On a brand new prefix installation I see some path reported by perl are not prefixed by $EPREFIX: $ perl -V Summary of my perl5 (revision 5 version 32 subversion 1) configuration: Platform: osname=linux osvers=3.10.0-1160.15.2.el7.x86_64 archname=x86_64-linux uname='linux ursa.cerit-sc.cz 3.10.0-1160.15.2.el7.x86_64 #1 smp thu jan 21 16:15:07 est 2021 x86_64 intel(r) xeon(r) gold 6254 cpu @ 3.10ghz genuineintel gnulinux ' config_args='-des -Dinstallprefix=/storage/brno3-cerit/home/mmokrejs/gentoo/usr -Dinstallusrbinperl=n -Ui_xlocale -Di_ndbm -Di_gdbm -Di_db -DDEBUGGING=none -Dlibpth=/storage/brno3-cerit/home/mmokrejs/gentoo/lib64 /storage/brno3-cerit/home/mmokrejs/gentoo/usr/lib64 /lib/*-linux-gnu /usr/lib/*-linux-gnu /lib64 /lib/64 /usr/lib64 /usr/lib/64 /lib32 /usr/lib32 /lib /usr/lib -Dnoextensions=ODBM_File -Duseshrplib -Darchname=x86_64-linux -Dcc=x86_64-pc-linux-gnu-gcc -Dar=x86_64-pc-linux-gnu-ar -Dnm=x86_64-pc-linux-gnu-nm -Dcpp=x86_64-pc-linux-gnu-gcc -E -Dranlib=x86_64-pc-linux-gnu-ranlib -Doptimize=-O2 -pipe -mtune=native -ftree-vectorize -Dldflags=-Wl,-O1 -Wl,--as-needed -Dprefix=/storage/brno3-cerit/home/mmokrejs/gentoo/usr -Dsiteprefix=/storage/brno3-cerit/home/mmokrejs/gentoo/usr/local -Dvendorprefix=/storage/brno3-cerit/home/mmokrejs/gentoo/usr -Dscriptdir=/storage/brno3-cerit/home/mmokrejs/gentoo/usr/bin -Dprivlib=/storage/brno3-cerit/home/mmokrejs/gentoo/usr/lib64/perl5/5.32 -Darchlib=/storage/brno3-cerit/home/mmokrejs/gentoo/usr/lib64/perl5/5.32/x86_64-linux -Dsitelib=/storage/brno3-cerit/home/mmokrejs/gentoo/usr/local/lib64/perl5/5.32 -Dsitearch=/storage/brno3-cerit/home/mmokrejs/gentoo/usr/local/lib64/perl5/5.32/x86_64-linux -Dvendorlib=/storage/brno3-cerit/home/mmokrejs/gentoo/usr/lib64/perl5/vendor_perl/5.32 -Dvendorarch=/storage/brno3-cerit/home/mmokrejs/gentoo/usr/lib64/perl5/vendor_perl/5.32/x86_64-linux -Dman1dir=/storage/brno3-cerit/home/mmokrejs/gentoo/usr/share/man/man1 -Dman3dir=/storage/brno3-cerit/home/mmokrejs/gentoo/usr/share/man/man3 -Dsiteman1dir=/storage/brno3-cerit/home/mmokrejs/gentoo/usr/local/man/man1 -Dsiteman3dir=/storage/brno3-cerit/home/mmokrejs/gentoo/usr/local/man/man3 -Dvendorman1dir=/storage/brno3-cerit/home/mmokrejs/gentoo/usr/share/man/man1 -Dvendorman3dir=/storage/brno3-cerit/home/mmokrejs/gentoo/usr/share/man/man3 -Dman1ext=1 -Dman3ext=3pm -Dlibperl=libperl.so.5.32.1 -Dlocincpth=/storage/brno3-cerit/home/mmokrejs/gentoo/usr/include -Dglibpth=/storage/brno3-cerit/home/mmokrejs/gentoo/lib64 /storage/brno3-cerit/home/mmokrejs/gentoo/usr/lib64 -Duselargefiles -Dd_semctl_semun -Dcf_by=Gentoo -Dmyhostname=localhost -Dperladmin=root@localhost -Ud_csh -Dsh=/storage/brno3-cerit/home/mmokrejs/gentoo/bin/sh -Dtargetsh=/storage/brno3-cerit/home/mmokrejs/gentoo/bin/sh -Uusenm -Ui_xlocale -Di_ndbm -Di_gdbm -Di_db -DDEBUGGING=none -Dlibpth=/storage/brno3-cerit/home/mmokrejs/gentoo/lib64 /storage/brno3-cerit/home/mmokrejs/gentoo/usr/lib64 /lib/*-linux-gnu /usr/lib/*-linux-gnu /lib64 /lib/64 /usr/lib64 /usr/lib/64 /lib32 /usr/lib32 /lib /usr/lib -Dnoextensions=ODBM_File' hint=recommended useposix=true d_sigaction=define useithreads=undef usemultiplicity=undef use64bitint=define use64bitall=define uselongdouble=undef usemymalloc=n default_inc_excludes_dot=define bincompat5005=undef Compiler: cc='x86_64-pc-linux-gnu-gcc' ccflags ='-fwrapv -fno-strict-aliasing -pipe -I/storage/brno3-cerit/home/mmokrejs/gentoo/usr/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64' optimize='-O2 -pipe -mtune=native -ftree-vectorize' cppflags='-fwrapv -fno-strict-aliasing -pipe -I/storage/brno3-cerit/home/mmokrejs/gentoo/usr/include' ccversion='' gccversion='10.2.0' gccosandvers='' intsize=4 longsize=8 ptrsize=8 doublesize=8 byteorder=12345678 doublekind=3 d_longlong=define longlongsize=8 d_longdbl=define longdblsize=16 longdblkind=3 ivtype='long' ivsize=8 nvtype='double' nvsize=8 Off_t='off_t' lseeksize=8 alignbytes=8 prototype=define Linker and Libraries: ld='x86_64-pc-linux-gnu-gcc' ldflags ='-Wl,-O1 -Wl,--as-needed' libpth=/storage/brno3-cerit/home/mmokrejs/gentoo/lib64 /storage/brno3-cerit/home/mmokrejs/gentoo/usr/lib64 /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu /lib64 /lib/64 /usr/lib64 /usr/lib/64 /lib32 /usr/lib32 /lib /usr/lib /mnt/storage-brno3-cerit/nfs4/home/mmokrejs/gentoo/usr/x86_64-pc-linux-gnu/gcc-bin/10.2.0/../../../lib/gcc/x86_64-pc-linux-gnu/10.2.0/include-fixed /storage/brno3-cerit/home/mmokrejs/gentoo/usr/lib /lib/../lib64 /usr/lib/../lib64 libs=-lgdbm -ldb -ldl -lm -lcrypt -lutil -lc -lgdbm_compat perllibs=-ldl -lm -lcrypt -lutil -lc libc=libc-2.17.so so=so useshrplib=true libperl=libperl.so.5.32.1 gnulibc_version='2.32' Dynamic Linking: dlsrc=dl_dlopen.xs dlext=so d_dlsymun=undef ccdlflags='-Wl,-E' cccdlflags='-fPIC' lddlflags='-shared -O2 -pipe -mtune=native -ftree-vectorize -Wl,-O1 -Wl,--as-needed' Characteristics of this binary (from libperl): Compile-time options: HAS_TIMES PERLIO_LAYERS PERL_COPY_ON_WRITE PERL_DONT_CREATE_GVSV PERL_MALLOC_WRAP PERL_OP_PARENT PERL_PRESERVE_IVUV USE_64_BIT_ALL USE_64_BIT_INT USE_LARGE_FILES USE_LOCALE USE_LOCALE_COLLATE USE_LOCALE_CTYPE USE_LOCALE_NUMERIC USE_LOCALE_TIME USE_PERLIO USE_PERL_ATOF Locally applied patches: 0001-Fix-hpux-hints.patch - Fix hpux hints 0002-aix-gcc-detection-and-shared-library-soname-support.patch - aix gcc detection and shared library soname support 0003-cpan-ExtUtils-MakeMaker-drop-PORTAGE_TMPDIR-from-LD_.patch - cpan/ExtUtils-MakeMaker: drop $PORTAGE_TMPDIR from LD_RUN_PATH - Bug: https://bugs.gentoo.org/105054 0004-Remove-rpath-and-append-LDFLAGS-to-lddlflags.patch - Remove -rpath and append LDFLAGS to lddlflags 0005-Add-headers-for-opensolaris.patch - Add headers for opensolaris 0006-List-packaged-patches-in-patchlevel.h.patch - List packaged patches for perl-5.32.1(perl-5.32.0-patches-1) in patchlevel.h - Bug: https://bugs.debian.org/567489 0007-Cleanup-PATH-and-shrpenv.patch - Cleanup PATH and shrpenv 0008-Tweak-enc2xs-to-follow-symlinks-and-ignore-missing-I.patch - Tweak enc2xs to follow symlinks and ignore missing @INC directories. - Bug: https://bugs.debian.org/290336 0009-darwin-Use-CC-to-link.patch - darwin: Use $CC to link - Bug: https://bugs.gentoo.org/297751 0010-Provide-a-sensible-INSTALLDIRS-default-for-modules-i.patch - Provide a sensible INSTALLDIRS default for modules installed from CPAN. 0011-Fix-interix-hints.patch - Fix interix hints 0012-Set-libperl-soname.patch - Set libperl soname - Bug: https://bugs.gentoo.org/286840 0013-Add-etc-perl-to-INC.patch - Add /etc/perl to @INC 0014-cpan-ExtUtils-MakeMaker-remove-targets-that-generate.patch - cpan/ExtUtils-MakeMaker: remove targets that generate perllocal.pod 0015-Don-t-force-fstack-protector-on-everyone.patch - Don't force -fstack-protector on everyone - Bug: https://bugs.gentoo.org/348557 0016-Do-not-set-custom-CFLAGS-in-cpan-Digest-SHA.patch - Do not set custom CFLAGS in cpan/Digest-SHA - Bug: https://bugs.gentoo.org/506818 0017-Configure-Don-t-include-sources-in-usr-local-for-com.patch - Configure: Don't include sources in /usr/local/ for compiling perl 0018-cpan-IO-Socket-IP-Disable-network-tests.patch - cpan/IO-Socket-IP: Disable network tests 0019-Fix-EUMM-podlocal-tests.patch - Fix EUMM podlocal tests 0020-Skip-auto-linking-nsl-and-cl.patch - Skip auto-linking nsl and cl - Bug: https://rt.perl.org/Public/Bug/Display.html?id=13148 0021-Disable-porting-tests-which-create-fun-false-failure.patch - Disable porting tests which create fun false-failures all over travis 0022-Disable-PathTools-tests-which-fails-under-sandboxing.patch - Disable PathTools tests which fails under sandboxing - Bug: https://bugs.gentoo.org/645084 0023-Fix-CPAN-FirstTime-defaults-with-nonexisting-site-di.patch - Fix CPAN::FirstTime defaults with nonexisting site dirs if a parent is writable - Bug: https://bugs.debian.org/688842 0024-Pass-LD-settings-through-to-subdirectories.patch - Pass LD settings through to subdirectories - Bug: https://bugs.debian.org/758471 0025-Memoize-Storable-respect-nstore-option-not-respected.patch - Memoize::Storable: respect 'nstore' option not respected - Bug: https://bugs.debian.org/587650 - Bug: https://rt.cpan.org/Public/Bug/Display.html?id=77790 0026-Better-errors-for-man-pages-from-standard-input.patch - Better errors for man pages from standard input - Bug: https://bugs.debian.org/777405 0027-Respect-umask-during-installation.patch - Respect umask during installation 0028-Document-that-CCFLAGS-should-include-Config-ccflags.patch - Document that CCFLAGS should include $Config{ccflags} - Bug: https://bugs.debian.org/628522 - Bug: https://rt.cpan.org/Public/Bug/Display.html?id=68613 0029-Fix-parallel-building.patch - Fix parallel building 0030-Add-support-for-Dgentoolibdirs.patch - Add support for -Dgentoolibdirs Built under linux Compiled at Mar 17 2021 19:40:31 @INC: /etc/perl /storage/brno3-cerit/home/mmokrejs/gentoo/usr/local/lib64/perl5/5.32/x86_64-linux /storage/brno3-cerit/home/mmokrejs/gentoo/usr/local/lib64/perl5/5.32 /storage/brno3-cerit/home/mmokrejs/gentoo/usr/lib64/perl5/vendor_perl/5.32/x86_64-linux /storage/brno3-cerit/home/mmokrejs/gentoo/usr/lib64/perl5/vendor_perl/5.32 /storage/brno3-cerit/home/mmokrejs/gentoo/usr/lib64/perl5/5.32/x86_64-linux /storage/brno3-cerit/home/mmokrejs/gentoo/usr/lib64/perl5/5.32 $ $ emerge --info Portage 3.0.17 (python 3.8.8-final-0, default/linux/amd64/17.1/no-multilib/prefix/kernel-3.2+, gcc-10.2.0, glibc-2.32-r8, 3.10.0-1160.15.2.el7.x86_64 x86_64) ================================================================= System uname: Linux-3.10.0-1160.15.2.el7.x86_64-x86_64-Intel-R-_Xeon-R-_Gold_6254_CPU_@_3.10GHz-with-glibc2.2.5 KiB Mem: 10563841808 total, 722431560 free KiB Swap: 4194300 total, 3895952 free Timestamp of repository gentoo: Wed, 17 Mar 2021 01:00:01 +0000 Head commit of repository gentoo: 7f45254f083ec6d66c62d554198d449ea52e3420 sh bash 5.1_p4 ld GNU ld (Gentoo 2.35.2 p1) 2.35.2 app-shells/bash: 5.1_p4::gentoo dev-java/java-config: 2.3.1::gentoo dev-lang/perl: 5.32.1::gentoo dev-lang/python: 3.8.8::gentoo, 3.9.2::gentoo dev-util/cmake: 3.19.7::gentoo sys-apps/baselayout: 2.7-r1::gentoo sys-apps/sandbox: 2.21::gentoo sys-devel/autoconf: 2.71::gentoo sys-devel/automake: 1.16.3-r1::gentoo sys-devel/binutils: 2.35.2::gentoo sys-devel/gcc: 9.3.0-r2::gentoo, 10.2.0-r5::gentoo sys-devel/gcc-config: 2.4::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.11::gentoo (virtual/os-headers) sys-libs/glibc: 2.32-r8::gentoo Repositories: gentoo location: /mnt/storage-brno3-cerit/nfs4/home/mmokrejs/gentoo/var/db/repos/gentoo sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-jobs: 1 sync-rsync-verify-max-age: 24 sync-rsync-extra-opts: sync-rsync-verify-metamanifest: no science location: /mnt/storage-brno3-cerit/nfs4/home/mmokrejs/gentoo/var/lib/layman/science masters: gentoo priority: 50 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="@FREE Intel-SDP intel-ucode fasta meme mRNAmarkup ApE modeller gmap abyss swiss-prot Aladdin AVASYS pyvcf Non-profit-OSL-3.0 estscan blat staden CeCILL-1.1 phrap STRIDE cctbx-2.0 bh-luxi ARIADNE unRAR trf freedist free-noncomm genscan no-source-code BSD MIT BSD-2 unicode Subversion" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -mtune=native -ftree-vectorize" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /storage/brno3-cerit/home/mmokrejs/gentoo/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /storage/brno3-cerit/home/mmokrejs/gentoo/etc/env.d /storage/brno3-cerit/home/mmokrejs/gentoo/etc/gentoo-release" CXXFLAGS="-O2 -pipe -mtune=native -ftree-vectorize" DISTDIR="/storage/brno3-cerit/home/mmokrejs/gentoo/var/cache/distfiles" ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" FCFLAGS="-O2 -pipe -mtune=native -ftree-vectorize" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles force-prefix ipc-sandbox merge-sync multilib-strict network-sandbox news nostrip parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans unprivileged" FFLAGS="-O2 -pipe -mtune=native -ftree-vectorize" GENTOO_MIRRORS="http://distfiles.gentoo.org" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j100" PKGDIR="/storage/brno3-cerit/home/mmokrejs/gentoo/var/cache/binpkgs" PORTAGE_CONFIGROOT="/storage/brno3-cerit/home/mmokrejs/gentoo/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" PORTAGE_TMPDIR="/scratch.ssd/mmokrejs/job_2285717.cerit-pbs.cerit-sc.cz" USE="acl amd64 asm avx avx2 berkdb boost bzip2 cli crypt dri emboss fortran gdbm gmp iconv icu java jpeg jpg lapack libglvnd libtirpc mariadb mmx ncurses nfs nls nptl nptlonly objc openmp openssl pbs pcre pcre16 pdf perl png prefix readline sctp seccomp server session split-usr sqlite sse sse2 sse3 sse4_1 sse4_2 ssl sslv3 ssse3 svg tcl tcpd threads tiff tk truetype unicode vim-syntax xml zlib" ABI_X86="64" ADA_TARGET="gnat_2018" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-3 php7-4" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_8" PYTHON_TARGETS="python3_8" RUBY_TARGETS="ruby26" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq proto steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
you're specifically referring to @INC?
Not only @INC, also "libpth=" which could be a real problem on a different ARCH or ABI system.
0013-Add-etc-perl-to-INC.patch - Add /etc/perl to @INC This should be disabled prefix systems.
Long gone.