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Bug 583038

Summary: sci-chemistry/numbat-0.999-r2 : /.../pcsfit_metal.c:1823:29: error: ‘gsl_multifit_fdfsolver {aka struct <anonymous>}’ has no member named ‘J’
Product: Gentoo Linux Reporter: Toralf Förster <toralf>
Component: Current packagesAssignee: Gentoo Chemistry-Related Packages <sci-chemistry>
Severity: normal CC: sam, treecleaner
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
Package list:
Runtime testing required: ---
Bug Depends on: 862486    
Bug Blocks:    
Attachments: emerge-history.txt

Description Toralf Förster gentoo-dev 2016-05-14 18:07:53 UTC
/var/tmp/portage/sci-chemistry/numbat-0.999-r1/work/Numbat-0.999/src/pcsfit_metal.c: In function ‘calculate_single_tensor’:
/var/tmp/portage/sci-chemistry/numbat-0.999-r1/work/Numbat-0.999/src/pcsfit_metal.c:1823:29: error: ‘gsl_multifit_fdfsolver {aka struct <anonymous>}’ has no member named ‘J’
        gsl_multifit_covar (s->J, 0.0, covar);

$ cat emerge-info.txt

  This is an unstable amd64 chroot image (named amd64-gnome-unstable_20160509-190516) at a hardened host acting as a tinderbox.


  make.conf: USE="mmx sse sse2 pax_kernel xtpax -cdinstall -oci8 -bindist alsa apache2 avformat bzip2 cddb clang -cups egl fortran -gnome-keyring gnutls gtkstyle havege imlib -inifile ipv6 isag -javascript lapack -logrotate mssql mysqli pdo -qt3support qt4 semantic-desktop sse4_1 ssh-askpass ssl system-icu -system-libs system-llvm theora thinkpad tk tls uml v4l2 widgets xinetd -xmlreader xz"


Portage 2.2.28 (python 3.4.3-final-0, default/linux/amd64/13.0/desktop/gnome, gcc-5.3.0, glibc-2.23-r2, 4.5.4-hardened-r2 x86_64)
System uname: Linux-4.5.4-hardened-r2-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2
KiB Mem:    16157888 total,   4743332 free
KiB Swap:   16777212 total,  16777212 free
Timestamp of repository gentoo: Sat, 14 May 2016 16:03:52 +0000
sh bash 4.3_p42-r2
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
app-shells/bash:          4.3_p42-r2::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.22.2::gentoo
dev-lang/python:          2.7.11-r2::gentoo, 3.4.3-r7::gentoo, 3.5.1-r2::gentoo
dev-util/cmake:           3.5.2::gentoo
dev-util/pkgconfig:       0.29.1::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.20.5::gentoo
sys-apps/sandbox:         2.10-r2::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r2::gentoo
sys-devel/automake:       1.11.6-r2::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo
sys-devel/binutils:       2.25.1-r1::gentoo
sys-devel/gcc:            4.9.3::gentoo, 5.3.0::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r2::gentoo
sys-devel/make:           4.1-r1::gentoo
sys-kernel/linux-headers: 4.5::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r2::gentoo

    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://
    priority: 1

    location: /usr/local/portage
    masters: gentoo
    priority: 2

ACCEPT_KEYWORDS="amd64 ~amd64"
CFLAGS="-march=native -O2 -pipe"
CONFIG_PROTECT="/etc /etc/omega.conf /usr/share/gnupg/qualified.txt /var/lib/hsqldb /var/rancid/.cloginrc"
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=native -O2 -pipe"
EMERGE_DEFAULT_OPTS="--verbose-conflicts --color=n --nospinner --tree --quiet-build"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS=" rsync:// rsync://"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
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 acpi alsa amd64 apache2 avformat berkdb bluetooth branding bzip2 cairo cdda cddb cdr clang cli colord consolekit cracklib crypt cxx dbus dri dts dvd dvdr eds egl emboss encode evo exif fam firefox flac fortran gdbm gif glamor gnome gnome-online-accounts gnutls gpm gstreamer gtk gtkstyle havege iconv imlib introspection ipv6 isag jpeg lapack lcms ldap libnotify libsecret mad mmx mmxext mng modules mp3 mp4 mpeg mssql multilib mysqli nautilus ncurses nls nptl ogg opengl openmp pam pango pax_kernel pcre pdf pdo png policykit ppds pulseaudio qt4 readline sdl seccomp semantic-desktop session spell sse sse2 sse4_1 ssh-askpass ssl startup-notification svg system-icu system-llvm tcpd theora thinkpad tiff tk tls tracker truetype udev udisks uml unicode upower usb v4l2 vorbis widgets wxwidgets x264 xattr xcb xinetd xml xtpax xv xvid xz zlib" ABI_X86="64" 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="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" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en en_GB" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="intel i965" 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"
Comment 1 Toralf Förster gentoo-dev 2016-05-14 18:07:56 UTC
Created attachment 434284 [details]
Comment 2 Toralf Förster gentoo-dev 2016-05-14 18:07:58 UTC
Created attachment 434286 [details]
Comment 3 Toralf Förster gentoo-dev 2016-05-14 18:08:01 UTC
Created attachment 434288 [details]
Comment 4 Larry the Git Cow gentoo-dev 2021-03-28 01:14:42 UTC
The bug has been referenced in the following commit(s):

commit 68a82908d3282885a11131b8609a7f7ac2438bc2
Author:     Sam James <>
AuthorDate: 2021-03-28 00:38:17 +0000
Commit:     Sam James <>
CommitDate: 2021-03-28 01:13:50 +0000

    sci-chemistry/numbat: port to EAPI 7
    * Port to EAPI 7
    * Drop autotools-utils.eclass
    Still doesn't seem to build with newer gsl(?)
    but this unblocks autotools-utils removal anyway.
    Signed-off-by: Sam James <>

 sci-chemistry/numbat/numbat-0.999-r1.ebuild | 42 ++++++++++++++++-------------
 1 file changed, 23 insertions(+), 19 deletions(-)
Comment 5 Agostino Sarubbo gentoo-dev 2022-07-31 07:27:36 UTC
lto_tinderbox has reproduced this issue with version 0.999-r2 - Updating summary.
Comment 6 Larry the Git Cow gentoo-dev 2022-08-29 08:07:42 UTC
The bug has been closed via the following commit(s):

commit 5f26b5938812d41ebfd3712a9c59ba8a49f13d1b
Author:     Jakov Smolić <>
AuthorDate: 2022-08-29 08:06:35 +0000
Commit:     Jakov Smolić <>
CommitDate: 2022-08-29 08:07:22 +0000

    sci-chemistry/numbat: treeclean
    Signed-off-by: Jakov Smolić <>

 profiles/package.mask                              |  5 --
 sci-chemistry/numbat/Manifest                      |  1 -
 .../numbat/files/numbat-0.999-gnuplot.patch        | 42 ----------------
 sci-chemistry/numbat/metadata.xml                  | 19 --------
 sci-chemistry/numbat/numbat-0.999-r2.ebuild        | 56 ----------------------
 5 files changed, 123 deletions(-)