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Subject:

Re: help me to install voidoo on ubuntu11.10

From:

Tim Gruene <[log in to unmask]>

Reply-To:

Tim Gruene <[log in to unmask]>

Date:

Sat, 17 Dec 2011 14:21:43 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (569 lines)

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi     ,

I could not find error messages but only some warnings. Why do you think
anything goes wrong?

I recommend you repost your scientific question at the very end again
with a different thread as I guess that most readers will not have made
it through to the end of your email.

Best,
Tim

On 12/17/2011 02:19 AM, 王瑞 wrote:
> I am sorry for a little off-topic! Could anyone tells me how to install
> voidoo on 32-bits ubuntu11.10 ?
> For its distribution kit on http://xray.bmc.uu.se/markh/usf/, I have
> downloaded the distribution kit and Liniux_32_binaries executables, and
> followed their tutorial, but something goes wrong:
> 
> if ( !=  ) continue
> if ( -d sod && -e sod/Makefile_linux ) then
> echo Building sod
> Building sod
> cd sod
> rm sod sod.o
> cat Makefile_linux
> #
> OBJ= sod.o ../gklib/linux_kleylib  ../ccp4libs_latest_m32_linux/libccp4f.a
>  ../ccp4libs_latest_m32_linux/libccp4c.a
> EXEC = sod
> INCL= Makefile_linux
> SUBS =
> STATIC =
> ##SUBS## SUBS = sod_subs.o
> INCL = Makefile_linux sod.incl
> ##STATIC## STATIC = -static
> 
> fc = gfortran -DLINUX -m32
> 
> opt= -O -u -ffixed-line-length-132 -I..
> link= -O
> 
> $(EXEC): $(OBJ) $(SUBS)
> $(fc) $(link) -o $(EXEC) $(SUBS) $(OBJ) $(STATIC) ; strip $(EXEC)
> 
> sod.o: sod.fpp $(INCL)
> $(fc) $(opt) -c sod.fpp
> 
> ##SUBS## sod_subs.o: sod_subs.fpp $(INCL)
> ##SUBS## $(fc) $(opt) -c sod_subs.fpp
> make -f Makefile_linux
> gfortran -DLINUX -m32 -O -u -ffixed-line-length-132 -I.. -c sod.fpp
> gfortran -DLINUX -m32 -O -o sod  sod.o ../gklib/linux_kleylib
>  ../ccp4libs_latest_m32_linux/libccp4f.a
>  ../ccp4libs_latest_m32_linux/libccp4c.a  ; strip sod
> cp sod /home/dell/Documents/usf/usf_export/bin
> cd ..
> endif
> end
> if (  !=  &&  != solex ) continue
> if ( solex == gklib || solex == bin || solex == rave_package ) continue
> set ccp4_flag = `echo $prog | grep ccp4`
> grep ccp4
> echo solex
> if ( !=  ) continue
> if ( -d solex && -e solex/Makefile_linux ) then
> echo Building solex
> Building solex
> cd solex
> rm solex solex.o
> cat Makefile_linux
> #
> OBJ= solex.o ../gklib/linux_kleylib
>  ../ccp4libs_latest_m32_linux/libccp4f.a
>  ../ccp4libs_latest_m32_linux/libccp4c.a
> EXEC = solex
> INCL= Makefile_linux
> SUBS =
> STATIC =
> ##SUBS## SUBS = solex_subs.o
> ##INCL## INCL = Makefile_linux solex.incl
> ##STATIC## STATIC = -static
> 
> fc = gfortran -DLINUX -m32
> 
> opt= -O -u -ffixed-line-length-132 -I..
> link= -O
> 
> $(EXEC): $(OBJ) $(SUBS)
> $(fc) $(link) -o $(EXEC) $(SUBS) $(OBJ) $(STATIC) ; strip $(EXEC)
> 
> solex.o: solex.fpp $(INCL)
> $(fc) $(opt) -c solex.fpp
> 
> ##SUBS## solex_subs.o: solex_subs.fpp $(INCL)
> ##SUBS## $(fc) $(opt) -c solex_subs.fpp
> make -f Makefile_linux
> gfortran -DLINUX -m32 -O -u -ffixed-line-length-132 -I.. -c solex.fpp
> solex.fpp:71.24:
> 
>       call dosole (%val(iaptr),%val(ibptr),mapsize,masksize)
>                         1
> Warning: Type mismatch in argument 'mapa' at (1); passed INTEGER(4) to
> REAL(4)
> gfortran -DLINUX -m32 -O -o solex  solex.o ../gklib/linux_kleylib
>  ../ccp4libs_latest_m32_linux/libccp4f.a
>  ../ccp4libs_latest_m32_linux/libccp4c.a  ; strip solex
> cp solex /home/dell/Documents/usf/usf_export/bin
> cd ..
> endif
> end
> if (  !=  &&  != spancsi ) continue
> if ( spancsi == gklib || spancsi == bin || spancsi == rave_package )
> continue
> set ccp4_flag = `echo $prog | grep ccp4`
> grep ccp4
> echo spancsi
> if ( !=  ) continue
> if ( -d spancsi && -e spancsi/Makefile_linux ) then
> echo Building spancsi
> Building spancsi
> cd spancsi
> rm spancsi spancsi.o
> cat Makefile_linux
> #
> OBJ= spancsi.o ../gklib/linux_kleylib
>  ../ccp4libs_latest_m32_linux/libccp4f.a
>  ../ccp4libs_latest_m32_linux/libccp4c.a
> EXEC = spancsi
> INCL= Makefile_linux
> SUBS =
> STATIC =
> ##SUBS## SUBS = spancsi_subs.o
> ##INCL## INCL = Makefile_linux spancsi.incl
> ##STATIC## STATIC = -static
> 
> fc = gfortran -DLINUX -m32
> 
> opt= -O -u -ffixed-line-length-132 -I..
> link= -O
> 
> $(EXEC): $(OBJ) $(SUBS)
> $(fc) $(link) -o $(EXEC) $(SUBS) $(OBJ) $(STATIC) ; strip $(EXEC)
> 
> spancsi.o: spancsi.fpp $(INCL)
> $(fc) $(opt) -c spancsi.fpp
> 
> ##SUBS## spancsi_subs.o: spancsi_subs.fpp $(INCL)
> ##SUBS## $(fc) $(opt) -c spancsi_subs.fpp
> make -f Makefile_linux
> gfortran -DLINUX -m32 -O -u -ffixed-line-length-132 -I.. -c spancsi.fpp
> spancsi.fpp:69.24:
> 
>       call dospan (%val(iaptr),%val(ibptr),%val(idptr),
>                         1
> Warning: Type mismatch in argument 'mapa' at (1); passed INTEGER(4) to
> REAL(4)
> gfortran -DLINUX -m32 -O -o spancsi  spancsi.o ../gklib/linux_kleylib
>  ../ccp4libs_latest_m32_linux/libccp4f.a
>  ../ccp4libs_latest_m32_linux/libccp4c.a  ; strip spancsi
> cp spancsi /home/dell/Documents/usf/usf_export/bin
> cd ..
> endif
> end
> if (  !=  &&  != ssencs ) continue
> if ( ssencs == gklib || ssencs == bin || ssencs == rave_package ) continue
> set ccp4_flag = `echo $prog | grep ccp4`
> grep ccp4
> echo ssencs
> if ( !=  ) continue
> if ( -d ssencs && -e ssencs/Makefile_linux ) then
> echo Building ssencs
> Building ssencs
> cd ssencs
> rm ssencs ssencs.o
> cat Makefile_linux
> #
> OBJ= ssencs.o ../gklib/linux_kleylib
>  ../ccp4libs_latest_m32_linux/libccp4f.a
>  ../ccp4libs_latest_m32_linux/libccp4c.a
> EXEC = ssencs
> INCL= Makefile_linux
> SUBS =
> STATIC =
> ##SUBS## SUBS = ssencs_subs.o
> ##INCL## INCL = Makefile_linux ssencs.incl
> ##STATIC## STATIC = -static
> 
> fc = gfortran -DLINUX -m32
> 
> opt= -O -u -ffixed-line-length-132 -I..
> link= -O
> 
> $(EXEC): $(OBJ) $(SUBS)
> $(fc) $(link) -o $(EXEC) $(SUBS) $(OBJ) $(STATIC) ; strip $(EXEC)
> 
> ssencs.o: ssencs.fpp $(INCL)
> $(fc) $(opt) -c ssencs.fpp
> 
> ##SUBS## ssencs_subs.o: ssencs_subs.fpp $(INCL)
> ##SUBS## $(fc) $(opt) -c ssencs_subs.fpp
> make -f Makefile_linux
> gfortran -DLINUX -m32 -O -u -ffixed-line-length-132 -I.. -c ssencs.fpp
> gfortran -DLINUX -m32 -O -o ssencs  ssencs.o ../gklib/linux_kleylib
>  ../ccp4libs_latest_m32_linux/libccp4f.a
>  ../ccp4libs_latest_m32_linux/libccp4c.a  ; strip ssencs
> cp ssencs /home/dell/Documents/usf/usf_export/bin
> cd ..
> endif
> end
> if (  !=  &&  != usf_osx_bin ) continue
> if ( usf_osx_bin == gklib || usf_osx_bin == bin || usf_osx_bin ==
> rave_package ) continue
> set ccp4_flag = `echo $prog | grep ccp4`
> grep ccp4
> echo usf_osx_bin
> if ( !=  ) continue
> if ( -d usf_osx_bin && -e usf_osx_bin/Makefile_linux ) then
> echo Building usf_osx_bin
> Building usf_osx_bin
> cd usf_osx_bin
> rm usf_osx_bin usf_osx_bin.o
> rm: cannot remove `usf_osx_bin': No such file or directory
> rm: cannot remove `usf_osx_bin.o': No such file or directory
> cat Makefile_linux
> #
> OBJ= usf_osx_bin.o ../gklib/linux_kleylib
>  ../ccp4libs_latest_m32_linux/libccp4f.a
>  ../ccp4libs_latest_m32_linux/libccp4c.a
> EXEC = usf_osx_bin
> INCL= Makefile_linux
> SUBS =
> STATIC =
> ##SUBS## SUBS = usf_osx_bin_subs.o
> ##INCL## INCL = Makefile_linux usf_osx_bin.incl
> ##STATIC## STATIC = -static
> 
> fc = gfortran -DLINUX -m32
> 
> opt= -O -u -ffixed-line-length-132 -I..
> link= -O
> 
> $(EXEC): $(OBJ) $(SUBS)
> $(fc) $(link) -o $(EXEC) $(SUBS) $(OBJ) $(STATIC) ; strip $(EXEC)
> 
> usf_osx_bin.o: usf_osx_bin.fpp $(INCL)
> $(fc) $(opt) -c usf_osx_bin.fpp
> 
> ##SUBS## usf_osx_bin_subs.o: usf_osx_bin_subs.fpp $(INCL)
> ##SUBS## $(fc) $(opt) -c usf_osx_bin_subs.fpp
> make -f Makefile_linux
> make: *** No rule to make target `usf_osx_bin.fpp', needed by
> `usf_osx_bin.o'.  Stop.
> cp usf_osx_bin /home/dell/Documents/usf/usf_export/bin
> cp: cannot stat `usf_osx_bin': No such file or directory
> cd ..
> endif
> end
> if (  !=  &&  != voidoo ) continue
> if ( voidoo == gklib || voidoo == bin || voidoo == rave_package ) continue
> set ccp4_flag = `echo $prog | grep ccp4`
> grep ccp4
> echo voidoo
> if ( !=  ) continue
> if ( -d voidoo && -e voidoo/Makefile_linux ) then
> echo Building voidoo
> Building voidoo
> cd voidoo
> rm voidoo voidoo.o
> cat Makefile_linux
> #
> OBJ= voidoo.o ../gklib/linux_kleylib
>  ../ccp4libs_latest_m32_linux/libccp4f.a
>  ../ccp4libs_latest_m32_linux/libccp4c.a
> EXEC = voidoo
> INCL= Makefile_linux
> SUBS =
> STATIC =
> SUBS = voidoo_subs.o
> INCL = Makefile_linux voidoo.incl
> ##STATIC## STATIC = -static
> 
> fc = gfortran -DLINUX -m32
> 
> opt= -O -u -ffixed-line-length-132 -I..
> link= -O
> 
> $(EXEC): $(OBJ) $(SUBS)
> $(fc) $(link) -o $(EXEC) $(SUBS) $(OBJ) $(STATIC) ; strip $(EXEC)
> 
> voidoo.o: voidoo.fpp $(INCL)
> $(fc) $(opt) -c voidoo.fpp
> 
> voidoo_subs.o: voidoo_subs.fpp $(INCL)
> $(fc) $(opt) -c voidoo_subs.fpp
> make -f Makefile_linux
> gfortran -DLINUX -m32 -O -u -ffixed-line-length-132 -I.. -c voidoo.fpp
> gfortran -DLINUX -m32 -O -u -ffixed-line-length-132 -I.. -c voidoo_subs.fpp
> gfortran -DLINUX -m32 -O -o voidoo voidoo_subs.o voidoo.o
> ../gklib/linux_kleylib  ../ccp4libs_latest_m32_linux/libccp4f.a
>  ../ccp4libs_latest_m32_linux/libccp4c.a  ; strip voidoo
> cp voidoo /home/dell/Documents/usf/usf_export/bin
> cd ..
> endif
> end
> if (  !=  &&  != xpand ) continue
> if ( xpand == gklib || xpand == bin || xpand == rave_package ) continue
> set ccp4_flag = `echo $prog | grep ccp4`
> grep ccp4
> echo xpand
> if ( !=  ) continue
> if ( -d xpand && -e xpand/Makefile_linux ) then
> echo Building xpand
> Building xpand
> cd xpand
> rm xpand xpand.o
> cat Makefile_linux
> #
> OBJ= xpand.o ../gklib/linux_kleylib
>  ../ccp4libs_latest_m32_linux/libccp4f.a
>  ../ccp4libs_latest_m32_linux/libccp4c.a
> EXEC = xpand
> INCL= Makefile_linux
> SUBS =
> STATIC =
> ##SUBS## SUBS = xpand_subs.o
> INCL = Makefile_linux xpand.incl
> ##STATIC## STATIC = -static
> 
> fc = gfortran -DLINUX -m32
> 
> opt= -O -u -ffixed-line-length-132 -I..
> link= -O
> 
> $(EXEC): $(OBJ) $(SUBS)
> $(fc) $(link) -o $(EXEC) $(SUBS) $(OBJ) $(STATIC) ; strip $(EXEC)
> 
> xpand.o: xpand.fpp $(INCL)
> $(fc) $(opt) -c xpand.fpp
> 
> ##SUBS## xpand_subs.o: xpand_subs.fpp $(INCL)
> ##SUBS## $(fc) $(opt) -c xpand_subs.fpp
> make -f Makefile_linux
> gfortran -DLINUX -m32 -O -u -ffixed-line-length-132 -I.. -c xpand.fpp
> xpand.fpp:193.5:
> 
>  1990   continue
>      1
> xpand.fpp:207.72:
> 
>         if (ierr .ne. 0) goto 1990
>                                                                         2
> Warning: Label at (1) is not in the same block as the GOTO statement at (2)
> xpand.fpp:140.5:
> 
>  1000   continue
>      1
> xpand.fpp:211.72:
> 
>         if (length(ncsfil) .lt. 1) goto 1000
>                                                                         2
> Warning: Label at (1) is not in the same block as the GOTO statement at (2)
> xpand.fpp:193.5:
> 
>  1990   continue
>      1
> xpand.fpp:231.72:
> 
>         if (ierr .ne. 0) goto 1990
>                                                                         2
> Warning: Label at (1) is not in the same block as the GOTO statement at (2)
> xpand.fpp:193.5:
> 
>  1990   continue
>      1
> xpand.fpp:235.72:
> 
>         if (ierr .ne. 0) goto 1990
>                                                                         2
> Warning: Label at (1) is not in the same block as the GOTO statement at (2)
> xpand.fpp:426.5:
> 
>  2990   continue
>      1
> xpand.fpp:258.72:
> 
>         if (ierr .ne. 0) goto 2990
>                                                                         2
> Warning: Label at (1) is not in the same block as the GOTO statement at (2)
> xpand.fpp:426.5:
> 
>  2990   continue
>      1
> xpand.fpp:267.72:
> 
>           if (ierr .ne. 0) goto 2990
>                                                                         2
> Warning: Label at (1) is not in the same block as the GOTO statement at (2)
> xpand.fpp:426.5:
> 
>  2990   continue
>      1
> xpand.fpp:277.72:
> 
>           if (ierr .ne. 0) goto 2990
>                                                                         2
> Warning: Label at (1) is not in the same block as the GOTO statement at (2)
> xpand.fpp:426.5:
> 
>  2990   continue
>      1
> xpand.fpp:442.72:
> 
>         if (ierr .ne. 0) goto 2990
>                                                                         2
> Warning: Label at (1) is not in the same block as the GOTO statement at (2)
> xpand.fpp:426.5:
> 
>  2990   continue
>      1
> xpand.fpp:447.72:
> 
>           if (ierr .ne. 0) goto 2990
>                                                                         2
> Warning: Label at (1) is not in the same block as the GOTO statement at (2)
> xpand.fpp:426.5:
> 
>  2990   continue
>      1
> xpand.fpp:451.72:
> 
>           if (ierr .ne. 0) goto 2990
>                                                                         2
> Warning: Label at (1) is not in the same block as the GOTO statement at (2)
> xpand.fpp:193.5:
> 
>  1990   continue
>      1
> xpand.fpp:467.72:
> 
>           goto 1990
>                                                                         2
> Warning: Label at (1) is not in the same block as the GOTO statement at (2)
> gfortran -DLINUX -m32 -O -o xpand  xpand.o ../gklib/linux_kleylib
>  ../ccp4libs_latest_m32_linux/libccp4f.a
>  ../ccp4libs_latest_m32_linux/libccp4c.a  ; strip xpand
> cp xpand /home/dell/Documents/usf/usf_export/bin
> cd ..
> endif
> end
> if (  !=  &&  != xplo2d ) continue
> if ( xplo2d == gklib || xplo2d == bin || xplo2d == rave_package ) continue
> set ccp4_flag = `echo $prog | grep ccp4`
> grep ccp4
> echo xplo2d
> if ( !=  ) continue
> if ( -d xplo2d && -e xplo2d/Makefile_linux ) then
> echo Building xplo2d
> Building xplo2d
> cd xplo2d
> rm xplo2d xplo2d.o
> cat Makefile_linux
> #
> OBJ= xplo2d.o ../gklib/linux_kleylib
>  ../ccp4libs_latest_m32_linux/libccp4f.a
>  ../ccp4libs_latest_m32_linux/libccp4c.a
> EXEC = xplo2d
> INCL= Makefile_linux
> SUBS =
> STATIC =
> ##SUBS## SUBS = xplo2d_subs.o
> ##INCL## INCL = Makefile_linux xplo2d.incl
> ##STATIC## STATIC = -static
> 
> fc = gfortran -DLINUX -m32
> 
> opt= -O -u -ffixed-line-length-132 -I..
> link= -O
> 
> $(EXEC): $(OBJ) $(SUBS)
> $(fc) $(link) -o $(EXEC) $(SUBS) $(OBJ) $(STATIC) ; strip $(EXEC)
> 
> xplo2d.o: xplo2d.fpp $(INCL)
> $(fc) $(opt) -c xplo2d.fpp
> 
> ##SUBS## xplo2d_subs.o: xplo2d_subs.fpp $(INCL)
> ##SUBS## $(fc) $(opt) -c xplo2d_subs.fpp
> make -f Makefile_linux
> gfortran -DLINUX -m32 -O -u -ffixed-line-length-132 -I.. -c xplo2d.fpp
> xplo2d.fpp:3264.469:
> 
> \u0141\U00115186\U09B13EF8\U09C4E140
> 
>  1
> 
> 
> 
> 
> 
> Warning: Extraneous characters in format at (1)
> xplo2d.fpp:3272.476:
> 
> 
> 
>  1
> 
> 
> 
> 
> 
> Warning: Extraneous characters in format at (1)
> xplo2d.fpp:3280.483:
> 
> 
> 
>  1
> 
> 
> 
> 
> 
> Warning: Extraneous characters in format at (1)
> xplo2d.fpp:3286.486:
> 
> = list of atoms
> 
>  1
> 
> 
> 
> 
> 
> Warning: Extraneous characters in format at (1)
> gfortran -DLINUX -m32 -O -o xplo2d  xplo2d.o ../gklib/linux_kleylib
>  ../ccp4libs_latest_m32_linux/libccp4f.a
>  ../ccp4libs_latest_m32_linux/libccp4c.a  ; strip xplo2d
> cp xplo2d /home/dell/Documents/usf/usf_export/bin
> cd ..
> endif
> end
> goto exit
> exit 0
> 
> I have installed gfortran, could anyone help me ?
> By the way, could you give some advice on calculate the size of a pocket in
> the inside of a protein ?
> Thanks for your attention !
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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