>>> Unpacking source... >>> Unpacking kemistry-0.7.tar.bz2 to /var/tmp/portage/sci-chemistry/kemistry-0.7/work * Applying kemistry-0.7-gcc3.4.patch ...  [ ok ] * Applying kemistry-0.7-fPIC.patch ...  [ ok ] >>> Source unpacked. >>> Compiling source in /var/tmp/portage/sci-chemistry/kemistry-0.7/work/kemistry-0.7 ... * Running elibtoolize in: kemistry-0.7/admin * Applying install-sh-1.5.patch ... * Applying ltmain-1.5.patch ... * Applying portage-1.5.10.patch ... * Applying relink-1.4.0a.patch ... * Applying max_cmd_len-1.5.20.patch ... * Applying sed-1.5.6.patch ... * Applying tmp-1.3.5.patch ... * Applying uclibc-ltconf-1.3.0.patch ... * econf: updating kemistry-0.7/admin/config.guess with /usr/share/gnuconfig/config.guess * econf: updating kemistry-0.7/admin/config.sub with /usr/share/gnuconfig/config.sub ./configure --prefix=/usr --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --with-x --enable-mitshm --with-xinerama --with-qt-dir=/usr/qt/3 --enable-mt --with-qt-libraries=/usr/qt/3/lib64 --disable-dependency-tracking --disable-debug --without-debug --enable-libsuffix=64 --with-extra-includes=/usr/kde/3.5/include --with-extra-libs=/usr/kde/3.5/lib64 --libdir=/usr/lib64 --build=x86_64-pc-linux-gnu checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking for -p flag to install... yes checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets ${MAKE}... yes checking for style of include used by make... 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GNU/Linux ld.so checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no configure: creating libtool appending configuration tag "CXX" to libtool checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld) supports shared libraries... yes checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC works... no checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... no checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... yes checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking dynamic linker characteristics... GNU/Linux ld.so appending configuration tag "GCJ" to libtool checking if gcj supports -fno-rtti -fno-exceptions... (cached) no checking for gcj option to produce PIC... -fPIC checking if gcj PIC flag -fPIC works... no checking if gcj supports -c -o file.o... no checking whether the gcj linker (/usr/x86_64-pc-linux-gnu/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... yes checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking dynamic linker characteristics... 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(cached) yes checking for poll in -lpoll... no checking CoreAudio/CoreAudio.h usability... no checking CoreAudio/CoreAudio.h presence... no checking for CoreAudio/CoreAudio.h... no checking for res_init... no checking for killpg in -lucb... no checking for int... yes checking size of int... 4 checking for long... yes checking size of long... 8 checking for char *... yes checking size of char *... 8 checking for char... yes checking size of char... 1 checking for dlopen in -ldl... yes checking for shl_unload in -ldld... no checking for X... libraries /usr/lib64, headers . checking for IceConnectionNumber in -lICE... yes checking for libXext... yes checking for Xinerama... yes checking for pthread_create in -lpthread... yes checking for extra includes... added checking for extra libs... added checking for libz... -lz checking for libpng... -lpng -lz -lm checking for libjpeg6b... no checking for libjpeg... -ljpeg checking for Qt... libraries /usr/qt/3/lib64, headers /usr/qt/3/include using -mt checking for moc... /usr/qt/3/bin/moc checking for uic... /usr/qt/3/bin/uic checking whether uic supports -L ... yes checking whether uic supports -nounload ... yes checking if Qt needs -ljpeg... no checking for rpath... yes checking for KDE... libraries /usr/kde/3.5/lib, headers /usr/kde/3.5/include checking for KDE paths... defaults checking for dcopidl... /usr/kde/3.5/bin/dcopidl checking for dcopidl2cpp... /usr/kde/3.5/bin/dcopidl2cpp checking for mcopidl... /usr/kde/3.5/bin/mcopidl checking for artsc-config... /usr/bin/artsc-config checking for kde-config... /usr/kde/3.5/bin/kde-config checking for meinproc... /usr/kde/3.5/bin/meinproc checking if STL implementation is SGI like... yes KDrawChem KOffice part will not be built checking if tnt should be compiled... yes checking if po should be compiled... yes checking if openbabel should be compiled... yes checking if libkemistry should be compiled... yes checking if kmolcalc should be compiled... yes checking if kfile_plugins should be compiled... yes checking if kembabel should be compiled... yes checking if kdrawchem should be compiled... yes checking if docs should be compiled... yes configure: creating ./config.status fast creating ./Makefile fast creating docs/Makefile fast creating docs/en/Makefile fast creating docs/en/kdrawchem/Makefile fast creating docs/en/kembabel/Makefile fast creating docs/en/kmolcalc/Makefile fast creating docs/it/Makefile fast creating docs/it/kdrawchem/Makefile fast creating docs/it/kembabel/Makefile fast creating docs/it/kmolcalc/Makefile fast creating docs/it/po/Makefile fast creating docs/templates/Makefile fast creating kdrawchem/Makefile fast creating kdrawchem/kopart/Makefile fast creating kembabel/Makefile fast creating kfile_plugins/Makefile fast creating kmolcalc/Makefile fast creating libkemistry/Makefile fast creating openbabel/Makefile fast creating openbabel/mime/Makefile fast creating po/Makefile fast creating po/it/Makefile fast creating tnt/Makefile config.status: creating config.h config.status: executing default-1 commands make -j3 cd . \ && CONFIG_FILES= CONFIG_HEADERS=config.h \ /bin/sh ./config.status config.status: creating config.h config.status: config.h is unchanged config.status: executing default-1 commands make all-recursive make[1]: Entering directory `/var/tmp/portage/sci-chemistry/kemistry-0.7/work/kemistry-0.7' Making all in openbabel make[2]: Entering directory `/var/tmp/portage/sci-chemistry/kemistry-0.7/work/kemistry-0.7/openbabel' cd .. && \ /bin/sh /var/tmp/portage/sci-chemistry/kemistry-0.7/work/kemistry-0.7/admin/missing --run automake --gnu openbabel/Makefile cd .. && perl admin/am_edit openbabel/Makefile.in cd .. && \ CONFIG_HEADERS= CONFIG_LINKS= \ CONFIG_FILES=openbabel/Makefile /bin/sh ./config.status fast creating openbabel/Makefile config.status: executing default-1 commands make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/kemistry-0.7/work/kemistry-0.7/openbabel' make[2]: Entering directory `/var/tmp/portage/sci-chemistry/kemistry-0.7/work/kemistry-0.7/openbabel' Making all in mime make[3]: Entering directory `/var/tmp/portage/sci-chemistry/kemistry-0.7/work/kemistry-0.7/openbabel/mime' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/kemistry-0.7/work/kemistry-0.7/openbabel/mime' make[3]: Entering directory `/var/tmp/portage/sci-chemistry/kemistry-0.7/work/kemistry-0.7/openbabel' /bin/sh ../libtool --silent --mode=compile --tag=CXX x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/kde/3.5/include -I/usr/qt/3/include -I. -I/usr/kde/3.5/include -DQT_THREAD_SUPPORT -D_REENTRANT -Wnon-virtual-dtor -Wno-long-long -Wbad-function-cast -Wundef -Wall -pedantic -W -Wpointer-arith -Wmissing-prototypes -Wwrite-strings -ansi -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -Wcast-align -Wconversion -DNDEBUG -DNO_DEBUG -O2 -O2 -g -pipe -mtune=core2 -march=core2 -mssse3 -msse4.1 -fno-exceptions -fno-check-new -fexceptions -DDATADIR=\"/usr/share/apps/openbabel\" -fPIC -c -o atom.lo `test -f atom.cpp || echo './'`atom.cpp /bin/sh ../libtool --silent --mode=compile --tag=CXX x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/kde/3.5/include -I/usr/qt/3/include -I. -I/usr/kde/3.5/include -DQT_THREAD_SUPPORT -D_REENTRANT -Wnon-virtual-dtor -Wno-long-long -Wbad-function-cast -Wundef -Wall -pedantic -W -Wpointer-arith -Wmissing-prototypes -Wwrite-strings -ansi -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -Wcast-align -Wconversion -DNDEBUG -DNO_DEBUG -O2 -O2 -g -pipe -mtune=core2 -march=core2 -mssse3 -msse4.1 -fno-exceptions -fno-check-new -fexceptions -DDATADIR=\"/usr/share/apps/openbabel\" -fPIC -c -o base.lo `test -f base.cpp || echo './'`base.cpp /bin/sh ../libtool --silent --mode=compile --tag=CXX x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/kde/3.5/include -I/usr/qt/3/include -I. -I/usr/kde/3.5/include -DQT_THREAD_SUPPORT -D_REENTRANT -Wnon-virtual-dtor -Wno-long-long -Wbad-function-cast -Wundef -Wall -pedantic -W -Wpointer-arith -Wmissing-prototypes -Wwrite-strings -ansi -D_XOPEN_SOURCE=500 -D_BSD_SOURCE -Wcast-align -Wconversion -DNDEBUG -DNO_DEBUG -O2 -O2 -g -pipe -mtune=core2 -march=core2 -mssse3 -msse4.1 -fno-exceptions -fno-check-new -fexceptions -DDATADIR=\"/usr/share/apps/openbabel\" -fPIC -c -o binary.lo `test -f binary.cpp || echo './'`binary.cpp cc1plus: warning: command line option "-Wbad-function-cast" is valid for C/ObjC but not for C++ cc1plus: warning: command line option "-Wmissing-prototypes" is valid for Ada/C/ObjC but not for C++ cc1plus: warning: command line option "-Wbad-function-cast" is valid for C/ObjC but not for C++ cc1plus: warning: command line option "-Wmissing-prototypes" is valid for Ada/C/ObjC but not for C++ cc1plus: warning: command line option "-Wbad-function-cast" is valid for C/ObjC but not for C++ cc1plus: warning: command line option "-Wmissing-prototypes" is valid for Ada/C/ObjC but not for C++ In file included from mol.h:29, from atom.cpp:14: base.h: In member function 'void OpenBabel::OBNodeBase::SetIdx(int)': base.h:68: warning: conversion to 'short unsigned int' from 'int' may alter its value base.h: In member function 'virtual unsigned int OpenBabel::OBNodeBase::GetValence() const': base.h:75: warning: conversion to 'unsigned int' from 'size_t' may alter its value base.h: At global scope: base.h:133: warning: unused parameter 'bgn' base.h:133: warning: unused parameter 'end' base.h: In member function 'void OpenBabel::OBEdgeBase::SetIdx(int)': base.h:140: warning: conversion to 'short unsigned int' from 'int' may alter its value base.h: At global scope: base.h:183: warning: unused parameter 'src' base.h: In member function 'unsigned int OpenBabel::OBGraphBase::NumNodes()': base.h:189: warning: conversion to 'unsigned int' from 'long unsigned int' may alter its value base.h: In member function 'unsigned int OpenBabel::OBGraphBase::NumEdges()': base.h:190: warning: conversion to 'unsigned int' from 'long unsigned int' may alter its value In file included from mol.h:30, from atom.cpp:14: data.h: In constructor 'OpenBabel::OBElement::OBElement(int, const char*, float, float, float, int, float, float)': data.h:101: error: 'strcpy' was not declared in this scope In file included from math/vector3.h:31, from mol.h:32, from atom.cpp:14: ./obutil.h: In member function 'float OpenBabel::OBStopwatch::Lap()': ./obutil.h:56: warning: conversion to 'double' from 'long int' may alter its value ./obutil.h:56: warning: conversion to 'float' from 'double' may alter its value ./obutil.h: In member function 'float OpenBabel::OBSqrtTbl::Sqrt(float) const': ./obutil.h:74: warning: conversion to 'float' from 'double' may alter its value ./obutil.h: In member function 'void OpenBabel::OBSqrtTbl::Init(float, float)': ./obutil.h:86: warning: conversion to 'float' from 'double' may alter its value In file included from mol.h:32, from atom.cpp:14: math/vector3.h: In member function 'float OpenBabel::vector3::length() const': math/vector3.h:140: warning: conversion to 'float' from 'double' may alter its value In file included from base.cpp:14: base.h: In member function 'void OpenBabel::OBNodeBase::SetIdx(int)': base.h:68: warning: conversion to 'short unsigned int' from 'int' may alter its value base.h: In member function 'virtual unsigned int OpenBabel::OBNodeBase::GetValence() const': base.h:75: warning: conversion to 'unsigned int' from 'size_t' may alter its value base.h: At global scope: base.h:133: warning: unused parameter 'bgn' base.h:133: warning: unused parameter 'end' base.h: In member function 'void OpenBabel::OBEdgeBase::SetIdx(int)': base.h:140: warning: conversion to 'short unsigned int' from 'int' may alter its value In file included from mol.h:33, from atom.cpp:14: bitvec.h: In constructor 'OpenBabel::OBBitVec::OBBitVec()': bitvec.h:51: warning: conversion to 'int' from 'size_t' may alter its value bitvec.h: In constructor 'OpenBabel::OBBitVec::OBBitVec(int)': bitvec.h:53: warning: conversion to 'int' from 'size_t' may alter its value base.h: At global scope: base.h:183: warning: unused parameter 'src' base.h: In member function 'unsigned int OpenBabel::OBGraphBase::NumNodes()': base.h:189: warning: conversion to 'unsigned int' from 'long unsigned int' may alter its value base.h: In member function 'unsigned int OpenBabel::OBGraphBase::NumEdges()': base.h:190: warning: conversion to 'unsigned int' from 'long unsigned int' may alter its value In file included from mol.h:34, from atom.cpp:14: ring.h: In member function 'int OpenBabel::OBRing::Size() const': ring.h:58: warning: conversion to 'int' from 'size_t' may alter its value ring.h: In member function 'int OpenBabel::OBRing::PathSize() const': ring.h:59: warning: conversion to 'int' from 'size_t' may alter its value In file included from atom.cpp:14: mol.h: In member function 'unsigned int OpenBabel::OBResidue::DataSize()': mol.h:109: warning: conversion to 'unsigned int' from 'size_t' may alter its value mol.h: In member function 'void OpenBabel::OBAtom::SetFlag(int)': mol.h:170: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h: In member function 'void OpenBabel::OBAtom::SetIdx(int)': mol.h:185: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h:185: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h: In member function 'void OpenBabel::OBAtom::SetHyb(int)': mol.h:186: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h: In member function 'void OpenBabel::OBAtom::SetFormalCharge(int)': mol.h:191: warning: conversion to 'short int' from 'int' may alter its value mol.h: In member function 'void OpenBabel::OBAtom::SetType(char*)': mol.h:192: error: 'strcpy' was not declared in this scope mol.h: In member function 'void OpenBabel::OBAtom::SetType(std::string&)': mol.h:193: error: 'strcpy' was not declared in this scope mol.h: In member function 'void OpenBabel::OBAtom::SetCoordPtr(float**)': mol.h:200: warning: conversion to 'short unsigned int' from 'unsigned int' may alter its value mol.h: In member function 'void OpenBabel::OBAtom::UnsetAromatic()': mol.h:202: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h: In member function 'void OpenBabel::OBAtom::UnsetStereo()': mol.h:207: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h:208: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h:209: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h: In member function 'virtual unsigned int OpenBabel::OBAtom::GetValence() const': mol.h:227: warning: conversion to 'unsigned int' from 'long unsigned int' may alter its value mol.h: In member function 'unsigned int OpenBabel::OBAtom::DataSize()': mol.h:363: warning: conversion to 'unsigned int' from 'size_t' may alter its value mol.h: In member function 'void OpenBabel::OBBond::SetFlag(int)': mol.h:402: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h: In member function 'void OpenBabel::OBBond::SetIdx(int)': mol.h:412: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h: In member function 'void OpenBabel::OBBond::UnsetAromatic()': mol.h:427: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h: In member function 'unsigned int OpenBabel::OBBond::DataSize()': mol.h:478: warning: conversion to 'unsigned int' from 'size_t' may alter its value mol.h: In member function 'unsigned int OpenBabel::OBMol::DataSize()': mol.h:585: warning: conversion to 'unsigned int' from 'size_t' may alter its value mol.h: In member function 'unsigned int OpenBabel::OBMol::NumResidues()': mol.h:604: warning: conversion to 'unsigned int' from 'size_t' may alter its value mol.h: In member function 'int OpenBabel::OBMol::NumConformers()': mol.h:746: warning: conversion to 'int' from 'long unsigned int' may alter its value atom.cpp: In member function 'OpenBabel::OBAtom& OpenBabel::OBAtom::operator=(OpenBabel::OBAtom&)': atom.cpp:137: warning: conversion to 'short unsigned int' from 'unsigned int' may alter its value atom.cpp:138: warning: conversion to 'short unsigned int' from 'unsigned int' may alter its value atom.cpp:139: warning: conversion to 'char' from 'unsigned int' may alter its value atom.cpp:140: warning: conversion to 'short int' from 'int' may alter its value atom.cpp:141: error: 'strcpy' was not declared in this scope atom.cpp:144: warning: conversion to 'short unsigned int' from 'int' may alter its value atom.cpp: In member function 'bool OpenBabel::OBAtom::IsAxial()': atom.cpp:206: warning: conversion to 'float' from 'double' may alter its value In file included from mol.h:29, from binary.h:25, from binary.cpp:15: base.h: In member function 'void OpenBabel::OBNodeBase::SetIdx(int)': base.h:68: warning: conversion to 'short unsigned int' from 'int' may alter its value base.h: In member function 'virtual unsigned int OpenBabel::OBNodeBase::GetValence() const': base.h:75: warning: conversion to 'unsigned int' from 'size_t' may alter its value base.h: At global scope: base.h:133: warning: unused parameter 'bgn' base.h:133: warning: unused parameter 'end' base.h: In member function 'void OpenBabel::OBEdgeBase::SetIdx(int)': base.h:140: warning: conversion to 'short unsigned int' from 'int' may alter its value atom.cpp: In member function 'char* OpenBabel::OBAtom::GetType()': atom.cpp:363: error: 'strlen' was not declared in this scope atom.cpp:367: warning: deprecated conversion from string constant to 'char*' atom.cpp:368: warning: deprecated conversion from string constant to 'char*' base.h: At global scope: base.h:183: warning: unused parameter 'src' base.h: In member function 'unsigned int OpenBabel::OBGraphBase::NumNodes()': base.h:189: warning: conversion to 'unsigned int' from 'long unsigned int' may alter its value base.h: In member function 'unsigned int OpenBabel::OBGraphBase::NumEdges()': base.h:190: warning: conversion to 'unsigned int' from 'long unsigned int' may alter its value In file included from mol.h:30, from binary.h:25, from binary.cpp:15: data.h: In constructor 'OpenBabel::OBElement::OBElement(int, const char*, float, float, float, int, float, float)': data.h:101: error: 'strcpy' was not declared in this scope In file included from math/vector3.h:31, from mol.h:32, from binary.h:25, from binary.cpp:15: ./obutil.h: In member function 'float OpenBabel::OBStopwatch::Lap()': ./obutil.h:56: warning: conversion to 'double' from 'long int' may alter its value ./obutil.h:56: warning: conversion to 'float' from 'double' may alter its value ./obutil.h: In member function 'float OpenBabel::OBSqrtTbl::Sqrt(float) const': ./obutil.h:74: warning: conversion to 'float' from 'double' may alter its value ./obutil.h: In member function 'void OpenBabel::OBSqrtTbl::Init(float, float)': ./obutil.h:86: warning: conversion to 'float' from 'double' may alter its value atom.cpp: In member function 'bool OpenBabel::OBAtom::HtoMethyl()': atom.cpp:958: warning: deprecated conversion from string constant to 'char*' atom.cpp:984: warning: deprecated conversion from string constant to 'char*' In file included from mol.h:32, from binary.h:25, from binary.cpp:15: math/vector3.h: In member function 'float OpenBabel::vector3::length() const': math/vector3.h:140: warning: conversion to 'float' from 'double' may alter its value atom.cpp: In member function 'bool OpenBabel::OBAtom::SetHybAndGeom(int)': atom.cpp:1046: warning: conversion to 'float' from 'unsigned int' may alter its value atom.cpp:1046: warning: conversion to 'float' from 'double' may alter its value atom.cpp:1072: warning: suggest explicit braces to avoid ambiguous 'else' atom.cpp:1079: warning: suggest explicit braces to avoid ambiguous 'else' atom.cpp:1255: warning: deprecated conversion from string constant to 'char*' In file included from mol.h:33, from binary.h:25, from binary.cpp:15: bitvec.h: In constructor 'OpenBabel::OBBitVec::OBBitVec()': bitvec.h:51: warning: conversion to 'int' from 'size_t' may alter its value bitvec.h: In constructor 'OpenBabel::OBBitVec::OBBitVec(int)': bitvec.h:53: warning: conversion to 'int' from 'size_t' may alter its value In file included from mol.h:34, from binary.h:25, from binary.cpp:15: ring.h: In member function 'int OpenBabel::OBRing::Size() const': ring.h:58: warning: conversion to 'int' from 'size_t' may alter its value ring.h: In member function 'int OpenBabel::OBRing::PathSize() const': ring.h:59: warning: conversion to 'int' from 'size_t' may alter its value In file included from binary.h:25, from binary.cpp:15: mol.h: In member function 'unsigned int OpenBabel::OBResidue::DataSize()': mol.h:109: warning: conversion to 'unsigned int' from 'size_t' may alter its value mol.h: In member function 'void OpenBabel::OBAtom::SetFlag(int)': mol.h:170: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h: In member function 'void OpenBabel::OBAtom::SetIdx(int)': mol.h:185: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h:185: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h: In member function 'void OpenBabel::OBAtom::SetHyb(int)': mol.h:186: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h: In member function 'void OpenBabel::OBAtom::SetFormalCharge(int)': mol.h:191: warning: conversion to 'short int' from 'int' may alter its value mol.h: In member function 'void OpenBabel::OBAtom::SetType(char*)': mol.h:192: error: 'strcpy' was not declared in this scope mol.h: In member function 'void OpenBabel::OBAtom::SetType(std::string&)': mol.h:193: error: 'strcpy' was not declared in this scope mol.h: In member function 'void OpenBabel::OBAtom::SetCoordPtr(float**)': mol.h:200: warning: conversion to 'short unsigned int' from 'unsigned int' may alter its value mol.h: In member function 'void OpenBabel::OBAtom::UnsetAromatic()': mol.h:202: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h: In member function 'void OpenBabel::OBAtom::UnsetStereo()': mol.h:207: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h:208: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h:209: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h: In member function 'virtual unsigned int OpenBabel::OBAtom::GetValence() const': mol.h:227: warning: conversion to 'unsigned int' from 'long unsigned int' may alter its value mol.h: In member function 'unsigned int OpenBabel::OBAtom::DataSize()': mol.h:363: warning: conversion to 'unsigned int' from 'size_t' may alter its value mol.h: In member function 'void OpenBabel::OBBond::SetFlag(int)': mol.h:402: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h: In member function 'void OpenBabel::OBBond::SetIdx(int)': mol.h:412: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h: In member function 'void OpenBabel::OBBond::UnsetAromatic()': mol.h:427: warning: conversion to 'short unsigned int' from 'int' may alter its value mol.h: In member function 'unsigned int OpenBabel::OBBond::DataSize()': mol.h:478: warning: conversion to 'unsigned int' from 'size_t' may alter its value mol.h: In member function 'unsigned int OpenBabel::OBMol::DataSize()': mol.h:585: warning: conversion to 'unsigned int' from 'size_t' may alter its value mol.h: In member function 'unsigned int OpenBabel::OBMol::NumResidues()': mol.h:604: warning: conversion to 'unsigned int' from 'size_t' may alter its value mol.h: In member function 'int OpenBabel::OBMol::NumConformers()': mol.h:746: warning: conversion to 'int' from 'long unsigned int' may alter its value In file included from binary.h:26, from binary.cpp:15: rotor.h: In constructor 'OpenBabel::OBRotorRule::OBRotorRule(char*, int*, std::vector >&, float)': rotor.h:44: error: 'memcpy' was not declared in this scope rotor.h: In member function 'void OpenBabel::OBRotorRule::GetReferenceAtoms(int*)': rotor.h:52: error: 'memcpy' was not declared in this scope rotor.h: In member function 'int OpenBabel::OBRotor::Size()': rotor.h:92: warning: conversion to 'int' from 'long unsigned int' may alter its value rotor.h: In member function 'void OpenBabel::OBRotor::SetToAngle(float*, float)': rotor.h:107: warning: conversion to 'float' from 'double' may alter its value rotor.h:107: warning: conversion to 'float' from 'double' may alter its value rotor.h:111: warning: conversion to 'float' from 'double' may alter its value rotor.h:112: warning: conversion to 'float' from 'double' may alter its value rotor.h: In member function 'int OpenBabel::OBRotorList::Size()': rotor.h:153: warning: conversion to 'int' from 'long unsigned int' may alter its value binary.cpp: In function 'int OpenBabel::Swab(int)': binary.cpp:39: error: 'memcpy' was not declared in this scope binary.cpp: In member function 'void OpenBabel::OBRotamerList::AddRotamers(unsigned char*, int)': binary.cpp:219: error: 'memcpy' was not declared in this scope binary.cpp: In member function 'void OpenBabel::OBRotamerList::ExpandConformerList(OpenBabel::OBMol&, std::vector >&)': binary.cpp:236: error: 'memcpy' was not declared in this scope binary.cpp:241: warning: conversion to 'float' from 'double' may alter its value binary.cpp: In member function 'std::vector > OpenBabel::OBRotamerList::CreateConformerList(OpenBabel::OBMol&)': binary.cpp:267: error: 'memcpy' was not declared in this scope binary.cpp:272: warning: conversion to 'float' from 'double' may alter its value binary.cpp: In function 'bool OpenBabel::WriteBinary(std::string&, int&, OpenBabel::OBMol&)': binary.cpp:349: error: 'strlen' was not declared in this scope binary.cpp:454: warning: conversion to 'float' from 'double' may alter its value binary.cpp:586: error: 'memset' was not declared in this scope binary.cpp:617: error: 'memset' was not declared in this scope binary.cpp: In function 'bool OpenBabel::ReadBinary(std::istream&, unsigned char**)': binary.cpp:686: error: 'memcpy' was not declared in this scope binary.cpp: In function 'bool OpenBabel::ReadBinary(unsigned char*, OpenBabel::OBMol&, int)': binary.cpp:712: error: 'memcpy' was not declared in this scope binary.cpp:717: error: 'strcpy' was not declared in this scope binary.cpp:720: error: 'memcpy' was not declared in this scope binary.cpp:776: warning: conversion to 'float' from 'double' may alter its value binary.cpp: In function 'void OpenBabel::SetRotorToAngle(float*, OpenBabel::OBAtom**, float, std::vector >)': binary.cpp:947: warning: conversion to 'float' from 'double' may alter its value binary.cpp:952: warning: conversion to 'float' from 'double' may alter its value binary.cpp:953: warning: conversion to 'float' from 'double' may alter its value binary.cpp:962: warning: conversion to 'float' from 'double' may alter its value binary.cpp:962: warning: conversion to 'float' from 'double' may alter its value binary.cpp:964: warning: conversion to 'float' from 'double' may alter its value make[3]: *** [atom.lo] Error 1 make[3]: *** Waiting for unfinished jobs.... make[3]: *** [binary.lo] Error 1 make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/kemistry-0.7/work/kemistry-0.7/openbabel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/kemistry-0.7/work/kemistry-0.7/openbabel' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/kemistry-0.7/work/kemistry-0.7' make: *** [all] Error 2 * * ERROR: sci-chemistry/kemistry-0.7 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 4285: Called kde_src_compile * environment, line 3113: Called kde_src_compile 'all' * environment, line 3238: Called kde_src_compile 'myconf' 'configure' 'make' * environment, line 3234: Called die * The specific snippet of code: * emake || die "died running emake, $FUNCNAME:make" * The die message: * died running emake, kde_src_compile:make * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/tmp/portage/sci-chemistry/kemistry-0.7/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/kemistry-0.7/temp/environment'. *