Package: epcr Version: 2.3.10-1 User: [EMAIL PROTECTED] Usertags: ftbfs-gcc-4.4 Tags: patch
Your package fails to build with the upcoming GCC 4.4. Version 4.4 has not been released yet but I'm building with a snapshot in order to find errors and give people an advance warning. GCC 4.4 cleaned up some more C++ headers. You always have to #include headers directly and cannot rely for things to be included indirectly. You can reproduce this problem with gcc-snapshot from unstable. > Automatic build of epcr_2.3.10-1 on em64t by sbuild/amd64 0.53 ... > g++ -g -O2 -g -Wall -O2 -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.10\" > -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=10 -DSTANDALONE=1 -c stsmatch.cpp -o > stsmatch.o > stsmatch.cpp: In member function 'virtual bool > ncbi::pcr_tools::CStsFileCallbackDefault::Error(ncbi::pcr_tools::IStsFileCallback::EError)': > stsmatch.cpp:80: warning: enumeration value 'eErrTOTAL' not handled in switch > stsmatch.cpp: In member function 'virtual bool > ncbi::pcr_tools::CStsFileCallbackDefault::Done()': > stsmatch.cpp:95: error: 'stderr' was not declared in this scope > stsmatch.cpp:96: error: 'fprintf' was not declared in this scope > stsmatch.cpp:98: error: 'stderr' was not declared in this scope > stsmatch.cpp:99: error: 'fprintf' was not declared in this scope > stsmatch.cpp:101: error: 'stderr' was not declared in this scope > stsmatch.cpp:103: error: 'fprintf' was not declared in this scope > make[2]: *** [stsmatch.o] Error 1 > make[2]: Leaving directory `/build/tbm/epcr-2.3.10' > make[2]: Entering directory `/build/tbm/epcr-2.3.10' > if test -n "" ; then \ > test -L || ln -s . ; \ > fi > g++ -g -O2 -g -Wall -O2 -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.10\" > -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=10 -DSTANDALONE=1 -c e-PCR_main.cpp > -o e-PCR_main.o > e-PCR_main.cpp:69: error: 'stdout' was not declared in this scope > e-PCR_main.cpp: In member function 'int CMain::Help(FILE*)': > e-PCR_main.cpp:103: error: 'fprintf' was not declared in this scope > e-PCR_main.cpp: In member function 'int CMain::ParseCmdline()': > e-PCR_main.cpp:194: error: 'stderr' was not declared in this scope > e-PCR_main.cpp:195: error: 'fprintf' was not declared in this scope > e-PCR_main.cpp:237: error: 'stderr' was not declared in this scope > e-PCR_main.cpp:244: error: 'stderr' was not declared in this scope > e-PCR_main.cpp:276: error: 'stderr' was not declared in this scope > e-PCR_main.cpp:277: error: 'fprintf' was not declared in this scope > e-PCR_main.cpp:301: error: 'stderr' was not declared in this scope > e-PCR_main.cpp:301: error: 'fprintf' was not declared in this scope > e-PCR_main.cpp:306: error: 'stderr' was not declared in this scope > e-PCR_main.cpp: In constructor > 'CPcrProgressCallback::CPcrProgressCallback(int)': > e-PCR_main.cpp:350: error: 'stderr' was not declared in this scope > e-PCR_main.cpp:350: error: 'fileno' was not declared in this scope > e-PCR_main.cpp: In member function 'void > CPcrProgressCallback::Report(unsigned int, bool)': > e-PCR_main.cpp:361: error: 'stderr' was not declared in this scope > e-PCR_main.cpp:361: error: 'fputs' was not declared in this scope > e-PCR_main.cpp:366: error: 'stderr' was not declared in this scope > e-PCR_main.cpp:366: error: 'fputs' was not declared in this scope > e-PCR_main.cpp:368: error: 'stderr' was not declared in this scope > e-PCR_main.cpp:368: error: 'fprintf' was not declared in this scope > e-PCR_main.cpp:372: error: 'stderr' was not declared in this scope > e-PCR_main.cpp:372: error: 'fprintf' was not declared in this scope > e-PCR_main.cpp:373: error: 'stderr' was not declared in this scope > e-PCR_main.cpp:373: error: 'fprintf' was not declared in this scope > e-PCR_main.cpp:374: error: 'stderr' was not declared in this scope > e-PCR_main.cpp:374: error: 'putc' was not declared in this scope > e-PCR_main.cpp:377: error: 'stderr' was not declared in this scope > e-PCR_main.cpp:377: error: 'fputs' was not declared in this scope > e-PCR_main.cpp:378: error: 'putc' was not declared in this scope > e-PCR_main.cpp:381: error: 'stderr' was not declared in this scope > e-PCR_main.cpp:381: error: 'putc' was not declared in this scope > e-PCR_main.cpp:382: error: 'stderr' was not declared in this scope > e-PCR_main.cpp:382: error: 'fflush' was not declared in this scope > e-PCR_main.cpp: In member function 'void CMain::ParseVerbose(const char*)': > e-PCR_main.cpp:410: error: 'stderr' was not declared in this scope > e-PCR_main.cpp:410: error: 'fprintf' was not declared in this scope > e-PCR_main.cpp: In member function 'virtual int > CPcrMachineCallbackClassic::ReportHit(const char*, int, int, const > ncbi::pcr_tools::ISts*)': > e-PCR_main.cpp:446: error: 'sprintf' was not declared in this scope > e-PCR_main.cpp:448: error: 'sprintf' was not declared in this scope > e-PCR_main.cpp:454: error: 'fprintf' was not declared in this scope > e-PCR_main.cpp: In member function 'virtual void > CPcrMachineCallbackTabular::CbkMatch(const ncbi::pcr_tools::ISts*, unsigned > int, unsigned int, const ncbi::pcr_tools::IPcrMachineCallback::SScore*)': > e-PCR_main.cpp:539: error: 'fprintf' was not declared in this scope > e-PCR_main.cpp:554: error: 'fprintf' was not declared in this scope > e-PCR_main.cpp: In member function 'int CMain::Execute()': > e-PCR_main.cpp:615: error: 'fopen64' was not declared in this scope > e-PCR_main.cpp:615: error: 'stdout' was not declared in this scope > e-PCR_main.cpp:733: error: 'fclose' was not declared in this scope > e-PCR_main.cpp: In member function 'int CMain::Version()': > e-PCR_main.cpp:742: error: 'puts' was not declared in this scope > e-PCR_main.cpp: In function 'int main(int, char**)': > e-PCR_main.cpp:760: error: 'stderr' was not declared in this scope > e-PCR_main.cpp:760: error: 'fprintf' was not declared in this scope > e-PCR_main.cpp:763: error: 'stderr' was not declared in this scope > e-PCR_main.cpp:763: error: 'fprintf' was not declared in this scope > e-PCR_main.cpp:766: error: 'stderr' was not declared in this scope > e-PCR_main.cpp:766: error: 'fprintf' was not declared in this scope > make[2]: *** [e-PCR_main.o] Error 1 > make[2]: Leaving directory `/build/tbm/epcr-2.3.10' > make[2]: Entering directory `/build/tbm/epcr-2.3.10' > if test -n "" ; then \ > test -L || ln -s . ; \ > fi > g++ -g -O2 -g -Wall -O2 -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.10\" > -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=10 -DSTANDALONE=1 -c famap_main.cpp > -o famap_main.o > famap_main.cpp:54: error: 'stdout' was not declared in this scope > famap_main.cpp: In member function 'int CMain::Help(FILE*)': > famap_main.cpp:74: error: 'fprintf' was not declared in this scope > famap_main.cpp: In member function 'int CMain::ParseCmdline()': > famap_main.cpp:105: error: 'stderr' was not declared in this scope > famap_main.cpp:105: error: 'fprintf' was not declared in this scope > famap_main.cpp:110: error: 'stderr' was not declared in this scope > famap_main.cpp: In member function 'int CMain::Build()': > famap_main.cpp:121: error: 'stderr' was not declared in this scope > famap_main.cpp:122: error: 'fileno' was not declared in this scope > famap_main.cpp:123: error: 'fprintf' was not declared in this scope > famap_main.cpp:128: error: 'rename' was not declared in this scope > famap_main.cpp: In member function 'int CMain::Stat()': > famap_main.cpp:149: error: 'stdout' was not declared in this scope > famap_main.cpp:149: error: 'fprintf' was not declared in this scope > famap_main.cpp: In member function 'int CMain::Dump()': > famap_main.cpp:160: error: 'printf' was not declared in this scope > famap_main.cpp:163: error: 'stdout' was not declared in this scope > famap_main.cpp:163: error: 'fwrite' was not declared in this scope > famap_main.cpp:164: error: 'putc' was not declared in this scope > famap_main.cpp:170: warning: comparison between signed and unsigned integer > expressions > famap_main.cpp:172: warning: comparison between signed and unsigned integer > expressions > famap_main.cpp:173: error: 'stderr' was not declared in this scope > famap_main.cpp:173: error: 'fprintf' was not declared in this scope > famap_main.cpp:175: error: 'printf' was not declared in this scope > famap_main.cpp:178: error: 'stdout' was not declared in this scope > famap_main.cpp:178: error: 'fwrite' was not declared in this scope > famap_main.cpp:179: error: 'putc' was not declared in this scope > famap_main.cpp: In member function 'int CMain::List()': > famap_main.cpp:195: error: 'printf' was not declared in this scope > famap_main.cpp:205: warning: comparison between signed and unsigned integer > expressions > famap_main.cpp:207: warning: comparison between signed and unsigned integer > expressions > famap_main.cpp:208: error: 'stderr' was not declared in this scope > famap_main.cpp:208: error: 'fprintf' was not declared in this scope > famap_main.cpp:211: error: 'printf' was not declared in this scope > famap_main.cpp: In member function 'int CMain::Version()': > famap_main.cpp:223: error: 'puts' was not declared in this scope > famap_main.cpp: In function 'int main(int, char**)': > famap_main.cpp:241: error: 'stderr' was not declared in this scope > famap_main.cpp:241: error: 'fprintf' was not declared in this scope > famap_main.cpp:244: error: 'stderr' was not declared in this scope > famap_main.cpp:244: error: 'fprintf' was not declared in this scope > famap_main.cpp:247: error: 'stderr' was not declared in this scope > famap_main.cpp:247: error: 'fprintf' was not declared in this scope > make[2]: *** [famap_main.o] Error 1 > make[2]: Leaving directory `/build/tbm/epcr-2.3.10' > make[2]: Entering directory `/build/tbm/epcr-2.3.10' > if test -n "" ; then \ > test -L || ln -s . ; \ > fi > g++ -g -O2 -g -Wall -O2 -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.10\" > -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=10 -DSTANDALONE=1 -c fahash_main.cpp > -o fahash_main.o > fahash_main.cpp:57: error: 'stdout' was not declared in this scope > fahash_main.cpp: In member function 'int CMain::Help(FILE*)': > fahash_main.cpp:82: error: 'fprintf' was not declared in this scope > fahash_main.cpp: In member function 'int CMain::ParseCmdline()': > fahash_main.cpp:140: error: 'stderr' was not declared in this scope > fahash_main.cpp: In member function 'virtual void > CFaIndexerCallback::CbkSequence(const char*)': > fahash_main.cpp:157: error: 'stderr' was not declared in this scope > fahash_main.cpp:157: error: 'fprintf' was not declared in this scope > fahash_main.cpp:158: error: 'fflush' was not declared in this scope > fahash_main.cpp: In member function 'virtual void > CFaIndexerCallback::CbkProgress(unsigned int, unsigned int)': > fahash_main.cpp:166: error: 'stderr' was not declared in this scope > fahash_main.cpp:169: error: 'fprintf' was not declared in this scope > fahash_main.cpp:170: error: 'fflush' was not declared in this scope > fahash_main.cpp: In member function 'virtual void > CFaIndexerCallback::CbkFile(const char*)': > fahash_main.cpp:175: error: 'stderr' was not declared in this scope > fahash_main.cpp:175: error: 'fprintf' was not declared in this scope > fahash_main.cpp:176: error: 'fflush' was not declared in this scope > fahash_main.cpp: In member function 'virtual void > CFaIndexerCallback::CbkDumpProgress(unsigned int, unsigned int)': > fahash_main.cpp:184: error: 'stderr' was not declared in this scope > fahash_main.cpp:187: error: 'fprintf' was not declared in this scope > fahash_main.cpp:188: error: 'fflush' was not declared in this scope > fahash_main.cpp: In member function 'virtual void > CFaIndexerCallback::CbkDumpStart()': > fahash_main.cpp:193: error: 'stderr' was not declared in this scope > fahash_main.cpp:193: error: 'fprintf' was not declared in this scope > fahash_main.cpp:194: error: 'fflush' was not declared in this scope > fahash_main.cpp: In member function 'virtual void > CFaIndexerCallback::CbkDumpEnd()': > fahash_main.cpp:197: error: 'stderr' was not declared in this scope > fahash_main.cpp:197: error: 'fprintf' was not declared in this scope > fahash_main.cpp:198: error: 'fflush' was not declared in this scope > fahash_main.cpp: In member function 'virtual void > CFaIndexerCallback::CbkResetStart()': > fahash_main.cpp:201: error: 'stderr' was not declared in this scope > fahash_main.cpp:201: error: 'fprintf' was not declared in this scope > fahash_main.cpp:202: error: 'fflush' was not declared in this scope > fahash_main.cpp: In member function 'virtual void > CFaIndexerCallback::CbkResetEnd()': > fahash_main.cpp:205: error: 'stderr' was not declared in this scope > fahash_main.cpp:205: error: 'fprintf' was not declared in this scope > fahash_main.cpp: In member function 'int CMain::Build()': > fahash_main.cpp:247: error: 'rename' was not declared in this scope > fahash_main.cpp: In member function 'int CMain::Execute()': > fahash_main.cpp:256: warning: enumeration value 'eNone' not handled in switch > fahash_main.cpp: In member function 'int CMain::Stat()': > fahash_main.cpp:266: error: 'stderr' was not declared in this scope > fahash_main.cpp:266: error: 'fputs' was not declared in this scope > fahash_main.cpp:269: error: 'fopen64' was not declared in this scope > fahash_main.cpp:269: error: 'stdout' was not declared in this scope > fahash_main.cpp:292: warning: comparison between signed and unsigned integer > expressions > fahash_main.cpp:303: error: 'fprintf' was not declared in this scope > fahash_main.cpp:306: error: 'fclose' was not declared in this scope > fahash_main.cpp: In member function 'int CMain::Version()': > fahash_main.cpp:314: error: 'puts' was not declared in this scope > fahash_main.cpp: In function 'int main(int, char**)': > fahash_main.cpp:332: error: 'stderr' was not declared in this scope > fahash_main.cpp:332: error: 'fprintf' was not declared in this scope > fahash_main.cpp:335: error: 'stderr' was not declared in this scope > fahash_main.cpp:335: error: 'fprintf' was not declared in this scope > fahash_main.cpp:338: error: 'stderr' was not declared in this scope > fahash_main.cpp:338: error: 'fprintf' was not declared in this scope > make[2]: *** [fahash_main.o] Error 1 > make[2]: Leaving directory `/build/tbm/epcr-2.3.10' > make[2]: Entering directory `/build/tbm/epcr-2.3.10' > if test -n "" ; then \ > test -L || ln -s . ; \ > fi > g++ -g -O2 -g -Wall -O2 -I. -g2 -DDEALLOCATE=0 -DVERSION=\"2.3.10\" > -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=10 -DSTANDALONE=1 -c re-PCR_main.cpp > -o re-PCR_main.o > re-PCR_main.cpp:59: error: 'stdout' was not declared in this scope > re-PCR_main.cpp: In member function 'int CMain::Help(FILE*)': > re-PCR_main.cpp:89: error: 'fprintf' was not declared in this scope > re-PCR_main.cpp: In member function 'int CMain::ParseCmdline()': > re-PCR_main.cpp:161: error: 'stderr' was not declared in this scope > re-PCR_main.cpp: At global scope: > re-PCR_main.cpp:179: error: 'stdout' was not declared in this scope > re-PCR_main.cpp: In member function 'virtual bool > CFaLookupCallbackBase::Fail(const std::string&)': > re-PCR_main.cpp:181: error: 'fprintf' was not declared in this scope > re-PCR_main.cpp: In member function 'virtual bool > CFaLookupCallbackBase::Warn(const std::string&, const > ncbi::pcr_tools::ISts*)': > re-PCR_main.cpp:185: error: 'fprintf' was not declared in this scope > re-PCR_main.cpp: In member function 'virtual bool > CFaLookupCallbackBase::Done()': > re-PCR_main.cpp:189: error: 'stderr' was not declared in this scope > re-PCR_main.cpp:189: error: 'fileno' was not declared in this scope > re-PCR_main.cpp:190: error: 'fprintf' was not declared in this scope > re-PCR_main.cpp:191: error: 'fflush' was not declared in this scope > re-PCR_main.cpp:193: error: 'fprintf' was not declared in this scope > re-PCR_main.cpp: In member function 'virtual void > CFaLookupCallbackBase::Progress(unsigned int, unsigned int)': > re-PCR_main.cpp:197: error: 'stderr' was not declared in this scope > re-PCR_main.cpp:197: error: 'fileno' was not declared in this scope > re-PCR_main.cpp:207: error: 'fprintf' was not declared in this scope > re-PCR_main.cpp:208: error: 'fflush' was not declared in this scope > re-PCR_main.cpp: At global scope: > re-PCR_main.cpp:228: error: 'stdout' was not declared in this scope > re-PCR_main.cpp: In member function 'virtual bool > CFaLookupPrimerCallback::Start()': > re-PCR_main.cpp:230: error: 'fprintf' was not declared in this scope > re-PCR_main.cpp: In member function 'virtual bool > CFaLookupPrimerCallback::Match(const ncbi::pcr_tools::SFaMatchBlock*)': > re-PCR_main.cpp:245: error: 'fprintf' was not declared in this scope > re-PCR_main.cpp: At global scope: > re-PCR_main.cpp:254: error: 'stdout' was not declared in this scope > re-PCR_main.cpp: In member function 'virtual bool > CFaLookupStsCallback::Start()': > re-PCR_main.cpp:258: error: 'fprintf' was not declared in this scope > re-PCR_main.cpp: In member function 'virtual bool > CFaLookupStsCallback::Match(const ncbi::pcr_tools::SFaMatchBlock*, const > ncbi::pcr_tools::ISts*)': > re-PCR_main.cpp:273: error: 'fprintf' was not declared in this scope > re-PCR_main.cpp: In member function 'int CMain::Execute()': > re-PCR_main.cpp:344: warning: enumeration value 'eNone' not handled in switch > re-PCR_main.cpp: In member function 'int CMain::PrimerLookup()': > re-PCR_main.cpp:355: error: 'stdout' was not declared in this scope > re-PCR_main.cpp:361: error: 'snprintf' was not declared in this scope > re-PCR_main.cpp:373: error: 'fopen' was not declared in this scope > re-PCR_main.cpp:376: error: 'fgets' was not declared in this scope > re-PCR_main.cpp:377: error: 'feof' was not declared in this scope > re-PCR_main.cpp:399: error: 'fclose' was not declared in this scope > re-PCR_main.cpp:401: error: 'stderr' was not declared in this scope > re-PCR_main.cpp:402: error: 'fprintf' was not declared in this scope > re-PCR_main.cpp: In member function 'int CMain::STSLookup()': > re-PCR_main.cpp:415: error: 'fopen64' was not declared in this scope > re-PCR_main.cpp:415: error: 'stdout' was not declared in this scope > re-PCR_main.cpp:423: error: 'snprintf' was not declared in this scope > re-PCR_main.cpp:444: error: 'fopen' was not declared in this scope > re-PCR_main.cpp:451: error: 'fgets' was not declared in this scope > re-PCR_main.cpp:452: error: 'feof' was not declared in this scope > re-PCR_main.cpp:485: warning: comparison between signed and unsigned integer > expressions > re-PCR_main.cpp:486: error: 'stderr' was not declared in this scope > re-PCR_main.cpp:487: error: 'fprintf' was not declared in this scope > re-PCR_main.cpp:499: error: 'fclose' was not declared in this scope > re-PCR_main.cpp:500: error: 'stderr' was not declared in this scope > re-PCR_main.cpp:501: error: 'fprintf' was not declared in this scope > re-PCR_main.cpp:442: warning: unused variable 'tcount' > re-PCR_main.cpp: In member function 'int CMain::Version()': > re-PCR_main.cpp:517: error: 'puts' was not declared in this scope > re-PCR_main.cpp: In function 'int main(int, char**)': > re-PCR_main.cpp:535: error: 'stderr' was not declared in this scope > re-PCR_main.cpp:535: error: 'fprintf' was not declared in this scope > re-PCR_main.cpp:538: error: 'stderr' was not declared in this scope > re-PCR_main.cpp:538: error: 'fprintf' was not declared in this scope > re-PCR_main.cpp:541: error: 'stderr' was not declared in this scope > re-PCR_main.cpp:541: error: 'fprintf' was not declared in this scope > make[2]: *** [re-PCR_main.o] Error 1 > make[2]: Leaving directory `/build/tbm/epcr-2.3.10' --- re-PCR_main.cpp~ 2008-11-07 16:50:00.000000000 +0000 +++ re-PCR_main.cpp 2008-11-07 16:50:09.000000000 +0000 @@ -37,6 +37,7 @@ #include <errno.h> #include <stdexcept> +#include <cstdio> #include <string> #include <memory> --- fahash_main.cpp~ 2008-11-07 16:50:32.000000000 +0000 +++ fahash_main.cpp 2008-11-07 16:50:41.000000000 +0000 @@ -37,6 +37,7 @@ #include <math.h> #include <time.h> +#include <cstdio> #include <memory> USING_NCBI_SCOPE; --- famap_main.cpp~ 2008-11-07 16:51:14.000000000 +0000 +++ famap_main.cpp 2008-11-07 16:51:23.000000000 +0000 @@ -29,6 +29,7 @@ #include <epcr/fast_seqio.hpp> #include <stdexcept> +#include <cstdio> #include <cstdlib> #include <cstring> --- e-PCR_main.cpp~ 2008-11-07 16:51:34.000000000 +0000 +++ e-PCR_main.cpp 2008-11-07 16:51:42.000000000 +0000 @@ -36,6 +36,7 @@ #include <errno.h> #include <time.h> +#include <cstdio> #include <memory> #ifndef STANDALONE --- stsmatch.cpp~ 2008-11-07 16:51:51.000000000 +0000 +++ stsmatch.cpp 2008-11-07 16:51:59.000000000 +0000 @@ -33,6 +33,7 @@ #include <errno.h> #include <ctype.h> +#include <cstdio> #include <stdexcept> USING_NCBI_SCOPE; -- Martin Michlmayr http://www.cyrius.com/ -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". 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