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----
# nab, leap, and sleap:
(cd cifparse && make install )
# (cd nab && make install )
(cd nss && make install )
--------
but there is the following error
Please suggest how I can try to fix this.
Error
----------
gncp.Admin:~/Documents/GNCP/
MD/amber10/src$ make -f Makefile_at
mkdir /home/gncp/Documents/GNCP/MD/amber10/bin
/home/gncp/Documents/GNCP/MD/amber10/lib
/home/gncp/Documents/GNCP/MD/amber10/include
mkdir: cannot create directory `/home/gncp/Documents/GNCP/MD/amber10/bin':
File exists
mkdir: cannot create directory `/home/gncp/Documents/GNCP/MD/amber10/lib':
File exists
mkdir: cannot create directory
`/home/gncp/Documents/GNCP/MD/amber10/include': File exists
make: [install] Error 1 (ignored)
(cd ucpp-1.3 && make install )
make[1]: Entering directory
`/home/gncp/Documents/GNCP/MD/amber10/src/ucpp-1.3'
Makefile:35: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
gcc -o ucpp mem.o nhash.o cpp.o lexer.o assert.o macro.o eval.o
mv ucpp /home/gncp/Documents/GNCP/MD/amber10/bin
make[1]: Leaving directory
`/home/gncp/Documents/GNCP/MD/amber10/src/ucpp-1.3'
(cd byacc && make install )
make[1]: Entering directory `/home/gncp/Documents/GNCP/MD/amber10/src/byacc'
mv yacc /home/gncp/Documents/GNCP/MD/amber10/bin
make[1]: Leaving directory `/home/gncp/Documents/GNCP/MD/amber10/src/byacc'
(cd carpack && make install );
make[1]: Entering directory
`/home/gncp/Documents/GNCP/MD/amber10/src/carpack'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
ar rv arpack.a dgetv0.o dlaqrb.o dnaitr.o dnapps.o dnaup2.o dnaupd.o
dnconv.o dneigh.o dneupd.o dngets.o dsaitr.o dsapps.o dsaup2.o dsaupd.o
dsconv.o dseigt.o dsesrt.o dseupd.o dsgets.o dsortc.o dsortr.o dstatn.o
dstats.o dstqrb.o dsarpack.o wallclock.o dmout.o ivout.o dvout.o
ar: creating arpack.a
a - dgetv0.o
a - dlaqrb.o
a - dnaitr.o
a - dnapps.o
a - dnaup2.o
a - dnaupd.o
a - dnconv.o
a - dneigh.o
a - dneupd.o
a - dngets.o
a - dsaitr.o
a - dsapps.o
a - dsaup2.o
a - dsaupd.o
a - dsconv.o
a - dseigt.o
a - dsesrt.o
a - dseupd.o
a - dsgets.o
a - dsortc.o
a - dsortr.o
a - dstatn.o
a - dstats.o
a - dstqrb.o
a - dsarpack.o
a - wallclock.o
a - dmout.o
a - ivout.o
a - dvout.o
ranlib arpack.a
mv arpack.a /home/gncp/Documents/GNCP/MD/amber10/lib
make[1]: Leaving directory
`/home/gncp/Documents/GNCP/MD/amber10/src/carpack'
(cd clapack && make install )
make[1]: Entering directory
`/home/gncp/Documents/GNCP/MD/amber10/src/clapack'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
ar rv lapack.a dsyev.o dsyevd.o dormtr.o dormql.o dormqr.o dlansy.o
dsytrd.o dorgtr.o dsteqr.o dsterf.o dlascl.o dlamch.o ilaenv.o dlassq.o
dsytd2.o dorm2l.o dlatrd.o dorgql.o dorgqr.o dlasrt.o dlaset.o dlanst.o
dlaev2.o dlasr.o dlapy2.o dlartg.o dlae2.o dorg2r.o dlarft.o dlarfb.o
dorg2l.o dlarfg.o dlarf.o dspev.o dlansp.o dsptrd.o dopgtr.o dposv.o
dppsv.o dspsv.o dgeev.o dsptrs.o dsptrf.o dpptrs.o dpptrf.o dgebak.o
dtrevc.o dlacpy.o dhseqr.o dorghr.o dgehrd.o dgebal.o dlange.o dlabad.o
dlahqr.o dlarfx.o dlanhs.o dlaln2.o dgehd2.o dlahrd.o dlanv2.o dladiv.o
dgerq2.o dorm2r.o dlarnv.o dgeqr2.o dlaruv.o dspevd.o dstedc.o dopmtr.o
dlaed0.o dlaed1.o dlaed7.o dlaeda.o dlaed8.o dlaed9.o dlamrg.o dlaed2.o
dlaed3.o dsygv.o dsygst.o dsygs2.o dlaed4.o dlaed5.o dlaed6.o dpotrf.o
dpotrs.o dpotf2.o ieeeck.o dsyevd.o dormtr.o dormqr.o dormql.o dorm2l.o
ar: creating lapack.a
a - dsyev.o
a - dsyevd.o
a - dormtr.o
a - dormql.o
a - dormqr.o
a - dlansy.o
a - dsytrd.o
a - dorgtr.o
a - dsteqr.o
a - dsterf.o
a - dlascl.o
a - dlamch.o
a - ilaenv.o
a - dlassq.o
a - dsytd2.o
a - dorm2l.o
a - dlatrd.o
a - dorgql.o
a - dorgqr.o
a - dlasrt.o
a - dlaset.o
a - dlanst.o
a - dlaev2.o
a - dlasr.o
a - dlapy2.o
a - dlartg.o
a - dlae2.o
a - dorg2r.o
a - dlarft.o
a - dlarfb.o
a - dorg2l.o
a - dlarfg.o
a - dlarf.o
a - dspev.o
a - dlansp.o
a - dsptrd.o
a - dopgtr.o
a - dposv.o
a - dppsv.o
a - dspsv.o
a - dgeev.o
a - dsptrs.o
a - dsptrf.o
a - dpptrs.o
a - dpptrf.o
a - dgebak.o
a - dtrevc.o
a - dlacpy.o
a - dhseqr.o
a - dorghr.o
a - dgehrd.o
a - dgebal.o
a - dlange.o
a - dlabad.o
a - dlahqr.o
a - dlarfx.o
a - dlanhs.o
a - dlaln2.o
a - dgehd2.o
a - dlahrd.o
a - dlanv2.o
a - dladiv.o
a - dgerq2.o
a - dorm2r.o
a - dlarnv.o
a - dgeqr2.o
a - dlaruv.o
a - dspevd.o
a - dstedc.o
a - dopmtr.o
a - dlaed0.o
a - dlaed1.o
a - dlaed7.o
a - dlaeda.o
a - dlaed8.o
a - dlaed9.o
a - dlamrg.o
a - dlaed2.o
a - dlaed3.o
a - dsygv.o
a - dsygst.o
a - dsygs2.o
a - dlaed4.o
a - dlaed5.o
a - dlaed6.o
a - dpotrf.o
a - dpotrs.o
a - dpotf2.o
a - ieeeck.o
a - dsyevd.o
a - dormtr.o
a - dormqr.o
a - dormql.o
a - dorm2l.o
ranlib lapack.a
mv lapack.a /home/gncp/Documents/GNCP/MD/amber10/lib
make[1]: Leaving directory
`/home/gncp/Documents/GNCP/MD/amber10/src/clapack'
(cd cblas && make install )
make[1]: Entering directory `/home/gncp/Documents/GNCP/MD/amber10/src/cblas'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
ar rv blas.a dasum.o daxpy.o dcopy.o ddot.o dgbmv.o dgemm.o dgemv.o dger.o
dnrm2.o drot.o drotg.o dsbmv.o dscal.o dspmv.o dspr.o dspr2.o dswap.o
dsymm.o dsymv.o dsyr.o dsyr2.o dsyr2k.o dsyrk.o dtbmv.o dtbsv.o dtpmv.o
dtpsv.o dtrmm.o dtrmv.o dtrsm.o dtrsv.o idamax.o lsame.o xerbla.o
ar: creating blas.a
a - dasum.o
a - daxpy.o
a - dcopy.o
a - ddot.o
a - dgbmv.o
a - dgemm.o
a - dgemv.o
a - dger.o
a - dnrm2.o
a - drot.o
a - drotg.o
a - dsbmv.o
a - dscal.o
a - dspmv.o
a - dspr.o
a - dspr2.o
a - dswap.o
a - dsymm.o
a - dsymv.o
a - dsyr.o
a - dsyr2.o
a - dsyr2k.o
a - dsyrk.o
a - dtbmv.o
a - dtbsv.o
a - dtpmv.o
a - dtpsv.o
a - dtrmm.o
a - dtrmv.o
a - dtrsm.o
a - dtrsv.o
a - idamax.o
a - lsame.o
a - xerbla.o
ranlib blas.a
mv blas.a /home/gncp/Documents/GNCP/MD/amber10/lib
make[1]: Leaving directory `/home/gncp/Documents/GNCP/MD/amber10/src/cblas'
(cd f2c && make install )
make[1]: Entering directory `/home/gncp/Documents/GNCP/MD/amber10/src/f2c'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
ar rv f2c.a abort_.o d_atan.o d_cosh.o d_int.o d_nint.o d_sinh.o
d_abs.o d_atn2.o d_dim.o d_lg10.o d_prod.o d_sqrt.o exit_.o
d_acos.o d_exp.o d_log.o d_sign.o d_tan.o d_asin.o d_cos.o
d_mod.o d_sin.o d_tanh.o wsfe.o s_cmp.o s_copy.o s_paus.o s_rnge.o
s_stop.o wsle.o xwsne.o util.o wref.o wrtfmt.o rsne.o sfe.o sue.o uio.o
open.o rdfmt.o rewind.o rsfe.o rsli.o ilnw.o inquire.o lread.o fmtlib.o
ftell_.o iio.o err.o close.o dfe.o dolio.o due.o endfile.o backspace.o
fmt.o sig_die.o pow_dd.o pow_di.o pow_ii.o lwrite.o i_len.o s_cat.o
F77_aloc.o wsne.o typesize.o
ar: creating f2c.a
a - abort_.o
a - d_atan.o
a - d_cosh.o
a - d_int.o
a - d_nint.o
a - d_sinh.o
a - d_abs.o
a - d_atn2.o
a - d_dim.o
a - d_lg10.o
a - d_prod.o
a - d_sqrt.o
a - exit_.o
a - d_acos.o
a - d_exp.o
a - d_log.o
a - d_sign.o
a - d_tan.o
a - d_asin.o
a - d_cos.o
a - d_mod.o
a - d_sin.o
a - d_tanh.o
a - wsfe.o
a - s_cmp.o
a - s_copy.o
a - s_paus.o
a - s_rnge.o
a - s_stop.o
a - wsle.o
a - xwsne.o
a - util.o
a - wref.o
a - wrtfmt.o
a - rsne.o
a - sfe.o
a - sue.o
a - uio.o
a - open.o
a - rdfmt.o
a - rewind.o
a - rsfe.o
a - rsli.o
a - ilnw.o
a - inquire.o
a - lread.o
a - fmtlib.o
a - ftell_.o
a - iio.o
a - err.o
a - close.o
a - dfe.o
a - dolio.o
a - due.o
a - endfile.o
a - backspace.o
a - fmt.o
a - sig_die.o
a - pow_dd.o
a - pow_di.o
a - pow_ii.o
a - lwrite.o
a - i_len.o
a - s_cat.o
a - F77_aloc.o
a - wsne.o
a - typesize.o
ranlib f2c.a
mv f2c.a /home/gncp/Documents/GNCP/MD/amber10/lib
make[1]: Leaving directory `/home/gncp/Documents/GNCP/MD/amber10/src/f2c'
(cd c9x-complex && make skip )
make[1]: Entering directory
`/home/gncp/Documents/GNCP/MD/amber10/src/c9x-complex'
using built-in (C99) complex.h functionality
make[1]: Leaving directory
`/home/gncp/Documents/GNCP/MD/amber10/src/c9x-complex'
(cd cifparse && make install )
make[1]: Entering directory
`/home/gncp/Documents/GNCP/MD/amber10/src/cifparse'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
rm -f cifparse.a
ar rv cifparse.a lex.cif.o cifp.tab.o cifparse.o
ar: creating cifparse.a
a - lex.cif.o
a - cifp.tab.o
a - cifparse.o
ranlib cifparse.a
mv cifparse.a /home/gncp/Documents/GNCP/MD/amber10/lib
make[1]: Leaving directory
`/home/gncp/Documents/GNCP/MD/amber10/src/cifparse'
(cd nss && make install )
make[1]: Entering directory `/home/gncp/Documents/GNCP/MD/amber10/src/nss'
Makefile:17: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
/home/gncp/Documents/GNCP/MD/amber10/bin/nab -c symop.nab
make[1]: /home/gncp/Documents/GNCP/MD/amber10/bin/nab: Command not found
make[1]: *** [symop.o] Error 127
make[1]: Leaving directory `/home/gncp/Documents/GNCP/MD/amber10/src/nss'
make: *** [install] Error 2
gncp.Admin:~/Documents/GNCP/MD/amber10/src$
On Thu, Jul 19, 2012 at 9:03 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Thu, Jul 19, 2012, vaibhav dixit wrote:
>
>
> > During installation of ambertools1.5 I'm getting the following error. I'm
> > not able to understand the reason behind this error.
>
> > na_anal.c: In function ‘helixanal’:
> > na_anal.c:2417:16: error: expected ‘)’ before ‘is’
> > na_anal.c:2417:16: error: stray ‘\’ in program
> > na_anal.c:2417:41: warning: missing terminating " character [enabled by
> > default]
>
> The fix is here:
>
> http://archive.ambermd.org/201201/0318.html
>
> Somehow this never got put in as a bugfix for AmberTools1.5 (I think
> because
> it was discovered during the process of creating AmberTools12, and it only
> affects gcc 4.6, which became common after AmberTools1.5 was created.
>
> In spite of Jason's heroic efforts, there are many good reasons for people
> to
> upgrade to the current codes if at all possible. The number of
> combinations
> of possible incompatibilities between multiple compilers and multiple
> versions
> of Amber is enormous.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Fri Jul 20 2012 - 04:30:02 PDT