Bug 303491 – sci-chemistry/rasmol-2.7.5: if.h:208:17: error: cbf.h: Does not exist

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description David Kredba 2010-02-04 19:24:14 UTC]

sci-chemistry/rasmol-2.7.5 does not compile on ~amd64:

x86_64-pc-linux-gnu-gcc -O2 -g -ggdb -pipe      -I/usr/include    -Dlinux -D__amd64__ -D_POSIX_C_SOURCE=199309L                                 -D_POSIX_SOURCE -D_XOPEN_SOURCE                                 -D_BSD_SOURCE -D_SVID_SOURCE                                 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64                                                                   -DFUNCPROTO=15 -DNARROWPROTO   -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pango-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12   -DGTKWIN -DRASMOLDIR=\"/usr/lib64/rasmol/\" -DTHIRTYTWOBIT            -D_USE_RASMOL_H_  -I/usr/include -I/usr/include/cbflib    -c -o infile.o infile.c
script.c: In function ‘WriteScriptSelectBond’:
script.c:802: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘Long’
script.c:802: warning: format ‘%ld’ expects type ‘long int’, but argument 4 has type ‘Long’
script.c: In function ‘WriteScriptRibbons’:
script.c:1100: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘Long’
script.c: In function ‘WriteScriptMonitors’:
script.c:1232: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘Long’
script.c:1232: warning: format ‘%ld’ expects type ‘long int’, but argument 4 has type ‘Long’
script.c: In function ‘WriteScriptMaps’:
script.c:1313: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘Long’
script.c:1316: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘Long’
script.c:1316: warning: format ‘%ld’ expects type ‘long int’, but argument 4 has type ‘Long’
script.c:1335: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘Long’
script.c:1338: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘Long’
script.c:1338: warning: format ‘%ld’ expects type ‘long int’, but argument 4 has type ‘Long’
script.c: In function ‘WriteScriptFile’:
script.c:1462: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘Long’
script.c:1462: warning: format ‘%ld’ expects type ‘long int’, but argument 4 has type ‘Long’
script.c:1491: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘Long’
script.c:1491: warning: format ‘%ld’ expects type ‘long int’, but argument 4 has type ‘Long’
script.c:1491: warning: format ‘%ld’ expects type ‘long int’, but argument 5 has type ‘Long’
script.c: In function ‘OutputKinemageVector’:
script.c:1644: warning: format ‘%ld’ expects type ‘long int’, but argument 4 has type ‘Long’
script.c:1667: warning: format ‘%ld’ expects type ‘long int’, but argument 4 has type ‘Long’
script.c: In function ‘WriteKinemageSpheres’:
script.c:1745: warning: format ‘%ld’ expects type ‘long int’, but argument 4 has type ‘Long’
script.c: In function ‘POVWriteHeader’:
script.c:2884: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘Long’
script.c:2884: warning: format ‘%ld’ expects type ‘long int’, but argument 4 has type ‘Long’
script.c:2884: warning: format ‘%ld’ expects type ‘long int’, but argument 5 has type ‘Long’
In file included from infile.c:232:
cif.h:208:17: error: cbf.h: Adresář nebo soubor neexistuje
In file included from infile.c:232:
cif.h:212: error: expected ‘)’ before ‘handle’
cif.h:227: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘cif_handle’
infile.c: In function ‘LoadMol2Molecule’:
infile.c:1498: warning: format ‘%ld’ expects type ‘long int *’, but argument 4 has type ‘Long *’
infile.c:1498: warning: format ‘%ld’ expects type ‘long int *’, but argument 5 has type ‘Long *’
infile.c: In function ‘LoadAlchemyMolecule’:
infile.c:1581: warning: format ‘%ld’ expects type ‘long int *’, but argument 3 has type ‘Long *’
infile.c:1581: warning: format ‘%ld’ expects type ‘long int *’, but argument 4 has type ‘Long *’
infile.c:1581: warning: format ‘%ld’ expects type ‘long int *’, but argument 5 has type ‘Long *’
infile.c: At top level:
infile.c:2000: error: expected ‘)’ before ‘cif’
infile.c:2013: error: expected ‘)’ before ‘cif’
infile.c:2027: error: expected ‘)’ before ‘cif’
infile.c:2041: error: expected ‘)’ before ‘cif’
infile.c:2109: error: expected ‘)’ before ‘cif’
infile.c: In function ‘LoadCIFMolecule’:
infile.c:2160: error: ‘cif_handle’ undeclared (first use in this function)
infile.c:2160: error: (Each undeclared identifier is reported only once
infile.c:2160: error: for each function it appears in.)
infile.c:2160: error: expected ‘;’ before ‘cif’
infile.c:2177: error: ‘cif’ undeclared (first use in this function)
make: *** [infile.o] Error 1


Reproducible: Always

Steps to Reproduce:
1.be ~amd64 
2.emerge --oneshot =sci-chemistry/rasmol-2.7.5
3.

Actual Results:  
Fails due to missing header file cbf.h.

Expected Results:  
Compiles fine.

Portage 2.1.7.17 (default/linux/amd64/10.0/desktop, gcc-4.4.2, glibc-2.11-r1, 2.6.32-gentoo-r3-1d x86_64)
=================================================================
System uname: Linux-2.6.32-gentoo-r3-1d-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9300_@_2.50GHz-with-gentoo-2.0.1
Timestamp of tree: Thu, 04 Feb 2010 17:45:01 +0000
app-shells/bash:     4.0_p37
dev-java/java-config: 2.1.10
dev-lang/python:     2.6.4-r1, 3.1.1-r1
dev-util/cmake:      2.8.0-r2
sys-apps/baselayout: 2.0.1
sys-apps/openrc:     0.6.0-r1
sys-apps/sandbox:    2.2
sys-devel/autoconf:  2.13, 2.65
sys-devel/automake:  1.4_p6-r1, 1.7.9-r2, 1.8.5-r4, 1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils:  2.20
sys-devel/gcc:       4.4.2
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.6b
virtual/os-headers:  2.6.30-r1
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -g -ggdb -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config /var/bind /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/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="-O2 -g -ggdb -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests distlocks fixpackages news nostrip parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch"
FFLAGS="-O2 -g -ggdb -pipe"
GENTOO_MIRRORS="ftp://gentoo.inode.at/source/ ftp://gentoo.mirror.web4u.cz/ "
LANG="cs_CZ.UTF-8"
LDFLAGS="-Wl,-O1"
LINGUAS="cs en"
MAKEOPTS="-j5"
PKGDIR="/usr/portage/packages"
PORTAGE_COMPRESS="echo"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo caps cdr cli consolekit cracklib crypt cups cxx dbus djvu dri dts dvd dvdr eds emboss encode evo examples exif extras fam firefox flac fontconfig fontforge fortran gdbm gif gmp gnome gpm gstreamer gtk hal iconv idn ithreads java jpeg jpeg2k kde kerberos lcms ldap libedit libnotify mad mikmod mmx mng modules mp3 mp4 mpeg mudflap multilib mysql ncurses nls nptl nptlonly objc objc++ objc-gc odbc ogg openexr opengl openmp pam pch pcre pdf perl png policykit ppds pppd python qt3support qt4 quicktime readline reflection samba sdl session slang spell spl sqlite sse sse2 sse3 ssl startup-notification svg sysfs tcl tcpd threads thunar tiff tk truetype unicode usb utils vorbis x264 xattr xcb xinerama xml xorg xpm xulrunner xv xvid zlib" 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" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="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 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" ELIBC="glibc" INPUT_DEVICES="evdev keyboard mouse joystick" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="cs en" LIRC_DEVICES="inputlirc" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia nv vesa v4l"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY

[Comment 1 Henry Wertz 2010-02-05 02:14:26 UTC]

     Firstly, same bug on x86.  Secondly....
     This appears to be a bug in sci-libs/cbflib-0.8.1-r4.  So, CBFlib-0.8.1.tar.gz by default installs into $HOME, but if redirected into /usr, it would install several binaries in /usr/bin, several headers in /usr/include/cbflib, and a few libs into /usr/lib.   The ebuild *only* installs the libs.

     I just now extracted the tar (into /usr/src), and copied the include dir into /usr/include/cbflib.   Rasmol then installed fine.
------
emerge --info:
delta ~ # emerge --info                   
Portage 2.1.7.17 (default/linux/x86/10.0/desktop, gcc-4.4.2, glibc-2.11-r1, 2.6.28-gentoo-r3 i686)                                                              
=================================================================               
System uname: Linux-2.6.28-gentoo-r3-i686-AMD_Sempron-tm-_2500+-with-gentoo-2.0.1                                                                               
Timestamp of tree: Fri, 05 Feb 2010 00:20:01 +0000                              
distcc 3.1 i686-pc-linux-gnu [enabled]                                          
ccache version 2.4 [enabled]                                                    
app-shells/bash:     4.0_p37                                                    
dev-java/java-config: 1.3.7-r1, 2.1.10                                          
dev-lang/python:     2.4.4-r4, 2.5.4-r2, 2.6.4-r1, 3.1.1-r1                     
dev-python/pycrypto: 2.1.0                                                      
dev-util/ccache:     2.4-r8                                                     
dev-util/cmake:      2.8.0-r2                                                   
sys-apps/baselayout: 2.0.1                                                      
sys-apps/openrc:     0.6.0-r1                                                   
sys-apps/sandbox:    2.2                                                        
sys-devel/autoconf:  2.13, 2.65                                                 
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r4, 1.9.6-r3, 1.10.3, 1.11.1                                                                           
sys-devel/binutils:  2.20                                                       
sys-devel/gcc:       3.3.6-r1, 4.3.4, 4.4.2                                     
sys-devel/gcc-config: 1.4.1                                                     
sys-devel/libtool:   2.2.6b                                                     
virtual/os-headers:  2.6.30-r1                                                  
ACCEPT_KEYWORDS="x86 ~x86"                                                      
ACCEPT_LICENSE="* -@EULA"                                                       
CBUILD="i686-pc-linux-gnu"                                                      
CFLAGS="-O2 -march=athlon-xp -fomit-frame-pointer"                              
CHOST="i686-pc-linux-gnu"                                                       
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config /var/lib/hsqldb"                     
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/udev/rules.d"                               
CXXFLAGS="-O2 -march=athlon-xp -fomit-frame-pointer"                            
DISTDIR="/usr/portage/distfiles"                                                
FEATURES="assume-digests ccache distcc distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch"   
GENTOO_MIRRORS="http://gentoo.mirrors.tds.net/gentoo"                           
LDFLAGS="-Wl,-O1"                                                               
MAKEOPTS="-j3"                                                                  
PKGDIR="/usr/portage/packages"                                                  
PORTAGE_CONFIGROOT="/"                                                          
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"                                                  
PORTAGE_TMPDIR="/var/rtmp"                                                      
PORTDIR="/usr/portage"                                                          
PORTDIR_OVERLAY="/usr/local/portage"                                            
SYNC="rsync://rsync.us.gentoo.org/gentoo-portage"                               
USE="3dnow 3dnowext X a52 aac acl acpi alsa asf audiofile avahi berkdb bluetooth bonobo branding browserplugin bzip2 cairo cdr cjk cli consolekit cracklib crosscompile crypt css cups curl cxx dbus divx4linux dri dts dv dvb dvd dvdr dvdread eds emboss encode esd evo expat fam fame ffmpeg firefox flac foomaticdb fortran gd gdbm gif gimp gimpprint glut gmp gnome gnutls gpm gstreamer gtk gtk2 gtkhtml hal iconv idn ieee1394 imagemagick insecure-drivers insecure-savers ipv6 java jpeg junit kde kqemu latin1 lcms ldap libnotify lua mad matroska mikmod mjpeg mmx mng modules mozsvg mp3 mp4 mpeg mudflap mysql mythtv nas ncurses nls nptl nptlonly nsplugin offensive ogg opengl openmp pam pcre pdf perl pic plugin png posix ppds pppd pulseaudio python qt3support qt4 quicktime readline reflection samba scanner sdl semantic-desktop session spell spl sse ssl startup-notification subtitles svg sysfs tcltk tcpd threads threadsafe thunar tiff truetype unicode usb v4l v4l2 vorbis win32codecs wma wmf wmp x264 x86 xanim xine xml xorg xulrunner xv xvid xvmc zlib" ALSA_CARDS="via82xx" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="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 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" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="via"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

[Comment 2 Henry Wertz 2010-02-07 03:53:59 UTC]

     I saw sci-libs/cbflib-0.8.1-r5 came out today; it installls /usr/include/cbflib. 

     I did "emerge --oneshot rasmol" and it worked fine.

     Does original poster want to reply if this works for him too?  I assume it'll work fine and the bug can be closed.

     Thanks to everyone, particularly jlec for updating the ebuild!

[Comment 3 David Kredba 2010-02-08 16:20:41 UTC]

Thanks, it works for me too.

[Comment 4 Justin Lecher (RETIRED) 2010-02-08 22:51:12 UTC]

Sorry, that was my fault, I changed the installation part and dropped the header. It is fixed in sci-libs/cbflib-0.8.1-r5.