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Bug 489096 - dev-python/pycrypto-2.6-r2.ebuild fails with /usr/include/features.h:323:26: fatal error: bits/predefs.h: No such file or directory
Summary: dev-python/pycrypto-2.6-r2.ebuild fails with /usr/include/features.h:323:26: ...
Status: RESOLVED CANTFIX
Alias: None
Product: Gentoo/Alt
Classification: Unclassified
Component: Prefix Support (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Prefix
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2013-10-23 05:38 UTC by Steven Trogdon
Modified: 2014-02-01 20:31 UTC (History)
0 users

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Package list:
Runtime testing required: ---

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Description Steven Trogdon 2013-10-23 05:38:44 UTC 
The host OS here is Debian 7 (wheezy) a multiarch Debian. The error that's present during building is:

running build_ext
running build_configure
building 'Crypto.PublicKey._fastmath' extension
creating /storage/strogdon/gentoo-redlizard/var/tmp/portage/dev-python/pycrypto-2.6-r2/work/pycrypto-2.6-python2_7/temp.linux-x86_64-2.7
creating /storage/strogdon/gentoo-redlizard/var/tmp/portage/dev-python/pycrypto-2.6-r2/work/pycrypto-2.6-python2_7/temp.linux-x86_64-2.7/src
x86_64-pc-linux-gnu-gcc -pthread -march=native -pipe -fno-strict-aliasing -fPIC -std=c99 -O3 -fomit-frame-pointer -Isrc/ -I/usr/include/ -I/storage/strogdon/gentoo-redlizard/usr/include/python2.7 -c src/_fastmath.c -o /storage/strogdon/gentoo-redlizard/var/tmp/portage/dev-python/pycrypto-2.6-r2/work/pycrypto-2.6-python2_7/temp.linux-x86_64-2.7/src/_fastmath.o
In file included from /usr/include/stdio.h:28:0,
                 from src/_fastmath.c:29:
/usr/include/features.h:323:26: fatal error: bits/predefs.h: No such file or directory
compilation terminated.

I have Prefix installed with it's own glibc. On the host predefs.h is under
/usr/include/x86_64-linux-gnu/bits/!

emerge --info

Portage 2.2.7-prefix (prefix/linux/amd64, gcc-4.7.2, unavailable, 3.2.0-4-amd64 x86_64)
=================================================================
System uname: Linux-3.2.0-4-amd64-x86_64-Intel-R-_Xeon-R-_CPU_E5-1650_0_@_3.20GHz-with-debian-7.1
KiB Mem:    32945868 total,   9433484 free
KiB Swap:   33480700 total,  33480700 free
Timestamp of tree: Mon, 30 Sep 2013 19:14:10 +0000
ld GNU ld (GNU Binutils) 2.23
ccache version 3.1.9 [enabled]
app-shells/bash:          4.2_p39-r1
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.7.5-r2::rap, 3.3.2-r2::rap
dev-util/ccache:          3.1.9-r2::science
dev-util/cmake:           2.8.11.2
dev-util/pkgconfig:       0.28
sys-devel/autoconf:       2.69
sys-devel/automake:       1.12.4
sys-devel/binutils:       2.23
sys-devel/gcc:            4.6.3, 4.7.2-r1
sys-devel/gcc-config:     1.8-r00.1
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.11 (virtual/os-headers)
sys-libs/glibc:           2.17::heroxbd
Repositories: gentoo_prefix prefix-with-glibc local-overlay rap heroxbd sage-on-gentoo science
ACCEPT_KEYWORDS="~amd64-linux"
ACCEPT_LICENSE="* -@EULA Oracle-BCLA-JavaSE"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/terminfo"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/storage/strogdon/gentoo-redlizard/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs ccache collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles force-prefix merge-sync news parallel-fetch preserve-libs protect-owned sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1"
MAKEOPTS="-j13"
PKGDIR="/storage/strogdon/gentoo-redlizard/usr/portage/packages"
PORTAGE_CONFIGROOT="/storage/strogdon/gentoo-redlizard/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/storage/strogdon/gentoo-redlizard/var/tmp"
PORTDIR="/storage/strogdon/gentoo-redlizard/usr/portage"
PORTDIR_OVERLAY="/storage/strogdon/gentoo-prefix-libc/overlay /storage/strogdon/local-overlay /storage/strogdon/prefix-libc /storage/strogdon/heroxbd /storage/strogdon/sage-on-gentoo /storage/strogdon/sci"
SYNC="rsync://prefix.gentooexperimental.org/gentoo-portage-prefix"
USE="amd64 berkdb bzip2 cli cracklib crypt cxx dri fortran gdbm iconv ipv6 mmx modules mudflap ncurses nls nptl openmp pcre prefix readline session sse sse2 ssl tcpd unicode zlib" ABI_X86="64" 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" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19 ruby18" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga nouveau nv r128 radeon savage sis tdfx trident vesa via vmware dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
USE_PYTHON="2.7 3.3"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

The source of the failure is the following in setup.py

            # _fastmath (uses GNU mp library)
            Extension("Crypto.PublicKey._fastmath",
                      include_dirs=['src/','/usr/include/'],
                      libraries=['gmp'],
                      sources=["src/_fastmath.c"]),

Unless I have missed something the /usr/include/ is not needed in the "include_dirs=" Extension option. Without /usr/include the subject package builds in this Prefix as well as in Gentoo. And I can't see that is is would be needed in gentoo_prefix that uses a host glibc. setup.py for the master branch

https://github.com/dlitz/pycrypto/blob/master/setup.py

doesn't have /usr/include in the "include_dirs=" Extension option.
Comment 1 Steven Trogdon 2013-10-24 19:28:07 UTC 
There is now dev-python/pycrypto-2.6.1 in the tree that has this same failure for me.
Comment 2 Fabian Groffen gentoo-dev 2014-02-01 20:31:05 UTC 
You should probably have headers in your prefix if you also provide the glibc.  We can't work with the completely broken multiarch crap from Debilian.