FreeBSD Port: hmmer-2.2.g_1
Mauricio Herrera Cuadra
arareko at yahoo.com
Tue Aug 31 10:38:00 PDT 2004
Hola Fernan!
Thanks for your quick answer! Definitely an elegant solution instead of my
awful hacks :P Unfortunately we get stuck on the same step...
Also, I believe you are missing to declare some ENV variables after
installing pvm: PVM_ROOT and PVM_ARCH. I put them into /etc/login.conf as:
:setenv=MAIL=/var/mail/$,BLOCKSIZE=K,FTP_PASSIVE_MODE=YES,PVM_ROOT=/usr/local/lib/pvm,PVM_ARCH=FREEBSD:\
Remember to rebuild the database with:
[root at arareko] ~ # cap_mkdb /etc/login.conf
Now, this is what I get using your patch:
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
[root at arareko] /usr/ports/biology/hmmer # make WITH_PVM=yes
===> Vulnerability check disabled
===> Extracting for hmmer-2.2.g_1
>> Checksum OK for hmmer-2.2g.tar.gz.
===> hmmer-2.2.g_1 depends on file: /usr/local/bin/perl5.8.5 - found
===> Patching for hmmer-2.2.g_1
===> hmmer-2.2.g_1 depends on file: /usr/local/bin/perl5.8.5 - found
===> Applying FreeBSD patches for hmmer-2.2.g_1
===> hmmer-2.2.g_1 depends on executable: pvm - found
===> hmmer-2.2.g_1 depends on file: /usr/local/bin/perl5.8.5 - found
===> Configuring for hmmer-2.2.g_1
creating cache ./config.cache
Welcome to HMMER... configuring for your system.
checking for gcc... cc
checking whether the C compiler (cc -O -pipe ) works... yes
checking whether the C compiler (cc -O -pipe ) is a cross-compiler... no
checking whether we are using GNU C... yes
checking whether cc accepts -g... yes
checking whether ln -s works... yes
checking for ranlib... ranlib
checking whether your make is GNU make... nope, assuming sysv make.
Configuring for PVM
checking host system type... i386-portbld-freebsd4.10
checking how to run the C preprocessor... cc -E
Trying to enable default POSIX threads support
checking for pthread.h... yes
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... -D_THREAD_SAFE
checking for cc_r... cc
checking for pthread_setconcurrency... no
checking for pthread_attr_setscope... no
checking for ntohs... yes
checking for ntohl... yes
checking for htons... yes
checking for htonl... yes
Configuration complete. Writing Makefiles and such...
updating cache ./config.cache
creating ./config.status
creating Makefile
creating src/Makefile
creating testsuite/Makefile
configuring in squid
running /bin/sh ./configure --with-pvm --prefix=/usr/local
i386-portbld-freebsd4.10 --cache-file=.././config.cache --srcdir=.
loading cache .././config.cache
Welcome to SQUID... configuring for your system.
checking for gcc... (cached) cc
checking whether the C compiler (cc -O -pipe ) works... yes
checking whether the C compiler (cc -O -pipe ) is a cross-compiler... no
checking whether we are using GNU C... (cached) yes
checking whether cc accepts -g... (cached) yes
checking whether ln -s works... (cached) yes
checking for ranlib... (cached) ranlib
checking whether your make is GNU make... nope, assuming sysv make.
Configuring for PVM
checking whether byte ordering is bigendian... no
checking for ntohs... (cached) yes
checking for ntohl... (cached) yes
checking for htons... (cached) yes
checking for htonl... (cached) yes
checking size of unsigned short... 2
checking size of unsigned int... 4
checking size of unsigned long... 4
checking size of unsigned long long... 8
checking whether fpos_t is an arithmetic datatype... yes.
checking for ftello... yes
checking for fseeko... yes
checking for ftello64... no
checking for fseeko64... no
checking for ftell64... no
checking for fseek64... no
checking for stat64... no
checking size of off_t... 0
checking size of off64_t... 0
checking size of fpos_t... 8
Configuration complete. Writing Makefiles and such...
updating cache .././config.cache
creating ./config.status
creating Makefile
creating squid.h
creating squidconf.h
===> Building for hmmer-2.2.g_1
echo "/* version.h -- automatically generated by a Makefile. DO NOT EDIT.
*/" > version.h
echo "#define PACKAGE \""HMMER"\"" >> version.h
echo "#define RELEASE \""2.2g"\"" >> version.h
echo "#define RELEASEDATE \""August 2001"\"" >> version.h
echo "#define COPYRIGHT \""Copyright \(C\) 1992-2001 HHMI/Washington
University School of Medicine"\"" >> version.h
echo "#define LICENSE \""Freely distributed under the GNU General
Public License \(GPL\)"\"" >> version.h
cp version.h squid/
cp version.h src/
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c afetch_main.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c a2m.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c aligneval.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c alignio.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c clustal.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c cluster.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c dayhoff.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c eps.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c file.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c getopt.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c gki.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c gsi.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c hsregex.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c iupac.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c msa.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c msf.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c phylip.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c revcomp.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c rk.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c selex.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c seqencode.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c shuffle.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c sqerror.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c sqio.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c squidcore.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c sre_ctype.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c sre_math.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c sre_string.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c ssi.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c stack.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c stockholm.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c stopwatch.c
stopwatch.c:62: pvm3.h: No such file or directory
*** Error code 1
Stop in /usr/ports/biology/hmmer/work/hmmer-2.2g/squid.
*** Error code 1
Stop in /usr/ports/biology/hmmer/work/hmmer-2.2g.
*** Error code 1
Stop in /usr/ports/biology/hmmer.
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Then I do another of my awful tricks to keep going:
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
[root at arareko] /usr/ports/biology/hmmer # cd /usr/local/lib/pvm/
[root at arareko] /usr/local/lib/pvm # ln -s /usr/local/include/ include
[root at arareko] /usr/local/lib/pvm # cd /usr/ports/biology/hmmer/
[root at arareko] /usr/ports/biology/hmmer # make WITH_PVM=yes
===> Building for hmmer-2.2.g_1
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c stopwatch.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c translate.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c types.c
cc -O -pipe -DSRE_ENABLE_PVM -I/usr/local/lib/pvm/include -DHAVE_CONFIG_H
-c weight.c
cc -O -pipe -DHAVE_CONFIG_H -L/usr/local/lib/pvm/lib/FREEBSD -o afetch
afetch_main.o a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o
eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o
revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o
sre_ctype.o sre_math.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o
translate.o types.o weight.o -lpvm3 -lm
/usr/libexec/elf/ld: cannot find -lpvm3
*** Error code 1
Stop in /usr/ports/biology/hmmer/work/hmmer-2.2g/squid.
*** Error code 1
Stop in /usr/ports/biology/hmmer/work/hmmer-2.2g.
*** Error code 1
Stop in /usr/ports/biology/hmmer.
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
And then I'm again on the same step as yesterday... :)
I hope anyone can help us with this step. Anyway, thanks again for your
quick and good advice.
Me gustaría que mantuvieramos el contacto, yo soy de México y tal vez
podamos desarrollar algo de bioinformática juntos...
Suerte y saludos!
Mauricio.
--- Fernan Aguero <fernan at iib.unsam.edu.ar> wrote:
> +----[ Mauricio Herrera Cuadra <arareko at yahoo.com> (31.Aug.2004 03:12):
> |
> | Hi. Is it possible to install this port with PVM support? I've been
> | tweaking the Makefiles, but no good results. I've symlinked
> | /usr/local/include into /usr/local/lib/pvm in order to find pvm3.h
> during
> | compilation, but then I get this and I'm stuck on it:
>
> [output error snipped]
>
> Hola Mauricio!
>
> I believe that the right way to do this is to modify the
> port so that it allows you to build hmmer using the
> supported --with-pvm argument to configure.
>
> Attached is a preliminary patch that will get you near the
> beginning. After applying the patch you will need to call
> make like this:
> make WITH_PVM=yes
> so that WITH_PVM gets set. Then the port will do the right
> thing: check if net/pvm is installed and install it if this
> is not the case, and run hmmer's configure with the right
> arguments.
>
> After saying this, I have to say that I tested the modified
> port and it is still failing. But on a different error this
> time (attached is the output in case a porter with some
> insight can help). For some reason pvm3.h is not being
> found, although it is present under /usr/local/include (I
> just installed pvm from ports to test this, pvm-3.4.4).
>
> If I have some more time, I'll try to get back to this. But
> this is a horrible week for me in terms of spare time.
>
> Fernan
>
> |
> | Thanks in advance.
> | Regards,
> |
> +----]
>
> de nada. Saludos,
>
> Fernan
>
> --
> Fernan Aguero - fernan at iib.unsam.edu.ar
> Phone: +54 11 4580-7255/7 ext 310, Fax: +54 11 4752-9639
> Check http://genoma.unsam.edu.ar/~fernan for more info.
> > --- /usr/ports/biology/hmmer/Makefile Sat Mar 8 01:03:33 2003
> +++ Makefile Tue Aug 31 09:34:01 2004
> @@ -25,6 +25,11 @@
> hmmpfam.1 hmmsearch.1 seqstat.1 sfetch.1 shuffle.1 \
> sreformat.1
>
> +.if defined(WITH_PVM)
> +CONFIGURE_ARGS+= --with-pvm
> +BUILD_DEPENDS+= pvm:${PORTSDIR}/net/pvm
> +.endif
> +
> post-install:
> .if !defined(NOPORTDOCS)
> @ ${MKDIR} ${DOCSDIR}
> > Script started on Tue Aug 31 10:18:57 2004
> pi# portinstall net/pvm ; exit[26D[4h../test_p[4lort.sh
> WITH_PVM=yes[7C
> [port_test] ===> clean before use
> mkdir: /usr/tmp/pkgdb: File exists
> [port_test] ===> make clean
> ===> Cleaning for perl-5.6.1_15
> ===> Cleaning for hmmer-2.2.g_1
> [port_test] ===> clean old files
> [port_test] ===> prepare test
> ./bin missing (created)
> ./etc missing (created)
> ./etc/rc.d missing (created)
> ./include missing (created)
> ./info missing (created)
> ./lib missing (created)
> ./lib/perl5 missing (created)
> ./lib/perl5/5.00503 missing (created)
> ./lib/perl5/5.00503/man missing (created)
> ./lib/perl5/5.00503/man/man3 missing (created)
> ./lib/perl5/site_perl missing (created)
> ./lib/perl5/site_perl/5.005 missing (created)
> ./lib/perl5/site_perl/5.005/alpha-freebsd missing (created)
> ./lib/perl5/site_perl/5.005/alpha-freebsd/auto missing (created)
> ./lib/perl5/site_perl/5.005/auto missing (created)
> ./lib/perl5/site_perl/5.005/i386-freebsd missing (created)
> ./lib/perl5/site_perl/5.005/i386-freebsd/auto missing (created)
> ./libdata missing (created)
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> ./share/nls/ja_JP.eucJP missing (created)
> ./share/nls/ko_KR.eucKR missing (created)
> ./share/nls/la_LN.ISO8859-1 missing (created)
> ./share/nls/la_LN.ISO8859-15 missing (created)
> ./share/nls/la_LN.ISO8859-2 missing (created)
> ./share/nls/la_LN.ISO8859-4 missing (created)
> ./share/nls/la_LN.US-ASCII missing (created)
> ./share/nls/lt_LT.ISO8859-4 missing (created)
> ./share/nls/nl_BE.ISO8859-1 missing (created)
> ./share/nls/nl_BE.ISO8859-15 missing (created)
> ./share/nls/nl_NL.ISO8859-1 missing (created)
> ./share/nls/nl_NL.ISO8859-15 missing (created)
> ./share/nls/no_NO.ISO8859-1 missing (created)
> ./share/nls/no_NO.ISO8859-15 missing (created)
> ./share/nls/pl_PL.ISO8859-2 missing (created)
> ./share/nls/pt_BR.ISO8859-1 missing (created)
> ./share/nls/pt_PT.ISO8859-1 missing (created)
> ./share/nls/pt_PT.ISO8859-15 missing (created)
> ./share/nls/ro_RO.ISO8859-2 missing (created)
> ./share/nls/ru_RU.CP1251 missing (created)
> ./share/nls/ru_RU.CP866 missing (created)
> ./share/nls/ru_RU.ISO8859-5 missing (created)
> ./share/nls/ru_RU.KOI8-R missing (created)
> ./share/nls/sk_SK.ISO8859-2 missing (created)
> ./share/nls/sl_SI.ISO8859-2 missing (created)
> ./share/nls/sv_SE.ISO8859-1 missing (created)
> ./share/nls/sv_SE.ISO8859-15 missing (created)
> ./share/nls/tr_TR.ISO8859-9 missing (created)
> ./share/nls/uk_UA.ISO8859-5 missing (created)
> ./share/nls/uk_UA.KOI8-U missing (created)
> ./share/nls/zh_CN.eucCN missing (created)
> ./share/nls/zh_CN.GB18030 missing (created)
> ./share/nls/zh_CN.GBK missing (created)
> ./share/nls/zh_TW.Big5 missing (created)
> ./share/sgml missing (created)
> ./share/skel missing (created)
> ./share/xml missing (created)
> [port_test] ===> make depends
> ===> hmmer-2.2.g_1 depends on file: /usr/local/bin/perl5.6.1 - found
> ===> hmmer-2.2.g_1 depends on file: /usr/local/bin/perl5.6.1 - found
> ===> hmmer-2.2.g_1 depends on file: /usr/local/bin/perl5.6.1 - found
> ===> hmmer-2.2.g_1 depends on file: /usr/local/bin/perl5.6.1 - found
> [port_test] ===> make install
> ===> Vulnerability check disabled, database not found
> ===> Extracting for hmmer-2.2.g_1
> >> Checksum OK for hmmer-2.2g.tar.gz.
> ===> hmmer-2.2.g_1 depends on file: /usr/local/bin/perl5.6.1 - found
> ===> Patching for hmmer-2.2.g_1
> ===> hmmer-2.2.g_1 depends on file: /usr/local/bin/perl5.6.1 - found
> ===> Applying FreeBSD patches for hmmer-2.2.g_1
> ===> hmmer-2.2.g_1 depends on executable: pvm - found
> ===> hmmer-2.2.g_1 depends on file: /usr/local/bin/perl5.6.1 - found
> ===> Configuring for hmmer-2.2.g_1
> creating cache ./config.cache
> Welcome to HMMER... configuring for your system.
> checking for gcc... cc
> checking whether the C compiler (cc -O -pipe ) works... yes
> checking whether the C compiler (cc -O -pipe ) is a cross-compiler...
> no
> checking whether we are using GNU C... yes
> checking whether cc accepts -g... yes
> checking whether ln -s works... yes
> checking for ranlib... ranlib
> checking whether your make is GNU make... nope, assuming sysv make.
> Configuring for PVM
> checking host system type... i386-portbld-freebsd4.10
> checking how to run the C preprocessor... cc -E
> Trying to enable default POSIX threads support
> checking for pthread.h... yes
> checking for the pthreads library -lpthreads... no
> checking whether pthreads work without any flags... no
> checking whether pthreads work with -Kthread... no
> checking whether pthreads work with -kthread... no
> checking for the pthreads library -llthread... no
> checking whether pthreads work with -pthread... yes
> checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
> checking if more special flags are required for pthreads...
> -D_THREAD_SAFE
> checking for cc_r... cc
> checking for pthread_setconcurrency... no
> checking for pthread_attr_setscope... no
> checking for ntohs... yes
> checking for ntohl... yes
> checking for htons... yes
> checking for htonl... yes
> Configuration complete. Writing Makefiles and such...
> updating cache ./config.cache
> creating ./config.status
> creating Makefile
> creating src/Makefile
> creating testsuite/Makefile
> configuring in squid
> running /bin/sh ./configure --with-pvm --prefix=/usr/tmp/ports
> i386-portbld-freebsd4.10 --cache-file=.././config.cache --srcdir=.
> loading cache .././config.cache
> Welcome to SQUID... configuring for your system.
> checking for gcc... (cached) cc
> checking whether the C compiler (cc -O -pipe ) works... yes
> checking whether the C compiler (cc -O -pipe ) is a cross-compiler...
> no
> checking whether we are using GNU C... (cached) yes
> checking whether cc accepts -g... (cached) yes
> checking whether ln -s works... (cached) yes
> checking for ranlib... (cached) ranlib
> checking whether your make is GNU make... nope, assuming sysv make.
> Configuring for PVM
> checking whether byte ordering is bigendian... no
> checking for ntohs... (cached) yes
> checking for ntohl... (cached) yes
> checking for htons... (cached) yes
> checking for htonl... (cached) yes
> checking size of unsigned short... 2
> checking size of unsigned int... 4
> checking size of unsigned long... 4
> checking size of unsigned long long... 8
> checking whether fpos_t is an arithmetic datatype... yes.
> checking for ftello... yes
> checking for fseeko... yes
> checking for ftello64... no
> checking for fseeko64... no
> checking for ftell64... no
> checking for fseek64... no
> checking for stat64... no
> checking size of off_t... 0
> checking size of off64_t... 0
> checking size of fpos_t... 8
> Configuration complete. Writing Makefiles and such...
> updating cache .././config.cache
> creating ./config.status
> creating Makefile
> creating squid.h
> creating squidconf.h
> ===> Building for hmmer-2.2.g_1
> echo "/* version.h -- automatically generated by a Makefile. DO NOT
> EDIT. */" > version.h
> echo "#define PACKAGE \""HMMER"\"" >> version.h
> echo "#define RELEASE \""2.2g"\"" >> version.h
> echo "#define RELEASEDATE \""August 2001"\"" >> version.h
> echo "#define COPYRIGHT \""Copyright \(C\) 1992-2001 HHMI/Washington
> University School of Medicine"\"" >> version.h
> echo "#define LICENSE \""Freely distributed under the GNU General
> Public License \(GPL\)"\"" >> version.h
> cp version.h squid/
> cp version.h src/
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c afetch_main.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c a2m.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c aligneval.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c alignio.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c clustal.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c cluster.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c dayhoff.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c eps.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c file.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c getopt.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c gki.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c gsi.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c hsregex.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c iupac.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c msa.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c msf.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c phylip.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c revcomp.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c rk.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c selex.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c seqencode.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c shuffle.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c sqerror.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c sqio.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c squidcore.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c sre_ctype.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c sre_math.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c sre_string.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c ssi.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c stack.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c stockholm.c
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c stopwatch.c
> stopwatch.c:62: pvm3.h: No such file or directory
> *** Error code 1
>
> Stop in /home/fernan/misc/freebsd-ports/hmmer/work/hmmer-2.2g/squid.
> *** Error code 1
>
> Stop in /home/fernan/misc/freebsd-ports/hmmer/work/hmmer-2.2g.
> *** Error code 1
>
> Stop in /home/fernan/misc/freebsd-ports/hmmer.
> [port_test] ===> make package
> ===> Building for hmmer-2.2.g_1
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c stopwatch.c
> stopwatch.c:62: pvm3.h: No such file or directory
> *** Error code 1
>
> Stop in /home/fernan/misc/freebsd-ports/hmmer/work/hmmer-2.2g/squid.
> *** Error code 1
>
> Stop in /home/fernan/misc/freebsd-ports/hmmer/work/hmmer-2.2g.
> *** Error code 1
>
> Stop in /home/fernan/misc/freebsd-ports/hmmer.
> [port_test] ===> make deinstall
> ===> Deinstalling for biology/hmmer
> ===> hmmer not installed, skipping
> [port_test] ===> pkg_add
> [port_test] ===> make deinstall
> ===> Deinstalling for biology/hmmer
> ===> hmmer not installed, skipping
> [port_test] ===> make reinstall
> ===> Building for hmmer-2.2.g_1
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c stopwatch.c
> stopwatch.c:62: pvm3.h: No such file or directory
> *** Error code 1
>
> Stop in /home/fernan/misc/freebsd-ports/hmmer/work/hmmer-2.2g/squid.
> *** Error code 1
>
> Stop in /home/fernan/misc/freebsd-ports/hmmer/work/hmmer-2.2g.
> *** Error code 1
>
> Stop in /home/fernan/misc/freebsd-ports/hmmer.
> *** Error code 1
>
> Stop in /home/fernan/misc/freebsd-ports/hmmer.
> [port_test] ===> make package
> ===> Building for hmmer-2.2.g_1
> cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c stopwatch.c
> stopwatch.c:62: pvm3.h: No such file or directory
> *** Error code 1
>
> Stop in /home/fernan/misc/freebsd-ports/hmmer/work/hmmer-2.2g/squid.
> *** Error code 1
>
> Stop in /home/fernan/misc/freebsd-ports/hmmer/work/hmmer-2.2g.
> *** Error code 1
>
> Stop in /home/fernan/misc/freebsd-ports/hmmer.
> [port_test] ===> Finished
>
> Check the pkg-plist and edit it to manually fix remaining issues.
> You should remove the entries for the pkgdb. This script creates
> the pkgdb under PREFIX, thus they appear in the pkg-plist.
> exit
>
> Script done on Tue Aug 31 10:19:22 2004
>
=====
MAURICIO HERRERA CUADRA
arareko at yahoo.com
http://www.geocities.com/arareko/
"I've seen 5.11 divided into 11 different grades of increasing difficulty, as follows: 5.11a, 5.10d, 5.11-, 5.11b, 5.11, 5.11c, 5.9 squeeze, 5.11+, 5.10 OW, 5.12a, 5.11d" — Brutus of Wyde.
-----BEGIN GEEK CODE BLOCK-----
Version: 3.12
GCM/CS/IT/LS/MD/MU/PA/S/TW/O>B/M/P/AT$ d-(---)>!$ s+:+>$ a26>+++>?$
C(++++)>---$ UBL+++>UAVHIOSCX*---$ P++++(--)>--- L->+$ E-(--)>+++$
W+(+++)>-- N+>- o+++(--) K?>$ w+(---)>$ !O M>+$ !V PS+(+++) PE(-) Y(+)
PGP(-)>+ t(-)>+++$ 5 X@>+$ R*>+++$ tv(+)>+$ b+>+++$ DI+++>+++$
D+++>++++$ G++(-)>++++$ e++>++++$ h!>---$ r%>++ y+(**)>+$
------END GEEK CODE BLOCK------
_______________________________
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