Bug 924622 – sci-chemistry/autodock_vina-1.1.2-r1 w/ boost-1.84.0-r3: error: #error This header is deprecated and will be removed. (You can define BOOST_TIMER_ENABLE_DEPRECATED to suppress this error.)

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description urcindalo 2024-02-15 08:41:27 UTC]

I use a mostly stable system. Recently, dev-libs/boost was upgraded from 1.82.0-r1 to 1.84.0-r3. As a result, stable sci-chemistry/autodock_vina-1.1.2-r1 fails to build:
=====
x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=znver2 -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -std=c++11 -o random.o -c ../../../src/lib/random.cpp 
In file included from /usr/include/boost/system/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/system/detail/config.hpp:11,
                 from /usr/include/boost/system/detail/error_category.hpp:13,
                 from /usr/include/boost/system/error_category.hpp:10,
                 from /usr/include/boost/filesystem/detail/path_traits.hpp:25,
                 from /usr/include/boost/filesystem/path.hpp:21,
                 from ../../../src/lib/common.h:41,
                 from ../../../src/lib/parallel.h:28,
                 from ../../../src/lib/parallel_mc.cpp:23:
/usr/include/boost/progress.hpp:27:1: note: ‘#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead.’
   27 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
      | ^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/boost/timer.hpp:25:1: note: ‘#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead.’
   25 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
      | ^~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=znver2 -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -std=c++11 -o ssd.o -c ../../../src/lib/ssd.cpp 
x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=znver2 -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -std=c++11 -o terms.o -c ../../../src/lib/terms.cpp 
x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=znver2 -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -std=c++11 -o weighted_terms.o -c ../../../src/lib/weighted_terms.cpp 
x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=znver2 -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -std=c++11 -I ../../../src/lib -o split.o -c ../../../src/split/split.cpp 
make: *** [../../makefile_common:18: parallel_mc.o] Error 1
make: *** Waiting for unfinished jobs....
In file included from /usr/include/boost/math/quaternion.hpp:14,
                 from ../../../src/lib/quaternion.h:26,
                 from ../../../src/lib/conf.h:28,
                 from ../../../src/lib/tree.h:26,
                 from ../../../src/lib/model.h:29,
                 from ../../../src/lib/ssd.h:26,
                 from ../../../src/lib/ssd.cpp:23:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
In file included from /usr/include/boost/math/quaternion.hpp:14,
                 from ../../../src/lib/quaternion.h:26,
                 from ../../../src/lib/conf.h:28,
                 from ../../../src/lib/tree.h:26,
                 from ../../../src/lib/model.h:29,
                 from ../../../src/lib/terms.h:27,
                 from ../../../src/lib/terms.cpp:23:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
In file included from /usr/include/boost/math/quaternion.hpp:14,
                 from ../../../src/lib/quaternion.h:26,
                 from ../../../src/lib/conf.h:28,
                 from ../../../src/lib/tree.h:26,
                 from ../../../src/lib/model.h:29,
                 from ../../../src/lib/terms.h:27,
                 from ../../../src/lib/weighted_terms.h:26,
                 from ../../../src/lib/weighted_terms.cpp:23:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
 * ERROR: sci-chemistry/autodock_vina-1.1.2-r1::gentoo failed (compile phase):
 *   emake failed
=====

[Comment 1 Andreas Sturmlechner 2024-02-15 08:50:29 UTC]

Missing emerge --info, missing build.log.

Your snippet does not contain the actual error.

[Comment 2 urcindalo 2024-02-15 10:06:42 UTC]

$ emerge --info
Portage 3.0.61 (python 3.11.7-final-0, default/linux/amd64/17.1/desktop/plasma/systemd/merged-usr, gcc-13, glibc-2.38-r10, 6.6.13-gentoo x86_64)
=================================================================
System uname: Linux-6.6.13-gentoo-x86_64-AMD_Ryzen_7_3700X_8-Core_Processor-with-glibc2.38
KiB Mem:    32800292 total,   8721168 free
KiB Swap:   33554428 total,  31311100 free
Timestamp of repository gentoo: Thu, 15 Feb 2024 08:30:01 +0000
Head commit of repository gentoo: 1a5aaff8d4e767c15b44149a73d7c5781dc19f05
Timestamp of repository 4nykey: Mon, 12 Feb 2024 16:35:50 +0000
Head commit of repository 4nykey: c646a9667e9e90880f7a58cc4e78392bc9d03b0c

Timestamp of repository Case_Of: Mon, 12 Feb 2024 23:18:19 +0000
Head commit of repository Case_Of: 90ed595f46c40fa2aea69981d4d921ea5efdb3de

Head commit of repository brave-overlay: 1f2c9eaca254f609602e50dc788c75387424f5fb

Timestamp of repository guru: Wed, 14 Feb 2024 16:18:34 +0000
Head commit of repository guru: 957e0a69f8e10f8e8f630efd7d1f30e6066d9652

Timestamp of repository torbrowser: Mon, 12 Feb 2024 16:35:46 +0000
Head commit of repository torbrowser: e99b51cd8f02febfbd054dce6f30a80b058d68c7

Timestamp of repository vowstar: Tue, 13 Feb 2024 15:03:31 +0000
Head commit of repository vowstar: a1d847506b475056dd0c3f8c07df5ddab772fce0

Head commit of repository qq-gentoo: 8d62fef7c30e88c23ff09994c922e1cc2d997862

sh bash 5.1_p16-r6
ld GNU ld (Gentoo 2.41 p4) 2.41.0
app-misc/pax-utils:        1.3.7::gentoo
app-shells/bash:           5.1_p16-r6::gentoo
dev-build/autoconf:        2.71-r6::gentoo
dev-build/automake:        1.16.5-r2::gentoo
dev-build/cmake:           3.27.9::gentoo
dev-build/libtool:         2.4.7-r1::gentoo
dev-build/make:            4.4.1-r1::gentoo
dev-build/meson:           1.3.0-r2::gentoo
dev-java/java-config:      2.3.3-r1::gentoo
dev-lang/perl:             5.38.2-r1::gentoo
dev-lang/python:           3.11.7::gentoo, 3.12.1_p1::gentoo
dev-lang/rust-bin:         1.74.1::gentoo
sys-apps/baselayout:       2.14-r2::gentoo
sys-apps/sandbox:          2.38::gentoo
sys-apps/systemd:          255.3::gentoo
sys-devel/binutils:        2.41-r3::gentoo
sys-devel/binutils-config: 5.5::gentoo
sys-devel/clang:           15.0.7-r3::gentoo, 17.0.6::gentoo
sys-devel/gcc:             13.2.1_p20240113-r1::gentoo
sys-devel/gcc-config:      2.11::gentoo
sys-devel/lld:             15.0.7::gentoo, 17.0.6::gentoo
sys-devel/llvm:            15.0.7-r3::gentoo, 17.0.6::gentoo
sys-kernel/linux-headers:  6.6::gentoo (virtual/os-headers)
sys-libs/glibc:            2.38-r10::gentoo
Repositories:

gentoo
    location: /var/db/repos/gentoo
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000
    volatile: True
    sync-rsync-verify-metamanifest: yes
    sync-rsync-verify-jobs: 1
    sync-rsync-verify-max-age: 24
    sync-rsync-extra-opts: 

4nykey
    location: /var/db/repos/4nykey
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/4nykey.git
    masters: gentoo
    volatile: False

Case_Of
    location: /var/db/repos/Case_Of
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/Case_Of.git
    masters: gentoo
    volatile: False

brave-overlay
    location: /var/db/repos/brave-overlay
    sync-type: git
    sync-uri: https://gitlab.com/jason.oliveira/brave-overlay.git
    masters: gentoo
    volatile: False

guru
    location: /var/db/repos/guru
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/guru.git
    masters: gentoo
    volatile: False

local
    location: /var/db/repos/local
    masters: gentoo
    priority: 0
    volatile: False

torbrowser
    location: /var/db/repos/torbrowser
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/torbrowser.git
    masters: gentoo
    volatile: False

vowstar
    location: /var/db/repos/vowstar
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/vowstar.git
    masters: gentoo
    volatile: False

qq-gentoo
    location: /var/db/repos/qq-gentoo
    sync-type: git
    sync-uri: https://gitlab.com/quilosaq/qq-gentoo.git
    masters: gentoo
    priority: 40
    volatile: False

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=znver2 -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /opt/cxoffice/etc/cxoffice.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/config /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/revdep-rebuild /etc/sandbox.d /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=znver2 -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=znver2 -O2 -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg-live config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox pkgdir-index-trusted 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=znver2 -O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
INSTALL_MASK="/usr/share/locale -/usr/share/locale/es -/usr/share/locale/es_ES -/usr/share/locale/en_US -/usr/share/locale/en /usr/share/gcc-data/x86_64-pc-linux-gnu/*/locale -/usr/share/gcc-data/x86_64-pc-linux-gnu/*/locale/es /usr/share/man/de /usr/share/man/el /usr/share/man/fr /usr/share/man/hu /usr/share/man/ja /usr/share/man/jp /usr/share/man/sk /usr/share/man/zh_TW"
LANG="es_ES.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LEX="flex"
LINGUAS="es_ES es en_US en"
MAKEOPTS="-j16"
PKGDIR="/var/cache/binpkgs"
PORTAGE_BINHOST="https://gentoo.osuosl.org/experimental/amd64/binpkg/default/linux/17.1/x86-64/"
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 acl acpi activities alsa amd64 amr atm bluetooth branding btrfs bzip2 cairo cdda cddb cdr clang cli contrib crypt cups curl daemon dbus declarative dga djvu dri dts dv dvd dvdr encode exif fbcon ffmpeg fftw flac fontconfig fortran ftp fuse gdbm geolocation gif gimp gmp gnome-keyring gphoto2 gpm grub gstreamer gtk gui iconv icu idn imagemagick imlib ipv6 jack java jbig jpeg jpeg2k kde kwallet lame lapack latex lcms libass libcaca libkms libnotify libtirpc lm-sensors lzma lzo mad mmap mng modplug mono mp3 mp4 mpeg mtp multilib musepack nas ncurses network networkmanager nls ogg openal opencl openexr opengl openmp oss pam pango pcre pdf pipewire pkcs11 plasma png policykit portaudio postscript ppds pulseaudio qml qt5 rar raw readline ruby samba sasl scanner screencast sdl seccomp semantic-desktop slang smartcard sound spell ssl startup-notification svg syslog systemd taglib tcl test-rust theora threads tiff tk truetype twolame udev udisks unicode upnp upower usb v4l vcd vdpau vnc vorbis vulkan wavpack wayland widgets wmf wxwidgets x264 xattr xcb xft xml xmp xv xvid zlib" ABI_X86="64" ADA_TARGET="gnat_2021" ALSA_CARDS="hda-intel" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon krita" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2 aes avx avx2 f16c fma3 pclmul popcnt rdrand sha sse3 sse4_1 sse4_2 sse4a ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 ntrip navcom oceanserver oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 tsip tripmate tnt ublox" GRUB_PLATFORMS="efi-64" INPUT_DEVICES="synaptics evdev" KERNEL="linux" L10N="es-ES es en-US en" LCD_DEVICES="bayrad cfontz glk hd44780 lb216 lcdm001 mtxorb text" LLVM_TARGETS="AArch64 AMDGPU X86 XCore" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php8-1" POSTGRES_TARGETS="postgres15" PYTHON_SINGLE_TARGET="python3_11" PYTHON_TARGETS="python3_11" RUBY_TARGETS="ruby31" SANE_BACKENDS="epson2 hp" VIDEO_CARDS="radeonsi amdgpu" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipp2p iface geoip fuzzy condition tarpit sysrq proto 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, LC_ALL, LD, LFLAGS, LIBTOOL, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PYTHONPATH, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS

[Comment 3 urcindalo 2024-02-15 10:11:28 UTC]

Created attachment 885012 [details]
build.log

[Comment 4 Charo del Genio 2024-02-17 12:35:54 UTC]

Easy workaround, add -DBOOST_TIMER_ENABLE_DEPRECATED within src_configure in the ebuild.
Attaching new ebuild.

[Comment 5 Charo del Genio 2024-02-17 12:36:31 UTC]

Created attachment 885223 [details]
Patched ebuild

[Comment 6 urcindalo 2024-02-20 10:35:47 UTC]

(In reply to Charo del Genio from comment #4)
> Easy workaround, add -DBOOST_TIMER_ENABLE_DEPRECATED within src_configure in
> the ebuild.
> Attaching new ebuild.

Thanks very much. It worked.

[Comment 7 Larry the Git Cow 2024-03-02 21:15:03 UTC]

The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8ff06565cfa9e2d6114008541f2fae2c23f9e12c

commit 8ff06565cfa9e2d6114008541f2fae2c23f9e12c
Author:     Alexey Shvetsov <[e-mail]>
AuthorDate: 2024-03-02 21:14:38 +0000
Commit:     Alexey Shvetsov <[e-mail]>
CommitDate: 2024-03-02 21:14:38 +0000

    sci-chemistry/autodock_vina: Fix build with recent boost
    
    Closes: https://bugs.gentoo.org/913037
    Closes: https://bugs.gentoo.org/924622
    Signed-off-by: Alexey Shvetsov <[e-mail]>

 sci-chemistry/autodock_vina/autodock_vina-1.1.2-r1.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)