Problems building boost inside TPP

[bmcnally]

Hello list,

I'm attempting to build TPP 4.3-1 on RHEL 5.4, gcc 4.1.2. I think I
have all of the required libraries specified here:

install-prerequisites-centos-5_2.sh

Here's what happens when I try and `make all`:

mkdir -p /tmp/trans_proteomic_pipeline/src/../build/linux
building boost libraries...
warning: No toolsets are configured.
warning: Configuring default toolset "gcc".
warning: If the default is wrong, your build may not work correctly.
warning: Use the "toolset=xxxxx" option to override our guess.
warning: For more configuration options, please consult
warning: http://boost.org/boost-build2/doc/html/bbv2/advanced/configuration.html
warning: Building Boost.Regex with the optional Unicode/ICU support
disabled.
note: Please refer to the Boost.Regex documentation for more
information
note: this is a strictly optional feature.
...failed updating 1 target...

real 0m2.283s
user 0m2.375s
sys 0m0.240s
[ERROR] Boost libary build failed (missing /tmp/
trans_proteomic_pipeline/src/../build/linux/boost/lib/
libboost_filesystem.a), please report the results of manually running
the following commands:
cd /tmp/trans_proteomic_pipeline/src/../extern/boost_1_39_0/; time /
tmp/trans_proteomic_pipeline/src/../extern/boost_1_39_0/tools/jam/src/
bin.linuxx86_64/bjam -q -d0 --stagedir=/tmp/trans_proteomic_pipeline/
src/../build/linux/boost --layout=system --build-type=minimal -j3
variant=release link=static runtime-link=shared --with-filesystem --
with-date_time --with-iostreams --with-program_options --with-regex --
with-serialization --with-thread stage
make: *** [boost-build-libs] Error 255

Manually running the recommend command above results in the same
output:

cd /tmp/trans_proteomic_pipeline/src/../extern/boost_1_39_0/; time /
tmp/trans_proteomic_pipeline/src/../extern/boost_1_39_0/tools/jam/src/
bin.linuxx86_64/bjam -q -d0 --stagedir=/tmp/trans_proteomic_pipeline/
src/../build/linux/boost --layout=system --build-type=minimal -j3
variant=release link=static runtime-link=shared --with-filesystem --
with-date_time --with-iostreams --with-program_options --with-regex --
with-serialization --with-thread stage
warning: No toolsets are configured.
warning: Configuring default toolset "gcc".
warning: If the default is wrong, your build may not work correctly.
warning: Use the "toolset=xxxxx" option to override our guess.
warning: For more configuration options, please consult
warning: http://boost.org/boost-build2/doc/html/bbv2/advanced/configuration.html
warning: Building Boost.Regex with the optional Unicode/ICU support
disabled.
note: Please refer to the Boost.Regex documentation for more
information
note: this is a strictly optional feature.
...failed updating 1 target...

real 0m2.339s
user 0m2.370s
sys 0m0.241s

Any thoughts?

Thanks.

[Jagan Kommineni]

I have installed boost-1.38.0 by following procedure prior to installation of TPP  ...

Here is the procedure ...

----------------------------
#############
##
## Step 1: Download and install boost 1.38.0
##
## I will install Boost 1.38.0 onto /opt/boost_1_38_0 to avoid conflict with
## the default version installed by RedHat
#############
cd /opt
wget -nd http://downloads.sourceforge.net/boost/boost_1_38_0.tar.gz?use_mirror...
tar xzf boost_1_38_0.tar.gz
ln -s boost_1_38_0 boost
cd boost
./configure --prefix=/opt/boost
make -j5
make install
echo "/opt/boost/lib" > /etc/ld.so.conf.d/boost-1_38_0.conf
ldconfig
----------------------------
 Create Makefile.config.incl in the trans_proteomic_pipeline/src/ directory ...
---------------------------------------------------------------------------------------------------------------------
############ Begin Makefile.config.incl ####################
TPP_ROOT=/mnt/sanfs/APCF/APCF_WEB/tpp/

## for Boost
BOOST_INCL=-I/opt/boost/
BOOST_LIBDIR=/opt/boost/lib
BOOST_LIBSPEC=-gcc41-mt
LINK=shared
LIBEXT=so

## for perl
PERL_LIB_CORE=/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE/
PERL_BIN=/usr/bin/perl
############ End Makefile.config.incl ####################
----------------------------------------------------------------------------------------------------------
You need to change TPP_ROOT to suit your directory structure ...
cd trans_proteomic_pipeline/src/
make all
make install

Best of luck ...

Jagan

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[bmcnally]

Thanks Jagan. I was able to get it working. It turns out I had some
issues with gcc.

On Jul 11, 7:30 pm, Jagan Kommineni <jagan.kommin...@gmail.com> wrote:
> I have installed boost-1.38.0 by following procedure prior to installation
> of TPP  ...
>
> Here is the procedure ...
>
> ----------------------------
> #############
> ##
> ## Step 1: Download and install boost 1.38.0
> ##
> ## I will install Boost 1.38.0 onto /opt/boost_1_38_0 to avoid conflict with
> ## the default version installed by RedHat
> #############
> cd /opt

> wget -ndhttp://downloads.sourceforge.net/boost/boost_1_38_0.tar.gz?use_mirror...

> > spctools-discu...@googlegroups.com<spctools-discuss%2Bunsu...@googlegroups.com>
> > .

[Han Jo]

Althoug this post is a little bit out of date I am having the same issue!

I am trying to install the TPP (TPP-4.6.3) and get the same error as in the initial post.  And I do not fully understand whats happening there...
So it seems like in the meantime TPP comes with its own boost in the extern/ directory so the cited workaround by Jagan doesn't work anymore? Since all the guides from the src installation are out of date I am not sure about configuring the make.config.in file. Is it still neccessary to do this?

I am on the following environment:
SUSE Linux Enterprise Server 11 (x86_64)
VERSION = 11.1


Does anyone have a solution for this?

Thanks,
best regards,
Sven



So here is my error from std when simply typing make in the src directory.

mkdir -p /data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../build/SUSE LINUX-x86_64

building boost libraries...
warning: No toolsets are configured.
warning: Configuring default toolset "gcc".
warning: If the default is wrong, your build may not work correctly.
warning: Use the "toolset=xxxxx" option to override our guess.
warning: For more configuration options, please consult
warning: http://boost.org/boost-build2/doc/html/bbv2/advanced/configuration.html

notice: could not find main target LINUX-x86_64/boost
notice: assuming it is a name of file to create.
notice: could not find main target LINUX-x86_64/boost/obj
notice: assuming it is a name of file to create.
Performing configuration checks

    - has_icu builds           : no
don't know how to make <e>LINUX-x86_64/boost
don't know how to make <e>LINUX-x86_64/boost/obj

real    0m7.481s
user    0m2.340s
sys     0m0.216s
[ERROR] Boost libary build failed (missing LINUX-x86_64/boost/lib/libboost_filesystem.a), please report the results of manually running the following commands:
cd /data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../extern/boost_1_45_0; time /data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../extern/boost_1_45_0/tools/build/v2/engine/src/bin.linuxx86_64/bjam -q -d0 --stagedir=/data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../build/SUSE LINUX-x86_64/boost --build-dir=/data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../build/SUSE LINUX-x86_64/boost/obj --layout=system --build-type=minimal -j3 variant=release link=static runtime-link=shared --with-filesystem --with-date_time --with-iostreams --with-program_options --with-regex --with-serialization --with-thread stage

[ChargedPeptide]

I just had this issue yesterday, building on Elementary OS. It seems the space in the linux name (ARCH = "Elementary OS_x86_64" caused this problem.
(I assume you've used the proper Makefile.config.incl, like the one further up this thread).
It seems possible for Suse Linux-x86_64 has a similiar issue.
Try starting over from the top (i.e. reunpack TPP-4.6.3.tgz and recopy Makefile.config.incl to the src dir).
Then run:
Make ARCH=x86_64

Did it for me.

[ChargedPeptide]

Also, I quoted the wrong text. This is in reply to Han Jo.

[Han Jo]

Thanks for sharing! But this still would't let me build TPP.

Did you download boost by yourself (as described in your quoted text) or did you just go straight to the src dir of TPP and perform the installations steps?

[Han Jo]

Okay, after finding the line:

"libs/regex/build/has_icu_test.cpp:12:30: fatal error: unicode/uversion.h: No such file or directory". I tried to remove -q flag from the bjam command as suggested here(http://boost.2283326.n4.nabble.com/error-unicode-uversion-h-No-such-file-building-Boost-1-44-0-td2581731.html), but without success.
As far as I understood with the current version the makefile.config.inc does not need to contain the boost dirs... since boost is now part of the distributed tar. So my config file is as sparse as:

TPP_ROOT=/data/software/TPP/bin/
TPP_WEB=/data/software/TPP/web/

And I only do the following commands:

1. tar xzf TPP-4.6.3.tgz
2. cd TPP-4.6.3/trans_proteomic_pipeline/src
3. make ARCH=x86_64
   

...done building FANN library source
mkdir -p /data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../build/x86_64
unpacking Boost source (this may take a few minutes)...
...applying Boost patch /data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../extern/boost_1_45_0.gcc47patch
done unpacking Boost source
building boost bjam...
###
### Using 'gcc' toolset.
###
rm -rf bootstrap
mkdir bootstrap
gcc -o bootstrap/jam0 command.c compile.c debug.c expand.c glob.c hash.c hdrmacro.c headers.c jam.c jambase.c jamgram.c lists.c make.c make1.c newstr.c option.c output.c parse.c pathunix.c pathvms.c regexp.c rules.c scan.c search.c subst.c timestamp.c variable.c modules.c strings.c filesys.c builtins.c pwd.c class.c native.c md5.c w32_getreg.c modules/set.c modules/path.c modules/regex.c modules/property-set.c modules/sequence.c modules/order.c execunix.c fileunix.c
./bootstrap/jam0 -f build.jam --toolset=gcc --toolset-root= clean
...found 1 target...
...updating 1 target...
...updated 1 target...
./bootstrap/jam0 -f build.jam --toolset=gcc --toolset-root=
...found 48 targets...
...updating 2 targets...
[MKDIR] bin.linuxx86_64
[COMPILE] bin.linuxx86_64/bjam
...updated 2 targets...
...done building boost bjam

building boost libraries...
warning: No toolsets are configured.
warning: Configuring default toolset "gcc".
warning: If the default is wrong, your build may not work correctly.
warning: Use the "toolset=xxxxx" option to override our guess.
warning: For more configuration options, please consult
warning: http://boost.org/boost-build2/doc/html/bbv2/advanced/configuration.html

libs/regex/build/has_icu_test.cpp:12:30: fatal error: unicode/uversion.h: No such file or directory
compilation terminated.
...skipped <p/data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/build/x86_64/boost/obj/boost/bin.v2/libs/regex/build/gcc-4.5/debug>has_icu for lack of <p/data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/build/x86_64/boost/obj/boost/bin.v2/libs/regex/build/gcc-4.5/debug>has_icu_test.o...
...failed updating 1 target...

Performing configuration checks

    - has_icu builds           : no

Component configuration:

    - date_time                : building
    - filesystem               : building
    - graph                    : not building
    - graph_parallel           : not building
    - iostreams                : building
    - math                     : not building
    - mpi                      : not building
    - program_options          : building
    - python                   : not building
    - random                   : not building
    - regex                    : building
    - serialization            : building
    - signals                  : not building
    - system                   : not building
    - test                     : not building
    - thread                   : building
    - wave                     : not building

In file included from ./boost/thread/pthread/mutex.hpp:14:0,
                 from ./boost/thread/mutex.hpp:16,
                 from ./boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/thread/thread.hpp:17,
                 from libs/thread/src/pthread/thread.cpp:10:
./boost/thread/xtime.hpp:23:5: error: expected identifier before numeric constant
./boost/thread/xtime.hpp:23:5: error: expected ‘}’ before numeric constant
./boost/thread/xtime.hpp:23:5: error: expected unqualified-id before numeric constant
./boost/thread/xtime.hpp:46:14: error: expected type-specifier before ‘system_time’
In file included from ./boost/thread/pthread/mutex.hpp:14:0,
                 from ./boost/thread/mutex.hpp:16,
                 from ./boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/thread/thread.hpp:17,
                 from libs/thread/src/pthread/thread.cpp:10:
./boost/thread/xtime.hpp: In function ‘int xtime_get(xtime*, int)’:
./boost/thread/xtime.hpp:73:40: error: ‘get_system_time’ was not declared in this scope
./boost/thread/xtime.hpp: At global scope:
./boost/thread/xtime.hpp:88:1: error: expected declaration before ‘}’ token
...failed updating 1 target...

real    0m48.564s
user    1m21.641s
sys     0m6.872s
[ERROR] Boost libary build failed (missing /data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../build/x86_64/boost/lib/libboost_filesystem.a), please report the results of manually running the following commands:
cd /data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../extern/boost_1_45_0; time /data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../extern/boost_1_45_0/tools/build/v2/engine/src/bin.linuxx86_64/bjam -q -d0 --stagedir=/data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../build/x86_64/boost --build-dir=/data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../build/x86_64/boost/obj --layout=system --build-type=minimal -j3 variant=release link=static runtime-link=shared --with-filesystem --with-date_time --with-iostreams --with-program_options --with-regex --with-serialization --with-thread stage

make: *** [boost-build-libs] Error 255

When I execute the last command again the following, with no direct errors appears: (but I still cannot build TPP)

cd /data/NG4/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../extern/boost_1_45_0; time /data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../extern/boost_1_45_0/tools/build/v2/engine/src/bin.linuxx86_64/bjam -q -d0 --stagedir=/data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../build/x86_64/boost --build-dir=/data/software/TPP/TPP-4.6.3/trans_proteomic_pipeline/src/../build/x86_64/boost/obj --layout=system --build-type=minimal -j3 variant=release link=static runtime-link=shared --with-filesystem --with-date_time --with-iostreams --with-program_options --with-regex --with-serialization --with-thread stage

warning: No toolsets are configured.
warning: Configuring default toolset "gcc".
warning: If the default is wrong, your build may not work correctly.
warning: Use the "toolset=xxxxx" option to override our guess.
warning: For more configuration options, please consult
warning: http://boost.org/boost-build2/doc/html/bbv2/advanced/configuration.html

Performing configuration checks

    - has_icu builds           : no

Component configuration:

    - date_time                : building
    - filesystem               : building
    - graph                    : not building
    - graph_parallel           : not building
    - iostreams                : building
    - math                     : not building
    - mpi                      : not building
    - program_options          : building
    - python                   : not building
    - random                   : not building
    - regex                    : building
    - serialization            : building
    - signals                  : not building
    - system                   : not building
    - test                     : not building
    - thread                   : building
    - wave                     : not building

In file included from ./boost/thread/pthread/mutex.hpp:14:0,
                 from ./boost/thread/mutex.hpp:16,
                 from ./boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/thread/thread.hpp:17,
                 from libs/thread/src/pthread/thread.cpp:10:
./boost/thread/xtime.hpp:23:5: error: expected identifier before numeric constant
./boost/thread/xtime.hpp:23:5: error: expected ‘}’ before numeric constant
./boost/thread/xtime.hpp:23:5: error: expected unqualified-id before numeric constant
./boost/thread/xtime.hpp:46:14: error: expected type-specifier before ‘system_time’
In file included from ./boost/thread/pthread/mutex.hpp:14:0,
                 from ./boost/thread/mutex.hpp:16,
                 from ./boost/thread/pthread/thread_data.hpp:12,
                 from ./boost/thread/thread.hpp:17,
                 from libs/thread/src/pthread/thread.cpp:10:
./boost/thread/xtime.hpp: In function ‘int xtime_get(xtime*, int)’:
./boost/thread/xtime.hpp:73:40: error: ‘get_system_time’ was not declared in this scope
./boost/thread/xtime.hpp: At global scope:
./boost/thread/xtime.hpp:88:1: error: expected declaration before ‘}’ token
...failed updating 1 target...

real    0m10.936s
user    0m6.284s
sys     0m1.288s

[Joseph Slagel]

What version of gcc are you using to do the build?

-Joe

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Joe Slagel
Institute for Systems Biology
jsl...@systemsbiology.org
(206) 732-1362

[Han Jo]

I am using 4.5... good guess. I will give it a shot with a later version!

2013/10/14 Joseph Slagel <Joseph...@systemsbiology.org>

[Joseph Slagel]

Actually we've been seeing some problems with the latest versions of gcc.  You might be running into some of the same issues.

-Joe

[Joseph Slagel]

I've identified one problem with compiling with recent versions of gcc.  It has to do with a new macro TIME_UTC  conflicting with a enum in boost.  You can read about it here (with a workaround):

https://svn.boost.org/trac/boost/ticket/6940
https://bbs.archlinux.org/viewtopic.php?pid=1126374

I'm working on fixing it on TPP's trunk now.

-Joe

[Amin Momin]

Hi

I am trying to install TPP-4.8.0 on our RHEL6.6 and I get an error due to BOOST. Is there a solution for this bug. Or I just need to install Boost separately.

Thanks
Amin


libs/iostreams/src/bzip2.cpp:20:56: error: bzlib.h: No such file or directory
libs/iostreams/src/bzip2.cpp:31: error: ‘BZ_OK’ was not declared in this scope
libs/iostreams/src/bzip2.cpp:32: error: ‘BZ_RUN_OK’ was not declared in this sco                                                                                      pe
libs/iostreams/src/bzip2.cpp:33: error: ‘BZ_FLUSH_OK’ was not declared in this s                                                                                      cope
libs/iostreams/src/bzip2.cpp:34: error: ‘BZ_FINISH_OK’ was not declared in this                                                                                       scope
libs/iostreams/src/bzip2.cpp:35: error: ‘BZ_STREAM_END’ was not declared in this                                                                                       scope
libs/iostreams/src/bzip2.cpp:36: error: ‘BZ_SEQUENCE_ERROR’ was not declared in                                                                                       this scope
libs/iostreams/src/bzip2.cpp:37: error: ‘BZ_PARAM_ERROR’ was not declared in thi                                                                                      s scope
libs/iostreams/src/bzip2.cpp:38: error: ‘BZ_MEM_ERROR’ was not declared in this                                                                                       scope
libs/iostreams/src/bzip2.cpp:39: error: ‘BZ_DATA_ERROR’ was not declared in this                                                                                       scope
libs/iostreams/src/bzip2.cpp:40: error: ‘BZ_DATA_ERROR_MAGIC’ was not declared i                                                                                      n this scope
libs/iostreams/src/bzip2.cpp:41: error: ‘BZ_IO_ERROR’ was not declared in this s                                                                                      cope
libs/iostreams/src/bzip2.cpp:42: error: ‘BZ_UNEXPECTED_EOF’ was not declared in                                                                                       this scope
libs/iostreams/src/bzip2.cpp:43: error: ‘BZ_OUTBUFF_FULL’ was not declared in th                                                                                      is scope
libs/iostreams/src/bzip2.cpp:44: error: ‘BZ_CONFIG_ERROR’ was not declared in th                                                                                      is scope
libs/iostreams/src/bzip2.cpp:48: error: ‘BZ_FINISH’ was not declared in this sco                                                                                      pe
libs/iostreams/src/bzip2.cpp:49: error: ‘BZ_RUN’ was not declared in this scope
libs/iostreams/src/bzip2.cpp: In static member function ‘static void boost::iost                                                                                      reams::bzip2_error::check(int)’:
libs/iostreams/src/bzip2.cpp:62: error: ‘BZ_OK’ was not declared in this scope
libs/iostreams/src/bzip2.cpp:63: error: ‘BZ_RUN_OK’ was not declared in this sco                                                                                      pe
libs/iostreams/src/bzip2.cpp:64: error: ‘BZ_FLUSH_OK’ was not declared in this s                                                                                      cope
libs/iostreams/src/bzip2.cpp:65: error: ‘BZ_FINISH_OK’ was not declared in this                                                                                       scope
libs/iostreams/src/bzip2.cpp:66: error: ‘BZ_STREAM_END’ was not declared in this                                                                                       scope
libs/iostreams/src/bzip2.cpp:68: error: ‘BZ_MEM_ERROR’ was not declared in this                                                                                       scope
libs/iostreams/src/bzip2.cpp: In constructor ‘boost::iostreams::detail::bzip2_ba                                                                                      se::bzip2_base(const boost::iostreams::bzip2_params&)’:
libs/iostreams/src/bzip2.cpp:80: error: expected type-specifier before ‘bz_strea                                                                                      m’
libs/iostreams/src/bzip2.cpp:80: error: expected ‘)’ before ‘bz_stream’
libs/iostreams/src/bzip2.cpp: In destructor ‘boost::iostreams::detail::bzip2_bas                                                                                      e::~bzip2_base()’:
libs/iostreams/src/bzip2.cpp:83: error: expected type-specifier before ‘bz_strea                                                                                      m’
libs/iostreams/src/bzip2.cpp:83: error: expected ‘>’ before ‘bz_stream’
libs/iostreams/src/bzip2.cpp:83: error: expected ‘(’ before ‘bz_stream’
libs/iostreams/src/bzip2.cpp:83: error: ‘bz_stream’ was not declared in this sco                                                                                      pe
libs/iostreams/src/bzip2.cpp:83: error: expected primary-expression before ‘>’ t                                                                                      oken
libs/iostreams/src/bzip2.cpp:83: error: expected ‘)’ before ‘;’ token
libs/iostreams/src/bzip2.cpp: In member function ‘void boost::iostreams::detail:                                                                                      :bzip2_base::before(const char*&, const char*, char*&, char*)’:
libs/iostreams/src/bzip2.cpp:88: error: ‘bz_stream’ was not declared in this sco                                                                                      pe
libs/iostreams/src/bzip2.cpp:88: error: ‘s’ was not declared in this scope
libs/iostreams/src/bzip2.cpp:88: error: expected type-specifier before ‘bz_strea                                                                                      m’
libs/iostreams/src/bzip2.cpp:88: error: expected ‘>’ before ‘bz_stream’
libs/iostreams/src/bzip2.cpp:88: error: expected ‘(’ before ‘bz_stream’
libs/iostreams/src/bzip2.cpp:88: error: expected primary-expression before ‘>’ t                                                                                      oken
libs/iostreams/src/bzip2.cpp:88: error: expected ‘)’ before ‘;’ token
libs/iostreams/src/bzip2.cpp: In member function ‘void boost::iostreams::detail:                                                                                      :bzip2_base::after(const char*&, char*&)’:
libs/iostreams/src/bzip2.cpp:97: error: ‘bz_stream’ was not declared in this sco                                                                                      pe
libs/iostreams/src/bzip2.cpp:97: error: ‘s’ was not declared in this scope
libs/iostreams/src/bzip2.cpp:97: error: expected type-specifier before ‘bz_strea                                                                                      m’
libs/iostreams/src/bzip2.cpp:97: error: expected ‘>’ before ‘bz_stream’
libs/iostreams/src/bzip2.cpp:97: error: expected ‘(’ before ‘bz_stream’
libs/iostreams/src/bzip2.cpp:97: error: expected primary-expression before ‘>’ t                                                                                      oken
libs/iostreams/src/bzip2.cpp:97: error: expected ‘)’ before ‘;’ token
libs/iostreams/src/bzip2.cpp: In member function ‘int boost::iostreams::detail::                                                                                      bzip2_base::check_end(const char*, const char*)’:
libs/iostreams/src/bzip2.cpp:104: error: ‘bz_stream’ was not declared in this sc                                                                                      ope
libs/iostreams/src/bzip2.cpp:104: error: ‘s’ was not declared in this scope
libs/iostreams/src/bzip2.cpp:104: error: expected type-specifier before ‘bz_stre                                                                                      am’
libs/iostreams/src/bzip2.cpp:104: error: expected ‘>’ before ‘bz_stream’
libs/iostreams/src/bzip2.cpp:104: error: expected ‘(’ before ‘bz_stream’
libs/iostreams/src/bzip2.cpp:104: error: expected primary-expression before ‘>’                                                                                       token
libs/iostreams/src/bzip2.cpp:104: error: expected ‘)’ before ‘;’ token
libs/iostreams/src/bzip2.cpp: In member function ‘void boost::iostreams::detail:                                                                                      :bzip2_base::end(bool)’:
libs/iostreams/src/bzip2.cpp:118: error: ‘bz_stream’ was not declared in this sc                                                                                      ope
libs/iostreams/src/bzip2.cpp:118: error: ‘s’ was not declared in this scope
libs/iostreams/src/bzip2.cpp:118: error: expected type-specifier before ‘bz_stre                                                                                      am’
libs/iostreams/src/bzip2.cpp:118: error: expected ‘>’ before ‘bz_stream’
libs/iostreams/src/bzip2.cpp:118: error: expected ‘(’ before ‘bz_stream’
libs/iostreams/src/bzip2.cpp:118: error: expected primary-expression before ‘>’                                                                                       token
libs/iostreams/src/bzip2.cpp:118: error: expected ‘)’ before ‘;’ token
libs/iostreams/src/bzip2.cpp:121: error: ‘BZ2_bzCompressEnd’ was not declared in                                                                                       this scope
libs/iostreams/src/bzip2.cpp:122: error: ‘BZ2_bzDecompressEnd’ was not declared                                                                                       in this scope
libs/iostreams/src/bzip2.cpp: In member function ‘int boost::iostreams::detail::                                                                                      bzip2_base::compress(int)’:
libs/iostreams/src/bzip2.cpp:128: error: expected type-specifier before ‘bz_stre                                                                                      am’
libs/iostreams/src/bzip2.cpp:128: error: expected ‘>’ before ‘bz_stream’
libs/iostreams/src/bzip2.cpp:128: error: expected ‘(’ before ‘bz_stream’
libs/iostreams/src/bzip2.cpp:128: error: ‘bz_stream’ was not declared in this sc                                                                                      ope
libs/iostreams/src/bzip2.cpp:128: error: expected primary-expression before ‘>’                                                                                       token
libs/iostreams/src/bzip2.cpp: In member function ‘int boost::iostreams::detail::                                                                                      bzip2_base::decompress()’:
libs/iostreams/src/bzip2.cpp:133: error: expected type-specifier before ‘bz_stre                                                                                      am’
libs/iostreams/src/bzip2.cpp:133: error: expected ‘>’ before ‘bz_stream’
libs/iostreams/src/bzip2.cpp:133: error: expected ‘(’ before ‘bz_stream’
libs/iostreams/src/bzip2.cpp:133: error: ‘bz_stream’ was not declared in this sc                                                                                      ope
libs/iostreams/src/bzip2.cpp:133: error: expected primary-expression before ‘>’                                                                                       token
libs/iostreams/src/bzip2.cpp: In member function ‘void boost::iostreams::detail:                                                                                      :bzip2_base::do_init(bool, void* (*)(void*, int, int), void (*)(void*, void*), v                                                                                      oid*)’:
libs/iostreams/src/bzip2.cpp:144: error: ‘bz_stream’ was not declared in this sc                                                                                      ope
libs/iostreams/src/bzip2.cpp:144: error: ‘s’ was not declared in this scope
libs/iostreams/src/bzip2.cpp:144: error: expected type-specifier before ‘bz_stre                                                                                      am’
libs/iostreams/src/bzip2.cpp:144: error: expected ‘>’ before ‘bz_stream’
libs/iostreams/src/bzip2.cpp:144: error: expected ‘(’ before ‘bz_stream’
libs/iostreams/src/bzip2.cpp:144: error: expected primary-expression before ‘>’                                                                                       token
libs/iostreams/src/bzip2.cpp:144: error: expected ‘)’ before ‘;’ token
libs/iostreams/src/bzip2.cpp:161: error: ‘BZ2_bzCompressInit’ was not declared i                                                                                      n this scope
libs/iostreams/src/bzip2.cpp:164: error: ‘BZ2_bzDecompressInit’ was not declared                                                                                       in this scope
...failed updating 1 target...

real    0m2.806s
user    0m4.915s
sys     0m0.531s
[ERROR] Boost libary build failed (missing /home/aamomin/ProteomicProcessing/TPP                                                                                      download/TPP4.8.0/TPP-4.8.0/trans_proteomic_pipeline/src/../build/RedHatEnterpri                                                                                      seServer-x86_64/boost/lib/libboost_iostreams.a), please report the results of ma                                                                                      nually running the following commands:
cd /home/aamomin/ProteomicProcessing/TPPdownload/TPP4.8.0/TPP-4.8.0/trans_proteo                                                                                      mic_pipeline/src/../extern/boost_1_54_0; time /home/aamomin/ProteomicProcessing/                                                                                      TPPdownload/TPP4.8.0/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/boost_1_54                                                                                      _0/tools/build/v2/engine/bin.linuxx86_64/bjam -q -d0 --stagedir=/home/aamomin/Pr                                                                                      oteomicProcessing/TPPdownload/TPP4.8.0/TPP-4.8.0/trans_proteomic_pipeline/src/..                                                                                      /build/RedHatEnterpriseServer-x86_64/boost --build-dir=/home/aamomin/ProteomicPr                                                                                      ocessing/TPPdownload/TPP4.8.0/TPP-4.8.0/trans_proteomic_pipeline/src/../build/Re                                                                                      dHatEnterpriseServer-x86_64/boost/obj --layout=system --build-type=minimal -j3 v                                                                                      ariant=release link=static runtime-link=shared --with-filesystem --with-date_tim                                                                                      e --with-iostreams --with-program_options --with-regex --with-serialization --wi                                                                                      th-thread stage

make: *** [boost-build-libs] Error 255

[Joseph Slagel]

Amin,

While its possible I wouldn't recommend it.  From the error message it looks like you may be missing the bzip libraries.  Make sure you have bzip and bzip-devel installed on your system (yum bzip-devel).

-Joe

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[Amin Momin]

Thanks Joe, That error was resolved. Now I get a different one. Please give your suggestion.

Amin

/home/aamomin/ProteomicProcessing/TPPdownload/TPP4.8.0/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz/pwiz/data/msdata/                                                               Serializer_MSn.cpp:263: error: expected ‘)’ before ‘const’
/home/aamomin/ProteomicProcessing/TPPdownload/TPP4.8.0/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz/pwiz/data/msdata/                                                               Serializer_MSn.cpp:266: error: ‘Z_OK’ was not declared in this scope
/home/aamomin/ProteomicProcessing/TPPdownload/TPP4.8.0/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz/pwiz/data/msdata/                                                               Serializer_MSn.cpp:288: error: ‘Z_OK’ was not declared in this scope
make: *** [/home/aamomin/ProteomicProcessing/TPPdownload/TPP4.8.0/TPP-4.8.0/trans_proteomic_pipeline/src/../build/RedHatEnterpriseServer-x8                                                               6_64/pwiz/pwiz/data/msdata/Serializer_MSn.o] Error 1

[Joseph Slagel]

Amin,

Did you run a full clean before trying to rebuild?  "make realclean".  Can you send the full log if you still see a problem?

Joe

[Amin Momin]

Hello Joe,
   Thanks for the suggession. I was able to install TPP after taking care of the dependencies. Here are some of the libraries that were needed to install TPP-4.8.0 on RHEL6.6. This may help others working on installation.

Amin

gcc-c++

gnuplot

xsltproc

boost

boost-devel

bzip2

bzip2-devel

zlib-devel

perl-XML-LibXML

perl-XML-Parser

expat-devel

gd-devel

[dann...@gmail.com]

Hello everyone, I got same problem.
I am trying to run TPP 4.8.0 on Ubuntu 15.04

I also used booster patch viz.
https://groups.google.com/forum/#!topicsearchin/spctools-discuss/has_icu$20builds$20$3A$20no/spctools-discuss/PKpva-j8YbU

and my Makefile.config.incl looks like:
############ Begin Makefile.config.incl ####################
TPP_ROOT=/usr/local/tpp/TPP-4.8.0/
TPP_WEB=/tpp/

LINK=shared
LIBEXT=so

## for perl

PERL_LIB_CORE=/usr/lib/perl/5.18/CORE

PERL_BIN=/usr/bin/perl
############ End Makefile.config.incl ####################

here are several pieces of output I though might be useful:
...
...failed updating 1 target...
Command exited with non-zero status 1
142.82user 5.01system 0:51.65elapsed 286%CPU (0avgtext+0avgdata 287392maxresident)k
8inputs+98984outputs (1major+1904875minor)pagefaults 0swaps
...done building boost libraries

building boost libraries...
warning: No toolsets are configured.
warning: Configuring default toolset "gcc".
warning: If the default is wrong, your build may not work correctly.
warning: Use the "toolset=xxxxx" option to override our guess.
warning: For more configuration options, please consult
warning: http://boost.org/boost-build2/doc/html/bbv2/advanced/configuration.html

Performing configuration checks

    - zlib                     : yes (cached)
    - has_icu builds           : yes (cached)

Component configuration:

    - atomic                   : not building
    - chrono                   : not building
    - context                  : not building
    - coroutine                : not building
    - date_time                : building
    - exception                : not building

    - filesystem               : building
    - graph                    : not building
    - graph_parallel           : not building
    - iostreams                : building

    - locale                   : not building
    - log                      : not building

    - math                     : not building
    - mpi                      : not building
    - program_options          : building
    - python                   : not building
    - random                   : not building
    - regex                    : building
    - serialization            : building
    - signals                  : not building
    - system                   : not building
    - test                     : not building
    - thread                   : building

    - timer                    : not building
    - wave                     : not building
...
[ERROR] Boost libary build failed (missing /usr/local/tpp/TPP-4.8.0/trans_proteomic_pipeline/src/../build/Ubuntu-x86_64/boost/lib/libboost_thread.a), please report the results of manually running the following commands:
cd /usr/local/tpp/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/boost_1_54_0; time /usr/local/tpp/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/boost_1_54_0/tools/build/v2/engine/bin.linuxx86_64/bjam -q -d0 --stagedir=/usr/local/tpp/TPP-4.8.0/trans_proteomic_pipeline/src/../build/Ubuntu-x86_64/boost --build-dir=/usr/local/tpp/TPP-4.8.0/trans_proteomic_pipeline/src/../build/Ubuntu-x86_64/boost/obj --layout=system --build-type=minimal -j3 variant=release link=static runtime-link=shared --with-filesystem --with-date_time --with-iostreams --with-program_options --with-regex --with-serialization --with-thread stage
/bin/sh: 1: exit: Illegal number: -1
Makefile.incl:441: recipe for target 'boost-build-libs' failed
make: *** [boost-build-libs] Error 2
...

Help would be much appreciated

Daniel