Re: blast+ packaging
Here is config.log
25+-src/c++$ cat config.log
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by ncbi-tools++ configure 0.0, which was
generated by GNU Autoconf 2.59. Invocation command line was
$ ./src/build-system/configure --srcdir=. --with-dll --with-mt
--without-autodep --without-makefile-auto-update --with-flat-makefile
--without-dbapi --without-lzo --with-runpath=/usr/lib/ncbi-blast+
--with-build-root=BUILD --without-debug
## --------- ##
## Platform. ##
## --------- ##
hostname = debiansid
uname -m = x86_64
uname -r = 2.6.32-5-amd64
uname -s = Linux
uname -v = #1 SMP Wed Jan 12 03:40:32 UTC 2011
/usr/bin/uname -p = unknown
/bin/uname -X = unknown
/bin/arch = unknown
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /bin
PATH: /usr/local/games
PATH: /usr/games
PATH: /usr/local/ec2/bin
## ----------- ##
## Core tests. ##
## ----------- ##
configure:1708: loading site script ./src/build-system/config.site
| #!/bin/sh
| # $Id: config.site 157355 2009-04-14 21:08:11Z ucko $
|
| # Customize configure's default behavior; see config.site.ex or
| # config.site.ncbi for examples of how to do so.
|
| if [ -d "$NCBI" ]; then
| . $srcdir/src/build-system/config.site.ncbi
| elif [ -r /usr/local/etc/config.site ]; then
| . /usr/local/etc/config.site
| else
| echo >&2 <<EOF
|
| **********************************************************************
|
| Warning: unable to find config.site information. If you would like to
| build the C++ Toolkit against third-party packages in non-standard
| locations or otherwise customize build settings, you may wish to edit
|
| $srcdir/src/build-system/config.site
|
| using .../config.site.ex and .../config.site.ncbi as examples.
|
| **********************************************************************
|
| EOF
| fi
configure:1719: loading cache config.cache
configure:3027: checking build system type
configure:3045: result: x86_64-unknown-linux-gnu
configure:3053: checking host system type
configure:3067: result: x86_64-unknown-linux-gnu
configure:3111: checking for a BSD-compatible install
configure:3166: result: /usr/bin/install -c
configure:3232: checking for gcc
configure:3248: found /usr/bin/gcc
configure:3258: result: gcc
configure:3502: checking for C compiler version
configure:3505: gcc --version </dev/null >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
gcc (Debian 4.4.6-3) 4.4.6
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:3508: $? = 0
configure:3510: gcc -v </dev/null >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
Using built-in specs.
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 4.4.6-3'
--with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs
--enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr
--program-suffix=-4.4 --enable-shared --enable-multiarch
--with-multiarch-defaults=x86_64-linux-gnu --enable-linker-build-id
--with-system-zlib --libexecdir=/usr/lib --without-included-gettext
--enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.4
--libdir=/usr/lib --enable-nls --enable-clocale=gnu
--enable-libstdcxx-debug --enable-objc-gc --with-arch-32=i586
--with-tune=generic --enable-checking=release --build=x86_64-linux-gnu
--host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.4.6 (Debian 4.4.6-3)
configure:3513: $? = 0
configure:3515: gcc -V </dev/null >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
gcc: '-V' option must have argument
configure:3518: $? = 1
configure:3541: checking for C compiler default output file name
configure:3544: gcc conftest.c >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
configure:3547: $? = 0
configure:3593: result: a.out
configure:3598: checking whether the C compiler works
configure:3604: ./a.out
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
configure:3607: $? = 0
configure:3624: result: yes
configure:3631: checking whether we are cross compiling
configure:3633: result: no
configure:3636: checking for suffix of executables
configure:3638: gcc -o conftest conftest.c >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
configure:3641: $? = 0
configure:3666: result:
configure:3672: checking for suffix of object files
configure:3693: gcc -c conftest.c >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
configure:3696: $? = 0
configure:3718: result: o
configure:3722: checking whether we are using the GNU C compiler
configure:3746: gcc -c conftest.c >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
configure:3752: $? = 0
configure:3756: test -z
|| test ! -s conftest.err
configure:3759: $? = 0
configure:3762: test -s conftest.o
configure:3765: $? = 0
configure:3778: result: yes
configure:3784: checking whether gcc accepts -g
configure:3805: gcc -c -g conftest.c >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
configure:3811: $? = 0
configure:3815: test -z
|| test ! -s conftest.err
configure:3818: $? = 0
configure:3821: test -s conftest.o
configure:3824: $? = 0
configure:3835: result: yes
configure:3852: checking for gcc option to accept ANSI C
configure:3922: gcc -c -g -O2 conftest.c >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
configure:3928: $? = 0
configure:3932: test -z
|| test ! -s conftest.err
configure:3935: $? = 0
configure:3938: test -s conftest.o
configure:3941: $? = 0
configure:3959: result: none needed
configure:3977: gcc -c -g -O2 conftest.c >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
conftest.c:2: error: expected '=', ',', ';', 'asm' or '__attribute__'
before 'me'
configure:3983: $? = 1
configure: failed program was:
| #ifndef __cplusplus
| choke me
| #endif
configure:4168: checking for g++
configure:4184: found /usr/bin/g++
configure:4194: result: g++
configure:4210: checking for C++ compiler version
configure:4213: g++ --version </dev/null >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
g++ (Debian 4.4.6-3) 4.4.6
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:4216: $? = 0
configure:4218: g++ -v </dev/null >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
Using built-in specs.
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 4.4.6-3'
--with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs
--enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr
--program-suffix=-4.4 --enable-shared --enable-multiarch
--with-multiarch-defaults=x86_64-linux-gnu --enable-linker-build-id
--with-system-zlib --libexecdir=/usr/lib --without-included-gettext
--enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.4
--libdir=/usr/lib --enable-nls --enable-clocale=gnu
--enable-libstdcxx-debug --enable-objc-gc --with-arch-32=i586
--with-tune=generic --enable-checking=release --build=x86_64-linux-gnu
--host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.4.6 (Debian 4.4.6-3)
configure:4221: $? = 0
configure:4223: g++ -V </dev/null >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
g++: '-V' option must have argument
configure:4226: $? = 1
configure:4229: checking whether we are using the GNU C++ compiler
configure:4253: g++ -c conftest.cc >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
configure:4259: $? = 0
configure:4263: test -z
|| test ! -s conftest.err
configure:4266: $? = 0
configure:4269: test -s conftest.o
configure:4272: $? = 0
configure:4285: result: yes
configure:4291: checking whether g++ accepts -g
configure:4312: g++ -c -g conftest.cc >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
configure:4318: $? = 0
configure:4322: test -z
|| test ! -s conftest.err
configure:4325: $? = 0
configure:4328: test -s conftest.o
configure:4331: $? = 0
configure:4342: result: yes
configure:4384: g++ -c -g -O2 conftest.cc >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
configure:4390: $? = 0
configure:4394: test -z
|| test ! -s conftest.err
configure:4397: $? = 0
configure:4400: test -s conftest.o
configure:4403: $? = 0
configure:4429: g++ -c -g -O2 conftest.cc >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
conftest.cc: In function 'int main()':
conftest.cc:13: error: 'exit' was not declared in this scope
configure:4435: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define NCBI_CXX_TOOLKIT 1
| #define HOST "x86_64-unknown-linux-gnu"
| #define HOST_CPU "x86_64"
| #define HOST_VENDOR "unknown"
| #define HOST_OS "linux-gnu"
| /* end confdefs.h. */
|
| int
| main ()
| {
| exit (42);
| ;
| return 0;
| }
configure:4384: g++ -c -g -O2 conftest.cc >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
conftest.cc:9: error: 'void std::exit(int)' should have been declared
inside 'std'
configure:4390: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define NCBI_CXX_TOOLKIT 1
| #define HOST "x86_64-unknown-linux-gnu"
| #define HOST_CPU "x86_64"
| #define HOST_VENDOR "unknown"
| #define HOST_OS "linux-gnu"
| /* end confdefs.h. */
| extern "C" void std::exit (int) throw (); using std::exit;
| #include <stdlib.h>
| int
| main ()
| {
| exit (42);
| ;
| return 0;
| }
configure:4384: g++ -c -g -O2 conftest.cc >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
conftest.cc:9: error: 'void std::exit(int)' should have been declared
inside 'std'
In file included from conftest.cc:10:
/usr/include/stdlib.h:544: error: declaration of 'void std::exit(int)
throw ()' throws different exceptions
conftest.cc:9: error: from previous declaration 'void std::exit(int)'
configure:4390: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define NCBI_CXX_TOOLKIT 1
| #define HOST "x86_64-unknown-linux-gnu"
| #define HOST_CPU "x86_64"
| #define HOST_VENDOR "unknown"
| #define HOST_OS "linux-gnu"
| /* end confdefs.h. */
| extern "C" void std::exit (int); using std::exit;
| #include <stdlib.h>
| int
| main ()
| {
| exit (42);
| ;
| return 0;
| }
configure:4384: g++ -c -g -O2 conftest.cc >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
configure:4390: $? = 0
configure:4394: test -z
|| test ! -s conftest.err
configure:4397: $? = 0
configure:4400: test -s conftest.o
configure:4403: $? = 0
configure:4429: g++ -c -g -O2 conftest.cc >&5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be
preloaded: ignored.
configure:4435: $? = 0
configure:4439: test -z
|| test ! -s conftest.err
configure:4442: $? = 0
configure:4445: test -s conftest.o
configure:4448: $? = 0
configure:4811: error: Do not know how to build MT-safe with compiler
/usr/bin/g++ ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD
cannot be preloaded: ignored.
4.4.6
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_build=x86_64-unknown-linux-gnu
ac_cv_build_alias=x86_64-unknown-linux-gnu
ac_cv_c_compiler_gnu=yes
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_CXXCPP_set=
ac_cv_env_CXXCPP_value=
ac_cv_env_CXXFLAGS_set=
ac_cv_env_CXXFLAGS_value=
ac_cv_env_CXX_set=
ac_cv_env_CXX_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_exeext=
ac_cv_host=x86_64-unknown-linux-gnu
ac_cv_host_alias=x86_64-unknown-linux-gnu
ac_cv_objext=o
ac_cv_path_install='/usr/bin/install -c'
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_ac_ct_CXX=g++
ac_cv_prog_cc_g=yes
ac_cv_prog_cc_stdc=
ac_cv_prog_cxx_g=yes
## ----------------- ##
## Output variables. ##
## ----------------- ##
ALLOW_UNDEF=''
AMQ=''
APP_LDFLAGS=''
APP_LIBS_SETTING=''
APP_LIB_SETTING=''
APP_NOCOPY=''
APP_OR_NULL=''
AR=''
AR_FILTER=''
AR_WRAPPER=''
BDB_CACHE_LIB=''
BDB_LIB=''
BERKELEYDB_CXX_LIBS=''
BERKELEYDB_CXX_STATIC_LIBS=''
BERKELEYDB_INCLUDE=''
BERKELEYDB_LIBS=''
BERKELEYDB_STATIC_LIBS=''
BINCOPY=''
BOOST_INCLUDE=''
BOOST_LIBPATH=''
BOOST_REGEX_LIBS=''
BOOST_REGEX_STATIC_LIBS=''
BOOST_TAG=''
BOOST_TEST_PEM_LIBS=''
BOOST_TEST_PEM_STATIC_LIBS=''
BOOST_TEST_TEM_LIBS=''
BOOST_TEST_TEM_STATIC_LIBS=''
BOOST_TEST_UTF_LIBS=''
BOOST_TEST_UTF_STATIC_LIBS=''
BOOST_THREAD_LIBS=''
BOOST_THREAD_STATIC_LIBS=''
BZ2_INCLUDE=''
BZ2_LIB=''
BZ2_LIBS=''
CC='/usr/bin/gcc '
CCACHE=''
CC_FILTER=''
CC_WRAPPER=''
CFLAGS='-g -O2'
CFLAGS_DLL=''
CHECK_ARG=''
CHECK_OS_NAME=''
CHECK_TOOLS=''
COMPILER=''
CONNEXT=''
CPP=''
CPPFLAGS=''
CPPUNIT_INCLUDE=''
CPPUNIT_LIBS=''
CRYPT_LIBS=''
CXX='/usr/bin/g++ '
CXXCPP=''
CXXFLAGS='-g -O2'
CXXFLAGS_DLL=''
CXX_FILTER=''
CXX_WRAPPER=''
C_LIBS=''
C_LINK='$(CC)'
DBAPI_CTLIB=''
DBAPI_DBLIB=''
DBAPI_MYSQL=''
DBAPI_ODBC=''
DEBUG_SFX=''
DEFS=''
DEMANGLE_LIBS=''
DEPFLAGS=''
DEPFLAGS_POST=''
DISTCC=''
DLL=''
DLL_LDFLAGS=''
DLL_LIB_SETTING=''
DL_LIBS=''
D_SFX=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP=''
EGREP_Q=''
EXEEXT=''
EXPAT_INCLUDE=''
EXPAT_LIBS=''
EXPAT_STATIC_LIBS=''
FASTCGI_INCLUDE=''
FASTCGI_LIBS=''
FASTCGI_OBJS=''
FAST_CFLAGS=''
FAST_CXXFLAGS=''
FAST_LDFLAGS=''
FLTK_CONFIG=''
FLTK_INCLUDE=''
FLTK_LIBS=''
FLTK_LIBS_ALL=''
FLTK_LIBS_GL=''
FLTK_LIBS_IMAGES=''
FLTK_STATIC_LIBS=''
FLTK_STATIC_LIBS_ALL=''
FLTK_STATIC_LIBS_GL=''
FLTK_STATIC_LIBS_IMAGES=''
FORBID_UNDEF=''
FORCE_STATIC_LIB=''
FREETYPE_INCLUDE=''
FREETYPE_LIBS=''
FTDS64_CTLIB_INCLUDE=''
FTDS64_CTLIB_LIB=''
FTDS64_CTLIB_LIBS=''
FTDS64_INCLUDE=''
FTDS64_LIB=''
FTDS64_LIBS=''
FTDS_INCLUDE=''
FTDS_LIB=''
FTDS_LIBS=''
GCCPCH=''
GIF_INCLUDE=''
GIF_LIBS=''
GLEW_INCLUDE=''
GLEW_LIBS=''
GLEW_STATIC_LIBS=''
GLUT_INCLUDE=''
GLUT_LIBS=''
GNUTLS_INCLUDE=''
GNUTLS_LIBS=''
HDF5_INCLUDE=''
HDF5_LIBS=''
ICONV_LIBS=''
ICU_CONFIG=''
ICU_INCLUDE=''
ICU_LIBS=''
ICU_STATIC_LIBS=''
IF_DEACTIVATING=''
IF_REBUILDING_CONDITIONALLY=''
IF_REBUILDING_LIBS=''
IF_WITH_DLL=''
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
JDK_INCLUDE=''
JDK_PATH=''
JPEG_INCLUDE=''
JPEG_LIBS=''
KSTAT_LIBS=''
KeepStateTarget=''
LDFLAGS=''
LIBGNUTLS_CONFIG=''
LIBIMR=''
LIBOB=''
LIBOBJS=''
LIBS=''
LIBSSSDB=''
LIBSSSUTILS=''
LIBXML_INCLUDE=''
LIBXML_LIBS=''
LIBXML_STATIC_LIBS=''
LIBXSLT_INCLUDE=''
LIBXSLT_LIBS=''
LIBXSLT_STATIC_LIBS=''
LIB_OR_DLL=''
LINK='$(CXX)'
LINK_DLL=''
LINK_FILTER=''
LINK_LOADABLE=''
LINK_WRAPPER=''
LN_S=''
LTLIBOBJS=''
LZO_INCLUDE=''
LZO_LIBS=''
MATH_LIBS=''
MT_SFX=''
MUPARSER_INCLUDE=''
MUPARSER_LIBS=''
MYSQL_INCLUDE=''
MYSQL_LIBS=''
NCBIATOMIC_LIB=''
NCBI_C_INCLUDE=''
NCBI_C_LIBPATH=''
NCBI_C_ncbi=''
NCBI_PLATFORM_BITS=''
NCBI_SSS_INCLUDE=''
NCBI_SSS_LIBPATH=''
NETWORK_LIBS=''
NETWORK_PURE_LIBS=''
NO_STRICT_ALIASING=''
OBJEXT='o'
ODBC_INCLUDE=''
ODBC_LIBS=''
OECHEM_INCLUDE=''
OECHEM_LIBS=''
OPENGL_INCLUDE=''
OPENGL_LIBS=''
OPENGL_STATIC_LIBS=''
OPENSSL_INCLUDE=''
OPENSSL_LIBS=''
OPENSSL_STATIC_LIBS=''
OPT_GROUPS=''
ORBACUS_INCLUDE=''
ORBACUS_LIBPATH=''
OSMESA_INCLUDE=''
OSMESA_LIBS=''
OSMESA_STATIC_LIBS=''
OSTYPE='linux-gnu'
PACKAGE_BUGREPORT='cpp-core@ncbi.nlm.nih.gov'
PACKAGE_NAME='ncbi-tools++'
PACKAGE_STRING='ncbi-tools++ 0.0'
PACKAGE_TARNAME='ncbi-tools--'
PACKAGE_VERSION='0.0'
PATH_SEPARATOR=':'
PCREPOSIX_LIBS=''
PCRE_INCLUDE=''
PCRE_LIB=''
PCRE_LIBS=''
PNG_INCLUDE=''
PNG_LIBS=''
PROJECTS=''
PYTHON23=''
PYTHON23_INCLUDE=''
PYTHON23_LIBS=''
PYTHON24=''
PYTHON24_INCLUDE=''
PYTHON24_LIBS=''
PYTHON25=''
PYTHON25_INCLUDE=''
PYTHON25_LIBS=''
PYTHON=''
PYTHON_INCLUDE=''
PYTHON_LIBS=''
RANLIB=''
RESOLVER_LIBS=''
RPCSVC_LIBS=''
RT_LIBS=''
RUNPATH_ORIGIN=''
Rules=''
SABLOT_INCLUDE=''
SABLOT_LIBS=''
SABLOT_STATIC_LIBS=''
SGE_INCLUDE=''
SGE_LIBS=''
SHELL='/bin/bash'
SP_INCLUDE=''
SP_LIBS=''
SQLITE3_INCLUDE=''
SQLITE3_LIBS=''
SQLITE3_STATIC_LIBS=''
SQLITE_INCLUDE=''
SQLITE_LIBS=''
STATIC=''
STRIP=''
SYBASE_DBLIBS=''
SYBASE_DLLS=''
SYBASE_INCLUDE=''
SYBASE_LCL_PATH=''
SYBASE_LIBS=''
SYBASE_PATH=''
TAIL=''
TAIL_N=''
TCHECK_CL=''
THREAD_LIBS=''
TIFF_INCLUDE=''
TIFF_LIBS=''
TLS_INCLUDE=''
TLS_LIBS=''
UNGIF_INCLUDE=''
UNGIF_LIBS=''
UNIX_SRC=''
UNIX_USR_PROJ=''
UNLESS_PUBSEQOS=''
UNLESS_WITH_DLL=''
USUAL_AND_DLL=''
USUAL_AND_LIB=''
UUID_LIBS=''
VALGRIND_PATH=''
WXWIDGETS_GL_LIBS=''
WXWIDGETS_GL_STATIC_LIBS=''
WXWIDGETS_INCLUDE=''
WXWIDGETS_LIBS=''
WXWIDGETS_POST_LINK=''
WXWIDGETS_STATIC_LIBS=''
WXWIN_GL_LIBS=''
WXWIN_GL_STATIC_LIBS=''
WXWIN_INCLUDE=''
WXWIN_LIBS=''
WXWIN_POST_LINK=''
WXWIN_STATIC_LIBS=''
XALAN_INCLUDE=''
XALAN_LIBS=''
XALAN_STATIC_LIBS=''
XCONNEXT=''
XERCES_INCLUDE=''
XERCES_LIBS=''
XERCES_STATIC_LIBS=''
XPM_INCLUDE=''
XPM_LIBS=''
XSLTPROC=''
X_CFLAGS=''
X_EXTRA_LIBS=''
X_LIBS=''
X_PRE_LIBS=''
Z_INCLUDE=''
Z_LIB=''
Z_LIBS=''
_ACJNI_JAVAC=''
ac_ct_CC='gcc'
ac_ct_CXX='g++'
ac_ct_RANLIB=''
algo=''
app=''
bdb=''
bindir='${exec_prefix}/bin'
build='x86_64-unknown-linux-gnu'
build_alias=''
build_cpu='x86_64'
build_os='linux-gnu'
build_root=''
build_vendor='unknown'
builddir=''
c_ncbi_runpath=''
check=''
compiler=''
compiler_root='/usr'
compiler_version='000'
configurables_mfname=''
datadir='${prefix}/share'
dbapi=''
dll_ext=''
exe_ext=''
exec_prefix='NONE'
f_compile=''
f_libpath=''
f_outexe=''
f_outlib=''
f_outobj=''
f_runpath=''
freetds=''
freetype_config=''
ftds64=''
gui=''
has_dll_loadable=''
host='x86_64-unknown-linux-gnu'
host_alias=''
host_cpu='x86_64'
host_os='linux-gnu'
host_vendor='unknown'
includedir='${prefix}/include'
infodir='${prefix}/info'
internal=''
lib_ext=''
lib_l_ext=''
lib_l_pre=''
lib_pre=''
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
loadable_ext=''
local_lbsm=''
localstatedir='${prefix}/var'
make_shell=''
mandir='${prefix}/man'
mysql_config=''
ncbi_crypt=''
ncbi_runpath=''
ncbi_xreader_pubseqos2=''
ncbi_xreader_pubseqos=''
ncbicntr=''
obj_ext=''
objects=''
oldincludedir='/usr/include'
prefix='NONE'
program_transform_name='s,x,x,'
runpath=''
sbindir='${exec_prefix}/sbin'
script_shell=''
serial=''
serial_ws50_rtti_kludge=''
sharedstatedir='${prefix}/com'
signature=''
sra=''
srcdir='.'
sssutils=''
status_dir=''
sysconfdir='${prefix}/etc'
target_alias=''
top_srcdir=''
wxconf=''
## ----------- ##
## confdefs.h. ##
## ----------- ##
#define HOST "x86_64-unknown-linux-gnu"
#define HOST_CPU "x86_64"
#define HOST_OS "linux-gnu"
#define HOST_VENDOR "unknown"
#define NCBI_COMPILER "UNKNOWN"
#define NCBI_COMPILER_UNKNOWN 1
#define NCBI_COMPILER_VERSION 000
#define NCBI_CXX_TOOLKIT 1
#endif
#ifdef __cplusplus
extern "C" void exit (int) throw ();
configure: exit 1
Le 5/30/11 3:27 PM, Aaron Ucko a écrit :
> That's a puzzling error; please send your c++/config.log, which should shed more light on it. Thanks!
>
> -- Sent from my Palm Pre
> On May 30, 2011 3:44, Olivier Sallou <olivier.sallou@irisa.fr> wrote:
>
> hi,
>
> after updating to your code, there is a compil (configure) error at
>
> build time:
>
>
>
> configure: error: Do not know how to build MT-safe with compiler
>
> /usr/bin/g++
>
>
>
> Maybe a missing dependency, do you have any idea?
>
>
>
> Olivier
>
>
>
> Le 5/29/11 6:12 PM, Aaron M. Ucko a écrit :
>
> > Olivier Sallou <olivier.sallou@irisa.fr> writes:
>
> >
>
> >> please feel free to commit in my dir. It will indeed be easier than merging.
>
> > Done, thanks. I also threw in some improvements to the copyright file that
>
> > I'd meant to propose earlier:
>
> >
>
> > * Remove the stanza for (c++/)scripts/projects/xmlwrapp/*, whose LICENSE
>
> > file documents material absent from the ncbi-blast+ archive.
>
> > * Adjust other upstream-related stanzas' Files specifications to prefix
>
> > c++/ and cover include in addition to src as appropriate.
>
> >
>
> >> For dir updates, be it ncbi-blast+ or ncbi-blast-plus, I would rather
>
> >> like you update directly in my branch. We can, after that, "mv" the svn
>
> >> dir to ncbi-blast+ once everything is ok from packaging point of view.
>
> > That's fair, and no problem -- quite the contrary, when I was starting to
>
> > commit to ncbi-blast+ (before the Alioth glitch and your latest reply), I
>
> > didn't split my changes into individual commits quite as cleanly as I'd
>
> > meant to, so re-committing them in ncbi-blast-plus gave me a good
>
> > opportunity to correct that.
>
> >
>
> >> Please tell me once you have included your updates so that I recheck the
>
> >> package on my side.
>
> > I have. Here are the remaining issues of which I'm aware, none of which
>
> > should necessarily hold up an initial upload:
>
> >
>
> > * As previously mentioned, the linkage is still somewhat of a mess.
>
> > * Also as mentioned, there are no individual manpages.
>
> > * The standards version is slightly outdated; somebody should review the
>
> > upgrading checklist to see if advancing it requires any packaging changes.
>
> > * As I recall, there was some interest in incorporating RMBLAST, the patch
>
> > for which risked changing the standard applications' behavior. I expect
>
> > it should be possible to stay out of trouble by building it in a separate
>
> > copy of the source tree and linking it statically against any patched
>
> > libraries (and their reverse dependencies).
>
> >
>
> >> Regarding legacy, I prefered keeping it as separate package to avoid some
>
> >> confusion and get it only if required on backward compatibility. Though,
>
> >> if you think we should keep it in the same package, it is ok for me.
>
> > OK, thanks for the explanation; I've kept the split.
>
> >
>
>
>
--
gpg key id: 4096R/326D8438 (pgp.mit.edu)
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