Bug 246589 – sci-libs/c{,x}sparse /usr/include/cs.h file collision

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Gerald Morgan 2008-11-13 10:08:06 UTC]

cxsparse (an extended version of csparse, needed for octave) attempts to overwrite the /usr/include/cs.h file which is part of csparse.

Reproducible: Always

Steps to Reproduce:
1. emerge csparse
2. emerge cxsparse

Actual Results:  
...
 * This package will overwrite one or more files that may belong to other
 * packages (see list below). You can use a command such as `portageq
 * owners / <filename>` to identify the installed package that owns a
 * file. If portageq reports that only one package owns a file then do
 * NOT file a bug report. A bug report is only useful if it identifies at
 * least two or more packages that are known to install the same file(s).
 * If a collision occurs and you can not explain where the file came from
 * then you should simply ignore the collision since there is not enough
 * information to determine if a real problem exists. Please do NOT file
 * a bug report at http://bugs.gentoo.org unless you report exactly which
 * two packages install the same file(s). Once again, please do NOT file
 * a bug report unless you have completely understood the above message.
 * 
 * Detected file collision(s):
 * 
 *      /usr/include/cs.h
 * 
 * Searching all installed packages for file collisions...
 * 
 * Press Ctrl-C to Stop
 * 
 * sci-libs/csparse-2.2.1
 *      /usr/include/cs.h
 * 
 * Package 'sci-libs/cxsparse-2.2.1' NOT merged due to file collisions.
 * If necessary, refer to your elog messages for the whole content of the
 * above message.
...

Expected Results:  
cxsparse should have been emerged. I can't see any compelling reason why I shouldn't be able to have both packages together.

$ emerge --info
Portage 2.2_rc14 (default/linux/amd64/2008.0, gcc-4.3.2, glibc-2.8_p20080602-r0, 2.6.27-gentoo-r2 x86_64)
=================================================================
System uname: Linux-2.6.27-gentoo-r2-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9650_@_3.00GHz-with-glibc2.2.5
Timestamp of tree: Wed, 12 Nov 2008 22:45:01 +0000
app-shells/bash:     3.2_p39
dev-java/java-config: 1.3.7, 2.1.6-r1
dev-lang/python:     2.4.4-r13, 2.5.2-r8
dev-python/pycrypto: 2.0.1-r6
dev-util/cmake:      2.6.2
sys-apps/baselayout: 2.0.0
sys-apps/openrc:     0.3.0-r1
sys-apps/sandbox:    1.2.18.1-r3
sys-devel/autoconf:  2.13, 2.63
sys-devel/automake:  1.5, 1.9.6-r2, 1.10.1-r1
sys-devel/binutils:  2.19
sys-devel/gcc-config: 1.4.0-r4
sys-devel/libtool:   2.2.6a
virtual/os-headers:  2.6.27-r2
ABI="amd64"
ACCEPT_KEYWORDS="amd64 ~amd64"
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"
ARCH="amd64"
ASFLAGS_x86="--32"
AUTOCLEAN="yes"
CBUILD="x86_64-pc-linux-gnu"
CDEFINE_amd64="__x86_64__"
CDEFINE_x86="__i386__"
CFLAGS="-march=nocona -O2 -pipe"
CFLAGS_x86="-m32"
CHOST="x86_64-pc-linux-gnu"
CHOST_amd64="x86_64-pc-linux-gnu"
CHOST_x86="i686-pc-linux-gnu"
CLASSPATH="."
CLEAN_DELAY="5"
COLLISION_IGNORE="/lib/modules"
CONFIG_PROTECT="/etc"
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/terminfo /etc/texmf/web2c /etc/udev/rules.d"
CVS_RSH="ssh"
CXXFLAGS="-march=nocona -O2 -pipe"
DEFAULT_ABI="amd64"
DISPLAY=":0.0"
DISTDIR="/usr/portage/distfiles"
EDITOR="/bin/nano"
ELIBC="glibc"
EMERGE_DEFAULT_OPTS="--verbose"
EMERGE_WARNING_DELAY="10"
FEATURES="distlocks parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-orphans userfetch"
FETCHCOMMAND="/usr/bin/wget -t 5 -T 60 --passive-ftp -O "${DISTDIR}/${FILE}" "${URI}""
GCC_SPECS=""
GDK_USE_XFT="1"
GENTOO_MIRRORS="http://mirror.bytemark.co.uk/gentoo/ http://www.mirrorservice.org/sites/www.ibiblio.org/gentoo/ ftp://ftp.mirrorservice.org/sites/www.ibiblio.org/gentoo/ http://mirror.qubenet.net/mirror/gentoo/ "
HOME="/root"
HUSHLOGIN="FALSE"
INFOPATH="/usr/share/info:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.19/info:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.2/info:/usr/share/info/emacs-22"
INPUT_DEVICES="keyboard mouse evdev"
JAVAC="/bin/javac"
JDK_HOME=""
KERNEL="linux"
LADSPA_PATH="/usr/lib64/ladspa"
LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text"
LDFLAGS="-Wl,-O1"
LDFLAGS_x86="-m elf_i386"
LESS="-R -M --shift 5"
LESSOPEN="|lesspipe.sh %s"
LIBDIR_amd64="lib64"
LIBDIR_ppc="lib32"
LIBDIR_ppc64="lib64"
LIBDIR_x86="lib32"
LOGNAME="root"
LS_COLORS="rs=0:di=01;34:ln=01;36:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:su=37;41:sg=30;43:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.pdf=00;32:*.ps=00;32:*.txt=00;32:*.patch=00;32:*.diff=00;32:*.log=00;32:*.tex=00;32:*.doc=00;32:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:"
MAKEOPTS="-j5"
MANPATH="/man:/usr/local/share/man:/usr/share/man:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.19/man:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.2/man:/etc/java-config/system-vm/man/:/usr/lib64/php5/man/"
MULTILIB_ABIS="amd64 x86"
MULTILIB_STRICT_DENY="64-bit.*shared object"
MULTILIB_STRICT_DIRS="/lib32 /lib /usr/lib32 /usr/lib /usr/kde/*/lib32 /usr/kde/*/lib /usr/qt/*/lib32 /usr/qt/*/lib /usr/X11R6/lib32 /usr/X11R6/lib"
MULTILIB_STRICT_EXEMPT="(perl5|gcc|gcc-lib|binutils|eclipse-3|debug|portage)"
OPENGL_PROFILE="xorg-x11"
PAGER="/usr/bin/less"
PATH="/sbin:/bin:/usr/sbin:/usr/bin"
PKGDIR="/usr/portage/packages"
PORTAGE_ARCHLIST="ppc s390 amd64 x86 ppc64 x86-fbsd m68k arm sparc sh mips ia64 alpha hppa sparc-fbsd"
PORTAGE_BINHOST_CHUNKSIZE="3000"
PORTAGE_BIN_PATH="/usr/lib64/portage/bin"
PORTAGE_COMPRESS_EXCLUDE_SUFFIXES="css gif htm[l]? jp[e]?g js pdf png"
PORTAGE_CONFIGROOT="/"
PORTAGE_COUNTER_HASH="276d13b9720731d1dc918373fcfdddb2"
PORTAGE_DEBUG="0"
PORTAGE_DEPCACHEDIR="/var/cache/edb/dep"
PORTAGE_ELOG_CLASSES="warn error log"
PORTAGE_ELOG_MAILFROM="portage@localhost"
PORTAGE_ELOG_MAILSUBJECT="[portage] ebuild log for ${PACKAGE} on ${HOST}"
PORTAGE_ELOG_MAILURI="root"
PORTAGE_ELOG_SYSTEM="save_summary echo"
PORTAGE_FETCH_CHECKSUM_TRY_MIRRORS="5"
PORTAGE_FETCH_RESUME_MIN_SIZE="350K"
PORTAGE_GID="250"
PORTAGE_INST_GID="0"
PORTAGE_INST_UID="0"
PORTAGE_PYM_PATH="/usr/lib64/portage/pym"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_RSYNC_RETRIES="3"
PORTAGE_TMPDIR="/var/tmp"
PORTAGE_VERBOSE="1"
PORTAGE_WORKDIR_MODE="0700"
PORTDIR="/usr/portage"
PROFILE_ONLY_VARIABLES="ARCH ELIBC KERNEL USERLAND"
PWD="/home/gerald"
RESUMECOMMAND="/usr/bin/wget -c -t 5 -T 60 --passive-ftp -O "${DISTDIR}/${FILE}" "${URI}""
ROOT="/"
ROOTPATH="/opt/bin:/usr/x86_64-pc-linux-gnu/gcc-bin/4.3.2"
RPMDIR="/usr/portage/rpm"
SHELL="/bin/bash"
SHLVL="5"
STAGE1_USE="multilib nptl nptlonly unicode"
SYMLINK_LIB="yes"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
TERM="xterm"
USE="X acl alsa amd64 automount bash-completion berkdb bzip2 cairo cli cracklib crypt cups dbus directfb doc dri emacs examples fortran gd gdbm gif gpm gtk gzip iconv ipv6 isdnlog java jpeg jpeg2k midi mmx mudflap multilib ncurses nls nptl nptlonly opengl openmp pam pcre perl php png pppd python readline reflection samba session sound spell spl sse sse2 ssh ssl svg swat sysfs tcl tcpd threads tiff tk truetype unicode xinerama xml xorg zip 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="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="radeonhd radeon vga vesa fglrx"
USER="root"
USERLAND="GNU"
USE_EXPAND="ALSA_CARDS ALSA_PCM_PLUGINS APACHE2_MODULES APACHE2_MPMS CAMERAS CROSSCOMPILE_OPTS DVB_CARDS ELIBC FCDSL_CARDS FOO2ZJS_DEVICES FRITZCAPI_CARDS INPUT_DEVICES KERNEL LCD_DEVICES LINGUAS LIRC_DEVICES MISDN_CARDS USERLAND VIDEO_CARDS"
USE_EXPAND_HIDDEN="CROSSCOMPILE_OPTS ELIBC KERNEL USERLAND"
USE_ORDER="env:pkg:conf:defaults:pkginternal:env.d"
VIDEO_CARDS="radeonhd radeon vga vesa fglrx"
WINDOWID="8388621"
WINDOWPATH="7"
XAUTHORITY="/root/.xauthW0sGQU"
XERCESC_NLS_HOME="/usr/share/xerces-c/msg"
XTERM_LOCALE="C"
XTERM_SHELL="/bin/bash"
XTERM_VERSION="XTerm(237)"
_="/usr/bin/emerge"

[Comment 1 Markus Dittrich (RETIRED) 2008-11-14 14:19:49 UTC]

Thanks much for the note and I can confirm this. We can't really
have them block each other since they are both pulled in by
suitesparse at the moment. Is there actually any reason to have csparse 
around with cxsparse in the tree? As far as I know cxsparse is a superset 
of csparse but I may be wrong.

Thanks,
Markus

[Comment 2 Sébastien Fabbro (RETIRED) 2009-03-09 16:53:19 UTC]

*** Bug 248326 has been marked as a duplicate of this bug. ***

[Comment 3 Sébastien Fabbro (RETIRED) 2009-03-09 16:54:59 UTC]

Since csparse is more for educational purposes, I committed a fix to install its header in /usr/include/csparse. Please re-open if you see it as a problem.