| Summary: | sci-biology/ncbi-tools++ fails with libpng15 | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Justin Lecher (RETIRED) <jlec> |
| Component: | Current packages | Assignee: | Gentoo Science Biology related packages <sci-biology> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | CC: | mmokrejs |
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Bug Depends on: | |||
| Bug Blocks: | 354479 | ||
| Attachments: | proposed patch | ||
*** Bug 383789 has been marked as a duplicate of this bug. *** Created attachment 287207 [details, diff]
proposed patch
+ 23 Sep 2011; Lars Wendler <polynomial-c@gentoo.org> + ncbi-tools++-2010.06.15-r1.ebuild, + +files/ncbi-tools++-2010.06.15-libpng15.patch: + non-maintainer commit: Added a patch to fix compilation with libpng15 (bug + #383721). + |
/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/src/util/image/image_io_png.cpp: In function ‘void ncbi::s_PngWriteInit(png_struct*&, png_info*&, size_t, size_t, size_t, ncbi::CImageIO::ECompress)’: /var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/src/util/image/image_io_png.cpp:150:44: error: ‘Z_NO_COMPRESSION’ was not declared in this scope /var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/src/util/image/image_io_png.cpp:153:44: error: ‘Z_BEST_SPEED’ was not declared in this scope /var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/src/util/image/image_io_png.cpp:156:44: error: ‘Z_DEFAULT_COMPRESSION’ was not declared in this scope /var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/src/util/image/image_io_png.cpp:159:44: error: ‘Z_BEST_COMPRESSION’ was not declared in this scope /var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/src/util/image/image_io_png.cpp: In function ‘void ncbi::s_PngReadValidate(png_structp, png_infop, size_t&, size_t&, size_t&, size_t&, size_t&, size_t&, size_t&)’: /var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/src/util/image/image_io_png.cpp:180:28: error: invalid use of incomplete type ‘png_info {aka struct png_info_def}’ /usr/include/png.h:696:16: error: forward declaration of ‘png_info {aka struct png_info_def}’ /var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/src/util/image/image_io_png.cpp:181:28: error: invalid use of incomplete type ‘png_info {aka struct png_info_def}’ /usr/include/png.h:696:16: error: forward declaration of ‘png_info {aka struct png_info_def}’ /var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/src/util/image/image_io_png.cpp:182:28: error: invalid use of incomplete type ‘png_info {aka struct png_info_def}’ /usr/include/png.h:696:16: error: forward declaration of ‘png_info {aka struct png_info_def}’ /var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/src/util/image/image_io_png.cpp:183:35: error: invalid use of incomplete type ‘png_info {aka struct png_info_def}’ /usr/include/png.h:696:16: error: forward declaration of ‘png_info {aka struct png_info_def}’ /var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15-r1/work/ncbi_cxx--Jun_15_2010/src/util/image/image_io_png.cpp:184:35: error: invalid use of incomplete type ‘png_info {aka struct png_info_def}’ /usr/include/png.h:696:16: error: forward declaration of ‘png_info {aka struct png_info_def}’ make[7]: *** [image_io_png.o] Error 1 make[7]: *** Waiting for unfinished jobs.... make[7]: Leaving directory `/var/tmp/portage/sci-biology/ncbi-tools++-2010.06.15 $ einfo ncbi-tools++ Portage 2.2.0_alpha59 (default/linux/amd64/10.0, gcc-4.6.1-asneeded, glibc-2.13-r4, 3.0.4-lh x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.0.4-lh-x86_64-Intel-R-_Core-TM-_i7_CPU_860_@_2.80GHz-with-gentoo-2.0.3 Timestamp of tree: Mon, 19 Sep 2011 05:30:01 +0000 ccache version 3.1.6 [disabled] app-shells/bash: 4.2_p10 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.5.4-r4, 2.6.7-r2, 2.7.2-r2, 3.1.4-r2, 3.2-r2 dev-util/ccache: 3.1.6 dev-util/cmake: 2.8.5-r2::science dev-util/pkgconfig: 0.26 sys-apps/baselayout: 2.0.3 sys-apps/openrc: 0.9.3-r1 sys-apps/sandbox: 2.5 sys-devel/autoconf: 2.13, 2.68 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.1-r1 sys-devel/binutils: 2.21.1-r1 sys-devel/gcc: 4.2.4-r1, 4.3.6-r1, 4.4.6-r1, 4.5.3-r1, 4.6.1-r1 sys-devel/gcc-config: 1.4.1-r1 sys-devel/libtool: 2.4-r1::last-hope sys-devel/make: 3.82-r1 sys-kernel/linux-headers: 2.6.39 (virtual/os-headers) sys-libs/glibc: 2.13-r4 Repositories: gentoo sunrise bicatali betagarden dummy Neurogeek-s-overlay science last-hope g-ctan Installed sets: ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -ftracer -march=corei7 -mcx16 -msahf -mpopcnt -msse4.2 -mtune=corei7 --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=8192 -mtune=corei7 -frecord-gcc-switches -g -Wimplicit-function-declaration" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/eselect/ /usr/share/gnupg/qualified.txt /usr/share/nano/ /usr/share/openvpn/easy-rsa /var/lib/hsqldb /var/spool/torque" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /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 -ftracer -march=corei7 -mcx16 -msahf -mpopcnt -msse4.2 -mtune=corei7 --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=8192 -mtune=corei7 -frecord-gcc-switches -g -Wenum-compare" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="-t --jobs=12 --load-average=12 --keep-going --autounmask-write --autounmask" FEATURES="assume-digests binpkg-logs buildsyspkg collision-protect distlocks ebuild-locks fixlafiles fixpackages metadata-transfer multilib-strict news noinfo parallel-fetch parallel-install preserve-libs protect-owned sandbox sfperms sign split-log splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync" FFLAGS="-O2 -pipe -ftracer -march=corei7 -mcx16 -msahf -mpopcnt -msse4.2 -mtune=corei7 --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=8192 -mtune=corei7 -frecord-gcc-switches -g" GENTOO_MIRRORS=" /mnt/tmpfs/ http://gentoo.j-schmitz.net/mirror/ ftp://ftp.gentoo.mesh-solutions.com/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.tu-clausthal.de/pub/linux/gentoo/" LANG="en_GB.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common" LINGUAS="en" MAKEOPTS="-j16 -l12" PKGDIR="/usr/portage/packages" PORTAGE_COMPRESS="xz" PORTAGE_COMPRESS_FLAGS="-z -e -9 -v" 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="/data/local/sunrise/reviewed /data/local/bicatali /data/local/betagarden /data/local/dummy /data/local/neurogeek /data/local/sci /data/local/lh/ebuilds /data/local/g-ctan" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="64bit 7zip X acpi additions alsa amd64 arpwarp atlas bash-completion berkdb blas branding bzip2 c++ cairo caps cblas ccache cleartype cli command-args consolekit corefonts cracklib crypt cups cupsddk custom-optimization cxx dbus dri dts exif fbcondecor fortran gdbm gif glib glibc-omitfp gmp gnome gnome-keyring gpm graphics gstreamer gtk hddtemp iconv icu ios ipod iproute2 iptables ipv6 ipython javascript jpeg jpeg2k kqemu lapack largefile lcms ldap libnotify libsexy lm_sensors lzma mailtrain md5sum mmx mmxext mng modules mp3 mudflap multilib multiuser nagios-dns nagios-ntp nagios-ping nagios-ssh nano-syntax ncurses network-cron nis nls nptl nptlonly nsplugin objc objc++ opengl openmp openntpd pam pcre pdf perl png policykit pppd pymol python qt-static qt3support readline rrdcgi rrdtool science sensord session smp sqlite sqlite3 sse sse2 sse3 sse4 sse4a sse5 ssl startup-notification svg sysfs system-sqlite tcpd threads tiff truetype type1 udev unicode vaapi vdpau x264 xcb xcomposite xinerama xorg xulrunner zlib" ALSA_CARDS="hda-intel" 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" DRACUT_MODULES="plymouth" 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="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 x86_64" QEMU_USER_TARGETS="i386 x86_64" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia" 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_RSYNC_EXTRA_OPTS ================================================================= Package Settings ================================================================= sci-biology/ncbi-tools++-2010.06.15-r1 was built with the following: USE="(multilib) sqlite -mysql" CFLAGS="-O2 -pipe -march=corei7 -mcx16 -msahf -mpopcnt -msse4.2 --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=8192 -mtune=corei7 -frecord-gcc-switches -g -Wdisabled-optimization -Wimplicit-function-declaration" CXXFLAGS="-O2 -pipe -march=corei7 -mcx16 -msahf -mpopcnt -msse4.2 --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=8192 -mtune=corei7 -frecord-gcc-switches -g -Wdisabled-optimization -Wenum-compare"