Bugzilla Bug 179700

The build process for AMD64 creates a lib64 directory under the working
directory, which is not mentioned in the ebuild, causing a build failure (for
amd64, but not x86).  Line 59 of the ebuid says 'LDFLAGS="-L${WORKDIR}/lib" \'.
 If I replace this with 'LDFLAGS="-L${WORKDIR}/lib -L${WORKDIR}/lib64" \' then
I can get it to build successfully (I don't know the proper way to do this).



Reproducible: Always

Steps to Reproduce:
1. edit /usr/portage/sci-mathematics/Macaulay2/Macaulay2-0.9.95-r1.ebuild and
add ~amd64 to KEYWORDS
2. emerge Macaulay2




You have to add the ~amd64 keyword to the ebuild to get it to attempt
compiling.

Portage 2.1.2.7 (default-linux/amd64/2007.0/desktop, gcc-4.1.2, glibc-2.5-r2,
2.6.20.6 x86_64)
=================================================================
System uname: 2.6.20.6 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor 4600+
Gentoo Base System release 1.12.9
Timestamp of tree: Thu, 24 May 2007 16:30:09 +0000
dev-lang/python:     2.4.4-r4
dev-python/pycrypto: 2.0.1-r5
sys-apps/sandbox:    1.2.17
sys-devel/autoconf:  2.13, 2.61
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10
sys-devel/binutils:  2.16.1-r3
sys-devel/gcc-config: 1.3.16
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.17-r2
ACCEPT_KEYWORDS="amd64"
AUTOCLEAN="yes"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=athlon64 -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config
/usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config"
CONFIG_PROTECT_MASK="/etc/env.d /etc/gconf /etc/terminfo /etc/texmf/web2c"
CXXFLAGS="-march=athlon64 -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="http://distfiles.gentoo.org
http://distro.ibiblio.org/pub/linux/distributions/gentoo"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress
--force --whole-file --delete --delete-after --stats --timeout=180
--exclude=/distfiles --exclude=/local --exclude=/packages
--filter=H_**/files/digest-*"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X acl acpi alsa amd64 arts berkdb bitmap-fonts cairo cdr cli cracklib
crypt cups dbus dri dvd dvdr dvdread eds emboss encode esd evo fam firefox
fortran gcj gdbm gif gnome gpm gstreamer gtk gtk2 hal iconv ipv6 isdnlog jpeg
kerberos ldap libg++ mad midi mikmod mmx mp3 mpeg mudflap ncurses nls nptl
nptlonly ogg opengl openmp pam pcre pdf png pppd python qt3support quicktime
readline reflection sdl session spell spl sse sse2 ssl svg tcpd theora threads
tiff truetype truetype-fonts type1-fonts unicode vorbis xml xorg xv zlib"
ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x
ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3
trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw
asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa
lfloat linear meter mulaw multi null plug rate route share shm softvol"
ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux"
LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses
text" USERLAND="GNU" VIDEO_CARDS="radeon vesa vmware fbdev"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS,
LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS,
PORTDIR_OVERLAY

Hi,

I just uploaded a small fix that should take care of this.
Please wait an hour or so and give it spin and report back.

Thanks,
Markus

(In reply to comment #2)
> Hi,
> 
> I just uploaded a small fix that should take care of this.
> Please wait an hour or so and give it spin and report back.
> 
> Thanks,
> Markus
> 

Thanks!  I'm getting the following error later in the ebuild:

**************************************************************************
checking whether ntl library is installed... yes
checking whether factory library is installed... yes
checking whether factory library, profiling version, is installed (-lcf-pg)...
no
checking whether (and where) the libfac library is installed (-lfac)... no
checking whether libfac library, profiling version, is installed (-lfac-pg)...
no
configure: error: missing library: libfac

!!! ERROR: sci-mathematics/Macaulay2-0.9.95-r1 failed.
Call stack:
  ebuild.sh, line 1615:   Called dyn_compile
  ebuild.sh, line 972:   Called qa_call 'src_compile'
  ebuild.sh, line 44:   Called src_compile
  Macaulay2-0.9.95-r1.ebuild, line 62:   Called die

!!! failed to configure Macaulay
!!! If you need support, post the topmost build error, and the call stack if
relevant.
!!! A complete build log is located at
'/var/tmp/portage/sci-mathematics/Macaulay2-0.9.95-r1/temp/build.log'.
*******************************************************************************

In comment #1 you mention that you were able to build it successfully.
Do you mean that it built before but doesn't any more after the fix?
I any case, can you please post the config.log containing the failing
check for libfac?

Thanks,
Markus

Created an attachment (id=120659) [details]
Macaulay2 build log

(In reply to comment #4)
> In comment #1 you mention that you were able to build it successfully.
> Do you mean that it built before but doesn't any more after the fix?

It built when I used 'LDFLAGS="-L${WORKDIR}/lib -L${WORKDIR}/lib64" \' instead
of 'LDFLAGS="-L${WORKDIR}/lib" \'.  With your fix, the error in the building
process occurs later.  Before, it happened near the beginning of the build
process.  Anyway, I removed the work directory in /var/tmp/portage and saw some
errors about "unterminated #ifndef", which disappear if I just emerge again, so
mayebe it's a gcc error (though I'm using stable gcc).

> I any case, can you please post the config.log containing the failing
> check for libfac?
> 

config.log for libfac looks clean, but here it is:

/var/tmp/portage/sci-mathematics/Macaulay2-0.9.95-r1/work/libfac/config.log
*********************************************************
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

configure:659: checking for c++
configure:691: checking whether the C++ compiler (c++ -march=athlon64 -O2 -pipe
-L. -L${exec_prefix}/lib ) works
configure:707: c++ -o conftest -march=athlon64 -O2 -pipe -I./factor
-I${prefix}/include
-I/var/tmp/portage/sci-mathematics/Macaulay2-0.9.95-r1/work/include -L.
-L${exec_prefix}/lib  conftest.C  1>&5
configure:733: checking whether the C++ compiler (c++ -march=athlon64 -O2 -pipe
-L. -L${exec_prefix}/lib ) is a cross-compiler
configure:738: checking whether we are using GNU C++
configure:747: c++ -E conftest.C
configure:766: checking whether c++ accepts -g
configure:798: checking how to run the C++ preprocessor
configure:816: c++ -E -I./factor -I${prefix}/include
-I/var/tmp/portage/sci-mathematics/Macaulay2-0.9.95-r1/work/include conftest.C
>/dev/null 2>conftest.out
configure:842: checking whether make sets ${MAKE}
configure:871: checking for ranlib
configure:901: checking for ar
configure:934: checking for factory.h
configure:944: c++ -E -I./factor -I${prefix}/include
-I/var/tmp/portage/sci-mathematics/Macaulay2-0.9.95-r1/work/include conftest.C
>/dev/null 2>conftest.out
***************************************

I'll attach the build log as well.

> Thanks,
> Markus
> 

Created an attachment (id=120665) [details]
ebuild cleanup

The attached patch might fix this problem since now proper portage
functions are used which should ensure that all libs are installed in
lib64. Unfortunately, I can't test it since I don't have an amd64 box.
If the build still fails please post the error and the config.log of the
configure that's failing .

Thanks,
Markus

Created an attachment (id=120669) [details]
improved cleanup patch

The previous patch didn't work properly with parallel make;
this one should.

Markus

(In reply to comment #8)
> Created an attachment (id=120669) [edit] [details]
> improved cleanup patch
> 
> The previous patch didn't work properly with parallel make;
> this one should.
> 

This works!  Thanks for all your work!  Much apprecited!  Can you add the
~amd64 keyword?

> Markus
> 

Thanks for testing! I've committed Macaulay2-0.9.95-r2 which includes
this patch an a few additional fixes. Unfortunately, I don't have an amd64
box to test and can't, therefore, mark it ~amd64.

@amd64@g.o: Could you guys please have a look at Macaulay2-0.9.95-r2
and see if we can keyword it on amd64. Thanks a lot!

cheers,
Markus 

(In reply to comment #10)
> Thanks for testing! I've committed Macaulay2-0.9.95-r2 which includes
> this patch an a few additional fixes. Unfortunately, I don't have an amd64
> box to test and can't, therefore, mark it ~amd64.
> 
> @amd64@g.o: Could you guys please have a look at Macaulay2-0.9.95-r2
> and see if we can keyword it on amd64. Thanks a lot!
> 
> cheers,
> Markus 

0.9.95-r2 builds just fine on amd64.  Thanks a million!!!

(In reply to comment #10)
> @amd64@g.o: Could you guys please have a look at Macaulay2-0.9.95-r2
> and see if we can keyword it on amd64. Thanks a lot!

sci-mathematics/Macaulay2-0.9.95-r2  USE="emacs" fails with FEATURES="test",
but without the testing phase - i.e. FEATURES="-test":

1. Emerges on AMD64.
2. No collisions.
3. Works (emacs interface too).

Portage 2.1.2.7 (default-linux/amd64/2007.0/desktop, gcc-4.1.2, glibc-2.5-r0,
2.6.20-gentoo-r8 x86_64)
=================================================================
System uname: 2.6.20-gentoo-r8 x86_64 Intel(R) Pentium(R) D CPU 3.00GHz
Gentoo Base System release 1.12.9
Timestamp of tree: Tue, 19 Jun 2007 06:20:01 +0000
ccache version 2.4 [enabled]
dev-java/java-config: 1.3.7, 2.0.32
dev-lang/python:     2.4.4-r4
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     2.4-r7
sys-apps/sandbox:    1.2.17
sys-devel/autoconf:  2.13, 2.61
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10
sys-devel/binutils:  2.16.1-r3
sys-devel/gcc-config: 1.3.16
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.17-r2
ACCEPT_KEYWORDS="amd64"
AUTOCLEAN="yes"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -march=nocona -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config
/usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/init.d
/etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/
/etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/terminfo
/etc/texmf/web2c"
CXXFLAGS="-O2 -march=nocona -pipe"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="-akv"
FEATURES="buildpkg ccache collision-protect distlocks fixpackages
metadata-transfer multilib-strict parallel-fetch sandbox sfperms strict test
userfetch userpriv usersandbox"
GENTOO_MIRRORS="ftp://mirrors1.netvisao.pt/gentoo
http://darkstar.ist.utl.pt/pub/gentoo http://distfiles.gentoo.org
http://www.ibiblio.org/pub/Linux/distributions/gentoo"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress
--force --whole-file --delete --delete-after --stats --timeout=180
--exclude=/distfiles --exclude=/local --exclude=/packages
--filter=H_**/files/digest-*"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="X acl acpi alsa amd64 apache2 arts bash-completion bitmap-fonts cairo cdr
cli cracklib crypt dbus dri dts dvd dvdr dvdread eds emboss encode evo fam
firefox flac fortran gif gpm hal iconv ipv6 isdnlog jpeg kde kdeenablefinal
kdehiddenvisibility libg++ mad midi mikmod mmx mp3 mpeg mudflap musepack
musicbrainz mysql ncurses nptl nptlonly offensive ogg opengl openmp pam pcre
pdf perl png postgres pppd python qt3 qt3support qt4 quicktime readline
reflection sdl session spell spl sse sse2 ssl svg tcpd test tiff truetype
truetype-fonts type1-fonts unicode vorbis xcomposite xml xorg xscreensaver xv
zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci
emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m
maestro3 trident usb-audio via82xx via82xx-modem ymfpci"
ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file
hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route
share shm softvol" ELIBC="glibc" INPUT_DEVICES="keyboard mouse" KERNEL="linux"
LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses
text" USERLAND="GNU" VIDEO_CARDS="i810"
Unset:  CTARGET, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS,
PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS,
PORTDIR_OVERLAY

Created an attachment (id=122553) [details]
emerge log of sci-mathematics/Macaulay2 with FEATURES="test"

Hi Tiago,

Thank you very much for testing! Unfortunately, Macaulay2's
tests are far from ideal and I've already disabled quite a few 
that fail on x86. Would you please be able to post all *.error
files from your build directory (should be in Macaulay2-0.9.95/Macaulay2/test)
so I can have a closer look. In your emerge log I only 
noticed "raw-monomial.errors" but I may have missed one.

Thanks,
Markus

Created an attachment (id=122617) [details]
raw-monomial error log

engine/raw-monomial.m2 test is the only test that fails.

Thank you!

I hope I can fix this over the weekend and will post a 
patch once it is done.

Best,
Markus

Could you please add amd64 keywords to the 0.9.95-r1 and 0.9.95-r2 ebuilds?

Could you please eleborate why this is needed?
The Macaulay2-1.0.ebuild has the ~amd64 keyword.

Thanks,
Markus

I can't get the 1.0 ebuild to compile, and I guess I don't want to have to edit
package.mask every time a new version of Macaulay2 enters portage.

Actually, I guess a better solution for me is that I create an overlay, copy
the ebuilds, and add the keywords.  No big deal.  I just assumed since you put
all that work into the 0.9.95 ebuilds, you would want the keywords in them.

Could you please file a NEW bug for 1.0 with the error message as
well as your emerge --info so I can try to fix it! 
It compiles fine for me on my opteron so amd64 should
work, at least in principle ;)

Thanks,
Markus

(In reply to comment #21)
> Could you please file a NEW bug for 1.0 with the error message as
> well as your emerge --info so I can try to fix it! 
> It compiles fine for me on my opteron so amd64 should
> work, at least in principle ;)
> 

My fault.  It compiles just fine.  I think it was just failing the testing
phase.  Thanks!

Great to hear! I haven't even started looking at all
the tests so I am not surprised that at least some of them
fail. They were pretty messed up in the 0.95 releases
as well. Since Macaulay2-1.0 works fine I will close this
one as fixed.

Thanks,
Markus