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Date: Fri, 19 Jan 2007 09:08:25 +0900 (JST)
From: Tsurutani Naoki <turutani@scphys.kyoto-u.ac.jp>
Reply-To: Tsurutani Naoki <turutani@scphys.kyoto-u.ac.jp>
To: FreeBSD-gnats-submit@freebsd.org
Cc:
Subject: building biology/platon fails.
X-Send-Pr-Version: 3.113
X-GNATS-Notify:

>Number:         108105
>Category:       ports
>Synopsis:       building biology/platon fails.
>Confidential:   no
>Severity:       serious
>Priority:       medium
>Responsible:    freebsd-ports-bugs
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          sw-bug
>Submitter-Id:   current-users
>Arrival-Date:   Fri Jan 19 00:10:20 GMT 2007
>Closed-Date:    Mon May 07 03:19:34 GMT 2007
>Last-Modified:  Mon May 07 03:19:34 GMT 2007
>Originator:     Tsurutani Naoki
>Release:        FreeBSD 6.2-STABLE i386
>Organization:
>Environment:
System: FreeBSD polymer3.scphys.kyoto-u.ac.jp 6.2-STABLE FreeBSD 6.2-STABLE #3: Mon Jan 15 16:38:16 JST 2007 turutani@polymer3.scphys.kyoto-u.ac.jp:/usr/local/work/usr/obj/usr/src/sys/POLYMER i386


	
>Description:
	building biology/platon fails with next messages:
	Warning: Obsolete: arithmetic IF statement at (1)
	cc -O -pipe -I/usr/X11R6/include -c xdrvr.c
	gfortran42 -o platon platon.o xdrvr.o -L/usr/X11R6/lib -lX11
	platon.o(.text+0x6c31): In function `setupcc_':
	: undefined reference to `signal_'
	platon.o(.text+0x196f3): In function `s937_':
	: undefined reference to `system_'
	platon.o(.text+0x1971a): In function `s937_':
	: undefined reference to `system_'
	platon.o(.text+0x19729): In function `s937_':
	: undefined reference to `system_'
	platon.o(.text+0x1974d): In function `s937_':
	: undefined reference to `system_'
	platon.o(.text+0x19768): In function `s937_':
	: undefined reference to `system_'
	platon.o(.text+0x19c10): more undefined references to `system_' follow
	collect2: ld returned 1 exit status

	
>How-To-Repeat:
	always build biology/platon with no option.
	
>Fix:
	here is a patch:
	--- files/Makefile.orig Fri Jan 19 04:30:05 2007
	+++ files/Makefile Fri Jan 19 08:58:52 2007
	@@ -10,7 +10,7 @@
	 FOPT=  ${FFLAGS} -Nx800 -NL400 -Nn802
	 .endif
	 COPT=  ${CFLAGS} -I%%X11BASE%%/include
	-LOPT=  -L%%X11BASE%%/lib -lX11
	+LOPT=  -L%%X11BASE%%/lib -lX11 -lg2c
	
	 all:   ${OBJS}
	 	${FC} -o ${TARGET} ${OBJS} ${LOPT}

	I do not know whether this is good for any FreeBSD version,
	but it seems to work well on my host.
	


>Release-Note:
>Audit-Trail:
Responsible-Changed-From-To: freebsd-ports-bugs->itetcu 
Responsible-Changed-By: itetcu 
Responsible-Changed-When: Fri Jan 19 22:41:04 UTC 2007 
Responsible-Changed-Why:  
I'll take it. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=108105 
State-Changed-From-To: open->feedback 
State-Changed-By: itetcu 
State-Changed-When: Sat Jan 20 02:56:46 UTC 2007 
State-Changed-Why:  
I can't reproduce this, at least on my amd64 tindy and on 5-STABLE on 
i386 one (build in progress for 6-STABLE and HEAD on i386). All 'base 
systems' are from 2006-12-25. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=108105 
Responsible-Changed-From-To: itetcu->freebsd-ports-bugs 
Responsible-Changed-By: itetcu 
Responsible-Changed-When: Thu Mar 15 11:03:19 UTC 2007 
Responsible-Changed-Why:  
It is of no use to keep this PRs for myself, the way real life keeps 
being I have to use en unlikely half hour of free time to sleep :( 

http://www.freebsd.org/cgi/query-pr.cgi?pr=108105 

From: Stefan Walter <sw@gegenunendlich.de>
To: Tsurutani Naoki <turutani@scphys.kyoto-u.ac.jp>
Cc: GNATS <FreeBSD-gnats-submit@FreeBSD.org>
Subject: Re: ports/108105: building biology/platon fails.
Date: Sun, 8 Apr 2007 17:10:36 +0200

 --RIYY1s2vRbPFwWeW
 Content-Type: text/plain; charset=us-ascii
 Content-Disposition: inline
 
 Hi,
 
 can you still reproduce the problem with an up-to-date ports tree, or has
 it been resolved in the meantime? In case the problem is still there: Do
 you have any customizations in e.g. /etc/make.conf that might have an
 influence here?
 
 Regards,
 Stefan
 
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From: Tsurutani Naoki <turutani@scphys.kyoto-u.ac.jp>
To: Stefan Walter <sw@gegenunendlich.de>
Cc: GNATS <FreeBSD-gnats-submit@FreeBSD.org>
Subject: Re: ports/108105: building biology/platon fails.
Date: Mon, 09 Apr 2007 13:04:21 +0900

 Yes, I still have the same problem.

From: Stefan Walter <stefan@freebsd.org>
To: Tsurutani Naoki <turutani@scphys.kyoto-u.ac.jp>
Cc: GNATS <FreeBSD-gnats-submit@FreeBSD.org>
Subject: Re: ports/108105: building biology/platon fails.
Date: Mon, 9 Apr 2007 09:31:06 +0200

 --JYK4vJDZwFMowpUq
 Content-Type: text/plain; charset=us-ascii
 Content-Disposition: inline
 
 Tsurutani Naoki, 09.04.07, 06:04h CEST:
 
 > Yes, I still have the same problem.
 
 What about local changes to the build environment? Something must be
 different on your system; itetcu reported it worked fine with him, and I
 was able to build it without problems as well. Could you send your
 /etc/make.conf, for instance?
 
 Regards,
 Stefan
 
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From: Tsurutani Naoki <turutani@scphys.kyoto-u.ac.jp>
To: Stefan Walter <stefan@freebsd.org>
Cc: GNATS <FreeBSD-gnats-submit@freebsd.org>
Subject: Re: ports/108105: building biology/platon fails.
Date: Mon, 09 Apr 2007 17:11:57 +0900

 % egrep -v -e '^#' -e '^\ *$' /etc/make.conf
 CPUTYPE?=athlon64
 NO_CPU_CFLAGS=	true	# Don't add -march=<cpu> to CFLAGS automatically
 CFLAGS=	-O2 -fno-strict-aliasing -pipe
 NO_BLUETOOTH=		# do not build Bluetooth related stuff
 NO_I4B=			# do not build isdn4bsd package
 NO_OPENSSH=	true	# do not build OpenSSH
 SUP_UPDATE=	yes
 SUP=		/usr/bin/csup
 SUPFLAGS=	-g -L 2
 SUPHOST=	cvsup3.jp.FreeBSD.org
 SUPFILE=	/usr/local/etc/stable-supfile
 PORTSSUPFILE=	/usr/local/etc/ports-supfile
 DOCSUPFILE=	/usr/local/etc/doc-supfile
 DOC_LANG=	en_US.ISO8859-1 ja_JP.eucJP
 SENDMAIL_MC=/etc/mail/polymer3.mc
 SENDMAIL_SUBMIT_MC=/etc/mail/polymer3.submit.mc
 SENDMAIL_CFLAGS=	-I/usr/local/include/sasl1 -DSASL -D_FFR_UNSAFE_SASL
 SENDMAIL_LDFLAGS=	-L/usr/local/lib
 SENDMAIL_LDADD=	-lsasl
 NO_WPA_SUPPLICANT_EAPOL=true
 X_WINDOW_SYSTEM=	xorg
 HAVE_MOTIF=	yes
 MASTER_SITE_OVERRIDE?= \
 	ftp://ftp4.jp.freebsd.org/pub/FreeBSD/ports/distfiles/${DIST_SUBDIR}/
 MASTER_SITE_RINGSERVER=	ftp://ring.ip-kyoto.ad.jp/pub/%SUBDIR%/
 MASTER_SITE_TEX_CTAN=	ftp://ftp.osaka-u.ac.jp/CTAN/%SUBDIR%/
 GNOME_DESKTOP_VERSION=	2
 RUBY_DEFAULT_VER=1.8
 WITH_APACHE2=1
 APACHE_PORT=www/apache22
 WITH_MOZILLA=firefox
 KERNCONF=POLYMER
 WITH_JPMAN=1
 WITH_GECKO=firefox thunderbird
 PERL_ARCH=mach
 NOPERL=yes
 NO_PERL=yes
 NO_PERL_WRAPPER=yes
 PERL_VER=5.8.8
 PERL_VERSION=5.8.8
 
 And here are all the logs after *removing* /etc/make.conf:
 % cd /usr/ports/biology/platon/
 % make
 ===>  Vulnerability check disabled, database not found
 ===>  Extracting for platon-2007.01.09
 ===>  Patching for platon-2007.01.09
 (cd /usr/ports/biology/platon/work/platon ; /usr/bin/gunzip -f platon.f.Z xdrvr.c.gz)
 /bin/cp /usr/ports/biology/platon/files/Makefile 
 /usr/ports/biology/platon/work/platon/Makefile
 /usr/bin/sed -i.bak -e "s+%%X11BASE%%+/usr/X11R6+"  
 /usr/ports/biology/platon/work/platon/Makefile
 ===>   platon-2007.01.09 depends on executable in : gfortran42 - found
 ===>   platon-2007.01.09 depends on shared library: X11.6 - found
 ===>  Configuring for platon-2007.01.09
 ===>  Building for platon-2007.01.09
 gfortran42 -O -c platon.f
 platon.f:4562.72:
 
               ASSIGN 50 TO LRET
                                                                        1
 Warning: Obsolete: ASSIGN statement at (1)
 platon.f:4594.72:
 
       ASSIGN 220 TO LRET
                                                                        1
 Warning: Obsolete: ASSIGN statement at (1)
 platon.f:4630.15:
 
       GOTO LRET, (50, 220)
               1
 Warning: Obsolete: Assigned GOTO statement at (1)
 platon.f:9050.72:
 
             ASSIGN 140 TO LRET
                                                                        1
 Warning: Obsolete: ASSIGN statement at (1)
 platon.f:9054.38:
 
             IF (IVAL .EQ. 1) GOTO LRET, (100, 140)
                                      1
 Warning: Obsolete: Assigned GOTO statement at (1)
 platon.f:9056.38:
 
             IF (IVAL .EQ. 1) GOTO LRET, (100, 140)
                                      1
 Warning: Obsolete: Assigned GOTO statement at (1)
 platon.f:9059.42:
 
             IF (NCN(NRT) .LT. 2) GOTO LRET, (100, 140)
                                          1
 Warning: Obsolete: Assigned GOTO statement at (1)
 platon.f:9062.51:
 
               IF (NCN(NRT) .GT. IPR(159)) GOTO LRET, (100, 140)
                                                   1
 Warning: Obsolete: Assigned GOTO statement at (1)
 platon.f:9064.55:
 
               IF (IATPR(IEN(NO1 + 1)) .GT. 4) GOTO LRET, (100, 140)
                                                       1
 Warning: Obsolete: Assigned GOTO statement at (1)
 platon.f:9066.72:
 
             ASSIGN 100 TO LRET
                                                                        1
 Warning: Obsolete: ASSIGN statement at (1)
 platon.f:47284.72:
 
         ASSIGN 250 TO IERR
                                                                        1
 Warning: Obsolete: ASSIGN statement at (1)
 platon.f:47296.72:
 
                 ASSIGN 250 TO IERR
                                                                        1
 Warning: Obsolete: ASSIGN statement at (1)
 platon.f:47298.72:
 
                 ASSIGN 240 TO IERR
                                                                        1
 Warning: Obsolete: ASSIGN statement at (1)
 platon.f:47306.72:
 
             ASSIGN 250 TO IERR
                                                                        1
 Warning: Obsolete: ASSIGN statement at (1)
 platon.f:47311.72:
 
             ASSIGN 240 TO IERR
                                                                        1
 Warning: Obsolete: ASSIGN statement at (1)
 platon.f:47314.17:
 
   230   GOTO IERR, (250, 240)
                 1
 Warning: Obsolete: Assigned GOTO statement at (1)
 platon.f:61881.72:
 
       ASSIGN 30 TO LRET
                                                                        1
 Warning: Obsolete: ASSIGN statement at (1)
 platon.f:62134.33:
 
         IF (IT .EQ. 0)  GOTO LRET, (30, 120)
                                 1
 Warning: Obsolete: Assigned GOTO statement at (1)
 platon.f:62219.15:
 
       GOTO LRET, (30, 120)
               1
 Warning: Obsolete: Assigned GOTO statement at (1)
 platon.f:62230.72:
 
       ASSIGN 120 TO LRET
                                                                        1
 Warning: Obsolete: ASSIGN statement at (1)
 platon.f:80250.72:
 
       ASSIGN 1110 TO LRET9
                                                                        1
 Warning: Obsolete: ASSIGN statement at (1)
 platon.f:80395.72:
 
           ASSIGN 2675 TO LRET9
                                                                        1
 Warning: Obsolete: ASSIGN statement at (1)
 platon.f:80441.72:
 
       ASSIGN 2675 TO LRET9
                                                                        1
 Warning: Obsolete: ASSIGN statement at (1)
 platon.f:80446.58:
 
       IF (JB .GT. 60 .OR. LINE(JB:JB) .EQ. ' ') GOTO LRET9, (2675, 1110)
                                                          1
 Warning: Obsolete: Assigned GOTO statement at (1)
 cc -O2 -fno-strict-aliasing -pipe   -I/usr/X11R6/include -c xdrvr.c
 gfortran42 -o platon platon.o xdrvr.o -L/usr/X11R6/lib -lX11
 platon.o(.text+0x6c24): In function `setupcc_':
 : undefined reference to `signal_'
 platon.o(.text+0x1967f): In function `s937_':
 : undefined reference to `system_'
 platon.o(.text+0x196a6): In function `s937_':
 : undefined reference to `system_'
 platon.o(.text+0x196b5): In function `s937_':
 : undefined reference to `system_'
 platon.o(.text+0x196d9): In function `s937_':
 : undefined reference to `system_'
 platon.o(.text+0x196f4): In function `s937_':
 : undefined reference to `system_'
 platon.o(.text+0x19b9c): more undefined references to `system_' follow
 collect2: ld returned 1 exit status
 *** Error code 1
 
 Stop in /usr/ports/biology/platon/work/platon.
 *** Error code 1
 
 Stop in /usr/ports/biology/platon.

From: Stefan Walter <stefan@freebsd.org>
To: Tsurutani Naoki <turutani@scphys.kyoto-u.ac.jp>
Cc: GNATS <FreeBSD-gnats-submit@freebsd.org>
Subject: Re: ports/108105: building biology/platon fails.
Date: Tue, 10 Apr 2007 14:19:07 +0200

 --lrZ03NoBR/3+SXJZ
 Content-Type: text/plain; charset=us-ascii
 Content-Disposition: inline
 
 Hi,
 
 since you're getting the same errors without /etc/make.conf as well and
 I'm not an gfortran expert, the last thing I can recommend now is trying
 to reinstall lang/gcc42 (if you didn't do that, yet). If that doesn't
 help, maybe someone on the ports mailing list or the Platon developers can
 help.
 
 Regards,
 Stefan
 
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From: Tsurutani Naoki <turutani@scphys.kyoto-u.ac.jp>
To: stefan@freebsd.org
Cc: FreeBSD-gnats-submit@freebsd.org
Subject: Re: ports/108105: building biology/platon fails.
Date: Tue, 10 Apr 2007 22:59:43 +0900

 Hello,
 
 I've already try reinstalling gcc-4.2.0_20070307 with package,
 and found nothing changed.
 I also built on 7-current host, and found no problem nor any warnings.
 Please someone help me !!
 
 ---
 Tsurutani Naoki
 turutani@scphys.kyoto-u.ac.jp

From: Tsurutani Naoki <turutani@scphys.kyoto-u.ac.jp>
To: FreeBSD-gnats-submit@freebsd.org, bug-followup@freebsd.org,
        Stefan Walter <stefan@freebsd.org>,
        Ion-Mihai Tetcu <itetcu@freebsd.org>
Cc:  
Subject: Re: ports/108105: building biology/platon fails.
Date: Mon, 07 May 2007 11:32:00 +0900

 The problem is resolved.
 It was caused by old distfile, and new distfile does not generate this problem.
 
 This port has no effective distinfo and the distfile name contains no version.
 I thought, if distfile(s) are old or not what to be expected, 
 error by make checksum is always raised.  But it was my misunderstanding.
 
 To prevent this problem, I think we should fix the distinfo file of this port,
 and if possible, add version string to distfile or add versioned directory
 to store downloaded file like biology/tinker.
 I cannot confirm how often distfile is updated, but if it is true, 
 the version number of this port has no meanings.
 
 ---
 Tsurutani Naoki
 turutani@scphys.kyoto-u.ac.jp

From: Tsurutani Naoki <turutani@scphys.kyoto-u.ac.jp>
To: FreeBSD-gnats-submit@FreeBSD.org, bug-followup@FreeBSD.org,
        Stefan Walter <stefan@FreeBSD.org>,
        Ion-Mihai Tetcu <itetcu@FreeBSD.org>
Cc:  
Subject: Re: ports/108105: building biology/platon fails.
Date: Mon, 07 May 2007 11:32:00 +0900

 The problem is resolved.
 It was caused by old distfile, and new distfile does not generate this problem.
 
 This port has no effective distinfo and the distfile name contains no version.
 I thought, if distfile(s) are old or not what to be expected, 
 error by make checksum is always raised.  But it was my misunderstanding.
 
 To prevent this problem, I think we should fix the distinfo file of this port,
 and if possible, add version string to distfile or add versioned directory
 to store downloaded file like biology/tinker.
 I cannot confirm how often distfile is updated, but if it is true, 
 the version number of this port has no meanings.
 
 ---
 Tsurutani Naoki
 turutani@scphys.kyoto-u.ac.jp
State-Changed-From-To: feedback->closed 
State-Changed-By: linimon 
State-Changed-When: Mon May 7 03:19:06 UTC 2007 
State-Changed-Why:  
The problem was apparently caused by an old distfile. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=108105 
>Unformatted:
