# emerge -av sci-libs/pdal These are the packages that would be merged, in order: Calculating dependencies... done! Dependency resolution took 3.29 s. [ebuild R ] sci-libs/pdal-2.4.3:0/14::gentoo USE="-postgres -test" 0 KiB Total: 1 package (1 reinstall), Size of downloads: 0 KiB Build fails with: ...8><... snip /var/tmp/portage/sci-libs/pdal-2.4.3/work/PDAL-2.4.3-src/pdal/Geometry.cpp:143:59: error: invalid conversion from 'const OGRSpatialReference*' to 'OGRSpatialReference*' [-fpermissive] 143 | OGRSpatialReference *srs = m_geom->getSpatialReference(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ | | | const OGRSpatialReference* /var/tmp/portage/sci-libs/pdal-2.4.3/work/PDAL-2.4.3-src/pdal/Geometry.cpp: In member function 'pdal::Utils::StatusWithReason pdal::Geometry::transform(pdal::SpatialReference)': /var/tmp/portage/sci-libs/pdal-2.4.3/work/PDAL-2.4.3-src/pdal/Geometry.cpp:162:61: error: invalid conversion from 'const OGRSpatialReference*' to 'OGRSpatialReference*' [-fpermissive] 162 | OGRSpatialReference *inSrs = m_geom->getSpatialReference(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ | | | const OGRSpatialReference* ...8><... snip Same error for =sci-libs/pdal-2.5.0 (with ~amd64 in accept_keywords). Reproducible: Always # emerge --info sci-libs/pdal Portage 3.0.47 (python 3.11.3-final-0, default/linux/amd64/17.1/desktop/plasma, gcc-13, glibc-2.37-r3, 6.3.1-gentoo-x86_64-venus x86_64) ================================================================= System Settings ================================================================= System uname: Linux-6.3.1-gentoo-x86_64-venus-x86_64-Intel-R-_Core-TM-_i7-9750H_CPU_@_2.60GHz-with-glibc2.37 KiB Mem: 16242660 total, 2510696 free KiB Swap: 16777212 total, 16776188 free Timestamp of repository gentoo: Thu, 11 May 2023 00:30:01 +0000 Head commit of repository gentoo: e3577ba5886bc955089cfc71c17ff64670f83f63 Timestamp of repository steam-overlay: Wed, 10 May 2023 18:18:35 +0000 Head commit of repository steam-overlay: e8c2b4ce5fa18d50d70c3c325626de6ec9ebc796 sh bash 5.1_p16-r2 ld GNU ld (Gentoo 2.39 p6) 2.39.0 app-misc/pax-utils: 1.3.7::gentoo app-shells/bash: 5.1_p16-r2::gentoo dev-java/java-config: 2.3.1::gentoo dev-lang/perl: 5.36.0-r2::gentoo dev-lang/python: 3.10.10_p3::gentoo, 3.11.3::gentoo dev-lang/rust: 1.69.0-r1::gentoo dev-util/cmake: 3.25.3::gentoo dev-util/meson: 1.1.0::gentoo sys-apps/baselayout: 2.13-r1::gentoo sys-apps/openrc: 0.46::gentoo sys-apps/sandbox: 2.29::gentoo sys-devel/autoconf: 2.13-r7::gentoo, 2.71-r5::gentoo sys-devel/automake: 1.16.5-r1::gentoo sys-devel/binutils: 2.39-r5::gentoo sys-devel/binutils-config: 5.5::gentoo sys-devel/clang: 15.0.7-r1::gentoo, 16.0.3::gentoo sys-devel/gcc: 13.1.0-r1::gentoo sys-devel/gcc-config: 2.10::gentoo sys-devel/libtool: 2.4.7-r1::gentoo sys-devel/lld: 15.0.7::gentoo sys-devel/llvm: 15.0.7::gentoo, 16.0.3::gentoo sys-devel/make: 4.4.1::gentoo sys-kernel/linux-headers: 6.3::gentoo (virtual/os-headers) sys-libs/glibc: 2.37-r3::gentoo Repositories: gentoo location: /var/db/repos/gentoo sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 volatile: False sync-rsync-verify-max-age: 24 sync-rsync-verify-metamanifest: yes sync-rsync-extra-opts: sync-rsync-verify-jobs: 1 localrepo location: /var/db/repos/localrepo masters: gentoo volatile: False steam-overlay location: /var/db/repos/steam-overlay sync-type: git sync-uri: https://github.com/gentoo-mirror/steam-overlay.git masters: gentoo volatile: False ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="@FREE" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-march=native -O2 -pipe" DISTDIR="/var/cache/distfiles" ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GDK_PIXBUF_MODULE_FILE 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 XDG_STATE_HOME" FCFLAGS="-march=native -O2 -pipe" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg-live config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-march=native -O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LEX="flex" MAKEOPTS="-j6" PKGDIR="/var/cache/binpkgs" PORTAGE_CONFIGROOT="/" 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="/var/tmp" SHELL="/bin/bash" USE="X a52 aac acl acpi activities alsa amd64 bluetooth branding bzip2 cairo cdda cdr cli crypt cups dbus declarative dri dts dvd dvdr elogind encode eselect-ldso exif flac fortran gdbm gif gpm grub2 gtk3 gui hwaccel iconv icu ipv6 jpeg kde kwallet lcms libglvnd libnotify libtirpc mad mng mp3 mp4 mpeg multilib ncurses nptl numa offensive ogg opencl opengl openmp pam pango pcre pdf pipewire plasma png policykit ppds pulseadio qml qt5 readline screencast sdl seccomp semantic-desktop sound spell split-usr ssl startup-notification svg synaptics test-rust tiff truetype udev udisks unicode upower usb vorbis vulkan wayland webp widgets wxwidgets x264 xattr xcb xft xinerama xml xv xvid zlib" ABI_X86="64" ADA_TARGET="gnat_2021" 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="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt rdrand sse sse2 sse3 sse4_1 sse4_2 ssse3" 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" GRUB_PLATFORMS="efi-64" INPUT_DEVICES="libinput" KERNEL="linux" L10N="en-US" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LLVM_TARGETS="BPF NVPTX WebAssembly X86" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-4 php8-0" POSTGRES_TARGETS="postgres14" PYTHON_SINGLE_TARGET="python3_11" PYTHON_TARGETS="python3_11" RUBY_TARGETS="ruby30" USERLAND="GNU" VIDEO_CARDS="nvidia intel i915 i965 iris" 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: ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EMERGE_DEFAULT_OPTS, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LC_ALL, LD, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS ================================================================= Package Settings ================================================================= sci-libs/pdal-2.4.3::gentoo was built with the following: USE="-postgres -test" ABI_X86="(64)" FEATURES="fixlafiles usersandbox qa-unresolved-soname-deps assume-digests binpkg-logs parallel-fetch unmerge-orphans userpriv protect-owned binpkg-docompress binpkg-dostrip config-protect-if-modified ebuild-locks strict sfperms news userfetch merge-sync distlocks pid-sandbox unknown-features-warn usersync buildpkg-live unmerge-logs binpkg-multi-instance sandbox network-sandbox ipc-sandbox preserve-libs xattr multilib-strict"
Created attachment 861465 [details] build.log of sci-libs/pdal-2.4.3
I should add that neither version 2.4.3 nor 2.5.3 (the ~amd64 one) ebuilds seems to accept user patches. Should I open another bug for this?
(In reply to José de Paula Rodrigues from comment #2) > I should add that neither version 2.4.3 nor 2.5.3 (the ~amd64 one) ebuilds > seems to accept user patches. Should I open another bug for this? That doesn't sound right to me. Note that patches must end in .patch (iirc .diff may be accepted too): ``` mkdir -p /etc/portage/patches/sci-libs/pdal && echo "--- a/foo.c" >> /etc/portage/patches/sci-libs/pdal/foo.patch ``` and then.. ``` $ e pdal-2.5.3.ebuild clean prepare Appending /home/sam/git/gentoo to PORTDIR_OVERLAY... * PDAL-2.5.3-src.tar.bz2 BLAKE2B SHA512 size ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking PDAL-2.5.3-src.tar.bz2 to /var/tmp/portage/sci-libs/pdal-2.5.3/work >>> Source unpacked in /var/tmp/portage/sci-libs/pdal-2.5.3/work >>> Preparing source in /var/tmp/portage/sci-libs/pdal-2.5.3/work/PDAL-2.5.3-src ... * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-libs/pdal-2.5.3/work/PDAL-2.5.3-src" * Build directory (BUILD_DIR): "/var/tmp/portage/sci-libs/pdal-2.5.3/work/PDAL-2.5.3-src_build" * ============================================================================================================================================================================================================= * Applying user patches from /etc/portage/patches ... * Applying foo.patch ... gpatch: **** Only garbage was found in the patch input. [ !! ] * ERROR: sci-libs/pdal-2.5.3::gentoo failed (prepare phase): * patch -p1 failed with /etc/portage/patches/sci-libs/pdal/foo.patch ``` so it does work.
Of course, the patch filename has to end with '.patch', my bad. Here is a user patch that allows building sci-libs/pdal-2.4.3 against gcc-13
Created attachment 861467 [details, diff] allow pdal-2.4.3 build with gcc-13
Created attachment 861468 [details, diff] allow pdal-2.5.3 build with gcc-13 pdal-2.5.3 doesn't need <cstdint> included in a vendor/lazperf header file, unlike version 2.4.3.
@Jose thx for your contribution... can you also suggest this patch to upstream?
(In reply to Thomas Bettler from comment #7) > @Jose thx for your contribution... can you also suggest this patch to > upstream? Hi, Thomas, while investigating the issue upstream, I found out that they already corrected in their master branch: https://github.com/PDAL/PDAL/commit/7b4b2d942bc0390d370d5b90f31daf77148005f6 They've used a different approach, I'm updating my user patch to reflect upstream change.
Created attachment 861527 [details, diff] allow pdal-2.5.3 build with gcc-13 Following upstream fix on master branch.
Created attachment 861528 [details, diff] allow pdal-2.4.3 build with gcc-13 Following upstream fix on master branch.
Created attachment 861529 [details, diff] allow pdal-2.4.3 build with gcc-13 Follow upstream fix.
*** Bug 906294 has been marked as a duplicate of this bug. ***
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d64174f63fa545f1c60913c1d244eba99483ec13 commit d64174f63fa545f1c60913c1d244eba99483ec13 Author: Thomas Bettler <thomas.bettler@gmail.com> AuthorDate: 2023-05-11 16:33:43 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2023-05-14 07:26:45 +0000 sci-libs/pdal: fix gcc-13 build Closes: https://bugs.gentoo.org/906102 Closes: https://github.com/gentoo/gentoo/pull/30999 Signed-off-by: Thomas Bettler <thomas.bettler@gmail.com> Signed-off-by: Sam James <sam@gentoo.org> sci-libs/pdal/files/pdal-2.4.3-fix-gcc13.patch | 29 ++++++++++++ sci-libs/pdal/files/pdal-2.4.3-fix-gdal37.patch | 37 +++++++++++++++ sci-libs/pdal/pdal-2.4.3-r1.ebuild | 63 +++++++++++++++++++++++++ sci-libs/pdal/pdal-2.5.3-r1.ebuild | 61 ++++++++++++++++++++++++ 4 files changed, 190 insertions(+)
