unmerging linux-headers and broken system

fuorviato · 02-19-2014, 09:57 AM

Thanks but here I'm loosing you again. What exactly happened? Glibc didn't merge due /etc files missing?
Shall I run the newest package from /root or under right category-dir?

i92guboj · 02-19-2014, 10:12 AM

It didn't merge because the glibc ebuild does something with some files that should be contained in the tarball. But in this case they were not there, because the packages created with the quickpkg tool omit some files. This is ok for most packages, but it seems it is not ok for glibc. So I repackaged it to include everYthing.

The package must be in /usr/portage/packages/sys-libs

fuorviato · 02-19-2014, 10:25 AM

Hmm. still fails with the same error as before
I used the link from your previous post just as you told me to.

Quote:

>>> Extracting info
[32;01m * [39;49;00mPackage: sys-libs/glibc-2.17
[32;01m * [39;49;00mRepository: gentoo
[32;01m * [39;49;00mUSE:
[32;01m * [39;49;00mFEATURES: preserve-libs sandbox userpriv usersandbox
>>> Extracting sys-libs/glibc-2.17
[32;01m*[39;49;00m checking 1693 files for package collisions
1000 files checked ...
>>> Merging sys-libs/glibc-2.17 to /
sed: can't read /home/tmp/portage/sys-libs/glibc-2.17/image//etc/host.conf: No such file or directory
[32;01m*[0m Defaulting /etc/host.conf:multi to on
/var/tmp/portage/sys-libs/glibc-2.17/temp/environment: line 2410: pushd: /home/tmp/portage/sys-libs/glibc-2.17/image//lib: No such file or directory
/var/tmp/portage/sys-libs/glibc-2.17/temp/environment: line 2418: ./ld-*.so: No such file or directory
[31;01m*[0m ERROR: sys-libs/glibc-2.17::gentoo failed (preinst phase):
[31;01m*[0m simple run test (/bin/date) failed
[31;01m*[0m
[31;01m*[0m Call stack:
[31;01m*[0m ebuild.sh, line 93: Called pkg_preinst
[31;01m*[0m environment, line 3111: Called eblit-run 'pkg_preinst'
[31;01m*[0m environment, line 982: Called eblit-glibc-pkg_preinst
[31;01m*[0m environment, line 796: Called glibc_sanity_check
[31;01m*[0m environment, line 2418: Called die
[31;01m*[0m The specific snippet of code:
[31;01m*[0m ./ld-*.so --library-path . ${x} > /dev/null || die "simple run test (${x}) failed";
[31;01m*[0m
[31;01m*[0m If you need support, post the output of `emerge --info '=sys-libs/glibc-2.17::gentoo'`,
[31;01m*[0m the complete build log and the output of `emerge -pqv '=sys-libs/glibc-2.17::gentoo'`.
[31;01m*[0m The complete build log is located at '/var/tmp/portage/sys-libs/glibc-2.17/temp/build.log'.
[31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sys-libs/glibc-2.17/temp/environment'.
[31;01m*[0m Working directory: '/'
[31;01m*[0m S: '/var/tmp/portage/sys-libs/glibc-2.17/work/glibc-2.17'
!!! FAILED preinst: 1

i92guboj · 02-19-2014, 11:19 AM

Admittedly, now that I think about it, I never emerged a binary for glibc. I have only done it the hard way, by untaring in /. I guess that's the sanest option that you have for that package. Just

Code:

$ cd /; tar xf /usr/portage/packages/sys-libs/glibc-2.17.tbz2

fuorviato · 02-19-2014, 11:41 AM

You've just made my day - Bzip2 made it! I'm now emerging the rest. So far so good

Keep your fingers crossed.

i92guboj · 02-19-2014, 12:06 PM

Quote:

Originally Posted by fuorviato

You've just made my day - Bzip2 made it! I'm now emerging the rest. So far so good

Keep your fingers crossed.

you can be sure I'll do :P

fuorviato · 02-19-2014, 01:16 PM

Argh. It's stuck with python now:

Quote:

32;01m * [39;49;00mPackage: dev-lang/python-2.7.5-r3
[32;01m * [39;49;00mRepository: gentoo
[32;01m * [39;49;00mMaintainer: python@gentoo.org
[32;01m * [39;49;00mUSE: abi_x86_32 elibc_glibc gdbm ipv6 kernel_linux ncurses readline ssl threads userland_GNU wide-unicode x86 xml
[32;01m * [39;49;00mFEATURES: preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking Python-2.7.5.tar.xz to /var/tmp/portage/dev-lang/python-2.7.5-r3/work
>>> Unpacking python-gentoo-patches-2.7.5-0.tar.xz to /var/tmp/portage/dev-lang/python-2.7.5-r3/work
>>> Source unpacked in /var/tmp/portage/dev-lang/python-2.7.5-r3/work
>>> Preparing source in /var/tmp/portage/dev-lang/python-2.7.5-r3/work/Python-2.7.5 ...
/var/tmp/portage/dev-lang/python-2.7.5-r3/temp/environment: line 1827: warning: setlocale: LC_COLLATE: cannot change locale (en_US.UTF-8): No such file or directory
/var/tmp/portage/dev-lang/python-2.7.5-r3/temp/environment: line 1827: warning: setlocale: LC_COLLATE: cannot change locale (en_US.UTF-8)
[32;01m*[0m Applying various patches (bugfixes/updates) ...
[32;01m*[0m 01_all_static_library_location.patch ...
[A[106C [34;01m[ [32;01mok[34;01m ][0m
[32;01m*[0m 02_all_disable_modules_and_ssl.patch ...
[A[106C [34;01m[ [32;01mok[34;01m ][0m
[32;01m*[0m 03_all_libdir.patch ...
[A[106C [34;01m[ [32;01mok[34;01m ][0m
[32;01m*[0m 04_all_non-zero_exit_status_on_failure.patch ...
[A[106C [34;01m[ [32;01mok[34;01m ][0m
[32;01m*[0m 05_all_loadable_sqlite_extensions.patch ...
[A[106C [34;01m[ [32;01mok[34;01m ][0m
[32;01m*[0m 06_all_regenerate_platform-specific_modules.patch ...
[A[106C [34;01m[ [32;01mok[34;01m ][0m
[32;01m*[0m 21_all_distutils_c++.patch ...
[A[106C [34;01m[ [32;01mok[34;01m ][0m
[32;01m*[0m 22_all_turkish_locale.patch ...
[A[106C [34;01m[ [32;01mok[34;01m ][0m
[32;01m*[0m 23_all_arm_OABI.patch ...
[A[106C [34;01m[ [32;01mok[34;01m ][0m
[32;01m*[0m 24_all_tests_environment.patch ...
[A[106C [34;01m[ [32;01mok[34;01m ][0m
[32;01m*[0m 61_all_process_data.patch ...
[A[106C [34;01m[ [32;01mok[34;01m ][0m
[32;01m*[0m 62_all_xml.use_pyxml.patch ...
[A[106C [34;01m[ [32;01mok[34;01m ][0m
[32;01m*[0m Done with patching
[32;01m*[0m Applying python-2.7.5-library-path.patch ...
[A[106C [34;01m[ [32;01mok[34;01m ][0m
[32;01m*[0m Applying python-2.7.5-re_unsigned_ptrdiff.patch ...
[A[106C [34;01m[ [32;01mok[34;01m ][0m
[32;01m*[0m Applying CVE-2013-4238_py27.patch ...
[A[106C [34;01m[ [32;01mok[34;01m ][0m
[32;01m*[0m Applying python-2.7-issue16248.patch ...
[A[106C [34;01m[ [32;01mok[34;01m ][0m
[32;01m*[0m Applying python-2.7.5-nonfatal-compileall.patch ...
[A[106C [34;01m[ [32;01mok[34;01m ][0m
[32;01m*[0m Running autoconf ...
[A[106C [34;01m[ [32;01mok[34;01m ][0m
[32;01m*[0m Running autoheader ...
[A[106C [34;01m[ [32;01mok[34;01m ][0m
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/dev-lang/python-2.7.5-r3/work/Python-2.7.5 ...
[32;01m*[0m Disabled modules: _bsddb _sqlite3 _tkinter
* econf: updating Python-2.7.5/config.guess with /usr/share/gnuconfig/config.guess
* econf: updating Python-2.7.5/config.sub with /usr/share/gnuconfig/config.sub
/var/tmp/portage/dev-lang/python-2.7.5-r3/work/Python-2.7.5/configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --with-fpectl --enable-shared --enable-ipv6 --with-threads --enable-unicode=ucs4 --infodir=${prefix}/share/info --mandir=${prefix}/share/man --with-dbmliborder=gdbm --with-libc= --enable-loadable-sqlite-extensions --with-system-expat --with-system-ffi
checking build system type... i686-pc-linux-gnu
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checking if sockaddr has sa_len member... no
checking whether va_list is an array... no
checking for gethostbyname_r... yes
checking gethostbyname_r with 6 args... yes
checking for __fpu_control... yes
checking for --with-fpectl... yes
checking for --with-libm=STRING... default LIBM="-lm"
checking for --with-libc=STRING... set LIBC=""
checking whether C doubles are little-endian IEEE 754 binary64... yes
checking whether C doubles are big-endian IEEE 754 binary64... no
checking whether C doubles are ARM mixed-endian IEEE 754 binary64... no
checking whether we can use gcc inline assembler to get and set x87 control word... yes
checking for x87-style double rounding... yes
checking whether tanh preserves the sign of zero... yes
checking for acosh... yes
checking for asinh... yes
checking for atanh... yes
checking for copysign... yes
checking for erf... yes
checking for erfc... yes
checking for expm1... yes
checking for finite... yes
checking for gamma... yes
checking for hypot... yes
checking for lgamma... yes
checking for log1p... yes
checking for round... yes
checking for tgamma... yes
checking whether isinf is declared... yes
checking whether isnan is declared... yes
checking whether isfinite is declared... yes
checking whether POSIX semaphores are enabled... no
checking for broken sem_getvalue... yes
checking digit size for Python's longs... no value specified
checking wchar.h usability... yes
checking wchar.h presence... yes
checking for wchar.h... yes
checking size of wchar_t... 4
checking for UCS-4 tcl... no
checking whether wchar_t is signed... yes
checking what type to use for unicode... unsigned long
checking whether byte ordering is bigendian... no
checking whether right shift extends the sign bit... yes
checking for getc_unlocked() and friends... yes
checking how to link readline libs... -lreadline
checking for rl_callback_handler_install in -lreadline... yes
checking for rl_pre_input_hook in -lreadline... yes
checking for rl_completion_display_matches_hook in -lreadline... yes
checking for rl_completion_matches in -lreadline... yes
checking for broken nice()... no
checking for broken poll()... no
checking for struct tm.tm_zone... (cached) yes
checking for working tzset()... yes
checking for tv_nsec in struct stat... yes
checking for tv_nsec2 in struct stat... no
checking whether mvwdelch is an expression... yes
checking whether WINDOW has _flags... yes
checking for is_term_resized... yes
checking for resize_term... yes
checking for resizeterm... yes
configure: checking for device files
checking for /dev/ptmx... yes
checking for /dev/ptc... no
checking for %lld and %llu printf() format support... yes
checking for %zd printf() format support... yes
checking for socklen_t... yes
checking for build directories... done
configure: creating ./config.status
config.status: creating Makefile.pre
config.status: creating Modules/Setup.config
config.status: creating Misc/python.pc
config.status: creating Modules/ld_so_aix
config.status: creating pyconfig.h
creating Modules/Setup
creating Modules/Setup.local
creating Makefile
[31;01m*[0m configure has detected that the sem_open function is broken.
[31;01m*[0m Please ensure that /dev/shm is mounted as a tmpfs with mode 1777.
[31;01m*[0m ERROR: dev-lang/python-2.7.5-r3::gentoo failed (configure phase):
[31;01m*[0m Broken sem_open function (bug 496328)
[31;01m*[0m
[31;01m*[0m Call stack:
[31;01m*[0m ebuild.sh, line 93: Called src_configure
[31;01m*[0m environment, line 3706: Called die
[31;01m*[0m The specific snippet of code:
[31;01m*[0m die "Broken sem_open function (bug 496328)";
[31;01m*[0m
[31;01m*[0m If you need support, post the output of `emerge --info '=dev-lang/python-2.7.5-r3::gentoo'`,
[31;01m*[0m the complete build log and the output of `emerge -pqv '=dev-lang/python-2.7.5-r3::gentoo'`.
[31;01m*[0m The complete build log is located at '/var/tmp/portage/dev-lang/python-2.7.5-r3/temp/build.log'.
[31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/dev-lang/python-2.7.5-r3/temp/environment'.
[31;01m*[0m Working directory: '/var/tmp/portage/dev-lang/python-2.7.5-r3/work/i686-pc-linux-gnu'
[31;01m*[0m S: '/var/tmp/portage/dev-lang/python-2.7.5-r3/work/Python-2.7.5'

Also, linux-headers poses some problems. I'm pastbining it here since the output would bee too long.

http://bpaste.net/show/Qg1y7pcM6K6OSmAg76Vb/

i92guboj · 02-19-2014, 01:29 PM

Is tmpfs mounted? What's the output for this command?

Code:

mount | grep shm

fuorviato · 02-19-2014, 03:24 PM

Quote:

mount|grep shm
shm on /dev/shm type tmpfs (rw,nosuid,nodev,noexec,relatime)

My di command shows it has only 10 MB.

Quote:

Filesystem Mount Size Used Avail %Used fs Type
rootfs / 8.8G 4.3G 4.1G 54% rootfs
/dev/sda3 / 8.8G 4.3G 4.1G 54% ext3
udev /dev 10.0M 0.0M 10.0M 0% devtmpfs
devpts /dev/pts 10.0M 0.0M 10.0M 0% devpts
shm /dev/shm 10.0M 0.0M 10.0M 0% tmpfs
tmpfs /run 8.8G 4.3G 4.1G 54% tmpfs
sysfs /sys 8.8G 4.3G 4.1G 54% sysfs

Does it have anything to do with temp directory with no space for saving compilation files?

i92guboj · 02-19-2014, 04:01 PM

Since python is a fairly complex package, I think that the simplest thing is to provide you the binaries as well hehe.

http://www.jesgue.es/files/gentoo-x8...-2.7.5-r3.tbz2
http://www.jesgue.es/files/gentoo-x8...hon-3.3.3.tbz2

If you can install them, after that run

Code:

$ eselect python list
$ eselect python set <X>

Where X is the desired version. 2.7 is the most stable one. Though nowadays 3.x should be ok for *most* setups. I'd say go with 2.7 at least until we sort this out. After that, you can set it to 3.

i92guboj · 02-20-2014, 08:23 AM

Mmm. Reviewing this I noticed the pastebin link. I didn't see it before. I should really stop and think before doing things. Anyway...

That thing you pasted is NOT AN ERROR. It"s just portage telling you that some files are to be overwritten, but that's neither a problem nor strange under this circumstances. You can continue emerging stuff. If you didn't install my python bins yet DON'T DO IT.

fuorviato · 02-20-2014, 08:33 AM

I emerged python and set it to 2.7. Then I went with emerge --resume and it seems to have recovered (at least went on) then it failed again:

Build log -----> http://bpaste.net/show/181136/

I don't know much about programming but this seems to be interesting part

Quote:

onfigure has detected that the sem_open function is broken.
[31;01m*[0m Please ensure that /dev/shm is mounted as a tmpfs with mode 1777.
[31;01m*[0m ERROR: dev-lang/python-2.7.5-r3::gentoo failed (configure phase):
[31;01m*[0m Broken sem_open function (bug 496328)

Doesn't mode 1777 mean also execution permission?
I can see /dev/shm is mounted with "noexec" parameter?

Sorry. If I'm wrong

fuorviato · 02-20-2014, 08:35 AM

Quote:

Originally Posted by i92guboj

Mmm. Reviewing this I noticed the pastebin link. I didn't see it before. I should really stop and think before doing things. Anyway...

That thing you pasted is NOT AN ERROR. It"s just portage telling you that some files are to be overwritten, but that's neither a problem nor strange under this circumstances. You can continue emerging stuff. If you didn't install my python bins yet DON'T DO IT.

Damnit. Did it 5 min ago, argh

i92guboj · 02-20-2014, 08:53 AM

Don't worry, as said, it won't be any worse than before. Just give me five minutes to put all the last info together.

i92guboj · 02-20-2014, 08:56 AM

Ok. So, linux-headers merged, that's ok.

Python did not merge, so it's ok that you used my bin files after all. In any case, make sure that you are using the python version that you emerged. If you emerge 2.7 then eselect that, else, eselect 3.3.

As for /dev/shm, in my experience that error can be triggered by a number of things. The permissions in /dev/shm look like this:

Code:

# ls -ld /dev/shm/
drwxrwxrwt 2 root root 40 feb 20 15:55 /dev/shm/

So, check that as well. Being mounted with "noexec" is fine for that fs.