Date: Tue, 31 Aug 2004 10:35:28 -0300 From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: Mauricio Herrera Cuadra <arareko@yahoo.com> Cc: wjv@freebsd.org Subject: Re: FreeBSD Port: hmmer-2.2.g_1 Message-ID: <20040831133528.GL464@iib.unsam.edu.ar> In-Reply-To: <20040831060727.32223.qmail@web12309.mail.yahoo.com> References: <20040831060727.32223.qmail@web12309.mail.yahoo.com>
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--nmemrqcdn5VTmUEE Content-Type: text/plain; charset=us-ascii Content-Disposition: inline +----[ Mauricio Herrera Cuadra <arareko@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. --nmemrqcdn5VTmUEE Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename="Makefile.diff" --- /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} --nmemrqcdn5VTmUEE Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename="test_pvm.out" Content-Transfer-Encoding: quoted-printable Script started on Tue Aug 31 10:18:57 2004 pi# portinstall net/pvm ; exit=1B[26D=1B[4h../test_p=1B[4lort.sh WITH_PVM= =3Dyes=1B[7C=0D=0D [port_test] =3D=3D=3D> clean before use=0D mkdir: /usr/tmp/pkgdb: File exists=0D [port_test] =3D=3D=3D> make clean=0D =3D=3D=3D> Cleaning for perl-5.6.1_15=0D =3D=3D=3D> Cleaning for hmmer-2.2.g_1=0D [port_test] =3D=3D=3D> clean old files=0D [port_test] =3D=3D=3D> prepare test=0D =2E/bin missing (created)=0D =2E/etc missing (created)=0D =2E/etc/rc.d missing (created)=0D =2E/include missing (created)=0D =2E/info missing (created)=0D =2E/lib missing (created)=0D =2E/lib/perl5 missing (created)=0D =2E/lib/perl5/5.00503 missing (created)=0D =2E/lib/perl5/5.00503/man missing (created)=0D =2E/lib/perl5/5.00503/man/man3 missing (created)=0D =2E/lib/perl5/site_perl missing (created)=0D =2E/lib/perl5/site_perl/5.005 missing (created)=0D =2E/lib/perl5/site_perl/5.005/alpha-freebsd missing (created)=0D =2E/lib/perl5/site_perl/5.005/alpha-freebsd/auto missing (created)=0D =2E/lib/perl5/site_perl/5.005/auto missing (created)=0D =2E/lib/perl5/site_perl/5.005/i386-freebsd missing (created)=0D =2E/lib/perl5/site_perl/5.005/i386-freebsd/auto missing (created)=0D =2E/libdata missing (created)=0D =2E/libexec missing (created)=0D =2E/man missing (created)=0D =2E/man/cat1 missing (created)=0D =2E/man/cat2 missing (created)=0D =2E/man/cat3 missing (created)=0D =2E/man/cat4 missing (created)=0D =2E/man/cat5 missing (created)=0D =2E/man/cat6 missing (created)=0D =2E/man/cat7 missing (created)=0D =2E/man/cat8 missing (created)=0D =2E/man/cat9 missing (created)=0D =2E/man/catl missing (created)=0D =2E/man/catn missing (created)=0D =2E/man/de.ISO8859-1 missing (created)=0D =2E/man/de.ISO8859-1/cat1 missing (created)=0D =2E/man/de.ISO8859-1/cat2 missing (created)=0D =2E/man/de.ISO8859-1/cat3 missing (created)=0D =2E/man/de.ISO8859-1/cat4 missing (created)=0D =2E/man/de.ISO8859-1/cat5 missing (created)=0D =2E/man/de.ISO8859-1/cat6 missing (created)=0D =2E/man/de.ISO8859-1/cat7 missing (created)=0D =2E/man/de.ISO8859-1/cat8 missing (created)=0D =2E/man/de.ISO8859-1/cat9 missing (created)=0D =2E/man/de.ISO8859-1/catl missing (created)=0D 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(created)=0D =2E/man/ru.KOI8-R/cat9 missing (created)=0D =2E/man/ru.KOI8-R/catl missing (created)=0D =2E/man/ru.KOI8-R/catn missing (created)=0D =2E/man/ru.KOI8-R/man1 missing (created)=0D =2E/man/ru.KOI8-R/man2 missing (created)=0D =2E/man/ru.KOI8-R/man3 missing (created)=0D =2E/man/ru.KOI8-R/man4 missing (created)=0D =2E/man/ru.KOI8-R/man5 missing (created)=0D =2E/man/ru.KOI8-R/man6 missing (created)=0D =2E/man/ru.KOI8-R/man7 missing (created)=0D =2E/man/ru.KOI8-R/man8 missing (created)=0D =2E/man/ru.KOI8-R/man9 missing (created)=0D =2E/man/ru.KOI8-R/manl missing (created)=0D =2E/man/ru.KOI8-R/mann missing (created)=0D =2E/sbin missing (created)=0D =2E/share missing (created)=0D =2E/share/aclocal missing (created)=0D =2E/share/dict missing (created)=0D =2E/share/doc missing (created)=0D =2E/share/doc/ja missing (created)=0D =2E/share/emacs missing (created)=0D =2E/share/emacs/site-lisp missing (created)=0D =2E/share/examples missing (created)=0D =2E/share/java missing (created)=0D =2E/share/java/classes missing (created)=0D =2E/share/misc missing (created)=0D =2E/share/nls missing (created)=0D =2E/share/nls/C missing (created)=0D =2E/share/nls/af_ZA.ISO8859-1 missing (created)=0D =2E/share/nls/af_ZA.ISO8859-15 missing (created)=0D =2E/share/nls/am_ET.UTF-8 missing (created)=0D =2E/share/nls/bg_BG.CP1251 missing (created)=0D =2E/share/nls/cs_CZ.ISO8859-2 missing (created)=0D =2E/share/nls/da_DK.ISO8859-1 missing (created)=0D =2E/share/nls/da_DK.ISO8859-15 missing (created)=0D =2E/share/nls/de_AT.ISO8859-1 missing (created)=0D =2E/share/nls/de_AT.ISO8859-15 missing (created)=0D =2E/share/nls/de_CH.ISO8859-1 missing (created)=0D =2E/share/nls/de_CH.ISO8859-15 missing (created)=0D =2E/share/nls/de_DE.ISO8859-1 missing (created)=0D =2E/share/nls/de_DE.ISO8859-15 missing (created)=0D =2E/share/nls/el_GR.ISO8859-7 missing (created)=0D =2E/share/nls/en_AU.ISO8859-1 missing (created)=0D =2E/share/nls/en_AU.ISO8859-15 missing (created)=0D =2E/share/nls/en_AU.US-ASCII missing (created)=0D =2E/share/nls/en_CA.ISO8859-1 missing (created)=0D =2E/share/nls/en_CA.ISO8859-15 missing (created)=0D =2E/share/nls/en_CA.US-ASCII missing (created)=0D =2E/share/nls/en_GB.ISO8859-1 missing (created)=0D =2E/share/nls/en_GB.ISO8859-15 missing (created)=0D =2E/share/nls/en_GB.US-ASCII missing (created)=0D =2E/share/nls/en_NZ.ISO8859-1 missing (created)=0D =2E/share/nls/en_NZ.ISO8859-15 missing (created)=0D =2E/share/nls/en_NZ.US-ASCII missing (created)=0D =2E/share/nls/en_US.ISO8859-1 missing (created)=0D =2E/share/nls/en_US.ISO8859-15 missing (created)=0D =2E/share/nls/es_ES.ISO8859-1 missing (created)=0D =2E/share/nls/es_ES.ISO8859-15 missing (created)=0D =2E/share/nls/et_EE.ISO8859-15 missing (created)=0D =2E/share/nls/fi_FI.ISO8859-1 missing (created)=0D =2E/share/nls/fi_FI.ISO8859-15 missing (created)=0D =2E/share/nls/fr_BE.ISO8859-1 missing (created)=0D =2E/share/nls/fr_BE.ISO8859-15 missing (created)=0D =2E/share/nls/fr_CA.ISO8859-1 missing (created)=0D =2E/share/nls/fr_CA.ISO8859-15 missing (created)=0D =2E/share/nls/fr_CH.ISO8859-1 missing (created)=0D =2E/share/nls/fr_CH.ISO8859-15 missing (created)=0D =2E/share/nls/fr_FR.ISO8859-1 missing (created)=0D =2E/share/nls/fr_FR.ISO8859-15 missing (created)=0D =2E/share/nls/hi_IN.ISCII-DEV missing (created)=0D =2E/share/nls/hr_HR.ISO8859-2 missing (created)=0D =2E/share/nls/hu_HU.ISO8859-2 missing (created)=0D =2E/share/nls/is_IS.ISO8859-1 missing (created)=0D =2E/share/nls/is_IS.ISO8859-15 missing (created)=0D =2E/share/nls/it_CH.ISO8859-1 missing (created)=0D =2E/share/nls/it_CH.ISO8859-15 missing (created)=0D =2E/share/nls/it_IT.ISO8859-1 missing (created)=0D =2E/share/nls/it_IT.ISO8859-15 missing (created)=0D =2E/share/nls/ja_JP.SJIS missing (created)=0D =2E/share/nls/ja_JP.eucJP missing (created)=0D =2E/share/nls/ko_KR.eucKR missing (created)=0D =2E/share/nls/la_LN.ISO8859-1 missing (created)=0D =2E/share/nls/la_LN.ISO8859-15 missing (created)=0D =2E/share/nls/la_LN.ISO8859-2 missing (created)=0D =2E/share/nls/la_LN.ISO8859-4 missing (created)=0D =2E/share/nls/la_LN.US-ASCII missing (created)=0D =2E/share/nls/lt_LT.ISO8859-4 missing (created)=0D =2E/share/nls/nl_BE.ISO8859-1 missing (created)=0D =2E/share/nls/nl_BE.ISO8859-15 missing (created)=0D =2E/share/nls/nl_NL.ISO8859-1 missing (created)=0D =2E/share/nls/nl_NL.ISO8859-15 missing (created)=0D =2E/share/nls/no_NO.ISO8859-1 missing (created)=0D =2E/share/nls/no_NO.ISO8859-15 missing (created)=0D =2E/share/nls/pl_PL.ISO8859-2 missing (created)=0D =2E/share/nls/pt_BR.ISO8859-1 missing (created)=0D =2E/share/nls/pt_PT.ISO8859-1 missing (created)=0D =2E/share/nls/pt_PT.ISO8859-15 missing (created)=0D =2E/share/nls/ro_RO.ISO8859-2 missing (created)=0D =2E/share/nls/ru_RU.CP1251 missing (created)=0D =2E/share/nls/ru_RU.CP866 missing (created)=0D =2E/share/nls/ru_RU.ISO8859-5 missing (created)=0D =2E/share/nls/ru_RU.KOI8-R missing (created)=0D =2E/share/nls/sk_SK.ISO8859-2 missing (created)=0D =2E/share/nls/sl_SI.ISO8859-2 missing (created)=0D =2E/share/nls/sv_SE.ISO8859-1 missing (created)=0D =2E/share/nls/sv_SE.ISO8859-15 missing (created)=0D =2E/share/nls/tr_TR.ISO8859-9 missing (created)=0D =2E/share/nls/uk_UA.ISO8859-5 missing (created)=0D =2E/share/nls/uk_UA.KOI8-U missing (created)=0D =2E/share/nls/zh_CN.eucCN missing (created)=0D =2E/share/nls/zh_CN.GB18030 missing (created)=0D =2E/share/nls/zh_CN.GBK missing (created)=0D =2E/share/nls/zh_TW.Big5 missing (created)=0D =2E/share/sgml missing (created)=0D =2E/share/skel missing (created)=0D =2E/share/xml missing (created)=0D [port_test] =3D=3D=3D> make depends=0D =3D=3D=3D> hmmer-2.2.g_1 depends on file: /usr/local/bin/perl5.6.1 - foun= d=0D =3D=3D=3D> hmmer-2.2.g_1 depends on file: /usr/local/bin/perl5.6.1 - foun= d=0D =3D=3D=3D> hmmer-2.2.g_1 depends on file: /usr/local/bin/perl5.6.1 - foun= d=0D =3D=3D=3D> hmmer-2.2.g_1 depends on file: /usr/local/bin/perl5.6.1 - foun= d=0D [port_test] =3D=3D=3D> make install=0D =3D=3D=3D> Vulnerability check disabled, database not found=0D =3D=3D=3D> Extracting for hmmer-2.2.g_1=0D >> Checksum OK for hmmer-2.2g.tar.gz.=0D =3D=3D=3D> hmmer-2.2.g_1 depends on file: /usr/local/bin/perl5.6.1 - foun= d=0D =3D=3D=3D> Patching for hmmer-2.2.g_1=0D =3D=3D=3D> hmmer-2.2.g_1 depends on file: /usr/local/bin/perl5.6.1 - foun= d=0D =3D=3D=3D> Applying FreeBSD patches for hmmer-2.2.g_1=0D =3D=3D=3D> hmmer-2.2.g_1 depends on executable: pvm - found=0D =3D=3D=3D> hmmer-2.2.g_1 depends on file: /usr/local/bin/perl5.6.1 - foun= d=0D =3D=3D=3D> Configuring for hmmer-2.2.g_1=0D creating cache ./config.cache=0D Welcome to HMMER... configuring for your system.=0D checking for gcc... cc=0D checking whether the C compiler (cc -O -pipe ) works... yes=0D checking whether the C compiler (cc -O -pipe ) is a cross-compiler... no=0D checking whether we are using GNU C... yes=0D checking whether cc accepts -g... yes=0D checking whether ln -s works... yes=0D checking for ranlib... ranlib=0D checking whether your make is GNU make... nope, assuming sysv make.=0D Configuring for PVM=0D checking host system type... i386-portbld-freebsd4.10=0D checking how to run the C preprocessor... cc -E=0D Trying to enable default POSIX threads support=0D checking for pthread.h... yes=0D checking for the pthreads library -lpthreads... no=0D checking whether pthreads work without any flags... no=0D checking whether pthreads work with -Kthread... no=0D checking whether pthreads work with -kthread... no=0D checking for the pthreads library -llthread... no=0D checking whether pthreads work with -pthread... yes=0D checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE=0D checking if more special flags are required for pthreads... -D_THREAD_SAFE= =0D checking for cc_r... cc=0D checking for pthread_setconcurrency... no=0D checking for pthread_attr_setscope... no=0D checking for ntohs... yes=0D checking for ntohl... yes=0D checking for htons... yes=0D checking for htonl... yes=0D Configuration complete. Writing Makefiles and such...=0D updating cache ./config.cache=0D creating ./config.status=0D creating Makefile=0D creating src/Makefile=0D creating testsuite/Makefile=0D configuring in squid=0D running /bin/sh ./configure --with-pvm --prefix=3D/usr/tmp/ports i386-port= bld-freebsd4.10 --cache-file=3D.././config.cache --srcdir=3D.=0D loading cache .././config.cache=0D Welcome to SQUID... configuring for your system.=0D checking for gcc... (cached) cc=0D checking whether the C compiler (cc -O -pipe ) works... yes=0D checking whether the C compiler (cc -O -pipe ) is a cross-compiler... no=0D checking whether we are using GNU C... (cached) yes=0D checking whether cc accepts -g... (cached) yes=0D checking whether ln -s works... (cached) yes=0D checking for ranlib... (cached) ranlib=0D checking whether your make is GNU make... nope, assuming sysv make.=0D Configuring for PVM=0D checking whether byte ordering is bigendian... no=0D checking for ntohs... (cached) yes=0D checking for ntohl... (cached) yes=0D checking for htons... (cached) yes=0D checking for htonl... (cached) yes=0D checking size of unsigned short... 2=0D checking size of unsigned int... 4=0D checking size of unsigned long... 4=0D checking size of unsigned long long... 8=0D checking whether fpos_t is an arithmetic datatype... yes.=0D checking for ftello... yes=0D checking for fseeko... yes=0D checking for ftello64... no=0D checking for fseeko64... no=0D checking for ftell64... no=0D checking for fseek64... no=0D checking for stat64... no=0D checking size of off_t... 0=0D checking size of off64_t... 0=0D checking size of fpos_t... 8=0D Configuration complete. Writing Makefiles and such...=0D updating cache .././config.cache=0D creating ./config.status=0D creating Makefile=0D creating squid.h=0D creating squidconf.h=0D =3D=3D=3D> Building for hmmer-2.2.g_1=0D echo "/* version.h -- automatically generated by a Makefile. DO NOT EDIT. *= /" > version.h=0D echo "#define PACKAGE \""HMMER"\"" >> version.h=0D echo "#define RELEASE \""2.2g"\"" >> version.h=0D echo "#define RELEASEDATE \""August 2001"\"" >> version.h=0D echo "#define COPYRIGHT \""Copyright \(C\) 1992-2001 HHMI/Washington Univ= ersity School of Medicine"\"" >> version.h=0D echo "#define LICENSE \""Freely distributed under the GNU General Publi= c License \(GPL\)"\"" >> version.h=0D cp version.h squid/=0D cp version.h src/=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c afetch_main.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c a2m.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c aligneval.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c alignio.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c clustal.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c cluster.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c dayhoff.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c eps.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c file.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c getopt.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c gki.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c gsi.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c hsregex.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c iupac.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c msa.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c msf.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c phylip.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c revcomp.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c rk.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c selex.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c seqencode.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c shuffle.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c sqerror.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c sqio.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c squidcore.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c sre_ctype.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c sre_math.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c sre_string.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c ssi.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c stack.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c stockholm.c=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c stopwatch.c=0D stopwatch.c:62: pvm3.h: No such file or directory=0D *** Error code 1=0D =0D Stop in /home/fernan/misc/freebsd-ports/hmmer/work/hmmer-2.2g/squid.=0D *** Error code 1=0D =0D Stop in /home/fernan/misc/freebsd-ports/hmmer/work/hmmer-2.2g.=0D *** Error code 1=0D =0D Stop in /home/fernan/misc/freebsd-ports/hmmer.=0D [port_test] =3D=3D=3D> make package=0D =3D=3D=3D> Building for hmmer-2.2.g_1=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c stopwatch.c=0D stopwatch.c:62: pvm3.h: No such file or directory=0D *** Error code 1=0D =0D Stop in /home/fernan/misc/freebsd-ports/hmmer/work/hmmer-2.2g/squid.=0D *** Error code 1=0D =0D Stop in /home/fernan/misc/freebsd-ports/hmmer/work/hmmer-2.2g.=0D *** Error code 1=0D =0D Stop in /home/fernan/misc/freebsd-ports/hmmer.=0D [port_test] =3D=3D=3D> make deinstall=0D =3D=3D=3D> Deinstalling for biology/hmmer=0D =3D=3D=3D> hmmer not installed, skipping=0D [port_test] =3D=3D=3D> pkg_add=0D [port_test] =3D=3D=3D> make deinstall=0D =3D=3D=3D> Deinstalling for biology/hmmer=0D =3D=3D=3D> hmmer not installed, skipping=0D [port_test] =3D=3D=3D> make reinstall=0D =3D=3D=3D> Building for hmmer-2.2.g_1=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c stopwatch.c=0D stopwatch.c:62: pvm3.h: No such file or directory=0D *** Error code 1=0D =0D Stop in /home/fernan/misc/freebsd-ports/hmmer/work/hmmer-2.2g/squid.=0D *** Error code 1=0D =0D Stop in /home/fernan/misc/freebsd-ports/hmmer/work/hmmer-2.2g.=0D *** Error code 1=0D =0D Stop in /home/fernan/misc/freebsd-ports/hmmer.=0D *** Error code 1=0D =0D Stop in /home/fernan/misc/freebsd-ports/hmmer.=0D [port_test] =3D=3D=3D> make package=0D =3D=3D=3D> Building for hmmer-2.2.g_1=0D cc -O -pipe -DSRE_ENABLE_PVM -I/include -DHAVE_CONFIG_H -c stopwatch.c=0D stopwatch.c:62: pvm3.h: No such file or directory=0D *** Error code 1=0D =0D Stop in /home/fernan/misc/freebsd-ports/hmmer/work/hmmer-2.2g/squid.=0D *** Error code 1=0D =0D Stop in /home/fernan/misc/freebsd-ports/hmmer/work/hmmer-2.2g.=0D *** Error code 1=0D =0D Stop in /home/fernan/misc/freebsd-ports/hmmer.=0D [port_test] =3D=3D=3D> Finished=0D =0D Check the pkg-plist and edit it to manually fix remaining issues.=0D You should remove the entries for the pkgdb. This script creates=0D the pkgdb under PREFIX, thus they appear in the pkg-plist.=0D exit=0D Script done on Tue Aug 31 10:19:22 2004 --nmemrqcdn5VTmUEE--
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