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 On Thursday, June 4, 2015 at 2:37:24 PM UTC-5, [email protected] wrote: > > 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 > > On Thu, Jun 4, 2015 at 12:21 PM, Amin Momin <[email protected] > <javascript:>> wrote: > >> 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 >> >> >> On Thursday, June 4, 2015 at 11:23:05 AM UTC-5, [email protected] >> wrote: >>> >>> 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 >>> >>> >>> On Thu, Jun 4, 2015 at 8:41 AM, Amin Momin <[email protected]> wrote: >>> >>>> 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 >>>> >>>> >>>> >>>> On Wednesday, October 16, 2013 at 4:22:51 PM UTC-5, >>>> [email protected] wrote: >>>>> >>>>> 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 >>>>> >>>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "spctools-discuss" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to [email protected]. >>>> To post to this group, send email to [email protected]. >>>> Visit this group at http://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> >>> >>> -- >>> Joe Slagel >>> Institute for Systems Biology >>> [email protected] >>> >>> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> Visit this group at http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > > > -- > Joe Slagel > Institute for Systems Biology > [email protected] <javascript:> > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
