x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -pthread -I/usr/include -g -O0 -O2 -pipe -march=nocona -MT genotype_score.o -MD -MP -MF .deps/genotype_score.Tpo -c -o genotype_score.o genotype_score.cc pph.cc: In function 'int<unnamed>::compute_free(int)': pph.cc:1817: warning: comparison between signed and unsigned integer expressions pph.cc: In function 'int<unnamed>::compute_locked(int)': pph.cc:1838: warning: comparison between signed and unsigned integer expressions pph.cc: In function 'void<unnamed>::outputENTsol()': pph.cc:1867: warning: comparison between signed and unsigned integer expressions pph.cc: In function 'int<unnamed>::traverse(<unnamed>::CComp*, int, int, double, double*, int)': pph.cc:2047: error: 'stderr' was not declared in this scope pph.cc:2047: error: 'fprintf' was not declared in this scope pph.cc:2052: warning: unused variable 'error' pph.cc: In function 'bool<unnamed>::fill_template(<unnamed>::Gen*)': pph.cc:2378: error: 'stderr' was not declared in this scope pph.cc:2378: error: 'fprintf' was not declared in this scope pph.cc: In function 'void<unnamed>::merge_cc(<unnamed>::CComp*, <unnamed>::CComp*)': pph.cc:2389: warning: comparison between signed and unsigned integer expressions pph.cc:2395: warning: comparison between signed and unsigned integer expressions pph.cc: In function '<unnamed>::CComp*<unnamed>::get_cc(<unnamed>::Gen*, <unnamed>::CComp*)': pph.cc:2411: warning: comparison between signed and unsigned integer expressions pph.cc: In function 'void<unnamed>::read_genotypes()': pph.cc:2534: warning: comparison between signed and unsigned integer expressions pph.cc:2541: warning: comparison between signed and unsigned integer expressions pph.cc:2546: warning: comparison between signed and unsigned integer expressions pph.cc:2552: warning: comparison between signed and unsigned integer expressions pph.cc:2554: warning: comparison between signed and unsigned integer expressions pph.cc:2562: warning: comparison between signed and unsigned integer expressions pph.cc:2575: warning: comparison between signed and unsigned integer expressions pph.cc:2581: error: 'stderr' was not declared in this scope pph.cc:2581: error: 'fprintf' was not declared in this scope make[1]: *** [pph.o] Error 1 make[1]: *** Waiting for unfinished jobs.... mv -f .deps/score.Tpo .deps/score.Po mv -f .deps/case_control_score.Tpo .deps/case_control_score.Po mv -f .deps/genotype_score.Tpo .deps/genotype_score.Po mv -f .deps/qt_score.Tpo .deps/qt_score.Po make[1]: Leaving directory `/var/tmp/portage/sci-biology/blossoc-1.4.0/work/blossoc-1.4.0' # emerge --info =sci-biology/blossoc-1.4.0 Portage 2.1.9.25 (default/linux/amd64/10.0, gcc-4.4.4, glibc-2.12.1-r3, 2.6.35.4 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-2.6.35.4-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9300_@_2.50GHz-with-gentoo-2.0.1 Timestamp of tree: Wed, 15 Dec 2010 11:00:01 +0000 app-shells/bash: 4.1_p9 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.5.4-r4, 2.6.6-r1, 2.7.1, 3.1.3 dev-util/cmake: 2.8.1-r2 sys-apps/baselayout: 2.0.1-r1 sys-apps/openrc: 0.6.8 sys-apps/sandbox: 2.4 sys-devel/autoconf: 2.13, 2.68 sys-devel/automake: 1.5, 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.21 sys-devel/gcc: 4.3.5, 4.4.4-r2, 4.5.1-r1 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82 virtual/os-headers: 2.6.36.1 (sys-kernel/linux-headers) ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=nocona" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/openvpn/easy-rsa /var/bind /var/lib/hsqldb /var/qmail/alias /var/qmail/control /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=nocona" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs distlocks fixlafiles fixpackages news nostrip parallel-fetch protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" GENTOO_MIRRORS="http://distfiles.gentoo.org" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="en cs cz" MAKEOPTS="-j5" 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="/usr/local/portage/layman/science /usr/local/portage/layman/sunrise /usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X amd64 berkdb bzip2 cracklib crypt cxx dbus dri fontconfig fortran gdbm gnutls hal iconv innodb java jce jpeg jpg kde laptop mmx modules mpi mpich2 multilib mysql ncurses nfs nls nptl nptlonly nsplugin opengl openmp openssl pam pcre perl png python qt3support qt4 readline server session sse sse2 ssl suexec svg sysfs syslog tcpd threads tiff truetype unicode usb 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 auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dbd deflate dir disk_cache env expires ext_filter file_cache filter headers icu ident imagemap include info log_config mem_cache mime mime_magic rewrite setenvif speling status unique_id userdir usertrack vhost_alias negotiation" 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 evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en cs cz" PHP_TARGETS="php5-2" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="vesa" 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, FFLAGS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS # gcc-config -l [1] x86_64-pc-linux-gnu-4.3.5 [2] x86_64-pc-linux-gnu-4.4.4 * [3] x86_64-pc-linux-gnu-4.5.1 #
This looks like a missing '#include <cstdio>'. There's already a patch for gcc-4.3, seems for 4.4 a bit more patching is required.
so it is the exact problem from 292949. Please attach full buildlog
Created attachment 259276 [details] build.log (In reply to comment #2) > so it is the exact problem from 292949. Please attach full buildlog Happens with gcc-4.4.4 while not 4.5.1.
(In reply to comment #3) > Created an attachment (id=259276) [details] > build.log > > (In reply to comment #2) > > so it is the exact problem from 292949. Please attach full buildlog This patch is supposedly not enough, it is already in blossoc-1.4.0 > Happens with gcc-4.4.4 while not 4.5.1. And if that means my boost was probably compiled with 4.5.1 and hence blossoc cannot be linked to it fine using gcc-4.4.4 then this bug is INVALID. :(
