# emerge -pqv '=sci-libs/vtk-9.1.0-r2::gentoo' [ebuild N ] sci-libs/vtk-9.1.0-r2 USE="boost doc examples ffmpeg gdal imaging mysql odbc openmp postgres python qt5 rendering tbb threads tk views web (-all-modules) (-cuda) -debug (-java) (-mpi) -test" PYTHON_SINGLE_TARGET="python3_9 -python3_8 -python3_10" VIDEO_CARDS="-nvidia" # emerge --info '=sci-libs/vtk-9.1.0-r2::gentoo' Portage 3.0.30 (python 3.9.13-final-0, default/linux/arm64/17.0/desktop/gnome/systemd, gcc-11.3.0, glibc-2.35-r7, 5.18.3-gentoo-arm64 aarch64) ================================================================= System Settings ================================================================= System uname: Linux-5.18.3-gentoo-arm64-aarch64-with-glibc2.35 KiB Mem: 16350188 total, 1739172 free KiB Swap: 8388604 total, 8388604 free Timestamp of repository gentoo: Sun, 12 Jun 2022 13:30:01 +0000 Head commit of repository gentoo: 26c58e9ef8e6d01e54c027f09f0b0b1c0d102774 sh bash 5.1_p16 ld GNU ld (Gentoo 2.37_p1 p2) 2.37 app-misc/pax-utils: 1.3.4::gentoo app-shells/bash: 5.1_p16::gentoo dev-java/java-config: 2.3.1::gentoo dev-lang/perl: 5.36.0::gentoo dev-lang/python: 3.9.13::gentoo, 3.10.5::gentoo, 3.11.0_beta3::gentoo dev-lang/rust-bin: 1.61.0::gentoo dev-util/cmake: 3.23.2::gentoo dev-util/meson: 0.62.2::gentoo sys-apps/baselayout: 2.8::gentoo sys-apps/sandbox: 2.29::gentoo sys-apps/systemd: 251.2::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.71-r1::gentoo sys-devel/automake: 1.16.5::gentoo sys-devel/binutils: 2.37_p1-r2::gentoo, 2.38-r2::gentoo sys-devel/binutils-config: 5.4.1::gentoo sys-devel/clang: 14.0.5::gentoo sys-devel/gcc: 11.3.0::gentoo sys-devel/gcc-config: 2.5-r1::gentoo sys-devel/libtool: 2.4.7::gentoo sys-devel/llvm: 13.0.1::gentoo, 14.0.5::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.18-r1::gentoo (virtual/os-headers) sys-libs/glibc: 2.35-r7::gentoo Repositories: gentoo location: /var/db/repos/gentoo sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-metamanifest: yes sync-rsync-extra-opts: sync-rsync-verify-jobs: 1 sync-rsync-verify-max-age: 24 guru location: /var/lib/layman/guru sync-type: laymansync sync-uri: https://anongit.gentoo.org/git/repo/proj/guru.git masters: gentoo priority: 50 ACCEPT_KEYWORDS="arm64 ~arm64" ACCEPT_LICENSE="* -@EULA AnyDesk-TOS geekbench TeamViewer Vivaldi" CBUILD="aarch64-unknown-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="aarch64-unknown-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/php/apache2-php8.1/ext-active/ /etc/php/cgi-php8.1/ext-active/ /etc/php/cli-php8.1/ext-active/ /etc/php/fpm-php8.1/ext-active/ /etc/php/phpdbg-php8.1/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=native -O2 -pipe" DISTDIR="/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="-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="https://mirror.isoc.org.il/pub/gentoo/" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j4" 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 aalib accessibility acl acpi alsa archive arm64 audit bash-completion berkdb bidi bluray branding brotli bzip2 cairo cdda cddb cdr cgi cli colord cracklib cron crypt cryptsetup cups curl dbi dbus designer device-mapper djvu doc dri dts dvb dvdr eds emacs encode evo examples exif expat experimental extras fam fbcon fftw flac fluidsynth fontconfig fortran ftp fuse game gamepad games gcrypt gd gdbm gdk-pixbuf geoip geolocation gif git glade gme gmp gnome gnome-keyring gnome-online-accounts gnutls go gpg gphoto2 gpm graphite graphviz gsm gssapi gstreamer gtk gtk-doc gtk3 gui guile harfbuzz hdf5 heif highlight html http http2 iconv icu idn imagemagick imlib introspection iodbc ipv6 jack java javascript jbig jemalloc joystick jpeg jpeg2k json kde kerberos latex lcms ldap libcaca libevent libglvnd libnotify libsecret libtirpc libxml2 lmdb lua lvm lz4 lzma lzo mad maildir man mbedtls mbox midi mng mp3 mp4 mpeg mtp musepack mysql nas nautilus ncurses netlink nettle network networkmanager nfs nls nptl nss ntlm odbc ogg openal openexr opengl openmp openssl opus pam pango pcap pcre pdf perl pkcs11 plasma plugins plymouth png policykit portaudio postgres postscript ppds pulseaudio python qdbm qml qrcode qt5 raw readline redis rss samba sasl savedconfig screencast sctp sdl seccomp session skey snappy sndfile sndio snmp sound source sox speech speex spell split-usr sql sqlite ssh ssl startup-notification svg symlink syslog systemd tcl theora threads tiff tk tools tracker tremor truetype twolame udev udisks unicode unwind upnp upower usb utils uuid v4l vala vim-syntax vnc vorbis vpx wavpack wayland webengine webkit webp widgets wmf wxwidgets x264 xattr xcb xface xinerama xml xmp xpm xscreensaver xv xvid yaml zeroconf zip zlib zsh-completion zstd" ADA_TARGET="gnat_2020" 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 stage words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_ARM="edsp thumb thumb2 v4 v5 v6 v7 v8 vfp vfp-d32 vfpv3 vfpv4" CPU_FLAGS_X86="edsp neon thumb vfp vfpv3 vfpv4 vfp-d32 sha1 sha2 crc32 v4 v5 v6 v7 v8 thumb2" 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="evdev" KERNEL="linux" L10N="en en-US he ru" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="nlpsolver" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-4 php8-0" POSTGRES_TARGETS="postgres12 postgres13" PYTHON_SINGLE_TARGET="python3_9" PYTHON_TARGETS="python3_9" RUBY_TARGETS="ruby26 ruby27 ruby30 ruby31" USERLAND="GNU" VIDEO_CARDS="virgl" 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, LEX, 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
Created attachment 784397 [details] build.log.xz
Downgrade to the latest 4.8 version of the netcdf package fixes the compilation.
/var/tmp/portage/sci-libs/vtk-9.1.0-r2/work/VTK-9.1.0/ThirdParty/exodusII/vtkexodusII/src/ex_utils.c: In function ‘vtkexodusII_ex__compress_variable’: /var/tmp/portage/sci-libs/vtk-9.1.0-r2/work/VTK-9.1.0/ThirdParty/exodusII/vtkexodusII/src/ex_utils.c:1773:19: error: expected identifier or ‘(’ before numeric constant 1773 | const int NC_SZIP_NN = 32; /* Selects nearest neighbor coding method for szip. */ | ^~~~~~~~~~
Could it be, this is an arm specific issue? On my amd64 machine, it builds without issues, using the use flag settings from the attached build log and built against netcdf 4.9.0.
(In reply to Bernd from comment #4) > Could it be, this is an arm specific issue? On my amd64 machine, it builds > without issues, using the use flag settings from the attached build log and > built against netcdf 4.9.0. Found https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1012703.
Still can't reproduce it. In my chroot the package builds with the given use flags. Did another build run, ensuring to use --usepkg=n, so no binary package might give a false negative.
If there's no objections, I'd patch out the line only if >=netcdf-4.9.0 is installed. If someone who actually has the issue could test the PR?
(In reply to Bernd from comment #7) > If there's no objections, I'd patch out the line only if >=netcdf-4.9.0 is > installed. > If someone who actually has the issue could test the PR? Tell me what do you want me to test?
Created attachment 786050 [details, diff] 0001-sci-libs-vtk-fix-build-against-netcdf-4.9.0.patch I'm currently testing if the patch doesn't break anything before opening a PR. See the attached file if you want to test the changes ahead.
Created attachment 786068 [details] build.log.xz
(In reply to Bernd from comment #9) > Created attachment 786050 [details, diff] [details, diff] > 0001-sci-libs-vtk-fix-build-against-netcdf-4.9.0.patch > > I'm currently testing if the patch doesn't break anything before opening a > PR. See the attached file if you want to test the changes ahead. now it fails with another error - attached build.log
(In reply to Leonid Kopylov from comment #11) > (In reply to Bernd from comment #9) > > Created attachment 786050 [details, diff] [details, diff] [details, diff] > > 0001-sci-libs-vtk-fix-build-against-netcdf-4.9.0.patch > > > > I'm currently testing if the patch doesn't break anything before opening a > > PR. See the attached file if you want to test the changes ahead. > > now it fails with another error - attached build.log I'm pretty sure you ran out of RAM.
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d699c8995b81d8cd0be7d051485af755d25cdf11 commit d699c8995b81d8cd0be7d051485af755d25cdf11 Author: Bernd Waibel <waebbl-gentoo@posteo.net> AuthorDate: 2022-06-18 10:29:13 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2022-06-26 07:09:32 +0000 sci-libs/vtk: fix build against netcdf-4.9.0 Closes: https://bugs.gentoo.org/851594 Signed-off-by: Bernd Waibel <waebbl-gentoo@posteo.net> Closes: https://github.com/gentoo/gentoo/pull/25954 Signed-off-by: Sam James <sam@gentoo.org> ...-avoid-naming-collision-with-netcdf-4.9.0.patch | 26 ++++++++++++++++++++++ sci-libs/vtk/vtk-9.1.0-r2.ebuild | 1 + 2 files changed, 27 insertions(+)
