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 <momin.a...@gmail.com> 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, jsl...@systemsbiology.org > 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 <momin...@gmail.com> 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, >>> jsl...@systemsbiology.org 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 spctools-discu...@googlegroups.com. >>> To post to this group, send email to spctools...@googlegroups.com. >>> 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 >> jsl...@systemsbiology.org >> >> -- > 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 spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > 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 jsla...@systemsbiology.org -- 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
