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Bug#: 166521
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Status: RESOLVED
Resolution: FIXED
Assigned To: AMD64 Project <amd64@gentoo.org>
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Reporter: Sylvain Raybaud <sraybaud@crans.org>
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Filename Description Type Creator Created Size Actions
sci-mathematics:scilab-4.1:20070212-152803.log compile log text/plain Sylvain Raybaud 2007-02-12 22:02 0000 116.61 KB Details
sci-mathematics:scilab-4.1:20070214-200458.log another log text/plain Scott Short 2007-02-14 20:24 0000 122.65 KB Details
scilab-4.1-java-pic.patch patch to fix screwed up scilab makefile text/plain Markus Dittrich 2007-03-11 18:38 0000 1.57 KB Details
Create a New Attachment (proposed patch, testcase, etc.) View All

Bug 166521 depends on: Show dependency tree
Bug 166521 blocks:
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Additional Comments: (this is where you put emerge --info)


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Description:   Opened: 2007-02-12 16:32 0000 
upgrade from 4.0 to 4.1 failed during linking :

Creation of ../../bin/libjavasci.so
linking
/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.1/../../../../x86_64-pc-linux-gnu/bin/ld:
../../routines/default/FTables.o: relocation R_X86_64_32 against `a local
symbol' can not be used when making a shared object; recompile with -fPIC
../../routines/default/FTables.o: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[1]: *** [../../bin/libjavasci.so] Error 1

USE="gtk java ocaml -Xaw3d -debug -tk"

Reproducible: Always

Steps to Reproduce:
emerge -auv scilab




I have been told by emerge to include the following information :

GENTOO_VM=sun-jdk-1.6  CLASSPATH="" JAVA_HOME="/opt/sun-jdk-1.6.0"
JAVACFLAGS="-source 1.4 -target 1.4" COMPILER=""

sylvain@wonderland ~/system $ emerge --info
Portage 2.1.2-r9 (!/usr/portage/profiles/default-linux/amd64/2006.1/desktop/,
gcc-4.1.1, glibc-2.5-r0, 2.6.18-gentoo-r3 x86_64)
=================================================================
System uname: 2.6.18-gentoo-r3 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor
4200+
Gentoo Base System release 1.12.9
Timestamp of tree: Sun, 11 Feb 2007 22:20:01 +0000
dev-java/java-config: 1.3.7, 2.0.31-r3
dev-lang/python:     2.4.4
dev-python/pycrypto: 2.0.1-r5
sys-apps/sandbox:    1.2.18.1
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:  2.17
sys-devel/gcc-config: 1.3.13-r3
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.20
ACCEPT_KEYWORDS="amd64 ~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/env.d/java/ /etc/gconf
/etc/java-config/vms/ /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c"
CXXFLAGS="-march=athlon64 -O2 -pipe"
DISTDIR="/var/portage/distfiles"
FEATURES="autoconfig ccache confcache distlocks metadat-transfer
metadata-transfer parallel-fetch sandbox sfperms strict userfetch userpriv
usersandbox"
GENTOO_MIRRORS="ftp://gentoo.imj.fr/pub/gentoo
http://cudlug.cudenver.edu/gentoo http://gentoo.modulix.net/gentoo
http://ftp.club-internet.fr/pub/mirrors/gentoo http://distfiles.gentoo.org
http://www.ibiblio.org/pub/Linux/distributions/gentoo"
LINGUAS="en fr en_GB"
MAKEOPTS="-j3"
PKGDIR="/var/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"
PORTAGE_TMPDIR="/dev/shm/portage"
PORTDIR="/var/portage"
PORTDIR_OVERLAY="/var/local/portage"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="X a52 aac aalib alsa amd64 arts bash-completion berkdb bitmap-fonts bzip2
cairo cddb cdr cli cracklib crypt dbus dlloader dri dvd dvdr dvdread eds emboss
encode esd fam firefox flac fortran gdbm gif gpm gstreamer gtk gtk2 hal iconv
ieee1394 ipv6 isdnlog java jpeg kde kdeenablefinal ldap libcaca libg++
lm_sensors mad mikmod mp3 mpeg ncurses nls nptl nptlonly nvidia ogg opengl oss
pam pcre pdf perl png ppds pppd python qt3 qt4 quicktime readline reflection
samba sdl session socks5 spell spl ssl svg tcpd tetex theora truetype
truetype-fonts type1-fonts udev unicode vorbis xml xorg xscreensaver xv zlib"
ELIBC="glibc" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LINGUAS="en fr
en_GB" USERLAND="GNU" VIDEO_CARDS="nvidia nv"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS,
PORTAGE_RSYNC_EXTRA_OPTS

It's the first time I fill a bugrepport so please tell me if I made something
wrong or if I didn't provide enough pieces of information.

------- Comment #1 From Simon Stelling (RETIRED) 2007-02-12 19:29:54 0000 ------- 
> sylvain@wonderland ~/system $ emerge --info
> Portage 2.1.2-r9 (!/usr/portage/profiles/default-linux/amd64/2006.1/desktop/,

Please reset your profile link. It should point to a directory within PORTDIR,
i.e. /var/portage/profiles/default-linux/amd64/2006.1/desktop in your case.

------- Comment #2 From James Brown 2007-02-12 20:12:39 0000 ------- 
Same build error here. I'm pretty sure this is a hardened gcc-related error.
Isn't gcc hardened by default on amd64?

(I will post my emerge --info if you want it, but I don't think it's relevant)

------- Comment #3 From Simon Stelling (RETIRED) 2007-02-12 21:11:21 0000 ------- 
(In reply to comment #2)
> Same build error here. I'm pretty sure this is a hardened gcc-related error.
> Isn't gcc hardened by default on amd64?

Nope, hardened is not standard. But I can't reproduce the problem here (using a
normal toolchain), even though I'm using the same USE flags. But it doesn't
look like a typical hardened problem to me. 

@hardened: could you give it a try and see whether it works/fails for you?

------- Comment #4 From Sylvain Raybaud 2007-02-12 21:52:26 0000 ------- 
(In reply to comment #1)
> > sylvain@wonderland ~/system $ emerge --info
> > Portage 2.1.2-r9 (!/usr/portage/profiles/default-linux/amd64/2006.1/desktop/,
> 
> Please reset your profile link. It should point to a directory within PORTDIR,
> i.e. /var/portage/profiles/default-linux/amd64/2006.1/desktop in your case.
> 

done, but scilab still fails to compile, with the exact same problem.
thanks for the tip anyway.

------- Comment #5 From Kevin F. Quinn (RETIRED) 2007-02-12 21:54:54 0000 ------- 
(In reply to comment #0)
> /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.1/../../../../x86_64-pc-linux-gnu/bin/ld:
> ../../routines/default/FTables.o: relocation R_X86_64_32 against `a local
> symbol' can not be used when making a shared object; recompile with -fPIC
> ../../routines/default/FTables.o: could not read symbols: Bad value

My amd64 box is down at the moment, so can't try - but since the compiler in
use by the reporter is 4.1.1, then it's unlikely to be hardened (I haven't put
it in the tree yet!).

The error message is complaining about non-PIC code in shared libraries -
x86-64 simply does not support non-PIC code in shared libraries; it doesn't do
TEXTRELs.  Doesn't need to - you have rip-relative addressing which really goes
a long way to removing one of the biggest limitations of x86.

Check the compilation line for FTables.o - if it doesn't contain '-fPIC' then
clearly it's a makefile issue.  Attaching a complete build log would be useful.

One other possibility I've come across recently, is local-exec TLS; if the code
is using thread data with the default TLS model (i.e. local-exec), it'll cause
this sort of error message.  Had a quick look at the code though, and couldn't
see anything like this.

------- Comment #6 From Sylvain Raybaud 2007-02-12 22:02:36 0000 ------- 
Created an attachment (id=110003) [edit]
compile log

this is the log file generated by portage

------- Comment #7 From Sylvain Raybaud 2007-02-12 22:05:27 0000 ------- 
(In reply to comment #5)
> (In reply to comment #0)
> > /usr/lib/gcc/x86_64-pc-linux-gnu/4.1.1/../../../../x86_64-pc-linux-gnu/bin/ld:
> > ../../routines/default/FTables.o: relocation R_X86_64_32 against `a local
> > symbol' can not be used when making a shared object; recompile with -fPIC
> > ../../routines/default/FTables.o: could not read symbols: Bad value
> 
> My amd64 box is down at the moment, so can't try - but since the compiler in
> use by the reporter is 4.1.1, then it's unlikely to be hardened (I haven't put
> it in the tree yet!).

indeed it's not.

> Check the compilation line for FTables.o - if it doesn't contain '-fPIC' then
> clearly it's a makefile issue.  Attaching a complete build log would be useful.

you mean something like that ? (full log attached)

sylvain@wonderland ~ $ grep FTables
system/sci-mathematics\:scilab-4.1\:20070212-152803.log
gcc -march=athlon64 -O2 -pipe `pkg-config gtk+-2.0 --cflags`   -c -o FTables.o
FTables.c

I indeed see no fPIC here...


> 
> One other possibility I've come across recently, is local-exec TLS; if the code
> is using thread data with the default TLS model (i.e. local-exec), it'll cause
> this sort of error message.  Had a quick look at the code though, and couldn't
> see anything like this.
> 

do you know of a way to test this hypothesis ?

------- Comment #8 From solar 2007-02-12 22:33:33 0000 ------- 
This does not appear to be limited to hardened. 
Removing hardened from the CC: list.

------- Comment #9 From Kevin F. Quinn (RETIRED) 2007-02-12 23:46:46 0000 ------- 
ok; as you say, the log clearly shows the object wasn't compiled -fPIC, yet it
tried linking it into a shared library.  blubb - how does your log compare?

FWIW I get the same when building on x86 (didn't let it complete because I
didn't want to install all the dependencies - but the object is not compiled
-fPIC so will likely generate TEXTRELS when linked into the shared library).

------- Comment #10 From Scott Short 2007-02-14 20:20:59 0000 ------- 
Just trying to help with some more info - slightly different system:

 Creation of ../../bin/libjavasci.so
linking
/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.2/../../../../x86_64-pc-linux-gnu/bin/ld:
../../routines/default/FTables.o: relocation R_X86_64_32 against `a local
symbol' can not be used when making a shared object; recompile with -fPIC
../../routines/default/FTables.o: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[1]: *** [../../bin/libjavasci.so] Error 1
make[1]: Leaving directory
`/var/tmp/portage/sci-mathematics/scilab-4.1/work/scilab-4.1/routines/Javasci'
make: *** [scilex-lib] Error 2

!!! ERROR: sci-mathematics/scilab-4.1 failed.
Call stack:
  ebuild.sh, line 1614:   Called dyn_compile
  ebuild.sh, line 971:   Called qa_call 'src_compile'
  environment, line 5123:   Called src_compile
  scilab-4.1.ebuild, line 108:   Called die

!!! emake failed
!!! If you need support, post the topmost build error, and the call stack if
relevant.
!!! A complete build log is located at
'/var/log/portage/sci-mathematics:scilab-4.1:20070214-200458.log'.

!!! When you file a bug report, please include the following information:
GENTOO_VM=blackdown-jdk-1.4.2  CLASSPATH=""
JAVA_HOME="/opt/blackdown-jdk-1.4.2.03"
JAVACFLAGS="-source 1.4 -target 1.4" COMPILER=""
and of course, the output of emerge --info

Portage 2.1.2-r9 (default-linux/amd64/2006.1, gcc-4.1.2, glibc-2.5-r0,
2.6.20-gentoo x86_64)
=================================================================
System uname: 2.6.20-gentoo x86_64 AMD Turion(tm) 64 Mobile Technology ML-34
Gentoo Base System version 1.12.9
Timestamp of tree: Wed, 14 Feb 2007 16:28:01 +0000
ccache version 2.4 [enabled]
dev-java/java-config: 1.3.7, 2.0.31-r3
dev-lang/python:     2.4.4
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     2.4-r6
sys-apps/sandbox:    1.2.18.1
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:  2.17
sys-devel/gcc-config: 1.3.14
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.20
ACCEPT_KEYWORDS="amd64 ~amd64"
AUTOCLEAN="yes"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=k8 -O2 -msse3 -pipe -fomit-frame-pointer"
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/java-config/vms/ /etc/revdep-rebuild /etc/terminfo"
CXXFLAGS="-march=k8 -O2 -msse3 -pipe -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig ccache distlocks fixpackages metadata-transfer sandbox
sfperms strict"
GENTOO_MIRRORS="http://node0.gensho http://www.gtlib.gatech.edu/pub/gentoo"
LANG="en_US.UTF-8"
LC_ALL="en_US.UTF-8"
MAKEOPTS="-j5"
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"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://node0.gensho/gentoo-portage"
USE="X acpi aiglx alsa amd64 berkdb bitmap-fonts bzip2 cairo cli cracklib crypt
cups curl dbus divx dlloader dri dvd dvdr dvdread fortran gdbm gif glitz gmedia
gnutls gpm gtk gtkhtml iconv ipv6 isdnlog java jpeg libg++ logrotate
mailwrapper mbox midi mikmod moznoirc moznomail mp3 ncurses nls nptl nptlonly
nsplugin objc objc++ offensive opengl oss pam pcre pdf perl png ppds pppd
python quicktime readline realmedia reflection ruby session spell spl ssl tcpd
tiff truetype truetype-fonts type1-fonts unicode usb wmp xorg zlib"
ALSA_CARDS="atiixp" 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="evdev
keyboard mouse synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633
glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU"
VIDEO_CARDS="radeon fglrx"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LDFLAGS, LINGUAS,
PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY

------- Comment #11 From Scott Short 2007-02-14 20:24:27 0000 ------- 
Created an attachment (id=110203) [edit]
another log

------- Comment #12 From emanuele 2007-03-08 17:08:25 0000 ------- 
same issue here.. any news?
thanks

------- Comment #13 From Markus Dittrich 2007-03-11 18:38:10 0000 ------- 
Created an attachment (id=112986) [edit]
patch to fix screwed up scilab makefile

This whole mess is likely due to a screwed up scilab makefile.
The object file FTables.o is not supposed to be linked into
libjavasci.so or any other *.so for that matter (since it is non PIC code).
I've attached a patch that might fix this. Please REPLACE the existing
scilab-4.0-java-pic.patch with it and give it a spin. Unfortunately, I don't
have an amd64 box to test it myself.

BTW: If you guys are compiling fortran code (such as scilab) you will have
to explicitly set FFLAGS otherwise no compiler flags are being passed
to gfortran. If you generally use gfortran, as opposed to, e.g., ifc/ifort, the
easiest
solution would be to just put  

FFLAGS="${CFLAGS}"

into your make.conf.

Thanks,
Markus

------- Comment #14 From emanuele 2007-03-19 14:14:55 0000 ------- 
Patch work fine for me.
thanks

(In reply to comment #13)
> Created an attachment (id=112986) [edit]
> patch to fix screwed up scilab makefile
> 
> This whole mess is likely due to a screwed up scilab makefile.
> The object file FTables.o is not supposed to be linked into
> libjavasci.so or any other *.so for that matter (since it is non PIC code).
> I've attached a patch that might fix this. Please REPLACE the existing
> scilab-4.0-java-pic.patch with it and give it a spin. Unfortunately, I don't
> have an amd64 box to test it myself.
> 
> BTW: If you guys are compiling fortran code (such as scilab) you will have
> to explicitly set FFLAGS otherwise no compiler flags are being passed
> to gfortran. If you generally use gfortran, as opposed to, e.g., ifc/ifort, the
> easiest
> solution would be to just put  
> 
> FFLAGS="${CFLAGS}"
> 
> into your make.conf.
> 
> Thanks,
> Markus
>

------- Comment #15 From Markus Dittrich 2007-03-20 13:13:37 0000 ------- 
Thanks for testing!

@amd64: I've just committed this patch to cvs and from my point
                of view this bug can be closed.

Thanks,
Markus

------- Comment #16 From Simon Stelling (RETIRED) 2007-03-24 09:57:27 0000 ------- 
cool, thanks
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