AMBER Archive (2008)

Subject: AMBER: Problems installing Amber Tools for Amber 10

From: Sam Danziger (sam.danziger_at_gmail.com)
Date: Mon May 12 2008 - 13:20:23 CDT

I've tried to install Amber Tools 1.0, but get an error message when I
try to compile.

I'm using Gentoo linux (Linux version 2.6.22-gentoo-r18), and have
tried gcc 3.4.1, 3.4.4 and 4.3.0 (4.3.0 gives me a different error
than below).

Please help!

Thank you,
-Sammake[2]: Entering directory `/extra/p530/software/amber10/src/gleap/leapsrc'
g++ -c -pipe -O2 -Wall -W -D_REENTRANT -I../mortsrc -I../mortsrc/guilib -I../pl
ugins -I../freelib -I. -o strmain.o strmain.cpp
strmain.cpp:14: warning: unused parameter 'sig'
g++ -c -pipe -O2 -Wall -W -D_REENTRANT -I../mortsrc -I../mortsrc/guilib -I../pl
ugins -I../freelib -I. -o strbuff.o strbuff.cpp
g++ -c -pipe -O2 -Wall -W -D_REENTRANT -I../mortsrc -I../mortsrc/guilib -I../pl
ugins -I../freelib -I. -o plugins.o plugins.cpp
g++ -static-libgcc -o sleap strmain.o strbuff.o plugins.o ../freelib/readl
ine/libreadline.a -lm ../plugins/libplugins.a ../mortsrc/libmort.a
`.gnu.linkonce.t._ZN5boost2io6detail22parse_printf_directiveIcSt11char_traitsIcE
SaIcEN9__gnu_cxx17__normal_iteratorIPKcSsEESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_
itemIT_T0_T1_EERKT3_jh' referenced in section `.rodata' of ../plugins/libplugins
.a(saveprm.o): defined in discarded section `.gnu.linkonce.t._ZN5boost2io6detail
22parse_printf_directiveIcSt11char_traitsIcESaIcEN9__gnu_cxx17__normal_iteratorI
PKcSsEESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_itemIT_T0_T1_EERKT3_jh' of ../plugin
s/libplugins.a(saveprm.o)
`.gnu.linkonce.t._ZN5boost2io6detail22parse_printf_directiveIcSt11char_traitsIcE
SaIcEN9__gnu_cxx17__normal_iteratorIPKcSsEESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_
itemIT_T0_T1_EERKT3_jh' referenced in section `.rodata' of ../mortsrc/libmort.a(
numvec.o): defined in discarded section `.gnu.linkonce.t._ZN5boost2io6detail22pa
rse_printf_directiveIcSt11char_traitsIcESaIcEN9__gnu_cxx17__normal_iteratorIPKcS
sEESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_itemIT_T0_T1_EERKT3_jh' of ../mortsrc/li
bmort.a(numvec.o)
`.gnu.linkonce.t._ZN5boost2io6detail22parse_printf_directiveIcSt11char_traitsIcE
SaIcEN9__gnu_cxx17__normal_iteratorIPKcSsEESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_
itemIT_T0_T1_EERKT3_jh' referenced in section `.rodata' of ../mortsrc/libmort.a(
nonbond-pbc.o): defined in discarded section `.gnu.linkonce.t._ZN5boost2io6detai
l22parse_printf_directiveIcSt11char_traitsIcESaIcEN9__gnu_cxx17__normal_iterator
IPKcSsEESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_itemIT_T0_T1_EERKT3_jh' of ../morts
rc/libmort.a(nonbond-pbc.o)
`.gnu.linkonce.t._ZN5boost2io6detail22parse_printf_directiveIcSt11char_traitsIcE
SaIcEN9__gnu_cxx17__normal_iteratorIPKcSsEESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_
itemIT_T0_T1_EERKT3_jh' referenced in section `.rodata' of ../mortsrc/libmort.a(
mdlfmt.o): defined in discarded section `.gnu.linkonce.t._ZN5boost2io6detail22pa
rse_printf_directiveIcSt11char_traitsIcESaIcEN9__gnu_cxx17__normal_iteratorIPKcS
sEESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_itemIT_T0_T1_EERKT3_jh' of ../mortsrc/li
bmort.a(mdlfmt.o)
`.gnu.linkonce.t._ZN5boost2io6detail22parse_printf_directiveIcSt11char_traitsIcE
SaIcEN9__gnu_cxx17__normal_iteratorIPKcSsEESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_
itemIT_T0_T1_EERKT3_jh' referenced in section `.rodata' of ../mortsrc/libmort.a(
parmfun.o): defined in discarded section `.gnu.linkonce.t._ZN5boost2io6detail22p
arse_printf_directiveIcSt11char_traitsIcESaIcEN9__gnu_cxx17__normal_iteratorIPKc
SsEESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_itemIT_T0_T1_EERKT3_jh' of ../mortsrc/l
ibmort.a(parmfun.o)
`.gnu.linkonce.t._ZN5boost2io6detail22parse_printf_directiveIcSt11char_traitsIcE
SaIcEN9__gnu_cxx17__normal_iteratorIPKcSsEESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_
itemIT_T0_T1_EERKT3_jh' referenced in section `.rodata' of ../mortsrc/libmort.a(
atom.o): defined in discarded section `.gnu.linkonce.t._ZN5boost2io6detail22pars
e_printf_directiveIcSt11char_traitsIcESaIcEN9__gnu_cxx17__normal_iteratorIPKcSsE
ESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_itemIT_T0_T1_EERKT3_jh' of ../mortsrc/libm
ort.a(atom.o)
`.gnu.linkonce.t._ZN5boost2io6detail22parse_printf_directiveIcSt11char_traitsIcE
SaIcEN9__gnu_cxx17__normal_iteratorIPKcSsEESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_
itemIT_T0_T1_EERKT3_jh' referenced in section `.rodata' of ../mortsrc/libmort.a(
bond.o): defined in discarded section `.gnu.linkonce.t._ZN5boost2io6detail22pars
e_printf_directiveIcSt11char_traitsIcESaIcEN9__gnu_cxx17__normal_iteratorIPKcSsE
ESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_itemIT_T0_T1_EERKT3_jh' of ../mortsrc/libm
ort.a(bond.o)
`.gnu.linkonce.t._ZN5boost2io6detail22parse_printf_directiveIcSt11char_traitsIcE
SaIcEN9__gnu_cxx17__normal_iteratorIPKcSsEESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_
itemIT_T0_T1_EERKT3_jh' referenced in section `.rodata' of ../mortsrc/libmort.a(
head.o): defined in discarded section `.gnu.linkonce.t._ZN5boost2io6detail22pars
e_printf_directiveIcSt11char_traitsIcESaIcEN9__gnu_cxx17__normal_iteratorIPKcSsE
ESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_itemIT_T0_T1_EERKT3_jh' of ../mortsrc/libm
ort.a(head.o)
`.gnu.linkonce.t._ZN5boost2io6detail22parse_printf_directiveIcSt11char_traitsIcE
SaIcEN9__gnu_cxx17__normal_iteratorIPKcSsEESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_
itemIT_T0_T1_EERKT3_jh' referenced in section `.rodata' of ../mortsrc/libmort.a(
amboff.o): defined in discarded section `.gnu.linkonce.t._ZN5boost2io6detail22pa
rse_printf_directiveIcSt11char_traitsIcESaIcEN9__gnu_cxx17__normal_iteratorIPKcS
sEESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_itemIT_T0_T1_EERKT3_jh' of ../mortsrc/li
bmort.a(amboff.o)
`.gnu.linkonce.t._ZN5boost2io6detail22parse_printf_directiveIcSt11char_traitsIcE
SaIcEN9__gnu_cxx17__normal_iteratorIPKcSsEESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_
itemIT_T0_T1_EERKT3_jh' referenced in section `.rodata' of ../mortsrc/libmort.a(
prmtop.o): defined in discarded section `.gnu.linkonce.t._ZN5boost2io6detail22pa
rse_printf_directiveIcSt11char_traitsIcESaIcEN9__gnu_cxx17__normal_iteratorIPKcS
sEESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_itemIT_T0_T1_EERKT3_jh' of ../mortsrc/li
bmort.a(prmtop.o)
`.gnu.linkonce.t._ZN5boost2io6detail22parse_printf_directiveIcSt11char_traitsIcE
SaIcEN9__gnu_cxx17__normal_iteratorIPKcSsEESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_
itemIT_T0_T1_EERKT3_jh' referenced in section `.rodata' of ../mortsrc/libmort.a(
fortran.o): defined in discarded section `.gnu.linkonce.t._ZN5boost2io6detail22p
arse_printf_directiveIcSt11char_traitsIcESaIcEN9__gnu_cxx17__normal_iteratorIPKc
SsEESt5ctypeIcEEEbRT2_RKSD_PNS1_11format_itemIT_T0_T1_EERKT3_jh' of ../mortsrc/l
ibmort.a(fortran.o)
collect2: ld returned 1 exit status
make[2]: *** [sleap] Error 1
make[2]: Leaving directory `/extra/p530/software/amber10/src/gleap/leapsrc'
make[1]: *** [sleap] Error 2
make[1]: Leaving directory `/extra/p530/software/amber10/src/gleap'
make: *** [install] Error 2
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