Bug 394545 – sci-biology/exonerate-2.2.0-r1 ignores CFLAGS / CC

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Linlin Yan 2011-12-13 11:49:12 UTC]

Sometimes the exonerate crashes, depending on the input data set. I checked the compiling options of exonerate. After I replaced all '-O3' to '-O2' in file 'configure' in its source package, the crash problem disappeared.

Reproducible: Sometimes

Steps to Reproduce:
I do not have the reproduable data now. However, I am sure that -O3 is not a good idea for compiling optimization.

[Comment 1 Jeroen Roovers (RETIRED) 2011-12-13 14:46:56 UTC]

I can confirm that it ignores CFLAGS and CC. That could easily be fixed and if it helps prevent it crashing, so the better.

[Comment 2 Justin Lecher (RETIRED) 2011-12-13 14:56:52 UTC]

+  13 Dec 2011; Justin Lecher <[e-mail]> exonerate-2.2.0-r1.ebuild:
+  Respect CFLAGS and CC, #394545
+

[Comment 3 Linlin Yan 2011-12-14 06:02:13 UTC]

Created attachment 295759 [details]
data for reproducting crash

$ ./test.sh 
Command line: [exonerate --querytype dna --targettype dna --gapextend -3 --query contigs.fa --bestn 100 --model affine:local --joinrangeext 300 --score 15 --target ref.fa --dnasubmat submat.txt --hspfilter 200 --dnahspdropoff 10 --showvulgar FALSE --ryo %S %pi %ql %C\n]
Hostname: [saturn]
./test.sh: line 7: 15092 Segmentation fault      exonerate --querytype dna --targettype dna --gapextend -3 --query contigs.fa --bestn 100 --model affine:local --joinrangeext 300 --score 15 --target ref.fa --dnasubmat submat.txt --hspfilter 200 --dnahspdropoff 10 --showvulgar FALSE --ryo "%S %pi %ql %C\n"

[Comment 4 Linlin Yan 2011-12-14 06:05:40 UTC]

Thanks for your quick response and great efforts!

For reproducing the crash, I finally found the data set and upload it now.

Here goes my 'emerge --info':
$ emerge --info
Portage 2.1.10.11 (default/linux/amd64/10.0/server, gcc-4.4.5, glibc-2.13-r4, 3.0.6-gentoo x86_64)
=================================================================
System uname: Linux-3.0.6-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_E7450_@_2.40GHz-with-gentoo-2.0.3
Timestamp of tree: Tue, 13 Dec 2011 14:30:01 +0000
app-shells/bash:          4.1_p9
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.6.6-r2, 2.7.2-r3, 3.1.4-r3
dev-util/cmake:           2.8.4-r1
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.0.3
sys-apps/openrc:          0.9.4
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13, 2.68
sys-devel/automake:       1.10.3, 1.11.1
sys-devel/binutils:       2.21.1-r1
sys-devel/gcc:            4.3.4, 4.4.5, 4.5.3-r1
sys-devel/gcc-config:     1.4.1-r1
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82-r1
sys-kernel/linux-headers: 2.6.39 (virtual/os-headers)
sys-libs/glibc:           2.13-r4
Repositories: gentoo science d-overlay
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=native -fomit-frame-pointer"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /var/spool/torque"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /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 -pipe -march=native -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv"
FFLAGS="-O2 -pipe -march=native -fomit-frame-pointer"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j8"
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/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/science /var/lib/layman/d-overlay"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="acl amd64 berkdb bzip2 cli cracklib crypt cups cxx doc dri examples fortran gdbm gpm iconv ipv6 mmx modules mudflap multilib ncurses nls nptl nptlonly openmp pam pcre pppd readline session snmp sse sse2 ssl sysfs tcpd test threads truetype unicode xml xorg 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 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 stage tables krita karbon braindump" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" 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 ubx" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="fglrx radeon" 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"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

[Comment 5 Justin Lecher (RETIRED) 2011-12-14 07:30:39 UTC]

Could you please add a build log with MAKEOPTS="-j1"?

[Comment 6 Justin Lecher (RETIRED) 2011-12-14 07:37:45 UTC]

not reproducable here.

[Comment 7 Linlin Yan 2011-12-14 14:16:37 UTC]

:( By adding 'MAKEOPTS="-j1"' when re-emerge exonerate, I can not reproduce the crash either. I confirmed that it is '-O2' rather than '-O3' this time. I tried to re-emerge by 'MAKEOPTS="-j8"' again, or to un-emerge before re-emerge it. All of them can not reproduce the crash. Only when I compile the package from source (not by emerge), it reproduces. I have no idea what was the problem before. Maybe there was some unknown conflicts on my server during the build process. Anyway, thank you very much!

[Comment 8 Justin Lecher (RETIRED) 2011-12-14 17:04:45 UTC]

it wasn't only the O3 but also -finline-functions. maybe it is somewhere around this.