Rememerging sci-geosciences/gmt-4.5.6 which is the stable version fails due to a compilation error: gmtdigitize.c: In function 'main': gmtdigitize.c:77:2: error: unknown type name 'gid_t' gid_t gid = 0; ^ gmtdigitize.c:78:2: error: unknown type name 'uid_t' uid_t uid = 0; ^ Settings: emerge --info '=sci-geosciences/gmt-4.5.6::gentoo' Portage 2.2.14 (python 2.7.9-final-0, default/linux/amd64/13.0/desktop/kde, gcc-4.8.3, glibc-2.19-r1, 3.7.10-gentoo-r1 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.7.10-gentoo-r1-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2 KiB Mem: 32911148 total, 7703032 free KiB Swap: 33554428 total, 33531964 free Timestamp of tree: Mon, 16 Mar 2015 18:30:01 +0000 ld GNU ld (Gentoo 2.24 p1.4) 2.24 app-shells/bash: 4.2_p53 dev-java/java-config: 2.2.0 dev-lang/perl: 5.20.1-r4 dev-lang/python: 2.7.9-r1, 3.3.5-r1, 3.4.1 dev-util/cmake: 2.8.12.2-r1 dev-util/pkgconfig: 0.28-r1 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.13.11 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.11.6-r1, 1.13.4 sys-devel/binutils: 2.24-r3 sys-devel/gcc: 4.7.3-r1, 4.8.3 sys-devel/gcc-config: 1.7.3 sys-devel/libtool: 2.4.4 sys-devel/make: 4.1-r1 sys-kernel/linux-headers: 3.18 (virtual/os-headers) sys-libs/glibc: 2.19-r1 Repositories: gentoo ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA dlj-1.1 skype-eula PUEL @EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=core2" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /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=core2" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fail-clean fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://mirrors.med.harvard.edu/gentoo ftp://mirror.datapipe.net/gentoo http://gentoo.mirrors.tds.net/gentoo http://gentoo.cites.uiuc.edu/pub/gentoo/" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j6" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="" USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo cdda cdr cli consolekit cpudetection cracklib crypt cups cxx dbus declarative dri dts dvd dvdr dvdread emboss encode exif fam firefox flac fortran gd gdbm gif glamor gpm gtk iconv imap ipv6 jpeg kde kipi lcms ldap libnotify mad mjpeg mmx mng modules mp3 mp4 mpeg multilib ncurses nls nptl odbc ogg openconnect opengl openmp pam pango pcre pdf phonon plasma plotutils png policykit postgres ppds python qt qt3support qt4 readline real samba sdl semantic-desktop session smp spell sse sse2 ssl startup-notification svg tcpd tiff truetype udev udisks unicode upower usb v4l v4l2 vorbis wmf wxwidgets x264 xcb xcomposite xinerama xml xscreensaver xv xvid zlib" ABI_X86="64" 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" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd 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 sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx sse sse2" 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 ublox ubx" GRUB_PLATFORMS="efi-64" INPUT_DEVICES="mouse keyboard evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="nv nvidia vesa fbdev" 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, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON ================================================================= Package Settings ================================================================= sci-geosciences/gmt-4.5.6 was built with the following: USE="doc gmtfull gmttria metric netcdf (policykit) -debug -gmthigh -mex -octave -postscript" ABI_X86="64" localhost ~ # emerge -pqv '=sci-geosciences/gmt-4.5.6::gentoo' [ebuild R ] sci-geosciences/gmt-4.5.6 USE="doc gmtfull gmttria metric netcdf -debug -gmthigh -mex -octave -postscript"
Created attachment 399130 [details] full build log
The same applies to sci-geosciences/gmt-4.5.9
It seems they fixed it in 4.5.13 (2015-01-01). At least this compiles for me: # diff -ubB /usr/portage/sci-geosciences/gmt/gmt-4.5.9.ebuild /usr/local/portage/sci-geosciences/gmt/gmt-4.5.13.ebuild --- /usr/portage/sci-geosciences/gmt/gmt-4.5.9.ebuild 2013-02-02 07:40:13.000000000 +0100 +++ /usr/local/portage/sci-geosciences/gmt/gmt-4.5.13.ebuild 2015-04-20 15:41:48.093099435 +0200 @@ -13,9 +13,9 @@ DESCRIPTION="Powerful map generator" HOMEPAGE="http://gmt.soest.hawaii.edu/" SRC_URI=" - mirror://gmt/${P}.tar.bz2 - mirror://gmt/${GSHHS}.tar.bz2 - gmttria? ( mirror://gmt/${P}-non-gpl.tar.bz2 )" + ftp://ftp.scc.u-tokai.ac.jp/pub/gmt/${P}-src.tar.bz2 + ftp://ftp.scc.u-tokai.ac.jp/pub/gmt/${GSHHS}.tar.bz2 + gmttria? ( ftp://ftp.scc.u-tokai.ac.jp/pub/gmt/${P}-non-gpl-src.tar.bz2 )" LICENSE="GPL-2 gmttria? ( Artistic )" SLOT="0" @@ -29,7 +29,7 @@ octave? ( sci-mathematics/octave )" DEPEND="${RDEPEND}" -S="${WORKDIR}/GMT${PV}" +S="${WORKDIR}/gmt-${PV}" # mex can use matlab too which i can't test REQUIRED_USE=" (since i hve no access to publish files into the gentoo mirror system i searched for a working mirror of the GMT distribution itself - they might not like the idea...)
Sorry for the noise, but since the guys @SOEST choose a kind of common default source directory structure we can remove the source definition in the ebuild: (In reply to Thomas Beutin from comment #3) > -S="${WORKDIR}/GMT${PV}"
Same in gmt-4.5.9 I am guessing this was caused by header cleanups in recent glibc versions.
*** Bug 554318 has been marked as a duplicate of this bug. ***
(In reply to Thomas Beutin from comment #3) > It seems they fixed it in 4.5.13 (2015-01-01). At least this compiles for me: > > # diff -ubB /usr/portage/sci-geosciences/gmt/gmt-4.5.9.ebuild > /usr/local/portage/sci-geosciences/gmt/gmt-4.5.13.ebuild > --- /usr/portage/sci-geosciences/gmt/gmt-4.5.9.ebuild 2013-02-02 > 07:40:13.000000000 +0100 > +++ /usr/local/portage/sci-geosciences/gmt/gmt-4.5.13.ebuild 2015-04-20 > 15:41:48.093099435 +0200 > @@ -13,9 +13,9 @@ > DESCRIPTION="Powerful map generator" > HOMEPAGE="http://gmt.soest.hawaii.edu/" > SRC_URI=" > - mirror://gmt/${P}.tar.bz2 > - mirror://gmt/${GSHHS}.tar.bz2 > - gmttria? ( mirror://gmt/${P}-non-gpl.tar.bz2 )" > + ftp://ftp.scc.u-tokai.ac.jp/pub/gmt/${P}-src.tar.bz2 > + ftp://ftp.scc.u-tokai.ac.jp/pub/gmt/${GSHHS}.tar.bz2 > + gmttria? ( > ftp://ftp.scc.u-tokai.ac.jp/pub/gmt/${P}-non-gpl-src.tar.bz2 )" > > LICENSE="GPL-2 gmttria? ( Artistic )" > SLOT="0" > @@ -29,7 +29,7 @@ > octave? ( sci-mathematics/octave )" > DEPEND="${RDEPEND}" > > -S="${WORKDIR}/GMT${PV}" > +S="${WORKDIR}/gmt-${PV}" If I try to use this patch for gmt-4.5.9, 'ebuild gmt-4.5.9.ebuild digest' fails with: root@lynx:/usr/local/portage/sci-geosciences/gmt(14)# ebuild gmt-4.5.9.ebuild digest >>> Downloading 'http://distfiles.gentoo.org/distfiles/gmt-4.5.9-src.tar.bz2' --2015-07-12 12:45:02-- http://distfiles.gentoo.org/distfiles/gmt-4.5.9-src.tar.bz2 Resolving distfiles.gentoo.org (distfiles.gentoo.org)... 137.226.34.42, 216.165.129.135, 140.211.166.134, ... Connecting to distfiles.gentoo.org (distfiles.gentoo.org)|137.226.34.42|:80... connected. HTTP request sent, awaiting response... 404 Not Found 2015-07-12 12:45:02 ERROR 404: Not Found. >>> Downloading 'ftp://ftp.scc.u-tokai.ac.jp/pub/gmt/gmt-4.5.9-src.tar.bz2' --2015-07-12 12:45:02-- ftp://ftp.scc.u-tokai.ac.jp/pub/gmt/gmt-4.5.9-src.tar.bz2 => ‘/net/caiman/usr/local/portage/distfiles_caiman/gmt-4.5.9-src.tar.bz2’ Resolving ftp.scc.u-tokai.ac.jp (ftp.scc.u-tokai.ac.jp)... 150.7.205.123 Connecting to ftp.scc.u-tokai.ac.jp (ftp.scc.u-tokai.ac.jp)|150.7.205.123|:21... connected. Logging in as anonymous ... Logged in! ==> SYST ... done. ==> PWD ... done. ==> TYPE I ... done. ==> CWD (1) /pub/gmt ... done. ==> SIZE gmt-4.5.9-src.tar.bz2 ... done. ==> PASV ... couldn't connect to 150.7.205.123 port 8234: No route to host !!! Couldn't download 'gmt-4.5.9-src.tar.bz2'. Aborting. !!! Fetch failed for gmt-4.5.9-src.tar.bz2, can't update Manifest
(In reply to Juergen Rose from comment #7) > (In reply to Thomas Beutin from comment #3) [...] > !!! Fetch failed for gmt-4.5.9-src.tar.bz2, can't update Manifest According to http://gmt.soest.hawaii.edu/projects/gmt/wiki/Download this still should be an official mirror. But if you check ftp://ftp.soest.hawaii.edu/gmt/ you won't find a v4.5.9 anymore (it has been moved to "legacy/"). I renamed my local gmt-4.5.11.ebuild to gmt-4.5.13.ebuild, kept the regular SRC_URI ("mirror://gmt/$..."), and after some timeouts i got everything from "ftp://ftp.iag.usp.br/". The diff to the latest ebuild in the official portage tree is: # diff -ubB /usr/portage/sci-geosciences/gmt/gmt-4.5.9.ebuild /usr/local/portage/sci-geosciences/gmt/gmt-4.5.13.ebuild --- /usr/portage/sci-geosciences/gmt/gmt-4.5.9.ebuild 2013-02-02 07:40:13.000000000 +0100 +++ /usr/local/portage/sci-geosciences/gmt/gmt-4.5.13.ebuild 2015-07-13 10:26:14.766574225 +0200 @@ -13,9 +13,9 @@ DESCRIPTION="Powerful map generator" HOMEPAGE="http://gmt.soest.hawaii.edu/" SRC_URI=" - mirror://gmt/${P}.tar.bz2 + mirror://gmt/${P}-src.tar.bz2 mirror://gmt/${GSHHS}.tar.bz2 - gmttria? ( mirror://gmt/${P}-non-gpl.tar.bz2 )" + gmttria? ( mirror://gmt/${P}-non-gpl-src.tar.bz2 )" LICENSE="GPL-2 gmttria? ( Artistic )" SLOT="0" @@ -29,8 +29,6 @@ octave? ( sci-mathematics/octave )" DEPEND="${RDEPEND}" -S="${WORKDIR}/GMT${PV}" - # mex can use matlab too which i can't test REQUIRED_USE=" mex? ( octave ) Does this help?
Created attachment 406846 [details] gmt-4.5.13.ebuild
(In reply to Thomas Beutin from comment #8) > (In reply to Juergen Rose from comment #7) > > (In reply to Thomas Beutin from comment #3) > [...] > > !!! Fetch failed for gmt-4.5.9-src.tar.bz2, can't update Manifest > > According to http://gmt.soest.hawaii.edu/projects/gmt/wiki/Download this > still should be an official mirror. But if you check > ftp://ftp.soest.hawaii.edu/gmt/ you won't find a v4.5.9 anymore (it has been > moved to "legacy/"). I renamed my local gmt-4.5.11.ebuild to > gmt-4.5.13.ebuild, kept the regular SRC_URI ("mirror://gmt/$..."), and after > some timeouts i got everything from "ftp://ftp.iag.usp.br/". > > The diff to the latest ebuild in the official portage tree is: > > # diff -ubB /usr/portage/sci-geosciences/gmt/gmt-4.5.9.ebuild > /usr/local/portage/sci-geosciences/gmt/gmt-4.5.13.ebuild > --- /usr/portage/sci-geosciences/gmt/gmt-4.5.9.ebuild 2013-02-02 > 07:40:13.000000000 +0100 > +++ /usr/local/portage/sci-geosciences/gmt/gmt-4.5.13.ebuild 2015-07-13 > 10:26:14.766574225 +0200 > @@ -13,9 +13,9 @@ > DESCRIPTION="Powerful map generator" > HOMEPAGE="http://gmt.soest.hawaii.edu/" > SRC_URI=" > - mirror://gmt/${P}.tar.bz2 > + mirror://gmt/${P}-src.tar.bz2 > mirror://gmt/${GSHHS}.tar.bz2 > - gmttria? ( mirror://gmt/${P}-non-gpl.tar.bz2 )" > + gmttria? ( mirror://gmt/${P}-non-gpl-src.tar.bz2 )" > > LICENSE="GPL-2 gmttria? ( Artistic )" > SLOT="0" > @@ -29,8 +29,6 @@ > octave? ( sci-mathematics/octave )" > DEPEND="${RDEPEND}" > > -S="${WORKDIR}/GMT${PV}" > - > # mex can use matlab too which i can't test > REQUIRED_USE=" > mex? ( octave ) > > > > > Does this help? Thank you Thomas, with the attached ebuild I was able after some timeouts to emerge gmt-4.5.13 .
Fixed by non-maintainer commit because sci-geo herd is apparently asleep at the wheel. @maintainers, please bump gmt, in portage this package hasn't been touched since 2013 and is thoroughly obsolete, while lots of new versions (including 5.1, a new major version) have been released upstream since then... + 18 Jul 2015; Alexandre Rostovtsev <tetromino@gentoo.org> gmt-4.5.6.ebuild, + gmt-4.5.9.ebuild, +files/gmt-4.5.9-unistd.h.patch: + Non-maintainer commit: fix build on modern glibc versions (bug #543624, + thanks to Andreas Plesch et al.)
