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Bug 55386 - Cleaning dev-lang/R dependencies
Summary: Cleaning dev-lang/R dependencies
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: New packages (show other bugs)
Hardware: AMD64 Linux
: High normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2004-06-27 23:08 UTC by Jeff Hubbs
Modified: 2004-10-10 12:01 UTC (History)
2 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments

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Description Jeff Hubbs 2004-06-27 23:08:32 UTC
emerge of R ends as follows:

   ztrmv:
   ztrsm:
   ztrsv:
gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H  -fPIC  -O3 -pipe -fomit-frame-pointer -funroll-loops -c cmplxblas.c -o cmplxblas.lo
gcc -shared -L/usr/local/lib  -o libRlapack.so dlapack0.lo dlapack1.lo dlapack2.lo dlapack3.lo cmplx.lo  cmplxblas.lo  -lf2c -lm
/usr/lib/gcc/x86_64-pc-linux-gnu/3.4.0/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib/gcc/x86_64-pc-linux-gnu/3.4.0/../../../libf2c.a(z_div.o): relocation R_X86_64_32 can not be used when making a shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-pc-linux-gnu/3.4.0/../../../libf2c.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[4]: *** [libRlapack.so] Error 1
make[4]: Leaving directory `/var/tmp/portage/R-1.9.0-r1/work/R-1.9.0/src/modules/lapack'
make[3]: *** [R] Error 2
make[3]: Leaving directory `/var/tmp/portage/R-1.9.0-r1/work/R-1.9.0/src/modules/lapack'
make[2]: *** [R] Error 1
make[2]: Leaving directory `/var/tmp/portage/R-1.9.0-r1/work/R-1.9.0/src/modules'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/var/tmp/portage/R-1.9.0-r1/work/R-1.9.0/src'
make: *** [R] Error 1

!!! ERROR: dev-lang/R-1.9.0-r1 failed.
!!! Function src_compile, Line 89, Exitcode 2
!!! (no error message)
!!! If you need support, post the topmost build error, NOT this status message.



Reproducible: Always
Steps to Reproduce:
1.emerge R
2.
3.

Actual Results:  
emerge R ends as follows:


   ztrmv:
   ztrsm:
   ztrsv:
gcc -I. -I../../../src/include -I../../../src/include -I/usr/local/include
-DHAVE_CONFIG_H  -fPIC  -O3 -pipe -fomit-frame-pointer -funroll-loops -c
cmplxblas.c -o cmplxblas.lo
gcc -shared -L/usr/local/lib  -o libRlapack.so dlapack0.lo dlapack1.lo
dlapack2.lo dlapack3.lo cmplx.lo  cmplxblas.lo  -lf2c -lm
/usr/lib/gcc/x86_64-pc-linux-gnu/3.4.0/../../../../x86_64-pc-linux-gnu/bin/ld:
/usr/lib/gcc/x86_64-pc-linux-gnu/3.4.0/../../../libf2c.a(z_div.o): relocation
R_X86_64_32 can not be used when making a shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-pc-linux-gnu/3.4.0/../../../libf2c.a: could not read
symbols: Bad value
collect2: ld returned 1 exit status
make[4]: *** [libRlapack.so] Error 1
make[4]: Leaving directory
`/var/tmp/portage/R-1.9.0-r1/work/R-1.9.0/src/modules/lapack'
make[3]: *** [R] Error 2
make[3]: Leaving directory
`/var/tmp/portage/R-1.9.0-r1/work/R-1.9.0/src/modules/lapack'
make[2]: *** [R] Error 1
make[2]: Leaving directory `/var/tmp/portage/R-1.9.0-r1/work/R-1.9.0/src/modules'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/var/tmp/portage/R-1.9.0-r1/work/R-1.9.0/src'
make: *** [R] Error 1

!!! ERROR: dev-lang/R-1.9.0-r1 failed.
!!! Function src_compile, Line 89, Exitcode 2
!!! (no error message)
!!! If you need support, post the topmost build error, NOT this status message.

Expected Results:  
Something a little less explosive, like finish emerging

# emerge info
Portage 2.0.51_pre10 (gcc34-amd64-2004.1, gcc-3.4.0, glibc-2.3.4.20040605-r0, 2.6.5)
=================================================================
System uname: 2.6.5 x86_64 4
Gentoo Base System version 1.4.16
Autoconf: sys-devel/autoconf-2.59-r4
Automake: sys-devel/automake-1.8.5-r1
Binutils: sys-devel/binutils-2.15.90.0.1.1-r3
ACCEPT_KEYWORDS="amd64 ~amd64"
AUTOCLEAN="yes"
CFLAGS="-O3 -pipe -fomit-frame-pointer -funroll-loops"
CHOST="x86_64-pc-linux-gnu"
COMPILER="gcc3"
CONFIG_PROTECT="/etc /usr/X11R6/lib/X11/xkb /usr/kde/2/share/config
/usr/kde/3.2/share/config /usr/kde/3/share/config /usr/lib/mozilla/defaults/pref
/usr/share/config /usr/share/texmf/dvipdfm/config/
/usr/share/texmf/dvips/config/ /usr/share/texmf/tex/generic/config/
/usr/share/texmf/tex/platex/config/ /usr/share/texmf/xdvi/ /var/qmail/control"
CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/env.d"
CXXFLAGS="-O3 -pipe -fomit-frame-pointer -funroll-loops"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoaddcvs ccache sandbox"
GENTOO_MIRRORS="http://gentoo.chem.wisc.edu/gentoo/"
MAKEOPTS="-j2"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY=""
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X alsa amd64 apm arts avi berkdb cdr crypt cups dvd dvdr encode esd
foomaticdb gdbm gif gnome gpm gtk gtk2 imagemagick imlib jpeg kde ldap libg++
libwww mikmod motif mozilla mpeg mysql ncurses nls odbc oggvorbis opengl oss pam
pcmcia pda pdflib perl png pnp postgres python qt quicktime readline ruby samba
sdl slang spell ssl tcpd tetex tiff truetype unicode usb wxwindows xinerama xml2
xmms xv xvid yahoo zlib"

# gcc --version
gcc (GCC) 3.4.0 20040601 (Gentoo Linux 3.4.0-r6, ssp-3.4-2, pie-8.7.6.3)

NOTE:  R is a dependency for app-misc/grass-5.0.3, which is why I'm emerging R
in the first place.
Comment 1 merwan kashouty 2004-06-28 08:30:40 UTC
libf2c needs to be compiled with -fPIC 
Comment 2 Patrick Kursawe (RETIRED) gentoo-dev 2004-06-30 12:00:37 UTC
Perhaps the guy who added libf2c to ~amd64 can comment on this bug?
Comment 3 Danny van Dyk (RETIRED) gentoo-dev 2004-06-30 12:19:59 UTC
-fPIC on amd64 is our buisness ;-) I will have a look now.
Comment 4 Danny van Dyk (RETIRED) gentoo-dev 2004-06-30 15:32:01 UTC
1) dev-libs/libf2c produced only static library w/o PIC. Fixed, libf2c-20021004-r1
   produces now a static library and a shared object.

2) dev-lang/R depends on f2c in case that is built with USE="-ifc -f77". Fixed for
   amd64. Reassigning to sci@g.o

Jeff: sync and remerge libf2c to test and report please.

sci-herd: Can someone try emerging f2c and libf2c-20021004-r1 on x86, sparc and ppc ? If they work on these platform, we can tidy up the dependencies a bit.
Comment 5 George Shapovalov (RETIRED) gentoo-dev 2004-06-30 18:30:51 UTC
Tested in 32 bit chroot
aldar work # uname -a
Linux aldar 2.6.5-gentoo-r1 #2 Sun May 30 19:56:37 MDT 2004 i686 AMD Athlon(tm) 64 Processor 3200+ AuthenticAMD GNU/Linux

Compiles (both libf2c and f2c) and converts fine (tested on some blas files).

BTW, you can too setup 32bit scroot, which is essentially a standard x86 (i686 as reported above) for just such purposes ;).
http://www.gentoo.org/proj/en/base/amd64/technotes.xml?part=2&chap=4

George
Comment 6 Jeff Hubbs 2004-06-30 20:04:40 UTC
I can report that libf2c-20021004-r1 appears to build just fine and so does R.
Comment 7 Danny van Dyk (RETIRED) gentoo-dev 2004-07-02 02:05:25 UTC
libf2c works on sparc as well... waiting for sparc to test virtual/blas & virtual lapack. In case they work, i will remove the atlas USE flag from dev-lang/R-1.9.0-r1 and set the dependencies on blas / lapack.

George: What do you think about going stable for 1.9.0-r1 ? I wanted to do it before this bug popped up and i think that this is only a minor one...
Comment 8 Patrick Kursawe (RETIRED) gentoo-dev 2004-07-28 07:27:33 UTC
Danny, you asked George but since he didn't reply so far and there are (as far as I can see) no other bugs open for R 1.9, I'd say just go ahead.
Comment 9 George Shapovalov (RETIRED) gentoo-dev 2004-07-28 15:07:01 UTC
Oops, sorry, slipped on this one (its pretty terse time for me now, setting up interviews and trying to organize my graduation..). Yes, I think you can go ahead on R as far as I am concerned. You should know the situation with R better than me at this point :).

George
Comment 10 Ferris McCormick (RETIRED) gentoo-dev 2004-08-05 15:53:00 UTC
On sparc, R-1.9.0-r1 builds with and without:
USE=f2c
USE=blas (== blas-atlas-3.6.0)
USE=gnome
(Actually, the USEs were USE="" [which gets "+tcltk -blas -gnome -f2c..." for me]
  USE="f2c"          ["+f2c -gnome -blas ..." ]
  USE="blas gnome"  [and so, gets "+tcltk +blas +gnome -f2c ..." ]

The second was built with (default) gcc-3-3-3, glibc-2.3.2-r9;
The others were built with hardened gcc-3,3,4-r1, glibc-2.3.3.20040420 (but the
gcc hardened version was built with its silly-for-sparc 'filter-flags -O?' DISabled)

In each case, the build, install went exactly as expected, and the resulting R can
run all of its demo() examples to make impressive graphs, alphabets, or whatever.
As a quick check of some of what is being checked here, I verified from 'ldd R.bin'
that the "USE=blas ..." build does in fact require:
libblas.so.0 => /usr/lib/libblas.so.0
libatlas.so.0 => /usr/lib/libatlas.so.0

In any event, the specific problem mentioned here concerning "USE=f2c" is not
currently a problem on sparc, and there were no errors in the build not in the
demos.

I don't know anything about R, so I can't test it further without reading its documentation.  But it seems OK on
sparc with any reasonable set of USE choices, so I am taking sparc off the CC
list.  I am adding myself in case this bug is asking for something I have missed.

Regards,
Ferris
Comment 11 Danny van Dyk (RETIRED) gentoo-dev 2004-08-06 03:16:35 UTC
Ok, dev-libs/libf2c and dev-lang/f2c are stable on amd64, x86 and ppc now.
Ferris: Could you mark those stable on sparc too ?

However, i can't mark app-sci/blas-atlas stable on x86 and ppc, cause it depends on >=sys-devel/libtool-1.5. We have to wait until that get's marked stable on x86, ppc and sparc.
Comment 12 Ferris McCormick (RETIRED) gentoo-dev 2004-08-06 03:48:45 UTC
I'll rebuild f2c+f2clib & do a quick check.  Then, yes, I'll mark them stable for sparc.
Comment 13 Ferris McCormick (RETIRED) gentoo-dev 2004-08-06 05:28:45 UTC
dev-libs/libf2c-20021004-r1, dev-lang/f2c-20030320 are now marked stable for sparc.
Comment 14 Pieter Van den Abeele (RETIRED) gentoo-dev 2004-08-19 18:43:36 UTC
removing ppc from cc
Comment 15 Danny van Dyk (RETIRED) gentoo-dev 2004-10-10 12:01:32 UTC
FIXED. blas-atlas is finally stable on ppc and x86.
R-1.8.1 is removed, cause R-1.9.0-r1 replaces it.