Bugzilla Bug 82498

Hi, I have a problem on ~x86 too.


>>> emerge (1 of 68) sci-biology/biopython-1.30 to /
>>> md5 src_uri ;-) biopython-1.30.tar.gz
>>> Unpacking source...
>>> Unpacking biopython-1.30.tar.gz to /var/tmp/portage/biopython-1.30/work
>>> Source unpacked.
running build
running build_py
creating build
creating build/lib.linux-i686-2.3
[cut]
i686-pc-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -march=pentium4 -mcpu=pentium4 -mmmx -msse -msse2 -msse3 -O3 -fomit-frame-pointer -funroll-loops -pipe -fPIC -IBio/Cluster -I/usr/include/python2.3 -c Bio/Cluster/cluster.c -o build/temp.linux-i686-2.3/Bio/Cluster/cluster.o
i686-pc-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -march=pentium4 -mcpu=pentium4 -mmmx -msse -msse2 -msse3 -O3 -fomit-frame-pointer -funroll-loops -pipe -fPIC -IBio/Cluster -I/usr/include/python2.3 -c Bio/Cluster/com.c -o build/temp.linux-i686-2.3/Bio/Cluster/com.o
i686-pc-linux-gnu-gcc -pthread -shared -march=pentium4 -mcpu=pentium4 -mmmx -msse -msse2 -msse3 -O3 -fomit-frame-pointer -funroll-loops -pipe build/temp.linux-i686-2.3/Bio/Cluster/clustermodule.o build/temp.linux-i686-2.3/Bio/Cluster/cluster.o build/temp.linux-i686-2.3/Bio/Cluster/ranlib.o build/temp.linux-i686-2.3/Bio/Cluster/com.o build/temp.linux-i686-2.3/Bio/Cluster/linpack.o -o build/lib.linux-i686-2.3/Bio/Cluster/cluster.so
building 'Bio.KDTree._CKDTree' extension
creating build/temp.linux-i686-2.3/Bio/KDTree
-I/usr/include/python2.3 -c Bio/KDTree/KDTree.swig.cpp -o build/temp.linux-i686-2.3/Bio/KDTree/KDTree.swig.o
unable to execute -I/usr/include/python2.3: No such file or directory
error: command '-I/usr/include/python2.3' failed with exit status 1

!!! ERROR: sci-biology/biopython-1.30 failed.
!!! Function distutils_src_compile, Line 38, Exitcode 1
!!! compilation failed
!!! If you need support, post the topmost build error, NOT this status message.

# python 
Python 2.3.5 (#1, Feb 18 2005, 20:07:19) 
[GCC 3.3.4 20040623 (Gentoo Linux 3.3.4-r1, ssp-3.3.2-2, pie-8.7.6)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> 

Portage 2.0.51-r15 (default-linux/x86/2004.0, gcc-3.3.4, glibc-2.3.4.20050125-r0, 2.4.30-pre1-bk4 i686)
=================================================================
System uname: 2.4.30-pre1-bk4 i686 Intel(R) Xeon(TM) CPU 3.06GHz
Gentoo Base System version 1.6.9
Python:              dev-lang/python-2.3.5 [2.3.5 (#1, Feb 18 2005, 20:07:19)]
dev-lang/python:     2.3.5
sys-devel/autoconf:  2.59-r6, 2.13
sys-devel/automake:  1.6.3, 1.7.9-r1, 1.5, 1.4_p6, 1.8.5-r3, 1.9.4
sys-devel/binutils:  2.15.92.0.2-r2
sys-devel/libtool:   1.5.10-r4
virtual/os-headers:  2.4.22-r1
ACCEPT_KEYWORDS="x86 ~x86"
AUTOCLEAN="yes"
CFLAGS="-march=pentium4 -mcpu=pentium4 -mmmx -msse -msse2 -msse3 -O3 -fomit-frame-pointer -funroll-loops -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config /usr/lib/X11/xkb /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/bind /var/qmail/alias /var/qmail/control"
CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/env.d"
CXXFLAGS="-march=pentium4 -mcpu=pentium4 -mmmx -msse -msse2 -msse3 -O3 -fomit-frame-pointer -funroll-loops -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoaddcvs autoconfig ccache distlocks sandbox sfperms"
GENTOO_MIRRORS="ftp://ftp.muni.cz/pub/linux/gentoo/ http://gentoo.mirror.icd.hu/ http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ http://gd.tuwien.ac.at/opsys/linux/gentoo/ ftp://ftp.tu-clausthal.de/pub/linux/gentoo/"
MAKEOPTS="-j2"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="x86 FFmpeg X Xaw3d aalib acpi afs alsa apache2 apm arts ati avi berkdb bidi bitmap-fonts caca cdparanoia cdr crypt cscope cups curl dba dga directfb divx divx4 divx4linux divx5 divx5linux doc dvb dvd dvdr dvdread emacs emacs-w3 encode esd ethereal evo f77 faad faad2 fam fame fbcon ffmpeg flac flash font-server foomaticdb fortran fvwm fvwm2 g77 gb gcj gd gdbm ggi gif gphoto2 gpm gstreamer gtk gtk2 gtkhtml guile i8x0 icc imagemagick imlib imlib2 innodb ipv6 java jpeg junit lcms leim libg++ libwww live lzo mad mcal mesa mikmod mmx mmx2 motif mozilla mpeg mule mysql ncurses network nls oggvorbis opengl oss pam pda pdflib perl php php4 plotutils png postgres ppds pthread pthreads python qt qtx quicktime readline rtc samba sdl slang slp spell sse sse2 sse3 ssl svga tcltk tcpd tetex theora thread threads tiff truetype truetype-fonts type1-fonts unicode usb v4l v4l2 win32 winvidix wmf xml xml2 xmms xosd xv xvid xvmc zeo zlib video_cards_radeon"
Unset:  ASFLAGS, CBUILD, CTARGET, LANG, LC_ALL, LDFLAGS, PORTDIR_OVERLAY



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

Thanks for reporting. The problem is the setup program tries to use "
-I/usr/include/python2.3" as the C++ compiler! This is a bug in "setup.py", and
could potentially affect all Python extensions written in C++. You can read on
this issue at: "http://bugzilla.open-bio.org/show_bug.cgi?id=1733".

I was able to reproduce this problem, but not to fix it. Instead, I added a new
version of Biopython (1.40b) which does not build the problematic module by
default. Please try this new version and tell me if it works for you.

george: This new version might fix the amd64 problem you mentionned in the
Biopython ChangeLog. (I suspect it was the same problem.)

1.40b installed fine. Close it. Thanks.

I will try to push version 1.40b to stable as soon as possible, and then remove
other versions from the tree.