ZFS upgrade failure

Message

MarkYork · Post by **MarkYork** » Thu Jul 31, 2025 5:31 am

Hello all,

I'm in the process of (trying) upgrading my Gentoo build. I have been running the system for a few weeks with ZFS as my rootfs without much of a problem, until I came into a ZFS upgrade. It is miserably failing during the pre-checks stating that CONFIG_MODULES is not set in the kernel config, but that is not true.
Below are the error logs and a confirmation that my kernel is set with CONFIG_MODULES

Code: Select all

# emerge --update --deep --newuse -v @world

These are the packages that would be merged, in order:

Calculating dependencies  
 * IMPORTANT: 30 news items need reading for repository 'gentoo'.
 * Use eselect news read to view new items.

... done!
Dependency resolution took 10.05 s (backtrack: 0/20).

[ebuild     U  ] sys-fs/zfs-kmod-2.3.3:0/2.3.3::gentoo [2.3.2:0/2.3.2::gentoo] USE="dist-kernel-cap initramfs rootfs strip -custom-cflags -debug -dist-kernel -modules-compress -modules-sign -verify-sig" 0 KiB
[ebuild     U  ] sys-fs/zfs-2.3.3:0/6::gentoo [2.3.2:0/6::gentoo] USE="nls pam rootfs -custom-cflags -debug -dist-kernel (-kernel-builtin) -minimal -python (-selinux) (-split-usr) (-test-suite) -unwind -verify-sig" PYTHON_TARGETS="python3_11 -python3_12 -python3_13" 0 KiB
[ebuild     U  ] dev-qt/qtbase-6.9.1-r3:6/6.9.1::gentoo [6.9.1-r2:6/6.9.1::gentoo] USE="X concurrent cups dbus gtk gui icu libinput libproxy network nls opengl sql sqlite ssl udev vulkan wayland widgets xml (zstd) -accessibility -brotli -custom-cflags -eglfs -evdev -gles2-only -gssapi -journald -mysql -oci8 -odbc -postgres -renderdoc -sctp -syslog -test -tslib" 0 KiB
[ebuild     U  ] sys-libs/kpmcore-25.04.3:6/10::gentoo [25.04.2:6/10::gentoo] USE="-debug" 0 KiB
[ebuild     U  ] kde-plasma/plasma-activities-6.3.6:6::gentoo [6.3.5:6::gentoo] USE="-debug -doc -test" 0 KiB
[ebuild     U  ] kde-plasma/kde-cli-tools-common-6.3.6::gentoo [6.3.5::gentoo] USE="handbook" 0 KiB
[ebuild  N     ] media-libs/libpulse-17.0::gentoo  USE="X asyncns dbus glib gtk -doc (-selinux) -systemd -test -valgrind" ABI_X86="32 (64) (-x32)" 0 KiB
[ebuild     U  ] www-client/firefox-bin-141.0:rapid::gentoo [140.0.4:rapid::gentoo] USE="gmp-autoupdate wayland (-selinux)" L10N="es-ES -ach -af -an -ar -ast -az -be -bg -bn -br -bs -ca -ca-valencia -cak -cs -cy -da -de -dsb -el -en-CA -en-GB -eo -es-AR -es-CL -es-MX -et -eu -fa -ff -fi -fr -fy -ga -gd -gl -gn -gu -he -hi -hr -hsb -hu -hy -ia -id -is -it -ja -ka -kab -kk -km -kn -ko -lij -lt -lv -mk -mr -ms -my -nb -ne -nl -nn -oc -pa -pl -pt-BR -pt-PT -rm -ro -ru -sco -si -sk -skr -sl -son -sq -sr -sv -ta -te -th -tl -tr -trs -uk -ur -uz -vi -xh -zh-CN -zh-TW" 0 KiB
[ebuild     U ~] net-im/zoom-6.5.7.3298::gentoo [6.5.3.2773::gentoo] USE="pulseaudio wayland zoom-symlink -opencl" 0 KiB
[ebuild   R    ] media-video/pipewire-1.4.6:0/0.4::gentoo  USE="X bluetooth dbus elogind gstreamer* readline sound-server ssl -doc -echo-cancel -extra -ffmpeg -fftw -flatpak -gsettings -ieee1394 -jack-client -jack-sdk -liblc3 -loudness -lv2 -man -modemmanager -pipewire-alsa -roc (-selinux) (-system-service) -systemd -test -v4l -zeroconf" ABI_X86="32 (64) (-x32)" 0 KiB
[ebuild     U  ] gnome-extra/gnome-calendar-47.0::gentoo [46.1::gentoo] USE="-test" 0 KiB
[ebuild     U  ] sys-block/partitionmanager-25.04.3:6::gentoo [25.04.2:6::gentoo] USE="handbook -debug" 0 KiB
[ebuild     U  ] kde-plasma/keditfiletype-6.3.6::gentoo [6.3.5::gentoo] USE="-debug -test" 0 KiB
[ebuild     U  ] kde-plasma/libplasma-6.3.6:6::gentoo [6.3.5:6::gentoo] USE="-debug -doc -gles2-only -test" 0 KiB
[ebuild     U  ] kde-plasma/polkit-kde-agent-6.3.6:6::gentoo [6.3.5:6::gentoo] USE="-debug" 0 KiB

Total: 15 packages (13 upgrades, 1 new, 1 reinstall), Size of downloads: 0 KiB

>>> Verifying ebuild manifests


>>> Running pre-merge checks for sys-fs/zfs-kmod-2.3.3

>>> Running pre-merge checks for sys-fs/zfs-2.3.3

>>> Emerging (1 of 15) sys-fs/zfs-kmod-2.3.3::gentoo
 * zfs-2.3.3.tar.gz BLAKE2B SHA512 size ;-) ...                          [ ok ]
 [32m*[0m Determining the location of the kernel source code
 [32m*[0m Found kernel source directory:
 [32m*[0m     /usr/src/linux
 [32m*[0m Found sources for kernel version:
 [32m*[0m     6.12.31-gentoo-gentoo-dist
 [32m*[0m Checking for suitable kernel configuration options ...
[A[72C [34;01m[ [32;01mok[34;01m ][0m
 [32m*[0m Preparing x86_64-pc-linux-gnu toolchain for kernel modules (override with KERNEL_CHOST) ...
 [32m*[0m Toolchain picked for kernel modules (override with KERNEL_CC, _LD, ...): '/usr/bin/x86_64-pc-linux-gnu-gcc-14' '/usr/bin/x86_64-pc-linux-gnu-g++-14' '/usr/bin/x86_64-pc-linux-gnu-ld.bfd' '/usr/bin/x86_64-pc-linux-gnu-gcc-ar' '/usr/bin/x86_64-pc-linux-gnu-gcc-nm' '/usr/bin/x86_64-pc-linux-gnu-objcopy' '/usr/bin/x86_64-pc-linux-gnu-objdump' '/usr/bin/x86_64-pc-linux-gnu-readelf' '/usr/bin/x86_64-pc-linux-gnu-strip'
>>> Unpacking source...
>>> Unpacking zfs-2.3.3.tar.gz to /var/tmp/portage/sys-fs/zfs-kmod-2.3.3/work
>>> Source unpacked in /var/tmp/portage/sys-fs/zfs-kmod-2.3.3/work
>>> Preparing source in /var/tmp/portage/sys-fs/zfs-kmod-2.3.3/work/zfs-2.3.3 ...
 [32m*[0m Applying zfs-kmod-2.1.11-gentoo.patch ...
patching file config/kernel.m4
Hunk #1 succeeded at 700 with fuzz 1 (offset 54 lines).
[A[72C [34;01m[ [32;01mok[34;01m ][0m
 [32m*[0m Running eautoreconf in '/var/tmp/portage/sys-fs/zfs-kmod-2.3.3/work/zfs-2.3.3' ...
 [32m*[0m Running 'libtoolize --install --copy --force --automake' ...
[A[72C [34;01m[ [32;01mok[34;01m ][0m
 [32m*[0m Running 'aclocal -I config --system-acdir=/var/tmp/portage/sys-fs/zfs-kmod-2.3.3/temp/aclocal' ...
[A[72C [34;01m[ [32;01mok[34;01m ][0m
 [32m*[0m Running 'autoconf --force' ...
[A[72C [34;01m[ [32;01mok[34;01m ][0m
 [32m*[0m Running 'autoheader --force' ...
[A[72C [34;01m[ [32;01mok[34;01m ][0m
 [32m*[0m Running 'automake --add-missing --copy --foreign --force-missing' ...
[A[72C [34;01m[ [32;01mok[34;01m ][0m
 (B[m[1m[32m*(B[m Running elibtoolize in: zfs-2.3.3/
 (B[m[1m[32m*(B[m Running elibtoolize in: zfs-2.3.3/config/
 (B[m[1m[32m*(B[m   Applying portage/1.2.0 patch ...
 (B[m[1m[32m*(B[m   Applying sed/1.5.6 patch ...
 (B[m[1m[32m*(B[m   Applying as-needed/2.5.0 patch ...
 (B[m[1m[32m*(B[m   Applying verbose-pic/2.4.7 patch ...
 (B[m[1m[32m*(B[m   Applying clang-runtime-ltmain/2.4.7 patch ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sys-fs/zfs-kmod-2.3.3/work/zfs-2.3.3 ...
 * econf: updating zfs-2.3.3/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating zfs-2.3.3/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating zfs-2.3.3/config/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating zfs-2.3.3/config/config.sub with /usr/share/gnuconfig/config.sub
./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --datarootdir=/usr/share --disable-dependency-tracking --disable-silent-rules --disable-static --docdir=/usr/share/doc/zfs-kmod-2.3.3 --htmldir=/usr/share/doc/zfs-kmod-2.3.3/html --with-sysroot=/ --libdir=/usr/lib64 --bindir=/bin --sbindir=/sbin --with-config=kernel --with-linux=/usr/src/linux --with-linux-obj=/usr/src/linux --disable-debug GENTOO_MAKEARGS_EVAL='ARCH=x86' 'V=1' 'KBUILD_VERBOSE=1' 'CONFIG_WERROR=' 'CONFIG_OBJTOOL_WERROR=' 'CONFIG_MODULE_SIG_ALL=' 'CONFIG_MODULE_COMPRESS_ALL=' 'CONFIG_MODULE_COMPRESS_GZIP=' 'CONFIG_MODULE_COMPRESS_XZ=' 'CONFIG_MODULE_COMPRESS_ZSTD=' 'DEPMOD=true' 'STRIP=true' 'CROSS_COMPILE=x86_64-pc-linux-gnu-' 'HOSTCC=x86_64-pc-linux-gnu-gcc' 'HOSTCXX=x86_64-pc-linux-gnu-g++' 'HOSTCFLAGS=-march=znver4 -O2 -pipe' 'HOSTCXXFLAGS=-march=znver4 -O2 -pipe' 'HOSTLDFLAGS=-Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs' 'HOSTPKG_CONFIG=x86_64-pc-linux-gnu-pkg-config' 'CC=/usr/bin/x86_64-pc-linux-gnu-gcc-14' 'CXX=/usr/bin/x86_64-pc-linux-gnu-g++-14' 'LD=/usr/bin/x86_64-pc-linux-gnu-ld.bfd' 'AR=/usr/bin/x86_64-pc-linux-gnu-gcc-ar' 'NM=/usr/bin/x86_64-pc-linux-gnu-gcc-nm' 'OBJCOPY=/usr/bin/x86_64-pc-linux-gnu-objcopy' 'OBJDUMP=/usr/bin/x86_64-pc-linux-gnu-objdump' 'READELF=/usr/bin/x86_64-pc-linux-gnu-readelf' TEST_JOBS=17
checking for gawk... gawk
checking metadata... META file
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking whether to enable maintainer-specific portions of Makefiles... no
checking whether make supports nested variables... yes
checking for a BSD-compatible install... /usr/lib/portage/python3.11/ebuild-helpers/xattr/install -c
checking whether sleep supports fractional seconds... yes
checking filesystem timestamp resolution... 0.01
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking whether make sets $(MAKE)... yes
checking xargs -n works... yes
checking how to print strings... printf
checking whether make supports the include directive... yes (GNU style)
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
checking for x86_64-pc-linux-gnu-gcc option to enable C11 features... none needed
checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes
checking dependency style of x86_64-pc-linux-gnu-gcc... none
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld
checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/x86_64-pc-linux-gnu-nm -B
checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r
checking for file... file
checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump
checking how to recognize dependent libraries... pass_all
checking for x86_64-pc-linux-gnu-dlltool... x86_64-pc-linux-gnu-dlltool
checking how to associate runtime and link libraries... printf %s\n
checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar
checking for archiver @FILE support... @
checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip
checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok
checking for sysroot... /
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for x86_64-pc-linux-gnu-mt... no
checking for mt... no
checking if : is a manifest tool... no
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no
checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC
checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes
checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes
checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes
checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes
checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for x86_64-pc-linux-gnu-gcc... (cached) x86_64-pc-linux-gnu-gcc
checking whether the compiler supports GNU C... (cached) yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... (cached) yes
checking for x86_64-pc-linux-gnu-gcc option to enable C11 features... (cached) none needed
checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... (cached) yes
checking dependency style of x86_64-pc-linux-gnu-gcc... (cached) none
checking whether ln -s works... yes
checking for x86_64-pc-linux-gnu-pkg-config... /usr/bin/x86_64-pc-linux-gnu-pkg-config
checking pkg-config is at least version 0.9.0... yes
checking dependency style of x86_64-pc-linux-gnu-gcc... none
checking whether to build with code coverage support... no
checking how to create a pax tar archive... gnutar
checking zfs author... OpenZFS
checking zfs license... CDDL
checking whether NLS is requested... yes
checking for msgfmt... /usr/bin/msgfmt
checking for gmsgfmt... /usr/bin/gmsgfmt
checking for xgettext... /usr/bin/xgettext
checking for msgmerge... /usr/bin/msgmerge
checking for ld... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64
checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes
checking for shared library run path origin... done
checking 32-bit host C ABI... no
checking for the common suffixes of directories in the library search path... lib64,lib64
checking zfs config... kernel
checking the number of available CPUs... 16
checking whether x86_64-pc-linux-gnu-gcc supports -Wno-clobbered... yes
checking whether x86_64-pc-linux-gnu-gcc supports -Winfinite-recursion... yes
checking whether  supports -Winfinite-recursion... yes
checking whether x86_64-pc-linux-gnu-gcc supports -Wimplicit-fallthrough... yes
checking whether x86_64-pc-linux-gnu-gcc supports -Wframe-larger-than=<size>... yes
checking whether x86_64-pc-linux-gnu-gcc supports -Wno-format-truncation... yes
checking whether x86_64-pc-linux-gnu-gcc supports -Wno-format-zero-length... yes
checking whether x86_64-pc-linux-gnu-gcc supports -Wformat-overflow... yes
checking whether x86_64-pc-linux-gnu-gcc supports -fno-omit-frame-pointer... yes
checking whether x86_64-pc-linux-gnu-gcc supports -fno-ipa-sra... yes
checking whether  supports -fno-ipa-sra... yes
checking whether to build with -fsanitize=address support... no
checking whether to build with -fsanitize=undefined support... no
checking whether host toolchain supports SSE... yes
checking whether host toolchain supports SSE2... yes
checking whether host toolchain supports SSE3... yes
checking whether host toolchain supports SSSE3... yes
checking whether host toolchain supports SSE4.1... yes
checking whether host toolchain supports SSE4.2... yes
checking whether host toolchain supports AVX... yes
checking whether host toolchain supports AVX2... yes
checking whether host toolchain supports AVX512F... yes
checking whether host toolchain supports AVX512CD... yes
checking whether host toolchain supports AVX512DQ... yes
checking whether host toolchain supports AVX512BW... yes
checking whether host toolchain supports AVX512IFMA... yes
checking whether host toolchain supports AVX512VBMI... yes
checking whether host toolchain supports AVX512PF... yes
checking whether host toolchain supports AVX512ER... yes
checking whether host toolchain supports AVX512VL... yes
checking whether host toolchain supports AES... yes
checking whether host toolchain supports PCLMULQDQ... yes
checking whether host toolchain supports MOVBE... yes
checking whether host toolchain supports XSAVE... yes
checking whether host toolchain supports XSAVEOPT... yes
checking whether host toolchain supports XSAVES... yes
checking for system type (linux-gnu)... Linux
checking for python3... python3
checking for python version... 3.11
checking for python platform... linux
checking for GNU default python prefix... ${prefix}
checking for GNU default python exec_prefix... ${exec_prefix}
checking for python script directory (pythondir)... ${PYTHON_PREFIX}/lib/python3.11/site-packages
checking for python extension module directory (pyexecdir)... ${PYTHON_EXEC_PREFIX}/lib/python3.11/site-packages
configure: Disabling pyzfs for kernel/srpm config
checking whether to enable pyzfs: ... no
checking for sed --in-place... --in-place
checking for cppcheck... no
checking for shellcheck... no
checking for checkbashisms... no
checking for parallel... no
checking kernel source and build directories... done
checking kernel source directory... /usr/src/linux
checking kernel build directory... /usr/src/linux
checking kernel source version... 6.12.31-gentoo-gentoo-dist
checking for kernel config option compatibility... done
checking whether CONFIG_MODULES is defined... no
configure: error: 
		*** This kernel does not include the required loadable module
		*** support!
		***
		*** To build OpenZFS as a loadable Linux kernel module
		*** enable loadable module support by setting
		*** `CONFIG_MODULES=y` in the kernel configuration and run
		*** `make modules_prepare` in the Linux source tree.
		***
		*** If you don't intend to enable loadable kernel module
		*** support, please compile OpenZFS as a Linux kernel built-in.
		***
		*** Prepare the Linux source tree by running `make prepare`,
		*** use the OpenZFS `--enable-linux-builtin` configure option,
		*** copy the OpenZFS sources into the Linux source tree using
		*** `./copy-builtin <linux source directory>`,
		*** set `CONFIG_ZFS=y` in the kernel configuration and compile
		*** kernel as usual.
			

!!! Please attach the following file when seeking support:
!!! /var/tmp/portage/sys-fs/zfs-kmod-2.3.3/work/zfs-2.3.3/config.log
 [31;01m*[0m ERROR: sys-fs/zfs-kmod-2.3.3::gentoo failed (configure phase):
 [31;01m*[0m   econf failed
 [31;01m*[0m 
 [31;01m*[0m Call stack:
 [31;01m*[0m               ebuild.sh, line  136:  Called src_configure
 [31;01m*[0m             environment, line 2828:  Called econf '--bindir=/bin' '--sbindir=/sbin' '--with-config=kernel' '--with-linux=/usr/src/linux' '--with-linux-obj=/usr/src/linux' '--disable-debug' 'GENTOO_MAKEARGS_EVAL='ARCH=x86' 'V=1' 'KBUILD_VERBOSE=1' 'CONFIG_WERROR=' 'CONFIG_OBJTOOL_WERROR=' 'CONFIG_MODULE_SIG_ALL=' 'CONFIG_MODULE_COMPRESS_ALL=' 'CONFIG_MODULE_COMPRESS_GZIP=' 'CONFIG_MODULE_COMPRESS_XZ=' 'CONFIG_MODULE_COMPRESS_ZSTD=' 'DEPMOD=true' 'STRIP=true' 'CROSS_COMPILE=x86_64-pc-linux-gnu-' 'HOSTCC=x86_64-pc-linux-gnu-gcc' 'HOSTCXX=x86_64-pc-linux-gnu-g++' 'HOSTCFLAGS=-march=znver4 -O2 -pipe' 'HOSTCXXFLAGS=-march=znver4 -O2 -pipe' 'HOSTLDFLAGS=-Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs' 'HOSTPKG_CONFIG=x86_64-pc-linux-gnu-pkg-config' 'CC=/usr/bin/x86_64-pc-linux-gnu-gcc-14' 'CXX=/usr/bin/x86_64-pc-linux-gnu-g++-14' 'LD=/usr/bin/x86_64-pc-linux-gnu-ld.bfd' 'AR=/usr/bin/x86_64-pc-linux-gnu-gcc-ar' 'NM=/usr/bin/x86_64-pc-linux-gnu-gcc-nm' 'OBJCOPY=/usr/bin/x86_64-pc-linux-gnu-objcopy' 'OBJDUMP=/usr/bin/x86_64-pc-linux-gnu-objdump' 'READELF=/usr/bin/x86_64-pc-linux-gnu-readelf'' 'TEST_JOBS=17'
 [31;01m*[0m        phase-helpers.sh, line  647:  Called __helpers_die 'econf failed'
 [31;01m*[0m   isolated-functions.sh, line  121:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m   		die "$@"
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of `emerge --info '=sys-fs/zfs-kmod-2.3.3::gentoo'`,
 [31;01m*[0m the complete build log and the output of `emerge -pqv '=sys-fs/zfs-kmod-2.3.3::gentoo'`.
 [31;01m*[0m The complete build log is located at '/var/tmp/portage/sys-fs/zfs-kmod-2.3.3/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sys-fs/zfs-kmod-2.3.3/temp/environment'.
 [31;01m*[0m Working directory: '/var/tmp/portage/sys-fs/zfs-kmod-2.3.3/work/zfs-2.3.3'
 [31;01m*[0m S: '/var/tmp/portage/sys-fs/zfs-kmod-2.3.3/work/zfs-2.3.3'

>>> Failed to emerge sys-fs/zfs-kmod-2.3.3, Log file:

>>>  '/var/tmp/portage/sys-fs/zfs-kmod-2.3.3/temp/build.log'
 * Messages for package sys-fs/zfs-kmod-2.3.3:
 * ERROR: sys-fs/zfs-kmod-2.3.3::gentoo failed (configure phase):
 *   econf failed
 * 
 * Call stack:
 *               ebuild.sh, line  136:  Called src_configure
 *             environment, line 2828:  Called econf '--bindir=/bin' '--sbindir=/sbin' '--with-config=kernel' '--with-linux=/usr/src/linux' '--with-linux-obj=/usr/src/linux' '--disable-debug' 'GENTOO_MAKEARGS_EVAL='ARCH=x86' 'V=1' 'KBUILD_VERBOSE=1' 'CONFIG_WERROR=' 'CONFIG_OBJTOOL_WERROR=' 'CONFIG_MODULE_SIG_ALL=' 'CONFIG_MODULE_COMPRESS_ALL=' 'CONFIG_MODULE_COMPRESS_GZIP=' 'CONFIG_MODULE_COMPRESS_XZ=' 'CONFIG_MODULE_COMPRESS_ZSTD=' 'DEPMOD=true' 'STRIP=true' 'CROSS_COMPILE=x86_64-pc-linux-gnu-' 'HOSTCC=x86_64-pc-linux-gnu-gcc' 'HOSTCXX=x86_64-pc-linux-gnu-g++' 'HOSTCFLAGS=-march=znver4 -O2 -pipe' 'HOSTCXXFLAGS=-march=znver4 -O2 -pipe' 'HOSTLDFLAGS=-Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs' 'HOSTPKG_CONFIG=x86_64-pc-linux-gnu-pkg-config' 'CC=/usr/bin/x86_64-pc-linux-gnu-gcc-14' 'CXX=/usr/bin/x86_64-pc-linux-gnu-g++-14' 'LD=/usr/bin/x86_64-pc-linux-gnu-ld.bfd' 'AR=/usr/bin/x86_64-pc-linux-gnu-gcc-ar' 'NM=/usr/bin/x86_64-pc-linux-gnu-gcc-nm' 'OBJCOPY=/usr/bin/x86_64-pc-linux-gnu-objcopy' 'OBJDUMP=/usr/bin/x86_64-pc-linux-gnu-objdump' 'READELF=/usr/bin/x86_64-pc-linux-gnu-readelf'' 'TEST_JOBS=17'
 *        phase-helpers.sh, line  647:  Called __helpers_die 'econf failed'
 *   isolated-functions.sh, line  121:  Called die
 * The specific snippet of code:
 *   		die "$@"
 * 
 * If you need support, post the output of `emerge --info '=sys-fs/zfs-kmod-2.3.3::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sys-fs/zfs-kmod-2.3.3::gentoo'`.
 * The complete build log is located at '/var/tmp/portage/sys-fs/zfs-kmod-2.3.3/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sys-fs/zfs-kmod-2.3.3/temp/environment'.
 * Working directory: '/var/tmp/portage/sys-fs/zfs-kmod-2.3.3/work/zfs-2.3.3'
 * S: '/var/tmp/portage/sys-fs/zfs-kmod-2.3.3/work/zfs-2.3.3'

Mod edit: [code] tags added for clarity. — JRG

MarkYork · Post by **MarkYork** » Thu Jul 31, 2025 9:25 pm

Adding some extra details to the case:

# uname -r
6.12.31-gentoo-gentoo-dist

# readlink /usr/src/linux
linux-6.12.31-gentoo

Post by **John R. Graham** » Fri Aug 01, 2025 9:53 pm

MarkYork wrote:Below are the error logs and a confirmation that my kernel is set with CONFIG_MODULES...

I don't see that confirmation. Could you post the output of

Code: Select all

grep CONFIG_MODULES= /usr/src/linux/.config

please?

- John

Asumi · Post by **Asumi** » Fri Aug 15, 2025 9:22 pm

I found this thread while googling the same error, my problem was that I had umask 0027 when building the kernel so emerging zfs-kmod was failing due to some messed up permissions, some files in the kernel tree were readable by portage and others were not.
Re-emerging gentoo-sources and rebuilding with umask 0022 seemed to fix the error for me.

shimbob · Post by **shimbob** » Sat Feb 07, 2026 11:07 pm

Getting hit with this error as well, while trying to install zfs-kmod-2.4.0(*) on kernel 6.18.8

...
checking kernel source directory... /usr/src/linux
checking kernel build directory... /usr/src/naztoo
checking kernel source version... 6.18.8-xanmod1
checking for kernel config option compatibility... done
checking whether CONFIG_MODULES is defined... error
...
naztoo ~ # grep CONFIG_MODULES= /usr/src/naztoo/.config
CONFIG_MODULES=y

(*) Disclaimer: I was getting impatient while waiting for zfs-kmod-2.4.0 to get stable so copied over the 2.3.5.ebuild into my local repo and tweaked it.

Post by **sam_** » Sat Feb 07, 2026 11:34 pm

The error is a generic one that can happen when it fails to probe the kernel configuration or run a make command in there. Check config.log and permissions as others did above.

(You wouldn't need to do that, you can just use package.accept_keywords.)

shimbob · Post by **shimbob** » Sun Feb 08, 2026 7:18 pm

I ended up extracting the ZFS-2.4.0 source manually, then copied and ran the configure command that portage was running:

$ ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --datarootdir=/usr/share --disable-dependency-tracking --disable-silent-rules --disable-static --docdir=/usr/share/doc/zfs-kmod-2.4.0 --htmldir=/usr/share/doc/zfs-kmod-2.4.0/html --with-sysroot=/ --libdir=/usr/lib64 --bindir=/bin --sbindir=/sbin --with-config=kernel --with-linux=/usr/src/linux --with-linux-obj=/usr/src/naztoo --disable-debug GENTOO_MAKEARGS_EVAL=\''ARCH=x86'\'' '\''V=1'\'' '\''KBUILD_VERBOSE=1'\'' '\''CONFIG_WERROR='\'' '\''CONFIG_OBJTOOL_WERROR='\'' '\''CONFIG_MODULE_SIG_ALL='\'' '\''CONFIG_MODULE_COMPRESS_ALL='\'' '\''CONFIG_MODULE_COMPRESS_GZIP='\'' '\''CONFIG_MODULE_COMPRESS_XZ='\'' '\''CONFIG_MODULE_COMPRESS_ZSTD='\'' '\''DEPMOD=true'\'' '\''STRIP=true'\'' '\''CROSS_COMPILE=x86_64-pc-linux-gnu-'\'' '\''HOSTCC=x86_64-pc-linux-gnu-gcc'\'' '\''HOSTCXX=x86_64-pc-linux-gnu-g++'\'' '\''HOSTCFLAGS=-O3 -pipe -flto -march=native -fomit-frame-pointer '\'' '\''HOSTCXXFLAGS=-O3 -pipe -flto -march=native -fomit-frame-pointer '\'' '\''HOSTLDFLAGS=-Wl,-O1 -Wl,--as-needed'\'' '\''HOSTPKG_CONFIG=x86_64-pc-linux-gnu-pkg-config'\'' '\''CC=/usr/bin/x86_64-pc-linux-gnu-gcc-15'\'' '\''CXX=/usr/bin/x86_64-pc-linux-gnu-g++-15'\'' '\''LD=/usr/bin/x86_64-pc-linux-gnu-ld.bfd'\'' '\''AR=/usr/bin/x86_64-pc-linux-gnu-gcc-ar'\'' '\''NM=/usr/bin/x86_64-pc-linux-gnu-gcc-nm'\'' '\''OBJCOPY=/usr/bin/x86_64-pc-linux-gnu-objcopy'\'' '\''OBJDUMP=/usr/bin/x86_64-pc-linux-gnu-objdump'\'' '\''READELF=/usr/bin/x86_64-pc-linux-gnu-readelf'\''' TEST_JOBS=6 --enable-linux-builtin

And that ran without problems.

Going back to my ebuild and digging into the error, config.log shows:

configure checking whether CONFIG_MODULES is defined
configure
KBUILD_MODPOST_NOFINAL= KBUILD_MODPOST_WARN=
make modules -k -j6

CONFIG_MODULES=y CFLAGS_MODULE=-DCONFIG_MODULES

-C /usr/src/naztoo M=/var/tmp/portage/sys-fs/zfs-kmod-2.4.0/work/zfs-2.4.0/build/conftest >build/conftest/build.log 2>&1
configure $? = 2
configure test -f build/conftest/conftest.o
configure $? = 1
configure result: error
configure error:
*** This kernel is unable to compile object files.
***
*** Please make sure you prepared the Linux source tree
*** by running `make prepare` there.

then digging deeper, .../build/conftest/build.log shows:

naztoo /var/tmp/portage/sys-fs/zfs-kmod-2.4.0/work/zfs-2.4.0/build/conftest # cat build.log
make: Entering directory '/usr/src/naztoo'
make[1]: Entering directory '/var/tmp/portage/sys-fs/zfs-kmod-2.4.0/work/zfs-2.4.0/build/conftest'
/usr/src/linux-6.18.8-xanmod/Makefile:813: /usr/src/linux-6.18.8-xanmod/arch/amd64/Makefile: No such file or directory
make[2]: *** No rule to make target '/usr/src/linux-6.18.8-xanmod/arch/amd64/Makefile'.
/usr/src/linux-6.18.8-xanmod/Makefile:813: Failed to remake makefile '/usr/src/linux-6.18.8-xanmod/arch/amd64/Makefile'.
make[1]: *** [/usr/src/linux-6.18.8-xanmod/Makefile:248: __sub-make] Error 2
make[1]: Target 'modules' not remade because of errors.
make[1]: Leaving directory '/var/tmp/portage/sys-fs/zfs-kmod-2.4.0/work/zfs-2.4.0/build/conftest'
make: *** [/usr/src/linux-6.18.8-xanmod/Makefile:248: __sub-make] Error 2
make: Target 'modules' not remade because of errors.
make: Leaving directory '/usr/src/naztoo'

And indeed, the entire linux-6.18.8-xanmod/arch/amd64 directory is missing. Just installed xanmod-sources-6.18.9 and that also seems to be missing arch/amd64.

(zfs-kmod-2.4.0 is not in portage yet)

ZFS upgrade failure

ZFS upgrade failure

Re: ZFS upgrade failure