It has happened several times for the last 10 years, a program to fail during the configure stage with a strange error:

checking whether we are cross compiling...  * /var/tmp/portage/sys-apps/sandbox-2.12/work/sandbox-2.12/libsandbox/libsandbox.c:check_syscall():968: failure (Value too large for defined data type):
 * ISE: fopen_wr(conftest.out)
        abs_path: (null)
        res_path: /var/tmp/portage/sys-apps/sandbox-2.13/work/sandbox-2.13-abi_x86_32.x86/conftest.out
configure: error: in `/var/tmp/portage/sys-apps/sandbox-2.13/work/sandbox-2.13-abi_x86_32.x86':
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details

It’s like the “./conftest” is made and the execution failed?

Last package it happened was when trying to build

sys-apps/sandbox-2.13

but it is not especially related to this Gentoo package or even to Gentoo!

And the debug.log is not informative neither:

configure:3793: ./conftest
/usr/lib32/libsandbox.so(+0xb238)[0xf7738238]
/usr/lib32/libsandbox.so(+0xb2c7)[0xf77382c7]
/usr/lib32/libsandbox.so(+0x40b1)[0xf77310b1]
/usr/lib32/libsandbox.so(+0x421e)[0xf773121e]
/usr/lib32/libsandbox.so(fopen+0x55)[0xf7733e45]
./conftest(+0x4a1)[0x565754a1]
/lib32/libc.so.6(__libc_start_main+0xf6)[0xf7561956]
./conftest(+0x508)[0x56575508]
/proc/23882/cmdline: ./conftest 

/var/tmp/portage/sys-apps/sandbox-2.13/work/sandbox-2.13/configure: line 3795: 23882 Aborted                 ./conftest$ac_cv_exeext
configure:3797: $? = 134
configure:3804: error: in `/var/tmp/portage/sys-apps/sandbox-2.13/work/sandbox-2.13-abi_x86_32.x86':
configure:3806: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details

After some debugging it turned out the problem was the

XFS filesystem

The root was formatted with XFS and therefore

/var/tmp/portage

where all the compilation occurred was on a xfs formatted partition!
It is easy to resolve the issue, just mount your “/var/tmp/portage” on another filesystem, if you do not have any spare devices or places with other filesystem, you could always mount it using

tmpfs

(using your memory for the directory) like this:

mount -t tmpfs -o size=4096m tmpfs /var/tmp/portage/

You can adjust the size with “size” parameter, but most of the program require a way below 4G of space. And do not forget mounting your build directory in the tmpfs speeds up the emerge process significantly!

And probably it is a good idea before mounting it to delete all old sub-directories, because they can take much space and they are left there after failed compilations of packages.

rm -R /var/tmp/portage/*

PS: It was the same with compilation of

sys-devel/gcc-7.3.0

configure: updating cache ./config.cache
 * /var/tmp/portage/sys-apps/sandbox-2.13/work/sandbox-2.13/libsandbox/libsandbox.c:check_syscall():968: failure (Value too large for defined data type):
 * ISE: fopen_wr(conftest.val)
        abs_path: (null)
        res_path: /var/tmp/portage/sys-devel/gcc-7.3.0/work/build/x86_64-pc-linux-gnu/32/libgomp/conftest.val
configure: error: unsupported system, cannot find sizeof (omp_lock_t)
make[2]: *** [Makefile:20106: configure-stage1-target-libgomp] Error 1
make[2]: Leaving directory '/var/tmp/portage/sys-devel/gcc-7.3.0/work/build'
make[1]: *** [Makefile:22189: stage1-bubble] Error 2
make[1]: Leaving directory '/var/tmp/portage/sys-devel/gcc-7.3.0/work/build'
make: *** [Makefile:22521: bootstrap-lean] Error 2
 * ERROR: sys-devel/gcc-7.3.0::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sys-devel/gcc-7.3.0::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sys-devel/gcc-7.3.0::gentoo'`.
 * The complete build log is located at '/var/tmp/portage/sys-devel/gcc-7.3.0/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sys-devel/gcc-7.3.0/temp/environment'.
 * Working directory: '/var/tmp/portage/sys-devel/gcc-7.3.0/work/build'
 * S: '/var/tmp/portage/sys-devel/gcc-7.3.0/work/gcc-7.3.0'
 * 
 * Please include /var/tmp/portage/sys-devel/gcc-7.3.0/work/gcc-build-logs.tar.bz2 in your bug report.
 * 

>>> Failed to emerge sys-devel/gcc-7.3.0, Log file:

The problem is the same, compiling on

XFS filesystem