Seems to conflict with sci-visualization/paraview-5.9.0.0: * Installing examples * Installing datafiles * Final size of build directory: 3455348 KiB (3.2 GiB) * Final size of installed tree: 2766468 KiB (2.6 GiB) * This package will overwrite one or more files that may belong to other * packages (see list below). You can use a command such as `portageq * owners / <filename>` to identify the installed package that owns a * file. If portageq reports that only one package owns a file then do * NOT file a bug report. A bug report is only useful if it identifies at * least two or more packages that are known to install the same file(s). * If a collision occurs and you can not explain where the file came from * then you should simply ignore the collision since there is not enough * information to determine if a real problem exists. Please do NOT file * a bug report at https://bugs.gentoo.org/ unless you report exactly * which two packages install the same file(s). See * https://wiki.gentoo.org/wiki/Knowledge_Base:Blockers for tips on how * to solve the problem. And once again, please do NOT file a bug report * unless you have completely understood the above message. * * package sci-libs/vtk-9.0.1 NOT merged * * Detected file collision(s): * * /usr/share/vtkm-1.5/VTKmLICENSE.txt * /usr/share/vtkm-1.5/VTKmREADME.md * * Searching all installed packages for file collisions... * * Press Ctrl-C to Stop * * sci-visualization/paraview-5.9.0:0::gentoo * /usr/share/vtkm-1.5/VTKmLICENSE.txt * /usr/share/vtkm-1.5/VTKmREADME.md * * Package 'sci-libs/vtk-9.0.1' NOT merged due to file collisions. If * necessary, refer to your elog messages for the whole content of the * above message. Reproducible: Always # emerge --info Portage 3.0.18 (python 3.8.9-final-0, default/linux/amd64/17.1/desktop/plasma, gcc-10.2.0, glibc-2.32-r7, 5.10.27-gentoo x86_64) ================================================================= System uname: Linux-5.10.27-gentoo-x86_64-AMD_Ryzen_9_3950X_16-Core_Processor-with-glibc2.2.5 KiB Mem: 65795288 total, 26975228 free KiB Swap: 33554428 total, 32547328 free Timestamp of repository gentoo: Mon, 31 May 2021 13:45:01 +0000 Head commit of repository gentoo: e420d181a07a0dcfef293eb85dc299511daf85cd sh bash 5.1_p8 ld GNU ld (Gentoo 2.35.2 p1) 2.35.2 app-shells/bash: 5.1_p8::gentoo dev-java/java-config: 2.3.1::gentoo dev-lang/perl: 5.32.1::gentoo dev-lang/python: 2.7.18_p9::gentoo, 3.8.9_p2::gentoo, 3.9.4_p1::gentoo dev-lang/rust: 1.51.0-r2::gentoo dev-util/cmake: 3.18.5::gentoo sys-apps/baselayout: 2.7::gentoo sys-apps/openrc: 0.42.1-r1::gentoo sys-apps/sandbox: 2.23::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r5::gentoo sys-devel/automake: 1.16.3-r1::gentoo sys-devel/binutils: 2.35.2::gentoo sys-devel/gcc: 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: 5.10::gentoo (virtual/os-headers) sys-libs/glibc: 2.32-r7::gentoo Repositories: gentoo location: /var/db/repos/gentoo sync-type: rsync sync-uri: rsync://rsync.namerica.gentoo.org/gentoo-portage/ priority: -1000 sync-rsync-verify-jobs: 1 sync-rsync-verify-metamanifest: yes sync-rsync-extra-opts: sync-rsync-verify-max-age: 24 local location: /usr/local/portage masters: gentoo 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/easy-rsa /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php7.4/ext-active/ /etc/php/cgi-php7.4/ext-active/ /etc/php/cli-php7.4/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" EMERGE_DEFAULT_OPTS="--jobs=8 --load-average=32" 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 cgroup collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch parallel-install 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" LINGUAS="en en_US" MAKEOPTS="--jobs=32 --load-average=35" 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" USE="X a52 aac acl acpi activities alsa amd64 apache2 berkdb bluetooth branding bzip2 cairo cdda cdr cli colord crypt cups curl dbus declarative doc dri dts dvd dvdr elogind emboss encode examples exif flac fontconfig fortran gcj gd gdbm gif gtk gtk-doc gui handbook iconv icu ipv6 jack java jbig jpeg kde kipi kpathsea kwallet lcms libglvnd libnotify libtirpc lzma mad mbox mng mp3 mp4 mpeg multilib ncurses nls nptl odbc ogg openexr opengl openmp pam pango pcre pdf phonon plasma png policykit postgres ppds qml qt5 readline screencast sdl seccomp semantic-desktop source spell split-usr ssl startup-notification svg t1lib tcpd threads tiff truetype udev udisks unicode upower usb vim-syntax vorbis webp widgets wxwidgets x264 xattr xcb xinerama xml xpm xv xvid zlib" ABI_X86="64 32" 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="actions alias auth_basic auth_digest authn_anon authn_core authn_dbd authn_dbm authn_default authn_file authz_core authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers http2 ident imagemap include info lbmethod_byrequests log_config log_forensic logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http proxy_http2 rewrite setenvif slotmem_shm socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias" APACHE2_MPMS="worker" CALLIGRA_FEATURES="karbon sheets words" CAMERAS="canon" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt rdrand sha sse sse2 sse3 sse4_1 sse4_2 sse4a 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 wacom joystick" KERNEL="linux" L10N="en en-US" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="nlpsolver wiki-publisher" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-4" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_8" PYTHON_TARGETS="python3_8" RUBY_TARGETS="ruby26" SANE_BACKENDS="epson2" USERLAND="GNU" VIDEO_CARDS="amdgpu radeonsi fbdev vesa" XFCE_PLUGINS="clock trash" 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, INSTALL_MASK, LC_ALL, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RUSTFLAGS
Thanks for the report. Honestly, I didn't check compatibility with paraview installations. For an easy fix, we could remove the two readme files from either vtk-9 or paraview. I wonder it worked with vtk-8, however. In the longer term, a more reliable solution would be to get a separate package for vtkm into ::gentoo. I thought about it, while working on the vtk-9 update but decided against it for now. IIRC it's not possible to build paraview against an external vtk. Although they both use the same codebase, paraview modifies some of the vtk code. I have to check if paraview would work against an external vtkm package, which is a 3rd-party library for vtk, and possibly also for paraview.
Just checked the toplevel CMakeLists.txt of paraview. It has a PARAVIEW_USE_EXTERNAL_VTK switch (https://github.com/Kitware/ParaView/blob/v5.9.0/CMakeLists.txt#L213), referencing version 9.0 of vtk, so we could check whether it will build with external vtk.
see https://bugs.gentoo.org/253881
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4342b5087bd84cbe64de318c152b5425ec7f8d7b commit 4342b5087bd84cbe64de318c152b5425ec7f8d7b Author: Sam James <sam@gentoo.org> AuthorDate: 2021-06-02 01:23:23 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2021-06-02 01:23:23 +0000 sci-libs/vtk: delete README from bundled vtkm for now Avoids collision with paraview. We'll ideally try to get paraview building with system VTK again but VTK takes a while to build so anything to prevent collisions for users now is important while we investigate that possibility. Bug: https://bugs.gentoo.org/253881 Bug: https://bugs.gentoo.org/793221 Signed-off-by: Sam James <sam@gentoo.org> sci-libs/vtk/vtk-9.0.1.ebuild | 5 +++++ 1 file changed, 5 insertions(+)
Sam, many thanks for the quick fix!
(In reply to Bernd from comment #5) > Sam, many thanks for the quick fix! np! (Bit late.) I suppose we may be able to close this one now and just revisit the general bundled issue...
VTK-9.2.2 has an cmake option to disable installation of readme file. We hopefully won't need this hack for the new version.
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=588025882a58b613f5ef08e02b96efbb7d4c7445 commit 588025882a58b613f5ef08e02b96efbb7d4c7445 Author: Bernd Waibel <waebbl-gentoo@posteo.net> AuthorDate: 2022-09-29 05:18:39 +0000 Commit: Joonas Niilola <juippis@gentoo.org> CommitDate: 2022-12-12 06:08:29 +0000 sci-libs/vtk: add 9.2.2 - add a new function to check memory and disk space requirements - don't drop bundled external libraries, it's only a few MB which are freed through this and upstream does a good job to avoid automagic deps - request more modules to build explicitly depending on USE flag settings - don't export CC and friends with USE=mpi, package builds fine with gcc and still links to MPI libraries - add USE flag to build vtk-m optional Bug: https://bugs.gentoo.org/793221 Bug: https://bugs.gentoo.org/835659 Bug: https://bugs.gentoo.org/880759 Closes: https://bugs.gentoo.org/820593 Closes: https://bugs.gentoo.org/827310 Closes: https://bugs.gentoo.org/846374 Closes: https://bugs.gentoo.org/874798 Signed-off-by: Bernd Waibel <waebbl-gentoo@posteo.net> Closes: https://github.com/gentoo/gentoo/pull/28250 Signed-off-by: Joonas Niilola <juippis@gentoo.org> sci-libs/vtk/Manifest | 6 + .../vtk-9.2.2-VTKm-respect-user-CXXFLAGS.patch | 81 +++ ...9.2.2-link-with-glut-library-for-freeglut.patch | 18 + ...metryFilter-add-missing-mutex-header-file.patch | 20 + sci-libs/vtk/metadata.xml | 11 +- sci-libs/vtk/vtk-9.2.2.ebuild | 728 +++++++++++++++++++++ 6 files changed, 863 insertions(+), 1 deletion(-)
Hello and happy 2023, let me reopen this bug with: >>> Installing (1 of 1) sci-visualization/paraview-5.11.0_rc2-r1::gentoo * checking 8730 files for package collisions * This package will overwrite one or more files that may belong to other * packages (see list below). You can use a command such as `portageq * owners / <filename>` to identify the installed package that owns a * file. If portageq reports that only one package owns a file then do * NOT file a bug report. A bug report is only useful if it identifies at * least two or more packages that are known to install the same file(s). * If a collision occurs and you can not explain where the file came from * then you should simply ignore the collision since there is not enough * information to determine if a real problem exists. Please do NOT file * a bug report at https://bugs.gentoo.org/ unless you report exactly * which two packages install the same file(s). See * https://wiki.gentoo.org/wiki/Knowledge_Base:Blockers for tips on how * to solve the problem. And once again, please do NOT file a bug report * unless you have completely understood the above message. * * Detected file collision(s): * * /usr/lib64/qt5/qml/VTK.9.2/plugins.qmltypes * /usr/lib64/qt5/qml/VTK.9.2/qmldir * /usr/lib64/qt5/qml/VTK.9.2/libqmlvtkplugin.so * * Searching all installed packages for file collisions... * * Press Ctrl-C to Stop * * sci-libs/vtk-9.2.2-r1:0::gentoo * /usr/lib64/qt5/qml/VTK.9.2/libqmlvtkplugin.so * /usr/lib64/qt5/qml/VTK.9.2/plugins.qmltypes * /usr/lib64/qt5/qml/VTK.9.2/qmldir * * Package 'sci-visualization/paraview-5.11.0_rc2-r1' NOT merged due to * file collisions. If necessary, refer to your elog messages for the * whole content of the above message. Seems the collision is back?
(In reply to Jordi PM from comment #9) > Hello and happy 2023, let me reopen this bug with: > While this is a similar issue, I'd ask you to file a new bug please. Different files are involved and it's likely caused by the new version of paraview.
