic_pipeline/src/../extern/pwiz -iwithprefix
pwiz -iwithprefix pwiz/utility/misc -iwithprefix pwiz/utility/math -I/
usr/local/include/boost-1_39/ -iwithprefix pwiz_boost_additions -I/
root/trans_proteomic_pipeline/src/Parsers/ramp -I /root/
trans_proteomic_pipeline/src/Parsers/ramp -c -o linuxloadmspectrum.o
loadmspectrum.cpp
In file included from saxgamlhandler.h:140,
from loadmspectrum.h:235,
from loadmspectrum.cpp:143:
saxhandler.h:240: error: ‘uint32_t’ has not been declared
saxhandler.h:241: error: ‘uint64_t’ does not name a type
I have hit another error in the TPP build. I've just started to
investigate ( I found another posting about this but on a windows
server) but if you have a quick answer please let me know.
g++ -D__LINUX__ -DDEFAULT_TPP_INSTALL_ROOT=\"/usr/local/labkey/bin/\" -
D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DXML_ONLY -D__INTEL__ -
DINLINING -DTPPLIB -fPIC -I. -I/root/trans_proteomic_pipeline/src/ -
I../extern/gzstream -I../extern/libarchive-2.2.7/libarchive -I/root/
trans_proteomic_pipeline/src/../extern/expat-2.0.0/lib -I/usr/local/
include/boost-1_39/ -iprefix /root/trans_proteomic_pipeline/src/../
extern/pwiz/ -iwithprefix pwiz/data/msdata -iwithprefix pwiz/data -I/
root/trans_proteomic_pipeline/src/../extern/pwiz -iwithprefix pwiz -
iwithprefix pwiz/utility/misc -iwithprefix pwiz/utility/math -I/usr/
local/include/boost-1_39/ -iwithprefix pwiz_boost_additions -I/root/
trans_proteomic_pipeline/src/Parsers/ramp -D_FILE_OFFSET_BITS=64 -
D_LARGEFILE_SOURCE -DPWIZ_USER_VERSION_INFO_H=\"common/TPPVersion.h
\" -c -O2 -I/usr/lib/perl5/5.10.0/x86_64-linux-thread-multi/
CORE -DTPPLIB_SWIG -o /root/trans_proteomic_pipeline/src/../build/
linux/tpplib_perl_wrap.o ./tpplib/tpplib_perl_wrap.cxx 2> /dev/null
g++ -I. -I/root/trans_proteomic_pipeline/src/ -I../extern/gzstream -
I../extern/libarchive-2.2.7/libarchive -I/root/
trans_proteomic_pipeline/src/../extern/expat-2.0.0/lib -I/usr/local/
include/boost-1_39/ -iprefix /root/trans_proteomic_pipeline/src/../
extern/pwiz/ -iwithprefix pwiz/data/msdata -iwithprefix pwiz/data -I/
root/trans_proteomic_pipeline/src/../extern/pwiz -iwithprefix pwiz -
iwithprefix pwiz/utility/misc -iwithprefix pwiz/utility/math -I/usr/
local/include/boost-1_39/ -iwithprefix pwiz_boost_additions -I/root/
trans_proteomic_pipeline/src/Parsers/ramp -D_FILE_OFFSET_BITS=64 -
D_LARGEFILE_SOURCE -O2 -shared -o /root/
trans_proteomic_pipeline/src/../build/linux/tpplib_perl.so /root/
trans_proteomic_pipeline/src/../build/linux/tpplib_perl_wrap.o /root/
trans_proteomic_pipeline/src/../build/linux/libtpp.a /root/
trans_proteomic_pipeline/src/../build/linux/libpwiz.a /lib//
libboost_filesystem-gcc44-mt.so /lib//libboost_system-gcc44-mt.so /
lib//libboost_iostreams-gcc44-mt.so /lib//libboost_thread-gcc44-
mt.so /lib//libboost_regex-gcc44-mt.so /lib//
libboost_program_options-gcc44-mt.so /lib//libboost_serialization-
gcc44-mt.so /root/trans_proteomic_pipeline/src/../build/linux/
libgzstream.a -lm -lz -lbz2 -lpthread
mkdir -p /root/trans_proteomic_pipeline/src/../build/linux/help
mkdir -p /root/trans_proteomic_pipeline/src/../build/linux/schema
mkdir -p /root/trans_proteomic_pipeline/src/../build/linux/images
cd perl_paths; export PERL=perl; make -f perl_paths.makefile all
make[1]: Entering directory `/root/trans_proteomic_pipeline/src/
perl_paths'
perl -pe "s/\/cygdrive\/c\/Inetpub\/tpp-bin\//\/usr\/local\/labkey\/bin
\/cgi\-bin\//g;s/\x24\{base_dir\}users\//\/usr\/local\/labkey\/bin\/
cgi-bin\/users\//g;s/\/tools\/bin\/TPP\/tpp\//\/usr\/local\/labkey\/bin
\//g;s/cygpath \-wp //g;s/\"\/cygdrive\/c\/Inetpub\/wwwroot\/\"/\
\x24ENV\{\'WEBSERVER_ROOT\'\}\.'\/'/g;s/\/tpp\-bin/\/tpp\/cgi\-bin/
g;s/'\/usr\/bin\//'/g;s/'\/bin\//'/g " < ../../perl/fileDownloader.pl
> ../../build/linux/fileDownloader.pl
perl -c ../../build/linux/fileDownloader.pl
../../build/linux/fileDownloader.pl syntax OK
perl -pe "s/\/cygdrive\/c\/Inetpub\/tpp-bin\//\/usr\/local\/labkey\/bin
\/cgi\-bin\//g;s/\x24\{base_dir\}users\//\/usr\/local\/labkey\/bin\/
cgi-bin\/users\//g;s/\/tools\/bin\/TPP\/tpp\//\/usr\/local\/labkey\/bin
\//g;s/cygpath \-wp //g;s/\"\/cygdrive\/c\/Inetpub\/wwwroot\/\"/\
\x24ENV\{\'WEBSERVER_ROOT\'\}\.'\/'/g;s/\/tpp\-bin/\/tpp\/cgi\-bin/
g;s/'\/usr\/bin\//'/g;s/'\/bin\//'/g " < ../../perl/filterMRM.pl
> ../../build/linux/filterMRM.pl
perl -c ../../build/linux/filterMRM.pl
../../build/linux/filterMRM.pl syntax OK
perl -pe "s/\/cygdrive\/c\/Inetpub\/tpp-bin\//\/usr\/local\/labkey\/bin
\/cgi\-bin\//g;s/\x24\{base_dir\}users\//\/usr\/local\/labkey\/bin\/
cgi-bin\/users\//g;s/\/tools\/bin\/TPP\/tpp\//\/usr\/local\/labkey\/bin
\//g;s/cygpath \-wp //g;s/\"\/cygdrive\/c\/Inetpub\/wwwroot\/\"/\
\x24ENV\{\'WEBSERVER_ROOT\'\}\.'\/'/g;s/\/tpp\-bin/\/tpp\/cgi\-bin/
g;s/'\/usr\/bin\//'/g;s/'\/bin\//'/g " < ../../perl/replaceall.pl
> ../../build/linux/replaceall.pl
perl -c ../../build/linux/replaceall.pl
../../build/linux/replaceall.pl syntax OK
perl -pe "s/\/cygdrive\/c\/Inetpub\/tpp-bin\//\/usr\/local\/labkey\/bin
\/cgi\-bin\//g;s/\x24\{base_dir\}users\//\/usr\/local\/labkey\/bin\/
cgi-bin\/users\//g;s/\/tools\/bin\/TPP\/tpp\//\/usr\/local\/labkey\/bin
\//g;s/cygpath \-wp //g;s/\"\/cygdrive\/c\/Inetpub\/wwwroot\/\"/\
\x24ENV\{\'WEBSERVER_ROOT\'\}\.'\/'/g;s/\/tpp\-bin/\/tpp\/cgi\-bin/
g;s/'\/usr\/bin\//'/g;s/'\/bin\//'/g " < ../../perl/updateAllPaths.pl
> ../../build/linux/updateAllPaths.pl
perl -c ../../build/linux/updateAllPaths.pl
../../build/linux/updateAllPaths.pl syntax OK
perl -pe "s/\/cygdrive\/c\/Inetpub\/tpp-bin\//\/usr\/local\/labkey\/bin
\/cgi\-bin\//g;s/\x24\{base_dir\}users\//\/usr\/local\/labkey\/bin\/
cgi-bin\/users\//g;s/\/tools\/bin\/TPP\/tpp\//\/usr\/local\/labkey\/bin
\//g;s/cygpath \-wp //g;s/\"\/cygdrive\/c\/Inetpub\/wwwroot\/\"/\
\x24ENV\{\'WEBSERVER_ROOT\'\}\.'\/'/g;s/\/tpp\-bin/\/tpp\/cgi\-bin/
g;s/'\/usr\/bin\//'/g;s/'\/bin\//'/g " < ../../perl/ProphetModels.pl
> ../../build/linux/ProphetModels.pl
perl -c ../../build/linux/ProphetModels.pl
Can't load '/root/trans_proteomic_pipeline/build/linux/tpplib_perl.so'
for module tpplib_perl: libboost_filesystem-gcc44-mt-1_39.so.1.39.0:
cannot open shared object file: No such file or directory at /usr/lib/
perl5/5.10.0/x86_64-linux-thread-multi/DynaLoader.pm line 203.
at /root/trans_proteomic_pipeline/build/linux/tpplib_perl.pm line 11
Compilation failed in require at ../../build/linux/ProphetModels.pl
line 44.
BEGIN failed--compilation aborted at ../../build/linux/
ProphetModels.pl line 44.
make[1]: *** [../../build/linux/ProphetModels.pl] Error 9
make[1]: *** Deleting file `../../build/linux/ProphetModels.pl'
make[1]: Leaving directory `/root/trans_proteomic_pipeline/src/
perl_paths'
make: *** [perl_paths] Error 2
amomics:~/trans_proteomic_pipeline/src #
amomics:~/trans_proteomic_pipeline/src # find / -name DynaLoader.pm
/usr/lib/perl5/5.10.0/x86_64-linux-thread-multi/DynaLoader.pm
amomics:~/trans_proteomic_pipeline/src #
amomics:~/trans_proteomic_pipeline/src # ls -l /usr/lib/perl5/5.10.0/
x86_64-linux-thread-multi/DynaLoader.pm
-r--r--r-- 1 root root 25002 Jul 15 2008 /usr/lib/perl5/5.10.0/x86_64-
linux-thread-multi/DynaLoader.pm
I'm going try setting the PERL_BIN in the Makefile.config.incld next.
Thanks again,
Bill
--~--~---------~--~----~------------~-------~--~----~
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To post to this group, send email to spctools-discuss@googlegroups.com
To unsubscribe from this group, send email to
spctools-discuss+unsubscr...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/spctools-discuss?hl=en
-~----------~----~----~----~------~----~------~--~---
