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Bug 257177 - sci-libs/hdf5-1.6.7 fails with /usr/include/bits/fcntl2.h:51: error: call to '__open_missing_mode' declared with attribute error: open with O_CREAT in second argument needs 3 arguments
Summary: sci-libs/hdf5-1.6.7 fails with /usr/include/bits/fcntl2.h:51: error: call to ...
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: New packages (show other bugs)
Hardware: All Linux
: High normal (vote)
Assignee: Gentoo Science Related Packages
Depends on:
Blocks: fortify-source
  Show dependency tree
Reported: 2009-02-01 02:01 UTC by Juergen Rose
Modified: 2009-02-17 22:00 UTC (History)
0 users

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

Suggested patch to fix compile error. (zip_perf.patch,412 bytes, patch)
2009-02-02 04:11 UTC, Simon C. Ion
Details | Diff

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Description Juergen Rose 2009-02-01 02:01:32 UTC
'emerge hdf5' fails with:

gcc -march=nocona -O2 -pipe -ansi -O3 -fomit-frame-pointer -finline-functions -I. -I. -I../src -I../src -I../test -I../tools/lib -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c zip_perf.c  -fPIC -DPIC -o .libs/zip_perf.lo
In function 'open',
    inlined from 'do_write_test' at zip_perf.c:549,
    inlined from 'main' at zip_perf.c:650:
/usr/include/bits/fcntl2.h:51: error: call to '__open_missing_mode' declared with attribute error: open with O_CREAT in second argument needs 3 arguments
make[2]: *** [zip_perf.lo] Error 1
make[2]: Leaving directory `/var/tmp/portage/sci-libs/hdf5-1.6.7/work/hdf5-1.6.7/perform'
make[1]: *** [tests] Error 1
make[1]: Leaving directory `/var/tmp/portage/sci-libs/hdf5-1.6.7/work/hdf5-1.6.7'
make: *** [all] Error 2
 * ERROR: sci-libs/hdf5-1.6.7 failed.

Fails on x86_64 and i686 systems.

Reproducible: Always

root@condor:/root(61)# emerge --info
Portage (default/linux/amd64/2008.0/desktop, gcc-4.3.3, glibc-2.9_p20081201-r1, x86_64)
System uname: Linux-
Timestamp of tree: Sat, 31 Jan 2009 05:40:01 +0000
distcc 3.1 x86_64-pc-linux-gnu [disabled]
app-shells/bash:     3.2_p48
dev-java/java-config: 1.3.7-r1, 2.1.7
dev-lang/python:     2.4.4-r15, 2.5.4-r2
dev-python/pycrypto: 2.0.1-r6
dev-util/cmake:      2.6.2-r1
sys-apps/baselayout: 2.0.0
sys-apps/openrc:     0.4.2
sys-apps/sandbox:    1.3.3
sys-devel/autoconf:  2.13, 2.63
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2
sys-devel/binutils:  2.19
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.6a
virtual/os-headers:  2.6.28-r1
ACCEPT_KEYWORDS="amd64 ~amd64"
CFLAGS="-march=nocona -O2 -pipe"
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/kde/4.1/env /usr/kde/4.1/share/config /usr/kde/4.
1/shutdown /usr/kde/4.2/env /usr/kde/4.2/share/config /usr/kde/4.2/shutdown /usr/share/config /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/gen
too-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 /etc/udev/rules.d"
CXXFLAGS="-march=nocona -O2 -pipe"
FEATURES="distlocks fixpackages parallel-fetch protect-owned sandbox sfperms strict unmerge-orphans userfetch"
FFLAGS="-march=nocona -O2 -pipe"
LINGUAS="de fr"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclud
e=/distfiles --exclude=/local --exclude=/packages"
PORTDIR_OVERLAY="/usr/local/portage/layman/java-overlay /usr/local/portage/layman/zugaina /usr/local/portage/layman/dotnet /usr/local/portag
e/layman/science /usr/local/portage/layman/jokey /usr/local/portage"
USE="X Xaw3d a52 aac acl acpi administrator afs aiglx alsa amd64 amrr ao aotuv apache2 asf atlas auctex audacious audiofile automount bash-c
ompletion beagle berkdb bjam blas bluetooth bonobo boo boost branding bzip2 c++ cairo cdda cddb cdf cdio cdparanoia cdr cgi chm cli corba cr
acklib cran crypt cups curl cxx daap dbus device-mapper dga dia divx djvu dlloader dmi doc dri ds3490 dv dvb dvd dvdr dvdread dvi dxr3 dynag
raph eds effects elf emacs emboss encode epiphany esd evo examples exif expat extra fam fame ffmpeg fftw firefox fits flac fltk foomaticdb f
ortran fpx galago gd gdal gdbm geos gif gimp gimpprint ginac glade glib glitz gml gmp gnokii gnome gnuplot gnutls gphoto2 gpm graphics graph
viz gs gsl gsm gstreamer gtk guile hal hardened harness hddtemp hdf hdf5 hlapi http hvm iconv icq icu id3 ide imagemagick imap innodb ipv6 i
rda irmc isdnlog ithreads jabber java jbig john jpeg jpeg2k kde kde4 kdeprefix kerberos kexi keyring ladspa lame lapack latex lcms ldap libf
fi libgda libnotify libsamplerate lirc lm_sensors lua lzo lzw mad maildir math matroska midi mikmod mmx mmxext mng mod mono motif mozdevelop
 mozilla mozsvg mozxmlterm mp3 mp4 mp4live mpeg mpeg2 mplayer mudflap multilib musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm 
network networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs numarray numeric nvidia obex ocaml octave odbc ogdi ogg ole opengl openmp pa
e pam pcre pda pdf perl plotutils plugins png posix postgres postscript ppds pppd preview-latex proj projectx pstricks python qhull qt3 qt3s
upport qt4 quicktime readline reflection reiserfs rhythmbox rle rpc rrdcgi rrdtool samba sasl science sdl session slang slp smp sndfile snmp
 soup sox speex spell spl sqlite sse sse2 ssl startup-notification stlport subtitles subversion suexec svg sysfs t1lib tcl tcpd tex theora t
hreads thunderbird tidy tiff tk truetype unicode usb userlocales utempter v4l2 vorbis webkit wmf wxwindows xattr xcb xemacs xext xine xml xm
lreader xmlrpc xorg xpm xulrunner xv xvid xvmc zlib zvbi" ALSA_CARDS="intel8x0" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop em
pty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULE
S="actions alias auth_basic auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile auth
z_host authz_owner authz_user autoindex cache dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter header
s ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http
 rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" DVB_CARDS="cx8800 cx88xx tda1004x saa713" ELIBC="glibc" INPUT_D
EVICES="keyboard mouse                " KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" L
INGUAS="de fr" NETBEANS_MODULES="ide websvccommon nb harness apisupport groovy gsf j2ee java xml" USERLAND="GNU" VIDEO_CARDS="nv nvidia vesa
Comment 1 Simon C. Ion 2009-02-02 03:53:04 UTC
Upstream knows of this issue. See:

The claim is that this patch will fix the issue:

--- hdf5-1.6.7/perform/zip_perf.c	2008-01-31 21:04:10.000000000 -0600
+++	2009-02-01 21:51:59.907431212 -0600
@@ -546,7 +546,7 @@
         /* do compressed data write */
-        output = open(filename, O_RDWR | O_CREAT);
+        output = open(filename, O_RDWR | O_CREAT, S_IRXW);
         if (output == -1)
Comment 2 Simon C. Ion 2009-02-02 04:11:22 UTC
Created attachment 180641 [details, diff]
Suggested patch to fix compile error.

Please ignore the previous patch. This one has the parameter spelled correctly.
Comment 3 Juergen Rose 2009-02-02 08:42:48 UTC
The patch worked for me.
Comment 4 Patrick Lauer gentoo-dev 2009-02-04 13:46:22 UTC
+  04 Feb 2009; Patrick Lauer <>
+  +files/hdf5-gcc4.3.3-fix.patch, hdf5-1.6.7.ebuild:
+  fortify_sources fix, patch from Simon C. Ion, closes #257177