Date: Mon, 9 Nov 2009 06:56:13 +0000 From: "b. f." <bf1783@googlemail.com> To: freebsd-questions@FreeBSD.org Cc: dougb@FreeBSD.org, Scott Bennett <bennett@cs.niu.edu> Subject: Re: math/py-numpy vs. math/atlas-devel Message-ID: <d873d5be0911082256y5c35d288i13b40f8d6e1f6285@mail.gmail.com>
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Scott Bennett wrote:
>I would like to install science/gnudatalanguage but have been running
>into various obstacles. Lars Engels very kindly just fixed one of them
>(devel/lasi) (Thanks, Lars!), so now I'm on to the next one, which may not
>be a showstopper, but it's at least a nuisance. One of the gnudatalanguage
>dependencies is math/py-numpy, which, in turn, depends upon math/atlas.
>However, I have math/atlas-devel installed and do not wish to revert to an
>older, slower version of the ATLAS library. Adding a "-x atlas-\*" onto
>the portmaster command to build math/py-numpy fails to prevent portmaster
>from trying to build math/atlas. Creating a
>/var/db/pkg/atlas-3.8.3_1,1/+IGNOREME file in addition doesn't help. How
>can I force math/py-numpy to accept the already installed math/atlas-devel
>libraries?
>Thanks in advance for any help!
Congratulations, you've managed to defeat three sets of safeguards in
portmaster.
Problem #1
math/atlas and math/atlas-devel don't have proper CONFLICTS entries in
their Makefiles (this should be fixed), so the following code in
portmaster, from dependency_check ():
1612 conflicts=''
1613 if pm_cd $d_port; then
1614 grep -ql ^CONFLICTS Makefile &&
1615 conflicts=`pm_make_b -V CONFLICTS`
1616 else
1617 fail "Cannot cd to $d_port"
1618 fi
1619 for glob in $conflicts; do
1620 confl_p=`pkg_info -I $glob 2>/dev/null`
1621 if [ -n "$confl_p" ]; then
1622 confl_p=${confl_p%% *}
1623 echo ''
1624 echo "===>>> The dependency
for ${origin}"
1625 echo " seems to be
handled by $confl_p"
1626 echo ''
1627 d_port="$pd/`origin_from_pdb $confl_p`"
1628 fi
1629 done
doesn't substitute your alternative dependency, math/atlas-devel, for
math/atlas.
Problem #2:
You're using the -x flag incorrectly. Or portmaster isn't
implementing it properly when the port to be excluded is not actually
installed, take your pick. It's not completely fool-proof. Since you
don't have math/atlas installed, the code in portmaster's
dependency_check ():
1632 origin="${d_port#$pd/}" ;
iport=`iport_from_origin ${origin}`
1633
1634 if [ -n "$iport" ]; then
1635 check_exclude $iport || continue
1636 else
1637 check_exclude $origin || continue
1638 fi
gives origin="math/atlas", and then uses:
385 iport_from_origin () {
386 local dir
387 dir=`grep -l "@comment ORIGIN:${1}$" $pdb/*/+CONTENTS`
388
389 # It should not happen that more than one port meets this
390 # requirement, but it can if the pkg data is corrupted.
391 dir="${dir%%/+CONTENTS*}"
392 echo ${dir#$pdb/}
393 }
to find that iport="" , so "check_exclude math/atlas" is called. Then,
in accordance with:
1483 check_exclude () {
1484 [ -n "$PM_EXCL" ] || return 0
1485
1486 local pat
1487
1488 for pat in $PM_EXCL; do
1489 case "$1" in
1490 *${pat}*)
1491 if [ -n "$PM_VERBOSE" ]; then
1492 echo "===>>> Skipping $1"
1493 echo " because it matches the
pattern: *${pat}*"
1494 echo ''
1495 fi
1496 return 1 ;;
1497 esac
1498 done
1499
1500 return 0
1501 }
check_exclude tries to match your patterns in PM_EXCL against
"math/atlas". But you've got "atlas-" in PM_EXCL (after portmaster's
globstrip removed the trailing asterisk, negating your attempt protect
it with quotes), which won't match because of the hyphen. It would
have matched if math/atlas were actually installed, in which case
iport="atlas-3.8.3_1,1" and portmaster would have compared iport with
*atlas-*. You must use a port origin glob with the -x flag when the
port that you wish to exclude isn't installed.
Problem #3:
The +IGNOREME checks in portmaster aren't properly implemented for
this case, so they fail to prevent math/atlas from being built. To
see this, Continue along in dependency_check (). Here, since iport="",
dependency_check () next calls "check_interactive math/atlas":
1459 check_interactive () {
1460 [ -n "$INTERACTIVE_UPDATE" ] || return 0
1461
1462 local update_to
1463
1464 [ -n "$2" ] && update_to=" to $2"
1465
1466 case "$INTERACTIVE_YES" in *:${1}:*) return 0 ;; esac
1467 case "$INTERACTIVE_NO" in *:${1}:*) return 1 ;; esac
1468
1469 if [ -e "$pdb/$1/+IGNOREME" ]; then
1470 echo ''
1471 echo "===>>> +IGNOREME file is present for $1"
1472 fi
1473
1474 echo '' ; echo -n "===>>> Update ${1}${update_to}? [y] "
1475 local answer ; read answer
1476 case "$answer" in
1477 [nN]*) INTERACTIVE_NO="${INTERACTIVE_NO}${1}:" ; return 1 ;;
1478 *) INTERACTIVE_YES="${INTERACTIVE_YES}${1}:" ;;
1479 esac
1480 return 0
1481 }
This subroutine can only fail if you've specified an interactive
update and you decline to update math/atlas. If that case,
portmaster will start to build math/py-numpy, and if math/atlas-devel
is installed with the needed static libraries, then math/py-numpy
should build normally. Apparently this didn't happen during your
attempts.
The +IGNOREME check is useless here because the subroutine checks only
for /var/db/pkg/math/atlas/+IGNOREME, not the usual
/var/db/pkg/atlas-3.8.3_1,1/+IGNOREME.
Returning to dependency_check (), "update_port math/atlas" is called
next, which then recursively calls "portmaster math/atlas" with many
of your original flags. This jumps to
1943 # Figure out what we are going to be working on
Shortly afterwards, portdir is found to be ="math/atlas", and
2020 [ -z "$upg_port" -a -z "$REPLACE_ORIGIN" ] &&
2021 upg_port=`iport_from_origin ${portdir}`
gives upg_port="", as before when computing iport in dependency_check (). Hence
2023 if [ -e "$pdb/$upg_port/+IGNOREME" ]; then
is false, and another +IGNOREME check is bypassed. math/atlas is then built.
So what can you do while these problems are being fixed? You could either:
1) Install math/atlas-devel, and use -x math/atlas on the portmaster
command line; or
2) Install math/atlas-devel, and use only interactive portmaster
builds in which you decline to build math/atlas; or
3) Install math/atlas-devel, and patch the math/atlas Makefile:
--- ports/math/atlas/Makefile.orig 2009-11-09 01:19:21.000000000 -0500
+++ ports/math/atlas/Makefile 2009-11-09 01:15:55.000000000 -0500
@@ -22,6 +22,7 @@
USE_GMAKE= yes
WRKSRC= ${WRKDIR}/ATLAS
USE_LDCONFIG= yes
+CONFLICTS= atlas-devel-[0-9]*
.include <bsd.port.pre.mk>
; or
4) Patch the math/py-numpy Makefile:
--- ports/math/py-numpy/Makefile.orig 2009-11-08 20:49:13.000000000 -0500
+++ ports/math/py-numpy/Makefile 2009-11-08 20:49:30.000000000 -0500
@@ -35,7 +35,7 @@
.include <bsd.port.pre.mk>
.if defined(WITH_ATLAS)
-LIB_DEPENDS+= atlas.2:${PORTSDIR}/math/atlas
+LIB_DEPENDS+= atlas.2:${PORTSDIR}/math/atlas-devel
.if !exists(${LOCALBASE}/lib/libalapack.a)
IGNORE= atlas needs to be built with WITH_STATICLIB for numpy
to function properly
.endif
; or
5) Use portupgrade for science/gnudatalanguage and math/py-numpy,
instead of portmaster, with ALT_PKGDEP set to substitute
math/atlas-devel for math/atlas in pkgtools.conf; or
6) Put an +IGNOREME in directories for science/gnudatalanguage and
math/py-numpy as well as math/atlas, and update these ports by hand,
with make -C ... deinstall clean install ... ; or
7) (Ugly hack) Install math/atlas-devel, and then math/py-numpy, by
hand. Thereafter, before each invocation of portmaster involving
math/py-numpy, edit that port's registration information, switching
it's math/atlas-related entries in +CONTENTS to math/atlas-devel.
b.
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