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[SOLVED] Can't compile sys-apps/sandbox

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kfiadeg
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[SOLVED] Can't compile sys-apps/sandbox

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Post by kfiadeg » Thu Jan 26, 2023 12:53 am

Howdy!
I have been upgrading live Gentoo server from it's state from 2018.

I have encountered problem upgrading sys-apps/sandbox from version 2.13 to 2.29.

When I try to emerge sys-apps/sandbox I do have following error:

Code: Select all

checking for i686-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc -m32 -mfpmath=sse
checking whether the C compiler works... no
configure: error: in `/var/tmp/portage/sys-apps/sandbox-2.29/work/sandbox-2.29-abi_x86_32.x86':
configure: error: C compiler cannot create executables
This is strange as other packages have compiled successfully. It must be noted that I have copied GCC compiler (v11) from chrooted stage3 on the same machine and using binary packaging (still could not recompile it on target machine).

I've already tried many things that came to my mind upon looking through the internet for solution:

1. copy sys-apps/sandbox from the chrooted current stage3 just as I did with GCC - unfortunatelly this can not be done due to internal collisions that IMO do not exist:

Code: Select all

>>> Emerging binary (1 of 1) sys-apps/sandbox-2.29::gentoo
 * sandbox-2.29-1.xpak size ;-) ...                                      [ ok ]
>>> Extracting info
>>> Extracting sys-apps/sandbox-2.29

>>> Installing (1 of 1) sys-apps/sandbox-2.29::gentoo
 * checking 11 files for package collisions
 * Package 'sys-apps/sandbox-2.29' has internal collisions between non-
 * identical files (located in separate directories in the installation
 * image (${D}) corresponding to merged directories in the target
 * filesystem (${ROOT})):
 * 
 * 	/usr/lib64/libsandbox.so
 * 		/usr/lib/libsandbox.so
 * 		/usr/lib64/libsandbox.so
 * 			Differences: size, content
 * 
 * Package 'sys-apps/sandbox-2.29' NOT merged due to internal collisions
 * between non-identical files. If necessary, refer to your elog messages
 * for the whole content of the above message.
 * If configure failed with a 'cannot run C compiled programs' error, try this:
 * FEATURES='-sandbox -usersandbox' emerge sandbox
/usr/lib/libsandbox.so and /usr/lib64/libsandbox.so are the same file as /usr/lib directory is a symlink to /usr/lib64.

2 I have desperatelly deleted file that causes collision hoping that this will move merging on. It did not - the same error about collisions and now, after emerging back the old version of sys-apps/sandbox from binary xpak package I have created as a "backup" I do have disturbing error for every emerge command I issue:

Code: Select all

>> Emerging (1 of 1) sys-apps/sandbox-2.29::gentoo
 * sandbox-2.29.tar.xz BLAKE2B SHA512 size ;-) ...                                                                                                                                                                                   [ ok ]
 * ACCESS DENIED:  open_wr:      /dev/tty
 * ACCESS DENIED:  open_wr:      /dev/tty
 * ACCESS DENIED:  open_wr:      /dev/null
/usr/lib/portage/python3.10/ebuild.sh: line 11: /dev/null: Permission denied
 * ACCESS DENIED:  open_wr:      /dev/null
(more at https://dpaste.com/EE346LT42).

Additiona information:

- emerge --info : https://dpaste.com/7RJ8B6QHJ
- emerge --info sandbox:

Code: Select all

=================================================================
                        Package Settings
=================================================================

sys-apps/sandbox-2.13::gentoo was built with the following:
USE="-abi_ppc_32 -abi_ppc_64" ABI_X86="(32) (64) (-x32)"
CFLAGS="-O2 -pipe -mtune=skylake --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=4096 -fomit-frame-pointer -fgcse-after-reload -fstack-protector-strong"
CXXFLAGS="-O2 -pipe -mtune=skylake --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=4096 -fomit-frame-pointer -fgcse-after-reload -fstack-protector-strong"
FEATURES="assume-digests binpkg-logs candy compress-build-logs config-protect-if-modified distlocks ebuild-locks fail-clean fixlafiles merge-sync metadata-transfer multilib-strict news nostrip parallel-fetch preserve-libs protect-owned sandbox sfperms split-elog split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
Please help. Case is urgent as @system and @world have been upgraded only partially and if it happens that server restarts it will probably not boot or operate properly.
Last edited by kfiadeg on Thu Jan 26, 2023 11:54 pm, edited 1 time in total.
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Post by kfiadeg » Thu Jan 26, 2023 1:08 am

One more thing: config.log from /var/tmp/portage/sys-apps/sandbox-2.29/work/sandbox-2.29-abi_x86_32.x86 directory: https://dpaste.com/HYHQ7JUKE

Oh, and also tried things like:

Code: Select all

# ABI_X86="64" emerge -va1 sandbox
but I can not "remove" "32" flag from the ABI_X86 this way:

Code: Select all

[ebuild     U  ] sys-apps/sandbox-2.29::gentoo [2.13::gentoo] USE="nnp%* (-abi_ppc_32%) (-abi_ppc_64%)" ABI_X86="(32) (64) (-x32)" 0 KiB
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Post by sam_ » Thu Jan 26, 2023 1:28 am

Did you attempt a partial migration from 17.0->17.1? It sounds like there might have been a partial migration.

This might be easier to try debug on #gentoo on IRC.
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Hu
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Re: Can't compile sys-apps/sandbox

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Post by Hu » Thu Jan 26, 2023 2:00 am

kfiadeg wrote:

Code: Select all

checking for i686-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc -m32 -mfpmath=sse
checking whether the C compiler works... no
configure: error: in `/var/tmp/portage/sys-apps/sandbox-2.29/work/sandbox-2.29-abi_x86_32.x86':
configure: error: C compiler cannot create executables
The error from config.log is:

Code: Select all

configure:4181: checking whether the C compiler works
configure:4203: x86_64-pc-linux-gnu-gcc -m32 -mfpmath=sse -O2 -pipe -mtune=skylake --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=4096 -fomit-frame-pointer -fgcse-after-reload -fstack-protector-strong -fno-lto  -Wl,-O1 -Wl,--as-needed -fno-lto conftest.c  >&5
/usr/lib/gcc/x86_64-pc-linux-gnu/11/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-pc-linux-gnu/11/../../../../lib/libc.so when searching for -lc
/usr/lib/gcc/x86_64-pc-linux-gnu/11/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-pc-linux-gnu/11/../../../../lib/libc.a when searching for -lc
/usr/lib/gcc/x86_64-pc-linux-gnu/11/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/../lib/libc.so when searching for -lc
/usr/lib/gcc/x86_64-pc-linux-gnu/11/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/../lib/libc.a when searching for -lc
/usr/lib/gcc/x86_64-pc-linux-gnu/11/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-pc-linux-gnu/11/../../../libc.so when searching for -lc
/usr/lib/gcc/x86_64-pc-linux-gnu/11/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-pc-linux-gnu/11/../../../libc.a when searching for -lc
/usr/lib/gcc/x86_64-pc-linux-gnu/11/../../../../x86_64-pc-linux-gnu/bin/ld: i386:x86-64 architecture of input file `/usr/lib/gcc/x86_64-pc-linux-gnu/11/../../../../lib/Scrt1.o' is incompatible with i386 output
/usr/lib/gcc/x86_64-pc-linux-gnu/11/../../../../x86_64-pc-linux-gnu/bin/ld: i386:x86-64 architecture of input file `/usr/lib/gcc/x86_64-pc-linux-gnu/11/../../../../lib/crti.o' is incompatible with i386 output
/usr/lib/gcc/x86_64-pc-linux-gnu/11/../../../../x86_64-pc-linux-gnu/bin/ld: i386:x86-64 architecture of input file `/usr/lib/gcc/x86_64-pc-linux-gnu/11/../../../../lib/crtn.o' is incompatible with i386 output
/usr/lib/gcc/x86_64-pc-linux-gnu/11/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib/gcc/x86_64-pc-linux-gnu/11/../../../../lib/Scrt1.o: file class ELFCLASS64 incompatible with ELFCLASS32
/usr/lib/gcc/x86_64-pc-linux-gnu/11/../../../../x86_64-pc-linux-gnu/bin/ld: final link failed: file in wrong format
collect2: error: ld returned 1 exit status
What is the output of emerge --verbose --info sys-devel/gcc sys-libs/glibc ; equery check sys-libs/glibc ; equery files sys-libs/glibc | grep 'libc.*\.so' ; namei -l /lib* /usr/lib*?
kfiadeg wrote:This is strange as other packages have compiled successfully. It must be noted that I have copied GCC compiler (v11) from chrooted stage3 on the same machine and using binary packaging (still could not recompile it on target machine).
How did you copy this?
kfiadeg wrote:1. copy sys-apps/sandbox from the chrooted current stage3 just as I did with GCC - unfortunatelly this can not be done due to internal collisions that IMO do not exist:

Code: Select all

 * 	/usr/lib64/libsandbox.so
 * 		/usr/lib/libsandbox.so
 * 		/usr/lib64/libsandbox.so
 * 			Differences: size, content
/usr/lib/libsandbox.so and /usr/lib64/libsandbox.so are the same file as /usr/lib directory is a symlink to /usr/lib64.
This looks to me like you are trying to copy a 17.1 profile sandbox package into a 17.0 profile directory tree.
kfiadeg wrote:2 I have desperatelly deleted file that causes collision hoping that this will move merging on.
That probably just made things worse. I think you should not have deleted it, and, when you wanted to restore, you should have restored the deleted file from backup, without using Portage.
kfiadeg wrote:after emerging back the old version of sys-apps/sandbox from binary xpak package I have created as a "backup" I do have disturbing error for every emerge command I issue:

Code: Select all

>> Emerging (1 of 1) sys-apps/sandbox-2.29::gentoo
 * sandbox-2.29.tar.xz BLAKE2B SHA512 size ;-) ...                                                                                                                                                                                   [ ok ]
 * ACCESS DENIED:  open_wr:      /dev/tty
 * ACCESS DENIED:  open_wr:      /dev/tty
 * ACCESS DENIED:  open_wr:      /dev/null
/usr/lib/portage/python3.10/ebuild.sh: line 11: /dev/null: Permission denied
 * ACCESS DENIED:  open_wr:      /dev/null
This looks like you lost the sandbox configuration file that normally marks these as permitted.
kfiadeg wrote: - emerge --info : https://dpaste.com/7RJ8B6QHJ
This confirms you are still on a 17.0 profile.
kfiadeg wrote:Please help. Case is urgent as @system and @world have been upgraded only partially and if it happens that server restarts it will probably not boot or operate properly.
Do you have a backup? We might be able to fix this, but knowing that your most recent backup is in good order would provide an alternate recovery path.
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Re: Can't compile sys-apps/sandbox

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Post by kfiadeg » Thu Jan 26, 2023 2:44 am

sam_, Hu - you're the best!
I have joined #gentoo as _sam suggested, then I tried to explain what is going on. And while creating this explanation I've been hacking around to make sure that I will give valid background. And then - MAGICALLY - sys-apps/sandbox emerged from chroot environment onto the host! I think it was the magic of good will of both of you! I swear I believe it! It has been 4+ hours of me trying to fix this myself! And then I ask other PEOPLE and good happens...

Thank you!

For the sake of this topic I point the things Hu asked about. See my answers below.
Hu wrote:What is the output of emerge --verbose --info sys-devel/gcc sys-libs/glibc ; equery check sys-libs/glibc ; equery files sys-libs/glibc | grep 'libc.*\.so' ; namei -l /lib* /usr/lib*?
1. # emerge --verbose --info sys-devel/gcc sys-libs/glibc → https://dpaste.com/5FZYR2RYA

2. equery check sys-libs/glibc

Code: Select all

# equery check sys-libs/glibc
!!! /etc/locale.gen has incorrect MD5sum
!!! /lib64/libcrypt.so.1 has incorrect MD5sum
* Checking sys-libs/glibc-2.36-r5 ...
   1837 out of 1839 files passed
3. # equery files sys-libs/glibc | grep 'libc.*\.so'

Code: Select all

/lib32/libc.so.6
/lib32/libc_malloc_debug.so.0
/lib64/libc.so.6
/lib64/libc_malloc_debug.so.0
/lib64/libcrypt.so.1
/usr/lib32/libc.so
/usr/lib32/libc_malloc_debug.so
/usr/lib64/libc.so
/usr/lib64/libc_malloc_debug.so
4. # namei -l /lib* /usr/lib*

Code: Select all

f: /lib
drwxr-xr-x root root /
lrwxrwxrwx root root lib -> lib64
drwxr-xr-x root root   lib64
f: /lib32
drwxr-xr-x root root /
drwxr-xr-x root root lib32
f: /lib64
drwxr-xr-x root root /
drwxr-xr-x root root lib64
f: /usr/lib
drwxr-xr-x root root /
drwxr-xr-x root root usr
lrwxrwxrwx root root lib -> lib64
drwxr-xr-x root root   lib64
f: /usr/lib32
drwxr-xr-x root root /
drwxr-xr-x root root usr
drwxr-xr-x root root lib32
f: /usr/lib64
drwxr-xr-x root root /
drwxr-xr-x root root usr
drwxr-xr-x root root lib64
f: /usr/libexec
drwxr-xr-x root root /
drwxr-xr-x root root usr
drwxr-xr-x root root libexec
Hu wrote:
kfiadeg wrote:This is strange as other packages have compiled successfully. It must be noted that I have copied GCC compiler (v11) from chrooted stage3 on the same machine and using binary packaging (still could not recompile it on target machine).
How did you copy this?
I followed this recipe: https://wiki.gentoo.org/wiki/Upgrading_ ... ld_systems and then used quickpg (on chroot) and emerge -K (on host).
Hu wrote:
kfiadeg wrote:1. copy sys-apps/sandbox from the chrooted current stage3 just as I did with GCC - unfortunatelly this can not be done due to internal collisions that IMO do not exist:

Code: Select all

 * 	/usr/lib64/libsandbox.so
 * 		/usr/lib/libsandbox.so
 * 		/usr/lib64/libsandbox.so
 * 			Differences: size, content
/usr/lib/libsandbox.so and /usr/lib64/libsandbox.so are the same file as /usr/lib directory is a symlink to /usr/lib64.
This looks to me like you are trying to copy a 17.1 profile sandbox package into a 17.0 profile directory tree.
This may be the case - the chrooted stage3 was 17.1 and host still uses 17.0.
Hu wrote:
kfiadeg wrote:2 I have desperatelly deleted file that causes collision hoping that this will move merging on.
That probably just made things worse. I think you should not have deleted it, and, when you wanted to restore, you should have restored the deleted file from backup, without using Portage.
Thanks for the tip. I will now not rely on the "backup" made of binary package.
Hu wrote:
kfiadeg wrote:after emerging back the old version of sys-apps/sandbox from binary xpak package I have created as a "backup" I do have disturbing error for every emerge command I issue:

Code: Select all

>> Emerging (1 of 1) sys-apps/sandbox-2.29::gentoo
 * sandbox-2.29.tar.xz BLAKE2B SHA512 size ;-) ...                                                                                                                                                                                   [ ok ]
 * ACCESS DENIED:  open_wr:      /dev/tty
 * ACCESS DENIED:  open_wr:      /dev/tty
 * ACCESS DENIED:  open_wr:      /dev/null
/usr/lib/portage/python3.10/ebuild.sh: line 11: /dev/null: Permission denied
 * ACCESS DENIED:  open_wr:      /dev/null
This looks like you lost the sandbox configuration file that normally marks these as permitted.
I see. Checking if sandbox configuration exists and is valid would be good step forward.
Hu wrote:
kfiadeg wrote: - emerge --info : https://dpaste.com/7RJ8B6QHJ
This confirms you are still on a 17.0 profile.
Yes. The profile upgrade guide suggests to have system fully updated before the switch, so I'm trying to do so.
Hu wrote:
kfiadeg wrote:Please help. Case is urgent as @system and @world have been upgraded only partially and if it happens that server restarts it will probably not boot or operate properly.
Do you have a backup? We might be able to fix this, but knowing that your most recent backup is in good order would provide an alternate recovery path.
I do have VM backups provided by hosting company, created every hour. It is good idea to use them as backup source. Thanks.

---

Currently sys-libs/libxcrypt can not be rebuild with 32 ABI_X86. I must rebuild it with:

Code: Select all

# ABI_X86="64" emerge -v1 sys-libs/libxcrypt
I wonder why this happens? Are building tools unable to create 32bit binaries at the moment? How to handle that?
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Re: Can't compile sys-apps/sandbox

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Post by Hu » Thu Jan 26, 2023 3:15 am

kfiadeg wrote:I think it was the magic of good will of both of you! I swear I believe it! It has been 4+ hours of me trying to fix this myself! And then I ask other PEOPLE and good happens...
I am glad that this worked out for you.
kfiadeg wrote:This may be the case - the chrooted stage3 was 17.1 and host still uses 17.0.
This may cause you problems with anything multilib related.
kfiadeg wrote:
Hu wrote:This looks like you lost the sandbox configuration file that normally marks these as permitted.
I see. Checking if sandbox configuration exists and is valid would be good step forward.
What is the output of wc /etc/sandbox.conf ; grep -e '^[^#]' /etc/sandbox.conf?
kfiadeg wrote:I followed this recipe: https://wiki.gentoo.org/wiki/Upgrading_ ... ld_systems and then used quickpg (on chroot) and emerge -K (on host).
The Wiki does not appear to mention use of quickpkg. It wants you to build in the chroot and install directly into the host. If you choose to use quickpkg, beware its defaults:

Code: Select all

       --include-config < y | n >
              Include all files protected by  CONFIG_PROTECT  (as  a  security
              precaution, default is 'n').

       --include-unmodified-config < y | n >
              Include  files  protected  by  CONFIG_PROTECT that have not been
              modified since installation (as a security  precaution,  default
              is 'n').
If you did not override those defaults, you may not have packaged the configuration files into the tbz2, and as a result would not receive them on the host when unpacking.
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Re: Can't compile sys-apps/sandbox

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Post by kfiadeg » Thu Jan 26, 2023 11:26 am

Hu wrote:What is the output of wc /etc/sandbox.conf ; grep -e '^[^#]' /etc/sandbox.conf?
Currently (as sys-apps/sandbox is already "fixed"), the result is:

Code: Select all

# wc /etc/sandbox.conf ; grep -e '^[^#]' /etc/sandbox.conf
 105  473 3280 /etc/sandbox.conf
SANDBOX_WRITE="/dev/fd:/proc/self/fd"
SANDBOX_WRITE="/dev/zero:/dev/null:/dev/full"
SANDBOX_WRITE="/dev/console:/dev/tty:/dev/vc/:/dev/pty:/dev/tts"
SANDBOX_WRITE="/dev/ptmx:/dev/pts/:/dev/shm"
SANDBOX_WRITE="/tmp/:/var/tmp/:/usr/tmp/"
SANDBOX_WRITE="${HOME}/.bash_history"
However I don't know how it looked when the problem was alive.

Hu wrote:The Wiki does not appear to mention use of quickpkg. It wants you to build in the chroot and install directly into the host. If you choose to use quickpkg, beware its defaults:

Code: Select all

       --include-config < y | n >
              Include all files protected by  CONFIG_PROTECT  (as  a  security
              precaution, default is 'n').

       --include-unmodified-config < y | n >
              Include  files  protected  by  CONFIG_PROTECT that have not been
              modified since installation (as a security  precaution,  default
              is 'n').
If you did not override those defaults, you may not have packaged the configuration files into the tbz2, and as a result would not receive them on the host when unpacking.
Indeed, Wiki does not say anything about using binaries with quickpkg. So it must have been my idea while raging with the "gentoo hell".
Thanks for the tip with config defaults - it might be the reason why sandbox didn't want to work properly after restoring it from binary-"backup" (made with quickpkg).
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Post by Hu » Thu Jan 26, 2023 3:10 pm

Perhaps not surprisingly since sandbox now works for you, your grep output matches mine. What is next for this system? Are there still problems to solve in this thread, or does it work to your satisfaction now that you have repaired the sandbox?
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Post by kfiadeg » Thu Jan 26, 2023 11:54 pm

It looks very good now. I keep updating @world - it will take some time. Then I'll do the backup, create binary packages (including configuration files) and reboot the system to make sure it can boot ;)
If it doesn't I'll get seriously mad, but having backup and binaries will calm me down after a while.
If it boots properly I'll try to switch to newer profile (17.1) and follow complete procedure (including recompiling).
At the end I may try to update kernel.

This topic may be marked as solved. Thanks again, folks, for your help and knowledge!
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