Bug 241178

Summary:	sci-chemistry/pdb2pqr fails to build: numpy or numeric needed
Product:	Gentoo Linux	Reporter:	Diego Elio Pettenò (RETIRED) <flameeyes>
Component:	New packages	Assignee:	Gentoo Chemistry-Related Packages <sci-chemistry>
Status:	RESOLVED FIXED
Severity:	normal
Priority:	High
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---
Attachments:	Build log

Description Diego Elio Pettenò (RETIRED) gentoo-dev

2008-10-10 21:18:45 UTC

Portage 2.2_rc11 (default/linux/x86/2008.0, gcc-4.1.2, glibc-2.8_p20080602-r0,
2.6.26-gentoo-r1 i686)
=================================================================
System uname:
Linux-2.6.26-gentoo-r1-i686-Quad-Core_AMD_Opteron-tm-_Processor_2350-with-glibc2.0
Timestamp of tree: Thu, 09 Oct 2008 18:30:10 +0000
app-shells/bash:     3.2_p39
dev-lang/python:     2.4.4-r6, 2.5.2-r7
dev-python/pycrypto: 2.0.1-r6
sys-apps/baselayout: 2.0.0
sys-apps/openrc:     0.2.5
sys-apps/sandbox:    1.2.18.1-r3
sys-devel/autoconf:  2.62-r1
sys-devel/automake:  1.7.9-r1, 1.9.6-r2, 1.10.1-r1
sys-devel/binutils:  2.18-r3
sys-devel/gcc-config: 1.4.0-r4
sys-devel/libtool:   2.2.4
virtual/os-headers:  2.6.26
ACCEPT_KEYWORDS="x86 ~x86"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf
/etc/gentoo-release /etc/terminfo /etc/udev/rules.d"
CXXFLAGS="-pipe"
DISTDIR="/usr/portage-distfiles"
FEATURES="distlocks parallel-fetch preserve-libs protect-owned sandbox sfperms
strict unmerge-orphans userfetch"
GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/
http://ftp.uni-erlangen.de/pub/mirrors/gentoo"
INSTALL_MASK="  /usr/share/doc  /usr/share/man  /usr/share/info"
LDFLAGS="-Wl,-O1"
MAKEOPTS="-j8"
PKGDIR="/usr/portage-packages"
PORTAGE_COMPRESS=""
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress
--force --whole-file --delete --stats --timeout=180 --exclude=/distfiles
--exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="acl berkdb bzip2 cli cracklib crypt cups custom-cflags dri fortran gdbm
gpm iconv ipv6 isdnlog midi mudflap ncurses nls nptl nptlonly openmp pam pcre
perl pppd python readline reflection session spl ssl sysfs tcpd unicode x86
xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci
emu10k1 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 mmap_emul mulaw multi null plug
rate route share shm softvol" APACHE2_MODULES="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
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" 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="fbdev glint i810 mach64 mga neomagic nv r128
radeon savage sis tdfx trident vesa vga via vmware voodoo"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, LANG, LC_ALL, LINGUAS,
PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY

Comment 1 Diego Elio Pettenò (RETIRED) gentoo-dev

2008-10-10 21:19:55 UTC

Created attachment 167930 [details]
Build log

Comment 2 Markus Dittrich (RETIRED) gentoo-dev

2008-10-11 11:22:33 UTC

Thank you very much for the note, Diego. I just
fixed this in cvs.

Best,
Markus

Comment 3 Robert Floor 2008-11-19 13:51:18 UTC

Dear Markus,

I have got the smae error can it also be fixed for the rsync Source Distributions?

Greeting en kind regards

Robert Floor

(In reply to comment #2)
> Thank you very much for the note, Diego. I just
> fixed this in cvs.
> 
> Best,
> Markus
>

Comment 4 Markus Dittrich (RETIRED) gentoo-dev

2008-11-20 00:07:03 UTC

Hi Robert,

This should be fixed in 1.1.2 and 1.3.0 on
all of our mirrors. Make sure to sync portage and then
please try again. If you still have problems please post 
the error you get, your emerge --info as well as the
the pdb2pqr version you are trying to emerge.

Thanks much,
Markus