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building tpp from svn (rev 4395) on ubuntu 9.04
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andreas quandt  
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 More options Jun 24, 11:35 am
From: andreas quandt <quandt.andr...@gmail.com>
Date: Wed, 24 Jun 2009 17:35:17 +0200
Local: Wed, Jun 24 2009 11:35 am
Subject: building tpp from svn (rev 4395) on ubuntu 9.04
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dear list,

i would like to test the trunk version of the tpp but have some trouble
to build it.
i was following the instructions for the installation of 4.2.1 on ubuntu
9.04 (specifying the latest boost library in the Makefile.config.incl)
but get following error during the compilation process:

In file included from
./Validation/DiscriminateFunction/DiscrimValMixtureDistr.h:6,
from ./Validation/MixtureModel/MixtureModel.h:14,
from
Validation/PeptideProphet/PeptideProphetParser/PeptideProphetParser.h:47,
from
Validation/PeptideProphet/PeptideProphetParser/PeptideProphetParserMain.cxx :2:
./Validation/Distribution/NonParametricDistribution.h:84: error: ‘Fit’
has not been declared
./Validation/Distribution/NonParametricDistribution.h:85: error:
expected ‘;’ before ‘(’ token
./Validation/Distribution/NonParametricDistribution.h:86: error:
expected ‘;’ before ‘(’ token
./Validation/Distribution/NonParametricDistribution.h:87: error:
expected ‘;’ before ‘(’ token
./Validation/Distribution/NonParametricDistribution.h:90: error: ‘Fit’
has not been declared
./Validation/Distribution/NonParametricDistribution.h:92: error: ‘Fit’
has not been declared
./Validation/Distribution/NonParametricDistribution.h:94: error: ‘Fit’
has not been declared
./Validation/Distribution/NonParametricDistribution.h:106: error: ISO
C++ forbids declaration of ‘Fit’ with no type
./Validation/Distribution/NonParametricDistribution.h:106: error:
expected ‘;’ before ‘*’ token
./Validation/Distribution/NonParametricDistribution.h:107: error: ISO
C++ forbids declaration of ‘Fit’ with no type
./Validation/Distribution/NonParametricDistribution.h:107: error:
expected ‘;’ before ‘*’ token
In file included from
./Validation/MixtureDistribution/AccurateMassDiffDiscrMixtureDistr.h:7,
from ./Validation/MixtureModel/MixtureModel.h:23,
from
Validation/PeptideProphet/PeptideProphetParser/PeptideProphetParser.h:47,
from
Validation/PeptideProphet/PeptideProphetParser/PeptideProphetParserMain.cxx :2:
./Validation/InterProphet/InterProphetParser/KDModel.h:118: error: ISO
C++ forbids declaration of ‘Fit’ with no type
./Validation/InterProphet/InterProphetParser/KDModel.h:118: error:
expected ‘;’ before ‘*’ token
./Validation/InterProphet/InterProphetParser/KDModel.h:119: error: ISO
C++ forbids declaration of ‘Fit’ with no type
./Validation/InterProphet/InterProphetParser/KDModel.h:119: error:
expected ‘;’ before ‘*’ token
make[1]: ***
[/usr/local/src/tpp-trunk-rev4395/src/../build/linux/PeptideProphetParserMa in.o]
Error 1
make[1]: Leaving directory `/usr/local/src/tpp-trunk-rev4395/src'
make: *** [default] Error 2

does anyone might have an idea what i am doing wrong?
and furthermore, i would like to ask if it is still necessary to build
the boost library separately and to set the Makefile.config.incl?
if not, i would very much appreciate if one of you could send me a brief
howto as i did not find any further information about this on the
spc-wiki...

many thanks in advance for any kind of help!

cheers,
andreas


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Brian Pratt  
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 More options Jun 24, 12:17 pm
From: "Brian Pratt" <brian.pr...@insilicos.com>
Date: Wed, 24 Jun 2009 09:17:58 -0700
Local: Wed, Jun 24 2009 12:17 pm
Subject: RE: [spctools-discuss] building tpp from svn (rev 4395) on ubuntu 9.04
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Hi Andreas,

You shouldn't need to mess with Boost config any more, TPP builds its own
copy for stability.

I'm hitting the same issue (such is life on the bleeding edge with trunk),
let me have a quick go at cleaning it up...

Brian


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andreas quandt  
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 More options Jun 24, 12:27 pm
From: andreas quandt <quandt.andr...@gmail.com>
Date: Wed, 24 Jun 2009 18:27:32 +0200
Local: Wed, Jun 24 2009 12:27 pm
Subject: Re: [spctools-discuss] Re: building tpp from svn (rev 4395) on ubuntu 9.04
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hey brian,

thanks for the fast reply.
also it would be great if you could send me a short howto for compiling
from trunk as i am not sure if it is still necessary to create
Makefile.config.incl and to define its content respectively.

many thanks in advance (again),
andreas


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Brian Pratt  
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 More options Jun 24, 12:32 pm
From: "Brian Pratt" <brian.pr...@insilicos.com>
Date: Wed, 24 Jun 2009 09:32:34 -0700
Local: Wed, Jun 24 2009 12:32 pm
Subject: RE: [spctools-discuss] Re: building tpp from svn (rev 4395) on ubuntu 9.04
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Customizing the makefile.config.incl is usually not necessary, and when it
is it's because a system is unusual so there's not really any standard
advice I can offer.

BTW trunk is just plain broken at the moment (developer forgot to add a
newly created file) - I've alerted the developer responsible for the error
and I'm sure it will be corrected soonest.  For the moment, add "-R 4391" to
your subversion statement to grab the code from just before the change that
broke the build.

From there a "make all install" should be all you need.  Conceivably you'll
hit some bumps due to gcc version, I'm not sure what ubuntu 9.04 ships with.

Brian


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andreas quandt  
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 More options Jun 24, 2:31 pm
From: andreas quandt <quandt.andr...@gmail.com>
Date: Wed, 24 Jun 2009 20:31:20 +0200
Local: Wed, Jun 24 2009 2:31 pm
Subject: Re: [spctools-discuss] Re: building tpp from svn (rev 4395) on ubuntu 9.04
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hi brian,

i tried the compilation but it fails with sqlite-3.6.11:
do you have potentially any suggestion what the cause might be?

cheers,
andreas

building SQLite3 library
cp
/usr/local/src/tpp-trunk-rev4391/src/../extern/sqlite-3.6.11/.libs/libsqlit e3.a
/usr/local/src/tpp-trunk-rev4391/src/../build/linux/libsqlite3.a
cp: cannot stat
`/usr/local/src/tpp-trunk-rev4391/src/../extern/sqlite-3.6.11/.libs/libsqli te3.a':
No such file or directory
make: ***
[/usr/local/src/tpp-trunk-rev4391/src/../build/linux/libsqlite3.a] Error 1
make[1]: Entering directory
`/usr/local/src/tpp-trunk-rev4391/extern/sqlite-3.6.11'
root@neo:/usr/local/src/tpp-trunk-rev4391/src#  rm -f sqlite3 sqlite3
test -z "libsqlite3.la" || rm -f libsqlite3.la
rm -f "./so_locations"
rm -rf .libs _libs
rm -f *.o
rm -f *.lo
if /bin/bash ./libtool --tag=CC --mode=compile gcc
-DPACKAGE_NAME=\"sqlite\" -DPACKAGE_TARNAME=\"sqlite\"
-DPACKAGE_VERSION=\"3.6.11\" -DPACKAGE_STRING=\"sqlite\ 3.6.11\"
-DPACKAGE_BUGREPORT=\"http://www.sqlite.org\" -DPACKAGE=\"sqlite\"
-DVERSION=\"3.6.11\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_FDATASYNC=1
-DHAVE_USLEEP=1 -DHAVE_LOCALTIME_R=1 -DHAVE_GMTIME_R=1 -I. -I.    
-DSQLITE_THREADSAFE=1  -g -O2 -MT sqlite3.lo -MD -MP -MF
".deps/sqlite3.Tpo" -c -o sqlite3.lo sqlite3.c; \
    then mv -f ".deps/sqlite3.Tpo" ".deps/sqlite3.Plo"; else rm -f
".deps/sqlite3.Tpo"; exit 1; fi
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... mkdir .libs
 gcc -DPACKAGE_NAME=\"sqlite\" -DPACKAGE_TARNAME=\"sqlite\"
-DPACKAGE_VERSION=\"3.6.11\" "-DPACKAGE_STRING=\"sqlite 3.6.11\""
-DPACKAGE_BUGREPORT=\"http://www.sqlite.org\" -DPACKAGE=\"sqlite\"
-DVERSION=\"3.6.11\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_FDATASYNC=1
-DHAVE_USLEEP=1 -DHAVE_LOCALTIME_R=1 -DHAVE_GMTIME_R=1 -I. -I.
-DSQLITE_THREADSAFE=1 -g -O2 -MT sqlite3.lo -MD -MP -MF
.deps/sqlite3.Tpo -c sqlite3.c  -fPIC -DPIC -o .libs/sqlite3.o
yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
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
checking dependency style of gcc... gcc3
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
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 ranlib... ranlib
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
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 ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking whether ln -s works... yes
checking how to recognise dependent libraries... pass_all
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 dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... 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 g77... no
checking for xlf... no
checking for f77... no
checking for frt... no
checking for pgf77... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for xlf90... no
checking for f90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... (cached) ranlib
checking for strip... strip
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC
checking if gcc PIC flag -fPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... 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
configure: creating libtool
appending configuration tag "CXX" to libtool
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
checking if g++ PIC flag -fPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
appending configuration tag "F77" to libtool
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC works... yes
checking if gfortran static flag -static works... yes
checking if gfortran supports -c -o file.o... yes
checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64)
supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for fdatasync... yes
checking for usleep... yes
checking for fullfsync... no
checking for localtime_r... yes
checking for gmtime_r... yes
checking for library containing tgetent... no
checking for library containing readline... no
checking for readline... no
checking for library containing pthread_create... -lpthread
checking for library containing dlopen... -ldl
checking for whether to support dynamic extensions... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating sqlite3.pc
config.status: executing depfiles commands
Assembler messages:
Fatal error: can't create .libs/sqlite3.o: No such file or directory
make[1]: *** [sqlite3.lo] Error 1
make[1]: Leaving directory
`/usr/local/src/tpp-trunk-rev4391/extern/sqlite-3.6.11'

...

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Brian Pratt  
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 More options Jun 24, 2:37 pm
From: "Brian Pratt" <brian.pr...@insilicos.com>
Date: Wed, 24 Jun 2009 11:37:52 -0700
Local: Wed, Jun 24 2009 2:37 pm
Subject: RE: [spctools-discuss] Re: building tpp from svn (rev 4395) on ubuntu 9.04
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Can you show me the subversion statement you used to grab the source code
tree?

Brian

...

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andreas quandt  
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 More options Jun 24, 2:39 pm
From: andreas quandt <quandt.andr...@gmail.com>
Date: Wed, 24 Jun 2009 20:39:46 +0200
Local: Wed, Jun 24 2009 2:39 pm
Subject: Re: [spctools-discuss] Re: building tpp from svn (rev 4395) on ubuntu 9.04
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svn -r 4391 co
https://sashimi.svn.sourceforge.net/svnroot/sashimi/trunk/trans_prote...
tpp-trunk-rev4391

hth
andreas

...

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Brian Pratt  
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 More options Jun 24, 2:40 pm
From: "Brian Pratt" <brian.pr...@insilicos.com>
Date: Wed, 24 Jun 2009 11:40:34 -0700
Local: Wed, Jun 24 2009 2:40 pm
Subject: RE: [spctools-discuss] Re: building tpp from svn (rev 4395) on ubuntu 9.04
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I should note that while I do build with MSVC, I also build with MinGW/gcc
and you're probably just hitting things I missed in MSVC because I built
with gcc first (that was the case with the boost decompression, for
example).  We'll work through this and get it cleaned up.

Brian

...

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andreas quandt  
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 More options Jun 24, 2:43 pm
From: andreas quandt <quandt.andr...@gmail.com>
Date: Wed, 24 Jun 2009 20:43:37 +0200
Local: Wed, Jun 24 2009 2:43 pm
Subject: Re: [spctools-discuss] Re: building tpp from svn (rev 4395) on ubuntu 9.04
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awesome, many thanks brian!

cheers,
andreas

...

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Brian Pratt  
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 More options Jun 24, 2:55 pm
From: "Brian Pratt" <brian.pr...@insilicos.com>
Date: Wed, 24 Jun 2009 11:55:10 -0700
Local: Wed, Jun 24 2009 2:55 pm
Subject: RE: [spctools-discuss] Re: building tpp from svn (rev 4395) on ubuntu 9.04
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Heh - got my wires crossed, you're working on ubuntu build issues, not msvc,
but the message is the same: we'll get this sorted.  Natalie is looking into
the sqlite issue now.

Brian

...

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Natalie Tasman  
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 More options Jun 24, 3:49 pm
From: Natalie Tasman <natalie.tas...@insilicos.com>
Date: Wed, 24 Jun 2009 12:49:06 -0700
Local: Wed, Jun 24 2009 3:49 pm
Subject: Re: [spctools-discuss] Re: building tpp from svn (rev 4395) on ubuntu 9.04
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Hello Andreas,

I have fixed the problem in trunk's Makefile.incl.  Please note that  
we're still waiting for another fix to get trunk working again; as you  
know, trunk is the "bleeding edge" and not guaranteed to build.

It seems that on Ubuntu, make and/or make's shell incorrectly  
interprets redirections (stderr, stdout ) which use '&' as the  
'background' directive.  I've simplly taken them out and things work  
fine now.  Previously, make was executing shell commands out-of-
sequence.  Also, this fixes the strange behavior in which you would  
see the shell prompt again, but the build was not really complete done.

And I've also taken the opportunity to update our included sqlite3 to  
the latest, 3.6.15.  You'll either need to do a "make  
distclean" (always a good idea with big trunk changes) or manually rm  
build/linux/libsqlite3.a, and then "make all".

-Natalie

On Jun 24, 2009, at 11:31 AM, andreas quandt wrote:

...

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Andreas Quandt  
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 More options Jun 24, 5:33 pm
From: Andreas Quandt <quandt.andr...@gmail.com>
Date: Wed, 24 Jun 2009 23:33:18 +0200
Local: Wed, Jun 24 2009 5:33 pm
Subject: Re: [spctools-discuss] Re: building tpp from svn (rev 4395) on ubuntu 9.04
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Hi Natalie

Many thanks for the fast bugfix.
Also it would be great if you (or brian) could let me know when the  
other bugfix is comitted so that I can continue with some small  
tests ;-)

Cheers
Andreas

On Jun 24, 2009, at 9:49 PM, Natalie Tasman <natalie.tas...@insilicos.com

...

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Natalie Tasman  
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 More options Jun 25, 6:26 pm
From: Natalie Tasman <natalie.tas...@insilicos.com>
Date: Thu, 25 Jun 2009 15:26:15 -0700
Local: Thurs, Jun 25 2009 6:26 pm
Subject: Re: [spctools-discuss] Re: building tpp from svn (rev 4395) on ubuntu 9.04
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Hello Andreas,

As of trunk rev. 4414, the TPP builds successfully.  This was tested  
on Ubuntu 9.04.

-Natalie

On Jun 24, 2009, at 2:33 PM, Andreas Quandt wrote:

...

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Andreas Quandt  
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 More options Jun 25, 7:48 pm
From: Andreas Quandt <quandt.andr...@gmail.com>
Date: Fri, 26 Jun 2009 01:48:20 +0200
Local: Thurs, Jun 25 2009 7:48 pm
Subject: Re: [spctools-discuss] Re: building tpp from svn (rev 4395) on ubuntu 9.04
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Hey Natalie

Many thanks for the info!
I will check it out in a few hours ;-)

Cheers
Andreas

On Jun 26, 2009, at 12:26 AM, Natalie Tasman <natalie.tas...@insilicos.com

...

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Andreas Quandt  
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 More options Jun 30, 5:29 pm
From: Andreas Quandt <quandt.andr...@gmail.com>
Date: Tue, 30 Jun 2009 23:29:11 +0200
Local: Tues, Jun 30 2009 5:29 pm
Subject: Re: [spctools-discuss] Re: building tpp from svn (rev 4395) on ubuntu 9.04
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Hey Natalie, hello Brian

Sorry for getting back to you so late.
I tried the compilation and it worked like a charm :-)
I am only a little bit confused about the structure as it completely  
differs from the stable branch.
Hence I am not exactly sure how to best integrate the trunk in an  
existing installation or to replace it respectively.
It would be great if one of you guys could give me a short explanation.

Cheers
Andreas

On Jun 26, 2009, at 12:26 AM, Natalie Tasman <natalie.tas...@insilicos.com

...

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Brian Pratt  
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 More options Jun 30, 6:16 pm
From: "Brian Pratt" <brian.pr...@insilicos.com>
Date: Tue, 30 Jun 2009 15:16:09 -0700
Local: Tues, Jun 30 2009 6:16 pm
Subject: RE: [spctools-discuss] Re: building tpp from svn (rev 4395) on ubuntu 9.04
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Can you be more specific?  While some files have changed, and some have been
added, the source code directory structure is pretty much the same.

Brian

...

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andreas quandt  
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 More options Jul 1, 5:43 am
From: andreas quandt <quandt.andr...@gmail.com>
Date: Wed, 01 Jul 2009 11:43:38 +0200
Local: Wed, Jul 1 2009 5:43 am
Subject: Re: [spctools-discuss] Re: building tpp from svn (rev 4395) on ubuntu 9.04
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hey brian,

now i know what you mean.
i did not see that the tpp binary folder is automatically created in the
parent directory....
so this seems to work fine.

many thanks!
andreas

...

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Discussion subject changed to "login to petunia when using trunk rev 4414" by andreas quandt
andreas quandt  
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 More options Jul 1, 5:47 am
From: andreas quandt <quandt.andr...@gmail.com>
Date: Wed, 01 Jul 2009 11:47:02 +0200
Local: Wed, Jul 1 2009 5:47 am
Subject: login to petunia when using trunk rev 4414
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dear list,

after checking out trunk rev 4414, i wanted to test the petunia
interface but there is a problem with the login when using guest/guest.
here, i get following error message: User guest not found. Please check
your user name, or log in as guest.

does anyone has an idea how to fix this?

cheers,
andreas


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andreas quandt  
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 More options Jul 1, 6:46 am
From: andreas quandt <quandt.andr...@gmail.com>
Date: Wed, 01 Jul 2009 12:46:49 +0200
Local: Wed, Jul 1 2009 6:46 am
Subject: Re: login to petunia when using trunk rev 4414
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hello,

i found the cause of my trouble: several paths in the cgi-bin/tpp_gui.pl
had to be adapted to the location of my tpp installation (among them,
the path to the users directory in cgi-bin/users).

cheers,
andreas


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Brian Pratt  
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 More options Jul 1, 11:33 am
From: "Brian Pratt" <brian.pr...@insilicos.com>
Date: Wed, 1 Jul 2009 08:33:43 -0700
Local: Wed, Jul 1 2009 11:33 am
Subject: RE: [spctools-discuss] Re: login to petunia when using trunk rev 4414
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You can (mostly, probably, are supposed to be able to) clean that up at
build time by modifying the Makefile.config.incl file.


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