Re: [gentoo-alt] bootstrap-prefix.sh -- how to properly resume "emerge -e system"

[Leho Kraav]

On P 18 nov   2012 23:15:07 EET, Fabian Groffen wrote:
> On 18-11-2012 22:57:49 +0200, Leho Kraav wrote:
>> On a couple of x86_64 Linux boxes, including a Gentoo instance,
>> everything seemed to be going
>> fine until some package bombs out towards the end during "emerge -e
>> system". Restarting the script wants to re-emerge all 92 packages from
>> the start, even though you might have 84 of them already installed.
>> Would it make sense to build binpkgs here btw and make the script do
>> "emerge -ek system" instead?
>>
>> Anyway, what's the sensible action here? I don't want it to start
>> rebuilding a hundred packages when only last 6 might be missing..
>
> In that stage, I'd just start a login shell from the prefix (e.g.
> /path/to/prefix/bin/bash -l) and run emerge --resume.  It may be wise to
> clean your environment, but portage should do that to a certain extent.
> (env -i HOME=$HOME TERM=$TERM USER=$USER /path/to/prefix/bin/bash -l)
>
> After emerge -e it does the startscript thing, but you can do that
> manually too.
>

Thanks. That seems to work. But the original problem of the bombing out 
seems to persist.
Python is failing on me. Everything seems to be correct to my eye, i.e. 
linking and include paths are all in the correct order.

1161 building 'dbm' extension
1162 x86_64-pc-linux-gnu-gcc -pthread -fPIC -fno-strict-aliasing -O2 
-pipe -O2 -pipe -fwrapv -DNDEBUG -DHAVE_GDBM_NDBM_H -I. -IInclude 
-I./Include -I/mnt/datapool/gentoo/     prefix/linux-amd64/usr/include 
-I/mnt/datapool/gentoo/prefix/linux-amd64/var/tmp/portage/dev-lang/python-2.7.3-r2/work/Python-2.7.3/Include 
-I/mnt/datapool/gentoo/pr     
efix/linux-amd64/var/tmp/portage/dev-lang/python-2.7.3-r2/work/Python-2.7.3 
-c 
/mnt/datapool/gentoo/prefix/linux-amd64/var/tmp/portage/dev-lang/python-2.7.3-r2/work/ 
    Python-2.7.3/Modules/dbmmodule.c -o 
build/temp.linux-x86_64-2.7/mnt/datapool/gentoo/prefix/linux-amd64/var/tmp/portage/dev-lang/python-2.7.3-r2/work/Python-2.7.3/Mod 
    ules/dbmmodule.o
1163 x86_64-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 
-L/mnt/datapool/gentoo/prefix/linux-amd64/lib 
-L/mnt/datapool/gentoo/prefix/linux-amd64/usr/lib -L/usr/lib32 -L/usr/  
   lib64 -L/lib32 -L/lib64 -L. -Wl,-O1 
-L/mnt/datapool/gentoo/prefix/linux-amd64/lib 
-L/mnt/datapool/gentoo/prefix/linux-amd64/usr/lib -L/usr/lib32 
-L/usr/lib64 -L/lib3     2 -L/lib64 -L. -fno-strict-aliasing -O2 -pipe 
-O2 -pipe -fwrapv -DNDEBUG -I. -IInclude -I./Include 
-I/mnt/datapool/gentoo/prefix/linux-amd64/usr/include build/temp.l     
inux-x86_64-2.7/mnt/datapool/gentoo/prefix/linux-amd64/var/tmp/portage/dev-lang/python-2.7.3-r2/work/Python-2.7.3/Modules/dbmmodule.o 
-L/mnt/datapool/gentoo/prefix/l     inux-amd64/lib 
-L/mnt/datapool/gentoo/prefix/linux-amd64/usr/lib -L/usr/lib32 
-L/usr/lib64 -L/lib32 -L/lib64 -L. -lgdbm -lgdbm_compat -lpython2.7 -o 
build/lib.linux-     x86_64-2.7/dbm.so
1164 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.2/../../../../x86_64-pc-linux-gnu/bin/ld: 
skipping incompatible /usr/lib32/libpthread.so when searching for 
-lpthread
1165 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.2/../../../../x86_64-pc-linux-gnu/bin/ld: 
skipping incompatible /usr/lib32/libpthread.a when searching for 
-lpthread
1166 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.2/../../../../x86_64-pc-linux-gnu/bin/ld: 
skipping incompatible /usr/lib32/libc.so when searching for -lc
1167 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.2/../../../../x86_64-pc-linux-gnu/bin/ld: 
skipping incompatible /usr/lib32/libc.a when searching for -lc
1168 *** WARNING: renaming "dbm" since importing it failed: 
libgdbm.so.4: cannot open shared object file: No such file or directory
1169 building 'gdbm' extension
1170 x86_64-pc-linux-gnu-gcc -pthread -fPIC -fno-strict-aliasing -O2 
-pipe -O2 -pipe -fwrapv -DNDEBUG -I. -IInclude -I./Include 
-I/mnt/datapool/gentoo/prefix/linux-amd64/     usr/include 
-I/mnt/datapool/gentoo/prefix/linux-amd64/var/tmp/portage/dev-lang/python-2.7.3-r2/work/Python-2.7.3/Include 
-I/mnt/datapool/gentoo/prefix/linux-amd64/va     
r/tmp/portage/dev-lang/python-2.7.3-r2/work/Python-2.7.3 -c 
/mnt/datapool/gentoo/prefix/linux-amd64/var/tmp/portage/dev-lang/python-2.7.3-r2/work/Python-2.7.3/Module 
    s/gdbmmodule.c -o 
build/temp.linux-x86_64-2.7/mnt/datapool/gentoo/prefix/linux-amd64/var/tmp/portage/dev-lang/python-2.7.3-r2/work/Python-2.7.3/Modules/gdbmmodule.o
1171 x86_64-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 
-L/mnt/datapool/gentoo/prefix/linux-amd64/lib 
-L/mnt/datapool/gentoo/prefix/linux-amd64/usr/lib -L/usr/lib32 -L/usr/  
   lib64 -L/lib32 -L/lib64 -L. -Wl,-O1 
-L/mnt/datapool/gentoo/prefix/linux-amd64/lib 
-L/mnt/datapool/gentoo/prefix/linux-amd64/usr/lib -L/usr/lib32 
-L/usr/lib64 -L/lib3     2 -L/lib64 -L. -fno-strict-aliasing -O2 -pipe 
-O2 -pipe -fwrapv -DNDEBUG -I. -IInclude -I./Include 
-I/mnt/datapool/gentoo/prefix/linux-amd64/usr/include build/temp.l     
inux-x86_64-2.7/mnt/datapool/gentoo/prefix/linux-amd64/var/tmp/portage/dev-lang/python-2.7.3-r2/work/Python-2.7.3/Modules/gdbmmodule.o 
-L/mnt/datapool/gentoo/prefix/     linux-amd64/lib 
-L/mnt/datapool/gentoo/prefix/linux-amd64/usr/lib -L/usr/lib32 
-L/usr/lib64 -L/lib32 -L/lib64 -L. -lgdbm -lpython2.7 -o 
build/lib.linux-x86_64-2.7/gd     bm.so
1172 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.2/../../../../x86_64-pc-linux-gnu/bin/ld: 
skipping incompatible /usr/lib32/libpthread.so when searching for 
-lpthread
1173 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.2/../../../../x86_64-pc-linux-gnu/bin/ld: 
skipping incompatible /usr/lib32/libpthread.a when searching for 
-lpthread
1174 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.2/../../../../x86_64-pc-linux-gnu/bin/ld: 
skipping incompatible /usr/lib32/libc.so when searching for -lc
1175 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.2/../../../../x86_64-pc-linux-gnu/bin/ld: 
skipping incompatible /usr/lib32/libc.a when searching for -lc
1176 *** WARNING: renaming "gdbm" since importing it failed: 
libgdbm.so.4: cannot open shared object file: No such file or directory

Prefix is installing the latest gdbm-1.9 series. But when it performs 
its tests, my host has gdbm-1.8.3 installed and the tests will fail.

$ /mnt/datapool/gentoo/prefix/linux-amd64 $ ldd 
var/tmp/portage/dev-lang/python-2.7.3-r2/work/Python-2.7.3/build/lib.linux-x86_64-2.7/dbm_failed.so
        linux-vdso.so.1 =>  (0x00007fffbddaf000)
        libgdbm.so.4 => not found
        libgdbm_compat.so.4 => not found
        libpython2.7.so.1.0 => /usr/lib64/libpython2.7.so.1.0 
(0x00007fe191f39000
...

How do I fight this one?