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Bug 591410 - sci-chemistry/coot-0.8.2-r1: "not using Guile" -> coot-glue-gtk2.c:8:22: fatal error: libguile.h: No such file or directory
Summary: sci-chemistry/coot-0.8.2-r1: "not using Guile" -> coot-glue-gtk2.c:8:22: fata...
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Chemistry-Related Packages
Depends on:
Blocks: guile-2-porting
  Show dependency tree
Reported: 2016-08-16 18:04 UTC by David Kredba
Modified: 2019-08-26 05:26 UTC (History)
1 user (show)

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

confi.log --with-guile=/usr (config.log,65.09 KB, text/plain)
2016-08-16 18:04 UTC, David Kredba
build.log (build.log,602.38 KB, text/plain)
2016-08-16 18:05 UTC, David Kredba
config.log of version 0.8.5 --with-guile (config.log,65.98 KB, text/plain)
2016-08-16 18:07 UTC, David Kredba
config.log --with-guile (config.log,66.02 KB, text/plain)
2016-08-16 18:09 UTC, David Kredba

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Description David Kredba 2016-08-16 18:04:17 UTC
Created attachment 443518 [details]
confi.log --with-guile=/usr

After I updated to =dev-scheme/guile-2.0.12-r1:12/22 I can't rebuild coot.
Configure reports: Not using guile.
Config.log file is attached, build.log too.

When I removed '=/usr' from configure command --with-guile it finds it:
Congratulations, you are using Guile
checking for guile... /usr/bin/guile
checking for guile-config... /usr/bin/guile-config
checking for guile-tools... /usr/bin/guile-tools
checking libguile compile flags... -pthread -I/usr/include/guile/2.0
checking libguile link flags... -lguile-2.0 -lgc
checking for Guile-Lib... yes
checking for guile-gui... ;;; note: auto-compilation is enabled, set GUILE_AUTO_COMPILE=0
;;;       or pass the --no-auto-compile argument to disable.
;;; compiling /usr/share/guile/gui/paren-match.scm
;;; compiled /var/tmp/portage/sci-chemistry/coot-0.8.2-r1/homedir/.cache/guile/ccache/2.0-LE-8-2.0/usr/share/guile/gui/paren-match.scm.go
checking GUILE_VERSION: 2.0

Later it fails due to:
c-inner-main.c: In function ‘c_inner_main’:
c-inner-main.c:137:3: error: ‘SCM_DEVAL_P’ undeclared (first use in this function)
   SCM_DEVAL_P = 1;
c-inner-main.c:137:3: note: each undeclared identifier is reported only once for each function it appears in
c-inner-main.c:138:3: error: ‘SCM_BACKTRACE_P’ undeclared (first use in this function)
c-inner-main.c:139:3: error: ‘SCM_RECORD_POSITIONS_P’ undeclared (first use in this function)

There is coot-0.8.5 released already which I tested with the same change in configure command, with two skipped icon patches and half of libtool patch and it finds guile but fails later due to: error: ‘SCM_DEVAL_P’ was not declared in this scope
   SCM_DEVAL_P = 1;
   ^ error: ‘SCM_BACKTRACE_P’ was not declared in this scope
   ^ error: ‘SCM_RECORD_POSITIONS_P’ was not declared in this scope
Comment 1 David Kredba 2016-08-16 18:05:19 UTC
Created attachment 443520 [details]
Comment 2 David Kredba 2016-08-16 18:07:21 UTC
Created attachment 443522 [details]
config.log of version 0.8.5 --with-guile
Comment 3 David Kredba 2016-08-16 18:09:37 UTC
Created attachment 443524 [details]
config.log --with-guile
Comment 4 David Kredba 2016-08-16 18:10:15 UTC
Portage 2.3.0 (python 2.7.12-final-0, default/linux/amd64/13.0/desktop/plasma, gcc-4.9.4, glibc-2.23-r2, 4.6.4-gentoo x86_64)
                         System Settings
System uname: Linux-4.6.4-gentoo-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9550_@_2.83GHz-with-gentoo-2.2
KiB Mem:     8169792 total,   2820480 free
KiB Swap:    8396796 total,   8396692 free
Timestamp of repository gentoo: Tue, 16 Aug 2016 15:30:01 +0000
sh bash 4.3_p46
ld GNU ld (Gentoo 2.26.1 p1.0) 2.26.1
app-shells/bash:          4.3_p46::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.24.0-r1::gentoo
dev-lang/python:          2.7.12::gentoo, 3.4.5::gentoo, 3.5.2::gentoo
dev-util/cmake:           3.6.1::gentoo
dev-util/pkgconfig:       0.29.1::gentoo
sys-apps/baselayout:      2.2-r1::gentoo
sys-apps/openrc:          0.21.3::gentoo
sys-apps/sandbox:         2.10-r2::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r2::gentoo
sys-devel/automake:       1.9.6-r4::gentoo, 1.11.6-r2::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo
sys-devel/binutils:       2.26.1::gentoo
sys-devel/gcc:            4.9.4::x-portage
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r2::gentoo
sys-devel/make:           4.2.1::gentoo
sys-kernel/linux-headers: 4.7::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r2::gentoo

    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://
    priority: -1000

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

ACCEPT_KEYWORDS="amd64 ~amd64"
CFLAGS="-O2 -march=core2 -ggdb -pipe"
CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt /var/bind"
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="-O2 -march=core2 -ggdb -pipe"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -march=core2 -ggdb -pipe"
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 aalib acl acpi alsa amd64 argyllcms berkdb blas bluetooth branding bzip2 cairo caps cdda cddb cdparanoia cdr cli consolekit cracklib crypt cups cvs cxx dbus declarative djvu dri dts dv dvb dvd dvdr emboss encode exif fam ffmpeg fftw firefox flac fontconfig fortran ftp gd gdbm geoip gif glamor gmp gnuplot gpm gps graphviz gsl gsm gstreamer gtk hdf5 iconv icu idn ieee1394 imagemagick imlib ipv6 ithreads javascript jbig jpeg jpeg2k kde kipi ladspa lame lapack lcms ldap libass libnotify libsamplerate lzma lzo mad matroska mms mmx mmxext mng modplug modules mp3 mp4 mpeg mplayer mtp multilib musepack musicbrainz ncurses netcdf nls nptl ogg opencl openexr opengl openmp pam pango pch pcre pdf perl phonon pic plasma plotutils png policykit postscript ppds pulseaudio python qml qt3support qt4 qt5 quicktime rdesktop readline sdl seccomp semantic-desktop session slang smp sndfile sox speex spell sse sse2 ssl ssse3 startup-notification svg szip tcpd theora threads tidy tiff truetype udev udisks unicode upower usb v4l vaapi vcd vdpau vnc vorbis wavpack widgets wmf wxwidgets x264 xattr xcb xcomposite xft xine xinerama xml xosd xpm xscreensaver xv xvid xvmc zlib" ABI_X86="64 32" 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="author braindump flow karbon kexi krita plan sheets stage words" CAMERAS="ptp2 adc65 agfa_cl20 aox ax203 barbie canon casio_qv clicksmart310 digigr8 digita dimagev dimera3500 directory enigma13 fuji gsmart300 hp215 iclick jamcam jd11 jl2005a jl2005c kodak_dc120 kodak_dc210 kodak_dc240 kodak_dc3200 kodak_ez200 konica konica_qm150 largan lg_gsm mars mustek panasonic_coolshot panasonic_dc1000 panasonic_dc1580 panasonic_l859 pccam300 pccam600 pentax polaroid_pdc320 polaroid_pdc640 polaroid_pdc700 ricoh ricoh_g3 samsung sierra sipix_blink2 sipix_web2 smal sonix sony_dscf1 sony_dscf55 soundvision spca50x sq905 st2205 stv0674 stv0680 sx330z topfield toshiba_pdrm11 tp6801" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2 sse3 sse4_1 ssse3" CURL_SSL="gnutls" ELIBC="glibc" FFTOOLS="aviocat cws2fws ffescape ffeval fourcc2pixfmt graph2dot ismindex pktdumper qt-faststart trasher ffhash sidxindex" GPSD_PROTOCOLS="aivdm ashtech earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 navcom nmea ntrip oceanserver oncore rtcm104v2 rtcm104v3 sirf superstar2 tnt tripmate tsip ubx fury geostar nmea2000" GRUB_PLATFORMS="pc" INPUT_DEVICES="evdev keyboard mouse joystick" KERNEL="linux" L10N="cs en" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer scripting-beanshell scripting-javascript nlpsolver" LINGUAS="cs en" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4 python3_5" QEMU_SOFTMMU_TARGETS="x86_64 arm i386" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby20" USERLAND="GNU" VIDEO_CARDS="nouveau" 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"
USE_PYTHON="2.7 3.4 3.5"

                        Package Settings

sci-chemistry/coot-0.8.3::x-portage was built with the following:
USE="openmp -static-libs -test" ABI_X86="64" PYTHON_TARGETS="python2_7"
Comment 5 David Kredba 2016-12-30 14:58:08 UTC
It seems to me, that for enabling guile-gtk works --with-guile-gtk-prefix="/usr" at configure.

For missing definitions extracted definitions from guile-1.8.8 works for compilation, but link fails:
SCM_API scm_t_option scm_read_opts[];

#define SCM_COPY_SOURCE_P      scm_read_opts[0].val
#define SCM_RECORD_POSITIONS_P scm_read_opts[1].val
#define SCM_CASE_INSENSITIVE_P scm_read_opts[2].val
#define SCM_KEYWORD_STYLE      scm_read_opts[3].val
#define SCM_ELISP_VECTORS_P    scm_read_opts[4].val
#define SCM_ESCAPED_PARENS_P   scm_read_opts[5].val

SCM_API scm_t_option scm_debug_opts[];

#define SCM_BREAKPOINTS_P       scm_debug_opts[1].val
#define SCM_TRACE_P             scm_debug_opts[2].val
#define SCM_REC_PROCNAMES_P     scm_debug_opts[3].val
#define SCM_BACKWARDS_P         scm_debug_opts[4].val
#define SCM_BACKTRACE_WIDTH     scm_debug_opts[5].val
#define SCM_BACKTRACE_INDENT    scm_debug_opts[6].val
#define SCM_N_FRAMES            scm_debug_opts[7].val
#define SCM_BACKTRACE_MAXDEPTH  scm_debug_opts[8].val
#define SCM_BACKTRACE_DEPTH     scm_debug_opts[9].val
#define SCM_BACKTRACE_P         scm_debug_opts[10].val
#define SCM_DEVAL_P             scm_debug_opts[11].val
#define SCM_STACK_LIMIT         scm_debug_opts[12].val
#define SCM_SHOW_FILE_NAME      scm_debug_opts[13].val
#define SCM_WARN_DEPRECATED     scm_debug_opts[14].val

#define SCM_DEVAL_P             scm_debug_opts[11].val
#define SCM_BACKTRACE_P         scm_debug_opts[10].val
#define SCM_RECORD_POSITIONS_P scm_read_opts[1].val

it needs its guile-1.8.8 eval.c definition to link:

scm_t_option scm_debug_opts[] = {
  { SCM_OPTION_BOOLEAN, "cheap", 1,
    "*This option is now obsolete.  Setting it has no effect." },
  { SCM_OPTION_BOOLEAN, "breakpoints", 0, "*Check for breakpoints." },
  { SCM_OPTION_BOOLEAN, "trace", 0, "*Trace mode." },
  { SCM_OPTION_BOOLEAN, "procnames", 1,
    "Record procedure names at definition." },
  { SCM_OPTION_BOOLEAN, "backwards", 0,
    "Display backtrace in anti-chronological order." },
  { SCM_OPTION_INTEGER, "width", 79, "Maximal width of backtrace." },
  { SCM_OPTION_INTEGER, "indent", 10, "Maximal indentation in backtrace." },
  { SCM_OPTION_INTEGER, "frames", 3,
    "Maximum number of tail-recursive frames in backtrace." },
  { SCM_OPTION_INTEGER, "maxdepth", 1000,
    "Maximal number of stored backtrace frames." },
  { SCM_OPTION_INTEGER, "depth", 20, "Maximal length of printed backtrace." },
  { SCM_OPTION_BOOLEAN, "backtrace", 0, "Show backtrace on error." },
  { SCM_OPTION_BOOLEAN, "debug", 0, "Use the debugging evaluator." },
  { SCM_OPTION_INTEGER, "stack", 20000, "Stack size limit (measured in words; 0 = no check)." },
  { SCM_OPTION_SCM, "show-file-name", (unsigned long)SCM_BOOL_T, "Show file names and line numbers in backtraces when not `#f'.  A value of `base' displays only base names, while `#t' displays full names."},
  { SCM_OPTION_BOOLEAN, "warn-deprecated", 0, "Warn when deprecated features are used." }

Deleting the lines assigning the value "1" to them (SCM_DEVAL_P, SCM_BACKTRACE_P and SCM_RECORD_POSITIONS_P) works too.

Later - "error: ‘scm_listofnull’ was not declared in this scope" is reported in the files at line 2066 and at line 2069.

It seems that enough is to prepend
#define scm_listofnull  scm_list_1 (SCM_EOL)

Coot 0.8.7 compiled this way was at least able to retrieve structure 1JY3 and offered fixing it and fixed (26 residues had their atoms swapped), rotated it etc.
Comment 6 Justin Lecher (RETIRED) gentoo-dev 2017-01-02 11:03:19 UTC
commit 5083ea5f1e067669f0e1bb65c33d9228506c5d3b
Author: Justin Lecher <>
Date:   Mon Jan 2 11:02:11 2017 +0000

    sci-chemistry/coot: Depend on guile-1 as workaround


    Package-Manager: Portage-2.3.3, Repoman-2.3.1
    Signed-off-by: Justin Lecher <>
Comment 7 Justin Lecher (RETIRED) gentoo-dev 2017-01-02 11:03:44 UTC
Upstream is still using guile-1. We have to closer look into this
Comment 8 Aaron W. Swenson gentoo-dev 2019-05-31 12:53:05 UTC
The version in portage (0.8.2) is now 4 years out of date.

The latest version available upstream is (released 2019-04-01) [1], and the test data has been updated, too [2]. Clearly, this package is no longer being maintained as there have been numerous intermediate releases that have not landed in Portage, and should be marked for tree cleaning.

Comment 9 Matt Turner gentoo-dev 2019-08-26 05:26:52 UTC
Removed by

commit c399a8bb15acd06ffef54b9c1b7f0e9c36f77c86
Author: Matt Turner <>
Date:   Fri Aug 9 21:03:09 2019 -0700

    sci-chemistry/coot: Remove
    Signed-off-by: Matt Turner <>