Build.log

build.log (text/plain), 33.84 KB, created by David Kredba on 2008-12-26 19:50:26 UTC

>>> Unpacking source...
>>> Unpacking kemistry-0.7.tar.bz2 to /var/tmp/portage/sci-chemistry/kemistry-0.7/work
 [32;01m*[0m Applying kemistry-0.7-gcc3.4.patch ...
[A[228C  [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying kemistry-0.7-fPIC.patch ...
[A[228C  [34;01m[ [32;01mok[34;01m ][0m
>>> Source unpacked.
>>> Compiling source in /var/tmp/portage/sci-chemistry/kemistry-0.7/work/kemistry-0.7 ...
 [32;01m*[0m Running elibtoolize in: kemistry-0.7/admin
 [32;01m*[0m   Applying install-sh-1.5.patch ...
 [32;01m*[0m   Applying ltmain-1.5.patch ...
 [32;01m*[0m   Applying portage-1.5.10.patch ...
 [32;01m*[0m   Applying relink-1.4.0a.patch ...
 [32;01m*[0m   Applying max_cmd_len-1.5.20.patch ...
 [32;01m*[0m   Applying sed-1.5.6.patch ...
 [32;01m*[0m   Applying tmp-1.3.5.patch ...
 [32;01m*[0m   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... GNU
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking for C compiler default output... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
checking dependency style of x86_64-pc-linux-gnu-gcc... none
checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
checking whether we are using the GNU C++ compiler... yes
checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
checking dependency style of x86_64-pc-linux-gnu-g++... none
checking whether x86_64-pc-linux-gnu-g++ supports -Wundef... yes
checking whether x86_64-pc-linux-gnu-g++ supports -Wbad-function-cast... yes
checking whether x86_64-pc-linux-gnu-g++ supports -Wno-long-long... yes
checking whether x86_64-pc-linux-gnu-g++ supports -Wnon-virtual-dtor... yes
checking whether x86_64-pc-linux-gnu-g++ supports -fno-exceptions... yes
checking whether x86_64-pc-linux-gnu-g++ supports -fno-check-new... yes
checking whether x86_64-pc-linux-gnu-g++ supports -fexceptions... yes
checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
checking whether x86_64-pc-linux-gnu-g++ supports -frepo... yes
checking for ld used by GCC... /usr/x86_64-pc-linux-gnu/bin/ld
checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes
checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/x86_64-pc-linux-gnu-nm -B
checking for a sed that does not truncate output... 
checking whether ln -s works... yes
checking how to recognise dependant libraries... pass_all
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok
checking for objdir... .libs
checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip
checking if x86_64-pc-linux-gnu-gcc static flag  works... no
checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no
checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC
checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC works... yes
checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes
checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking dynamic linker characteristics... 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... GNU/Linux ld.so
checking for msgfmt... /usr/bin/msgfmt
checking for gmsgfmt... /usr/bin/gmsgfmt
checking for xgettext... /usr/bin/xgettext
checking for main in -lutil... yes
checking for main in -lcompat... no
checking for crypt in -lcrypt... yes
checking for socklen_t... socklen_t
checking for dnet_ntoa in -ldnet... no
checking for dnet_ntoa in -ldnet_stub... no
checking for inet_ntoa... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking crt_externs.h usability... no
checking crt_externs.h presence... no
checking for crt_externs.h... no
checking for _NSGetEnviron... no
checking for sys/types.h... (cached) yes
checking for stdint.h... (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, std::allocator<float> >&, 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<float*, std::allocator<float*> >&)':
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<float*, std::allocator<float*> > 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<int, std::allocator<int> >)':
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
 [31;01m*[0m 
 [31;01m*[0m ERROR: sci-chemistry/kemistry-0.7 failed.
 [31;01m*[0m Call stack:
 [31;01m*[0m               ebuild.sh, line   49:  Called src_compile
 [31;01m*[0m             environment, line 4285:  Called kde_src_compile
 [31;01m*[0m             environment, line 3113:  Called kde_src_compile 'all'
 [31;01m*[0m             environment, line 3238:  Called kde_src_compile 'myconf' 'configure' 'make'
 [31;01m*[0m             environment, line 3234:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m                   emake || die "died running emake, $FUNCNAME:make"
 [31;01m*[0m  The die message:
 [31;01m*[0m   died running emake, kde_src_compile:make
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the topmost build error, and the call stack if relevant.
 [31;01m*[0m A complete build log is located at '/var/tmp/portage/sci-chemistry/kemistry-0.7/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/kemistry-0.7/temp/environment'.
 [31;01m*[0m