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Bug 629058 - sci-physics/meep-1.3 with >=dev-scheme/guile-2.0.13 fails at runtime
Summary: sci-physics/meep-1.3 with >=dev-scheme/guile-2.0.13 fails at runtime
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Physics related packages
Keywords: PMASKED
Depends on:
Blocks: guile-2-porting
  Show dependency tree
Reported: 2017-08-27 12:46 UTC by eroen
Modified: 2019-09-01 19:06 UTC (History)
2 users (show)

See Also:
Package list:
Runtime testing required: ---

sci-physics/meep-1.3:20170827-023022.log (meep-1.3:20170827-023022.log,120.31 KB, text/plain)
2017-08-27 12:46 UTC, eroen

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Description eroen 2017-08-27 12:46:11 UTC
Created attachment 490864 [details]

mpic++ -DHAVE_CONFIG_H -I. -I..  -I../src -DHAVE_CTL_HOOKS=1 -DHAVE_CTL_EXPORT_HOOK=1 -DCTL_SCM='"'/usr/share/libctl/base/ctl.scm'"' -DINCLUDE_SCM='"'/usr/share/libctl/base/include.scm'"' -DSPEC_SCM='"'/usr/share/meep/meep.scm'"' -DVERSION_STRING='"'"Meep 1.3, Copyright (C) 2005-2015 Massachusetts Insitute of Technology."'"'  -pthread -I/usr/include/guile/2.0  -march=corei7-avx -pipe -Og -g -gdwarf-4 -c -o meep_wrap.o meep_wrap.cxx
cp -f /usr/share/libctl/base/main.c main.cpp
cp -f /usr/share/libctl/utils/geom.c geom.cpp
gen-ctl-io --cxx --code -o ctl-io.cpp meep.scm /usr/share/libctl
meep_wrap.cxx: In function 'int SwigVector3_Check(SCM)':
meep_wrap.cxx:1384:23: error: 'SCM_VECTORP' was not declared in this scope
   return SCM_VECTORP(o) && SCM_VECTOR_LENGTH(o) == 3;
meep_wrap.cxx:1384:47: error: 'SCM_VECTOR_LENGTH' was not declared in this scope
   return SCM_VECTORP(o) && SCM_VECTOR_LENGTH(o) == 3;
make[3]: *** [Makefile:528: meep_wrap.o] Error 1
make[3]: Leaving directory '/var/tmp/portage/sci-physics/meep-1.3/work/meep-1.3/libctl'
make[2]: *** [Makefile:400: all] Error 2
make[2]: Leaving directory '/var/tmp/portage/sci-physics/meep-1.3/work/meep-1.3/libctl'
make[1]: *** [Makefile:491: all-recursive] Error 1
make[1]: Leaving directory '/var/tmp/portage/sci-physics/meep-1.3/work/meep-1.3'
make: *** [Makefile:400: all] Error 2
 * ERROR: sci-physics/meep-1.3::gentoo failed (compile phase):
 *   emake failed
Comment 1 eroen 2017-08-27 12:54:55 UTC
eroen@occam ~ $ emerge --info '=sci-physics/meep-1.3::gentoo'
Portage 2.3.7 (python 3.6.1-final-0, hardened/linux/amd64, gcc-6.4.0, glibc-2.25-r4, 4.9.24-hardened-o0 x86_64)
                         System Settings
System uname: Linux-4.9.24-hardened-o0-x86_64-Intel-R-_Core-TM-_i5-2520M_CPU_@_2.50GHz-with-gentoo-2.4.1
KiB Mem:     8000768 total,   2112620 free
KiB Swap:   16777212 total,  16343804 free
Timestamp of repository gentoo: Sun, 20 Aug 2017 12:30:01 +0000
Head commit of repository gentoo: f49b572487044b635dadd0db10851963ab42ffda
Timestamp of repository eroen: Sun, 30 Oct 2016 21:58:42 +0000
Head commit of repository sapher: 9ef31d0bf6a902342746fb03a445d4f8b7ddabef

Head commit of repository wiktorb: 722797c27affae074c3d7b0a628cad1bdff2041c

Head commit of repository stuff: bbd9d235512712091f976ceec47f66fa2914583e

sh bash 4.4_p12
ld GNU ld (Gentoo 2.27 p1.1) 2.27
ccache version 3.3.4 [disabled]
app-shells/bash:          4.4_p12::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.24.2::gentoo
dev-lang/python:          2.7.13::gentoo, 3.4.6::gentoo, 3.5.3::gentoo, 3.6.1-r1::gentoo
dev-util/ccache:          3.3.4::gentoo
dev-util/cmake:           3.9.1::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.4.1-r1::gentoo
sys-apps/openrc:          0.28::gentoo
sys-apps/sandbox:         2.10-r4::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r4::gentoo
sys-devel/automake:       1.15.1::gentoo
sys-devel/binutils:       2.27-r1::gentoo, 2.28.1::gentoo
sys-devel/gcc:            5.3.0::gentoo, 5.4.0-r3::gentoo, 6.3.0::gentoo, 6.4.0::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r4::gentoo
sys-devel/make:           4.2.1-r1::gentoo
sys-kernel/linux-headers: 4.10::gentoo (virtual/os-headers)
sys-libs/glibc:           2.25-r4::gentoo

    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://
    priority: -1000
    sync-rsync-extra-opts: --exclude ChangeLog* --exclude /metadata/cache/ --stats --delay-updates -c

    location: /usr/local/portage
    masters: gentoo
    priority: 0

    location: /var/lib/overlays/sapher
    sync-type: git
    masters: gentoo

    location: /var/lib/overlays/wiktorb
    sync-type: git
    masters: gentoo

    location: /var/lib/layman/enlightenment
    masters: gentoo
    priority: 50

    location: /var/lib/layman/flora
    masters: gentoo
    priority: 50

    location: /var/lib/layman/gamerlay
    masters: gentoo
    priority: 50

    location: /var/lib/layman/glc
    masters: gentoo
    priority: 50

    location: /var/lib/layman/hardened-development
    masters: gentoo
    priority: 50

    location: /var/lib/layman/haskell
    masters: gentoo
    priority: 50

    location: /var/lib/layman/hasufell
    masters: gentoo
    priority: 50

    location: /var/lib/layman/java
    masters: gentoo
    priority: 50

    location: /var/lib/layman/laurentb
    masters: gentoo
    priority: 50

    location: /var/lib/layman/roslin
    masters: gentoo
    priority: 50

    location: /var/lib/layman/science
    masters: gentoo
    priority: 50

    location: /var/lib/layman/stuff
    sync-type: git
    masters: gentoo
    priority: 50

    location: /var/lib/layman/sunrise
    masters: gentoo
    priority: 50

    location: /var/lib/layman/toolchain
    masters: gentoo
    priority: 50

    location: /var/lib/layman/v-fox
    masters: gentoo
    priority: 50

ACCEPT_KEYWORDS="amd64 ~amd64"
CFLAGS="-march=corei7-avx -pipe -Og -g -gdwarf-4"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/easy-rsa /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 /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=corei7-avx -pipe -Og -g -gdwarf-4"
EMERGE_DEFAULT_OPTS="--jobs=4 --autounmask --quiet-build --nospinner --verbose-conflicts --verbose-slot-rebuilds"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs binpkg-multi-instance cgroup collision-protect compressdebug config-protect-if-modified distlocks ebuild-locks fixlafiles installsources ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch parallel-install preserve-libs protect-owned sandbox sfperms split-log splitdebug strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu"
MAKEOPTS="-j4 -l10"
PORTAGE_RSYNC_EXTRA_OPTS="--exclude ChangeLog* --exclude /metadata/cache/ --stats --delay-updates -c"
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"
USE="X a52 aac acl alsa amd64 apng audio audiofile avresample avx bash-completion bdf berkdb bluray bzip2 cairo caps cb cdda cdparanoia cdr cjk cli corefonts cracklib crypt cups curl cxx ddate declarative detex device-mapper dga dia djvu dri dts dvd dvi2tty dvipdfm ebook egl exif fam ffmpeg fftw fits flac fontconfig g3dvl gallium gbm gcrypt gdbm gif gimp git glamor glib glibc-omitfp gmp gnuplot gnutls gold gpm graphics graphviz gs gstreamer gtk gtk3 hardened highlight hscolour iconv icu id3tag idn imagemagick imlib inotify iproute2 ipv6 jbig jpeg jpeg2k jpg json justify kde kde4 kpathsea latex lcms libffi libssh2 libv4l luatex lvm lvm2 lzma lzo man metric mikmod mkv mms mmx mng modules mp3 mpeg mpg123 multilib multimedia musepack ncurses netlink nptl nut ocr odbc offensive ogg opengl openmp openvg optimization optimized-qmake opus pam pango pax_kernel pcre pdf pgf phonon pie png postscript private-headers pstricks pth publishers python3 qt3support qt4 raw readline samba sbsms scanner science sdl seccomp session smp sna sndfile speex spell sqlite sse sse2 sse3 sse4 sse41 sse4_1 sse4_2 ssh ssl ssp ssse3 svg t1lib tcpd tesseract theora threads tiff tls truetype udev unicode urandom usb v4l v4l2 vaapi video vorbis vpx webp wmf x264 xanim xattr xcb xcomposite xetex xft xinerama xkb xml xmlpatterns xorg xosd xpm xrandr xtpax xv xvid xvmc xz zlib zsh-completion" ABI_X86="32 64" 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="kexi words flow plan sheets stage tables krita karbon braindump author" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx sse sse2 avx sse3 ssse3 sse4_1 aes avx mmxext popcnt sse3 sse4_1 sse4_2 ssse3" CURL_SSL="openssl" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock 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="mouse keyboard evdev synaptics wacom" KERNEL="linux" L10N="en en-US en-GB eng" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en gb us en_US en_GB eng jbo no nb nn no_NO nb_NO nn_NO nor" LLVM_TARGETS="BPF X86" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-3" POSTGRES_TARGETS="postgres9_5" PYTHON_SINGLE_TARGET="python3_4" PYTHON_TARGETS="python2_7 python3_4 python3_5 python3_6" QEMU_SOFTMMU_TARGETS="x86_64 i386" RUBY_TARGETS="ruby22" SANE_BACKENDS="plustek" USERLAND="GNU" VIDEO_CARDS="intel i965 ilo" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"

eroen@occam ~ $ emerge -pqv '=sci-physics/meep-1.3::gentoo'
[ebuild  N    ] sci-physics/meep-1.3  USE="examples guile hdf5 mpi"
Comment 2 eroen 2017-08-27 13:30:39 UTC
Actually, meep doesn't work with >=guile-2.0.13 at all[0] due to missing support in swig[1]. :-C

Comment 3 Aaron W. Swenson gentoo-dev 2019-05-31 12:31:43 UTC
Meep 1.6 allegedly fixes the Guile compatibility issue. [1]

Meep 1.3 is significantly out of date. The latest version is 1.9.0. [2]

Comment 4 Cyprien Nicolas (fulax) 2019-06-10 10:24:53 UTC
(In reply to Aaron W. Swenson from comment #3)
> Meep 1.6 allegedly fixes the Guile compatibility issue. [1]
> Meep 1.3 is significantly out of date. The latest version is 1.9.0. [2]
> [1]:
> [2]:

That would require to bump libctl to 4.x [1]. As meep does not have a dependency on guile, I'm not sure why this bug is a blocker to guile-2.

Comment 5 Larry the Git Cow gentoo-dev 2019-08-03 01:17:49 UTC
The bug has been referenced in the following commit(s):

commit 7fdc053024377382155383d3709f80089be930f0
Author:     Matt Turner <>
AuthorDate: 2019-08-03 01:11:32 +0000
Commit:     Matt Turner <>
CommitDate: 2019-08-03 01:13:03 +0000

    profiles: Mask sci-physics/meep and sci-libs/libctl for removal
    Mask sci-physics/harminv for removal as well as meep is the only reverse
    Signed-off-by: Matt Turner <>

 profiles/package.mask | 7 +++++++
 1 file changed, 7 insertions(+)
Comment 6 Larry the Git Cow gentoo-dev 2019-09-01 19:06:59 UTC
The bug has been closed via the following commit(s):

commit 22ad292fbdac49fba112703d6dc413edb2625728
Author:     Matt Turner <>
AuthorDate: 2019-09-01 19:02:18 +0000
Commit:     Matt Turner <>
CommitDate: 2019-09-01 19:06:49 +0000

    sci-physics/meep: Remove
    Signed-off-by: Matt Turner <>

 sci-physics/meep/Manifest                          |  1 -
 sci-physics/meep/files/meep-1.2-no-auto-mpb.patch  | 16 ------
 .../meep/files/meep-1.2-pc-no-ldflags.patch        | 12 -----
 sci-physics/meep/meep-1.3.ebuild                   | 58 ----------------------
 sci-physics/meep/metadata.xml                      | 14 ------
 5 files changed, 101 deletions(-)