FTBFS with GCC 4.4

Bug #394142 reported by Alessio Treglia on 2009-07-01
8
This bug affects 1 person
Affects Status Importance Assigned to Milestone
epcr (Debian)
Fix Released
Undecided
Unassigned
epcr (Ubuntu)
Medium
Unassigned

Bug Description

epcr FTBFS in Karmic:

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/buildd/epcr-2.3.11'
make[2]: Entering directory `/build/buildd/epcr-2.3.11'
if test -n "" ; then \
  test -L || ln -s . ; \
 fi
g++ -g -O2 -g -Wall -O2 -I. -g2 -DDEALLOCATE=0 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -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:70: error: 'stdout' was not declared in this scope
e-PCR_main.cpp: In member function 'int CMain::Help(FILE*)':
e-PCR_main.cpp:105: error: 'fprintf' was not declared in this scope
e-PCR_main.cpp: In member function 'int CMain::ParseCmdline()':
e-PCR_main.cpp:192: error: the default argument for parameter 0 of 'int CMain::Help(FILE*)' has not yet been parsed
e-PCR_main.cpp:198: error: 'stderr' was not declared in this scope
e-PCR_main.cpp:199: error: 'fprintf' was not declared in this scope
e-PCR_main.cpp:239: error: 'stderr' was not declared in this scope
e-PCR_main.cpp:246: error: 'stderr' was not declared in this scope
e-PCR_main.cpp:278: error: 'stderr' was not declared in this scope
e-PCR_main.cpp:279: error: 'fprintf' was not declared in this scope
e-PCR_main.cpp:304: error: 'stderr' was not declared in this scope
e-PCR_main.cpp:304: error: 'fprintf' was not declared in this scope
e-PCR_main.cpp:309: error: 'stderr' was not declared in this scope
e-PCR_main.cpp: In constructor 'CPcrProgressCallback::CPcrProgressCallback(int)':
e-PCR_main.cpp:353: error: 'stderr' was not declared in this scope
e-PCR_main.cpp:353: 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:364: error: 'stderr' was not declared in this scope
e-PCR_main.cpp:364: error: 'fputs' was not declared in this scope
e-PCR_main.cpp:369: error: 'stderr' was not declared in this scope
e-PCR_main.cpp:369: error: 'fputs' was not declared in this scope
e-PCR_main.cpp:371: error: 'stderr' was not declared in this scope
e-PCR_main.cpp:371: error: 'fprintf' was not declared in this scope
e-PCR_main.cpp:375: error: 'stderr' was not declared in this scope
e-PCR_main.cpp:375: error: 'fprintf' was not declared in this scope
e-PCR_main.cpp:376: error: 'stderr' was not declared in this scope
e-PCR_main.cpp:376: error: 'fprintf' 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: 'putc' was not declared in this scope
e-PCR_main.cpp:380: error: 'stderr' was not declared in this scope
e-PCR_main.cpp:380: error: 'fputs' was not declared in this scope
e-PCR_main.cpp:381: error: 'putc' was not declared in this scope
e-PCR_main.cpp:384: error: 'stderr' was not declared in this scope
e-PCR_main.cpp:384: error: 'putc' was not declared in this scope
e-PCR_main.cpp:385: error: 'stderr' was not declared in this scope
e-PCR_main.cpp:385: error: 'fflush' was not declared in this scope
e-PCR_main.cpp: In member function 'void CMain::ParseVerbose(const char*)':
e-PCR_main.cpp:413: error: 'stderr' was not declared in this scope
e-PCR_main.cpp:413: 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:449: error: 'sprintf' was not declared in this scope
e-PCR_main.cpp:451: error: 'sprintf' was not declared in this scope
e-PCR_main.cpp:457: 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:542: error: 'fprintf' was not declared in this scope
e-PCR_main.cpp:557: error: 'fprintf' was not declared in this scope
e-PCR_main.cpp: In member function 'int CMain::Execute()':
e-PCR_main.cpp:618: error: 'fopen64' was not declared in this scope
e-PCR_main.cpp:618: error: 'stdout' was not declared in this scope
e-PCR_main.cpp:737: error: 'fclose' was not declared in this scope
e-PCR_main.cpp: In member function 'int CMain::Version()':
e-PCR_main.cpp:746: error: 'puts' was not declared in this scope
e-PCR_main.cpp: In function 'int main(int, char**)':
e-PCR_main.cpp:764: error: 'stderr' was not declared in this scope
e-PCR_main.cpp:764: error: 'fprintf' was not declared in this scope
e-PCR_main.cpp:767: error: 'stderr' was not declared in this scope
e-PCR_main.cpp:767: error: 'fprintf' was not declared in this scope
e-PCR_main.cpp:770: error: 'stderr' was not declared in this scope
e-PCR_main.cpp:770: error: 'fprintf' was not declared in this scope
make[2]: *** [e-PCR_main.o] Error 1
make[2]: Leaving directory `/build/buildd/epcr-2.3.11'
make[2]: Entering directory `/build/buildd/epcr-2.3.11'
if test -n "" ; then \
  test -L || ln -s . ; \
 fi
g++ -g -O2 -g -Wall -O2 -I. -g2 -DDEALLOCATE=0 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -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:92: error: the default argument for parameter 0 of 'int CMain::Help(FILE*)' has not yet been parsed
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/buildd/epcr-2.3.11'
make[2]: Entering directory `/build/buildd/epcr-2.3.11'
if test -n "" ; then \
  test -L || ln -s . ; \
 fi
g++ -g -O2 -g -Wall -O2 -I. -g2 -DDEALLOCATE=0 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -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:106: error: the default argument for parameter 0 of 'int CMain::Help(FILE*)' has not yet been parsed
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/buildd/epcr-2.3.11'
make[2]: Entering directory `/build/buildd/epcr-2.3.11'
if test -n "" ; then \
  test -L || ln -s . ; \
 fi
g++ -g -O2 -g -Wall -O2 -I. -g2 -DDEALLOCATE=0 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -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:128: error: the default argument for parameter 0 of 'int CMain::Help(FILE*)' has not yet been parsed
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/buildd/epcr-2.3.11'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/build/buildd/epcr-2.3.11'
make: *** [debian/stamp-makefile-build] Error 2
dpkg-buildpackage: failure: debian/rules build gave error exit status 2

Related branches

Alessio Treglia (quadrispro) wrote :

A patch is available in BTS, however the Debian maintainer prefers to wait for a new upstream release.

Changed in epcr (Ubuntu):
importance: Undecided → Medium
status: New → Triaged
Changed in epcr (Debian):
status: Unknown → Confirmed
Fabrice Coutadeur (fabricesp) wrote :

Debdiff I have sent to debian (to not loose it)

Changed in epcr (Ubuntu):
status: Triaged → Fix Committed
Launchpad Janitor (janitor) wrote :

This bug was fixed in the package epcr - 2.3.11-1ubuntu1

---------------
epcr (2.3.11-1ubuntu1) karmic; urgency=low

  * debian/patch/gcc_4.4.patch: fix a FTBFS because of missing
    #include <cstdio> header in several sources (LP: #394142); patch taken
    from http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=504849.
  * debian/rules: added include of /usr/share/cdbs/1/rules/simple-patchsys.mk

 -- Fabrice Coutadeur <email address hidden> Wed, 01 Jul 2009 06:48:02 +0000

Changed in epcr (Ubuntu):
status: Fix Committed → Fix Released
Artur Rona (ari-tczew) wrote :

 epcr (2.3.12-1) unstable; urgency=low

   * New upstream release buildable with GCC 4.4 (Closes: #504849)
   * Version number updated in debian/rules.
   * debian/copyright refreshed to my latest exploration of the
     machine-readable format.
   * Added a BibTeX reference in debian/reference.

 -- Charles Plessy <email address hidden> Thu, 02 Jul 2009 09:31:29 +0900

Changed in epcr (Debian):
importance: Unknown → Undecided
status: Confirmed → New
status: New → Fix Released
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