FreeBSD Port: hmmer-2.2.g_1
Fernan Aguero
fernan at iib.unsam.edu.ar
Tue Aug 31 06:35:54 PDT 2004
+----[ 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.
-------------- next part --------------
--- /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}
-------------- next part --------------
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)
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./include missing (created)
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./share/sgml missing (created)
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[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
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