hdf5-1.8.1 was released on May 29, 2008. Could this version please be added to portage? It would be nice if openmpi could be supported, instead of defaulting to mpich2. Reproducible: Always Steps to Reproduce:
Created attachment 166659 [details, diff] minor changes to hdf5-1.6.7.ebuild I have only added new patches since there were some slight differences in the code. This required to change ${PN} => ${P}
Created attachment 166661 [details, diff] gcc4.3 patch
Created attachment 166663 [details, diff] Mpich2 patch
Compiled and tested on: Portage 2.1.4.4 (default/linux/amd64/2008.0, gcc-4.1.2, glibc-2.6.1-r0, 2.6.25-gentoo-r7 x86_64) ================================================================= System uname: 2.6.25-gentoo-r7 x86_64 AMD Opteron(tm) Processor 246 Timestamp of tree: Mon, 22 Sep 2008 07:34:01 +0000 with sys-cluster/mpich2-1.0.7
Created attachment 172333 [details] hdf5-1.8.2.ebuild This ebuild, which I have attached completely for convenience, is almost the same as the one for 1.8.1. The changes are: * The gcc-4.3 patch is no longer applied (the patch doesn't work any more; i guess this has been fixed upstream, but i've not verified that yet). * The USE flags "threads" and "fortran" are now mutually exclusive (otherwise configure dies anyway). Please note that I've only roughly verified that this ebuild works for me on amd64 with USE="fortran ssl zlib -cxx -debug -mpi -szip -threads -tools".
I tried using the 1.8.2 ebuild with USE="ssl szip threads zlib -cxx -debug -fortran* -mpi -tools" (I also renamed the mpich2 patch to 1.8.2, was this correct?), and got the following error : make[2]: Entering directory `/var/tmp/portage/sci-libs/hdf5-1.8.2/work/hdf5-1.8.2/perform' test -z "/var/tmp/portage/sci-libs/hdf5-1.8.2/image/usr/bin" || /bin/mkdir -p "/var/tmp/portage/sci-libs/hdf5-1.8.2/image/usr/bin" /bin/sh ../libtool --mode=install /usr/bin/install -c 'h5perf_serial' '/var/tmp/portage/sci-libs/hdf5-1.8.2/image/usr/bin/h5perf_serial' libtool: install: /usr/bin/install -c .libs/h5perf_serial /var/tmp/portage/sci-libs/hdf5-1.8.2/image/usr/bin/h5perf_serial make[2]: Nothing to be done for `install-data-am'. make[2]: Leaving directory `/var/tmp/portage/sci-libs/hdf5-1.8.2/work/hdf5-1.8.2/perform' make[1]: Leaving directory `/var/tmp/portage/sci-libs/hdf5-1.8.2/work/hdf5-1.8.2/perform' !!! dosed: /var/tmp/portage/sci-libs/hdf5-1.8.2/image/var/tmp/portage/sci-libs/hdf5-1.8.2/image/usr/bin/h5cc does not exist * * ERROR: sci-libs/hdf5-1.8.2 failed. * Call stack: * ebuild.sh, line 49: Called src_install * environment, line 3250: Called die * The specific snippet of code: * dosed "s/SHLIB:-no/SHLIB:-yes/g" "${D}"usr/bin/h5cc || die "dosed failed" * The die message: * dosed failed * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/log/portage/sci-libs:hdf5-1.8.2:20090112-155556.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/hdf5-1.8.2/temp/environment'. * This ebuild is from an overlay: '/usr/local/portage/' * * QA Notice: file does not exist: * * dosed: /var/tmp/portage/sci-libs/hdf5-1.8.2/image/var/tmp/portage/sci-libs/hdf5-1.8.2/image/usr/bin/h5cc does not exist my emerge --info: Portage 2.1.6.4 (default/linux/amd64/2008.0/desktop, gcc-4.3.2, glibc-2.9_p20081201-r1, 2.6.28-gentoo x86_64) ================================================================= System uname: Linux-2.6.28-gentoo-x86_64-Dual_Core_AMD_Opteron-tm-_Processor_275-with-gentoo-2.0.0 Timestamp of tree: Mon, 12 Jan 2009 12:10:01 +0000 app-shells/bash: 3.2_p48 dev-java/java-config: 1.3.7-r1, 2.1.6-r1 dev-lang/python: 2.6.1 dev-util/cmake: 2.6.2 sys-apps/baselayout: 2.0.0 sys-apps/openrc: 0.4.1-r1 sys-apps/sandbox: 1.3.2 sys-devel/autoconf: 2.13, 2.63 sys-devel/automake: 1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2 sys-devel/binutils: 2.19 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 2.2.6a virtual/os-headers: 2.6.28-r1 ACCEPT_KEYWORDS="amd64 ~amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -march=k8 -mtune=k8 -pipe -fomit-frame-pointer" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/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/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 /etc/udev/rules.d" CXXFLAGS="-O2 -march=k8 -mtune=k8 -pipe -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FEATURES="collision-protect distlocks fixpackages parallel-fetch protect-owned sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LANG="en_US.UTF-8" LC_ALL="en_US.UTF-8" LDFLAGS="-Wl,-O1" LINGUAS="en en_US" MAKEOPTS="-j5" PKGDIR="/usr/portage/packages" 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/soor-overlay /usr/local/portage/layman/devnull /usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="3dnow X aac acl acpi alsa amd64 apache2 atlas avahi bash-completion berkdb blas bluetooth bookmarks branding bzip2 cairo cblas cdr cli cracklib crypt ctype cups dbus dirac doc dri dvd dvdr dvdread eds emacs emboss encode esd evo examples f77 fam fftw firefox foomativdb fortran gdbm gfortran gif gimpprint glitz gpm gstreamer gtk hal iconv imagemagick imap isdnlog ivman java jpeg jpeg2k kde kdrive kpathsea lapack latex ldap libnotify lzo mad mdnsresponder-compat midi mikmod mime mmap mmx mozbranding mozilla mozsvg mp3 mpeg mplayer mudflap multilib multislot mysql ncurses newspr nptl nptlonly nsplugin ogg opengl openmp oss pam pcre pdf perl pertty pic png postgres ppds pppd python qt3 qt3support qt4 quicktime readline reflection rss samba sdl session spell spl sse sse2 ssl startup-notification subversion svg symlink sysfs tcltk tcpd tetex threads tiff tk transparency truetype ubuntu umfpack unicode usb v4l v4l2 vorbis webdav winbind xcomposite xfs xft xml xorg xulrunner xv zeroconf zlib" ALSA_CARDS="ali5451 als4000 atiixpatiixp-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 dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers 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" ELIBC="glibc" INPUT_DEVICES="evdev keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en en_US" USERLAND="GNU" VIDEO_CARDS="nvidia vga nv" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
See bug 255070 - I had the same problem with 1.6.7, I fixed by changing {D} to {ROOT} in src_install. I'm not sure if this is a sensible way to fix, but it works ;-) The clue is in the path: /var/tmp/portage/sci-libs/hdf5-1.8.2/image/var/tmp/portage/sci-libs/hdf5-1.8.2/image/usr/bin/h5cc Notice that /var/tmp/portage/sci-libs/hdf5-X.Y.Z/image is repeated twice. I don't understand why this ebuild works for some people though?
I have a new error cropping up when I try to install using gcc-4.3.3 and portage-2.2_rc23: mv -f .deps/overhead.Tpo .deps/overhead.Po /bin/sh ../libtool --tag=CC --mode=link gcc -O2 -march=k8 -mtune=k8 -pipe -fomit-frame-pointer -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -Wlogical-op -Wvla -O -fomit-frame-pointer -finline-functions -Wl,-O1 -o overhead overhead.o ../src/libhdf5.la -lpthread -lz -lm libtool: link: gcc -O2 -march=k8 -mtune=k8 -pipe -fomit-frame-pointer -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -Wlogical-op -Wvla -O -fomit-frame-pointer -finline-functions -Wl,-O1 -o .libs/overhead overhead.o ../src/.libs/libhdf5.so -lpthread -lz -lm gcc -DHAVE_CONFIG_H -I. -I../src -I../src -I../test -I../tools/lib -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -DNDEBUG -UH5_DEBUG_API -O2 -march=k8 -mtune=k8 -pipe -fomit-frame-pointer -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -Wlogical-op -Wvla -O -fomit-frame-pointer -finline-functions -MT zip_perf.o -MD -MP -MF .deps/zip_perf.Tpo -c -o zip_perf.o zip_perf.c zip_perf.c: In function 'error': zip_perf.c:186: warning: function might be possible candidate for 'printf' format attribute zip_perf.c: In function 'write_file': zip_perf.c:248: warning: conversion to 'uLongf' from 'int' may change the sign of the result zip_perf.c: In function 'get_unique_name': zip_perf.c:329: warning: passing argument 1 of 'strcat' discards qualifiers from pointer target type zip_perf.c:334: warning: passing argument 1 of 'strcat' discards qualifiers from pointer target type zip_perf.c:337: warning: request for implicit conversion from 'void *' to 'char *' not permitted in C++ zip_perf.c: In function 'fill_with_random_data': zip_perf.c:456: warning: conversion to 'long unsigned int' from 'ssize_t' may change the sign of the result zip_perf.c:466: warning: conversion to 'uLongf' from 'int' may change the sign of the result zip_perf.c: In function 'do_write_test': zip_perf.c:532: warning: conversion to 'long unsigned int' from 'ssize_t' may change the sign of the result zip_perf.c: In function 'fill_with_random_data': /usr/include/bits/fcntl2.h:45: warning: will never be executed /usr/include/bits/fcntl2.h:49: warning: will never be executed /usr/include/bits/fcntl2.h:51: warning: will never be executed /usr/include/bits/fcntl2.h:57: warning: will never be executed /usr/include/bits/fcntl2.h:60: warning: will never be executed /usr/include/bits/fcntl2.h:58: warning: will never be executed zip_perf.c: In function 'do_write_test': /usr/include/bits/fcntl2.h:45: warning: will never be executed /usr/include/bits/fcntl2.h:45: warning: will never be executed /usr/include/bits/fcntl2.h:57: warning: will never be executed /usr/include/bits/fcntl2.h:60: warning: will never be executed /usr/include/bits/fcntl2.h:58: warning: will never be executed /usr/include/bits/fcntl2.h:51: warning: will never be executed /usr/include/bits/fcntl2.h:57: warning: will never be executed /usr/include/bits/fcntl2.h:60: warning: will never be executed /usr/include/bits/fcntl2.h:58: warning: will never be executed /usr/include/bits/fcntl2.h:54: warning: will never be executed zip_perf.c: In function 'error': zip_perf.c:181: warning: function might be possible candidate for attribute 'noreturn' zip_perf.c: In function 'main': /usr/include/bits/unistd.h:39: warning: will never be executed /usr/include/bits/unistd.h:42: warning: will never be executed /usr/include/bits/unistd.h:43: warning: will never be executed /usr/include/bits/unistd.h:40: warning: will never be executed /usr/include/bits/string3.h:82: warning: will never be executed In function 'open', inlined from 'do_write_test' at zip_perf.c:552, inlined from 'main' at zip_perf.c:653: /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 zip_perf.c:69:1: warning: macro "GZ_SUFFIX" is not used zip_perf.c:50:1: warning: macro "SET_BINARY_MODE" is not used zip_perf.c:91:1: warning: macro "BUFLEN" is not used zip_perf.c:72:1: warning: macro "SUFFIX_LEN" is not used zip_perf.c:92:1: warning: macro "MAX_NAME_LEN" is not used make[2]: *** [zip_perf.o] Error 1 make[2]: Leaving directory `/var/tmp/portage/sci-libs/hdf5-1.8.2/work/hdf5-1.8.2/perform' make[1]: *** [all-local] Error 2 make[1]: Leaving directory `/var/tmp/portage/sci-libs/hdf5-1.8.2/work/hdf5-1.8.2' make: *** [all-recursive] Error 1 * * ERROR: sci-libs/hdf5-1.8.2 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 3232: Called die * The specific snippet of code: * make || die "make failed"; * The die message: * make failed * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/log/portage/sci-libs:hdf5-1.8.2:20090130-205200.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/hdf5-1.8.2/temp/environment'. * This ebuild is from an overlay named 'local': '/usr/local/portage/' # emerge --info Portage 2.2_rc23 (default/linux/amd64/2008.0/desktop, gcc-4.3.3, glibc-2.9_p20081201-r1, 2.6.28-gentoo-r1 x86_64) ================================================================= System uname: Linux-2.6.28-gentoo-r1-x86_64-Dual_Core_AMD_Opteron-tm-_Processor_275-with-gentoo-2.0.0 Timestamp of tree: Fri, 30 Jan 2009 18:30:01 +0000 app-shells/bash: 3.2_p48 dev-java/java-config: 1.3.7-r1, 2.1.7 dev-lang/python: 2.6.1 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: 1.5, 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" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -march=k8 -mtune=k8 -pipe -fomit-frame-pointer" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/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/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 /etc/udev/rules.d" CXXFLAGS="-O2 -march=k8 -mtune=k8 -pipe -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FEATURES="collision-protect distlocks fixpackages parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-orphans userfetch userpriv" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LANG="en_US.UTF-8" LC_ALL="en_US.UTF-8" LDFLAGS="-Wl,-O1" LINGUAS="en en_US" MAKEOPTS="-j5" PKGDIR="/usr/portage/packages" 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/soor-overlay /usr/local/portage/layman/devnull /usr/local/portage/layman/science /usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="3dnow X aac acl acpi alsa amd64 apache2 atlas avahi bash-completion berkdb blas bluetooth bookmarks branding bzip2 cairo cblas cdr cli cracklib crypt ctype cups dbus dirac doc dri dvd dvdr dvdread eds emacs emboss encode esd evo examples f77 fam fftw firefox foomativdb fortran gdbm gfortran gif gimpprint glitz gpm gstreamer gtk hal iconv imagemagick imap isdnlog ivman java jpeg jpeg2k kde kdrive kpathsea lapack latex ldap libnotify lzo mad mdnsresponder-compat midi mikmod mime mmap mmx mozbranding mozilla mozsvg mp3 mpeg mplayer mudflap multilib multislot mysql ncurses newspr nptl nptlonly nsplugin ogg opengl openmp oss pam pcre pdf perl pertty pic png postgres ppds pppd python qt3 qt3support qt4 quicktime readline reflection rss samba sdl session spell spl sse sse2 ssl startup-notification subversion svg symlink sysfs tcltk tcpd tetex threads tiff tk transparency truetype ubuntu umfpack unicode usb v4l v4l2 vorbis webdav webkit winbind xcomposite xfs xft xml xorg xulrunner xv zeroconf zlib" ALSA_CARDS="ali5451 als4000atiixp 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 dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers 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" ELIBC="glibc" INPUT_DEVICES="evdev keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en en_US" USERLAND="GNU" VIDEO_CARDS="nvidia vga nv" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
(In reply to comment #8) > In function 'open', > inlined from 'do_write_test' at zip_perf.c:552, > inlined from 'main' at zip_perf.c:653: > /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 This fcntl2.h problem has hit a couple other packages, for example bug #257139
(In reply to comment #9) > (In reply to comment #8) > > In function 'open', > > inlined from 'do_write_test' at zip_perf.c:552, > > inlined from 'main' at zip_perf.c:653: > > /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 > > This fcntl2.h problem has hit a couple other packages, for example bug #257139 > This O_CREAT issue was resolved in davfs2, the resolution and patch can be found in bug #257823
(In reply to comment #10) > > This O_CREAT issue was resolved in davfs2, the resolution and patch can be > found in bug #257823 > This change allowed me to compile: $ diff -r perform/zip_perf.c.old perform/zip_perf.c 552c552 < output = open(filename, O_RDWR | O_CREAT); --- > output = open(filename, O_RDWR | O_CREAT, S_IRWXU);
Created attachment 185734 [details, diff] As suggested in #11
Created attachment 185736 [details, diff] Patch to hdf5-1.8.2.ebuild Covers all the remarks from the discussion. Tested on: Portage 2.2_rc23 (default/linux/amd64/2008.0, gcc-4.3.3, glibc-2.9_p20081201-r2, 2.6.28-gentoo-r2 x86_64) =================================================================
(In reply to comment #13) > Created an attachment (id=185736) [edit] > Patch to hdf5-1.8.2.ebuild > > Covers all the remarks from the discussion. Tested on: > Portage 2.2_rc23 (default/linux/amd64/2008.0, gcc-4.3.3, > glibc-2.9_p20081201-r2, 2.6.28-gentoo-r2 x86_64) > ================================================================= > Did you run the test suite? It may be necessary to patch ./config/gnu-flags file in the HDF5 source code and setting PROD_CFLAGS from "-O" to "-O0". dt_arith conversion tests can fail with gcc, as discussed at http://www.hdfgroup.org/HDF5/release/known_problems5.html. Here is the code that needs to be modified: gcc-3.[0-4]*|gcc-4.[0123]*) # The optimization level is reduced for gcc 3.* and 4.* due to problems # with code generation for src/H5Tconv.c with the -O2 & -O3 # optimization levels (which shows up as failures for various integer # types -> long long conversions in the test/dtypes test). Perhaps # later versions of gcc will fix this bug... - QAK - 2003/10/20 PROD_CFLAGS="-O0" ;;
Created attachment 185749 [details, diff] As suggested in #14 (In reply to comment #13) No I didn't, but when I did, I got the error you'd reported. New patch fixes it.
(In reply to comment #15) > Created an attachment (id=185749) [edit] > As suggested in #14 > > (In reply to comment #13) > No I didn't, but when I did, I got the error you'd reported. New patch fixes > it. > Works for me. Thank you for all your effort on this ebuild.
hdf-1.8.3 has been released. This new version does not require the changes contained in hdf5-1.8.2-gcc4.3.3.patch. It does, however, include a bugfix, I think for compression filters, which required changes to downstream packages like pytables and h5py (both of which have already implemented the changes in their development branches, but have not made new releases at the time of this writing).
(In reply to comment #17) > hdf-1.8.3 has been released. This new version does not require the changes > contained in hdf5-1.8.2-gcc4.3.3.patch. It does, however, include a bugfix, I > think for compression filters, which required changes to downstream packages > like pytables and h5py (both of which have already implemented the changes in > their development branches, but have not made new releases at the time of this > writing). I've been doing some cleaning in this ebuild. Can anyone explain me why lines: mv "${ROOT}"usr/bin/h5pfc "${ROOT}"usr/bin/h5fc mv "${ROOT}"usr/bin/h5pcc "${ROOT}"usr/bin/h5cc are necessary?? Nothing in portage really depends on those wrappers...
Hi, I've been working on a tree candidate for hdf5-1.8.3, since the current 1.6.7 ebuild is very buggy. Lots of patches and ebuild cleaning. Please test the one in the science overlay against other packages and with different use flags combination. Report (and patches welcome) here! The plan is to push it to the tree in a couple weeks. Thanks
(In reply to comment #19) > Hi, > > I've been working on a tree candidate for hdf5-1.8.3, since the current 1.6.7 > ebuild is very buggy. Lots of patches and ebuild cleaning. Please test the one > in the science overlay against other packages and with different use flags > combination. Report (and patches welcome) here! The plan is to push it to the > tree in a couple weeks. > > Thanks > Thank you very much for this effort. hdf5-1.8.3 from the science overlay fails for me... first with my normal CFLAGS/LDFLAGS and then with out any at all (only default). Below, the following are provided: 1) Use flags 2) emerge --info (showing gentoo default CFLAGS/LDFLAGS) 3) Build log 4) automake.out 1) [ebuild N ] sci-libs/hdf5-1.8.3 USE="examples ssl threads zlib -cxx -fortran -mpi -szip 2) glacier ~ # emerge --info Portage 2.2_rc33 (default/linux/x86/2008.0, gcc-4.3.2, glibc-2.8_p20080602-r1, 2.6.27-gentoo-r8 i686) ================================================================= System uname: Linux-2.6.27-gentoo-r8-i686-Intel-R-_Pentium-R-_4_CPU_3.60GHz-with-glibc2.0 Timestamp of tree: Tue, 23 Jun 2009 23:00:01 +0000 ccache version 2.4 [enabled] app-shells/bash: 3.2_p39 dev-java/java-config: 2.1.7 dev-lang/python: 2.4.4-r13, 2.5.4-r2 dev-python/pycrypto: 2.0.1-r6 dev-util/ccache: 2.4-r7 dev-util/cmake: 2.6.4 sys-apps/baselayout: 1.12.11.1 sys-apps/sandbox: 2.0 sys-devel/autoconf: 2.13, 2.63 sys-devel/automake: 1.5, 1.7.9-r1, 1.9.6-r2, 1.10.2 sys-devel/binutils: 2.18-r3 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 1.5.26 virtual/os-headers: 2.6.27-r2 ACCEPT_KEYWORDS="x86" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=i686 -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/kde/4.2/env /usr/kde/4.2/share/config /usr/kde/4.2/shutdown /usr/kde/live/env /usr/kde/live/share/config /usr/kde/live/shutdown /usr/share/config" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /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="-O2 -march=i686 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="ccache distlocks fixpackages metadata-transfer parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-orphans userfetch userpriv usersandbox" GENTOO_MIRRORS="http://open-systems.ufl.edu/mirrors/gentoo http://www.gtlib.gatech.edu/pub/gentoo http://gentoo.osuosl.org http://www.ibiblio.org/pub/Linux/distributions/gentoo" LDFLAGS="-Wl,-O1" MAKEOPTS="-j3" 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/qting-edge /usr/local/portage/layman/berkano /usr/local/portage/layman/kde-testing /usr/local/portage/layman/travlr /usr/local/portage/layman/science" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X alsa bash-completion bzip2 cdr cli cracklib dbus dvd fftw fortran glib gpm iconv isdnlog java6 jpeg jpeg2k kde lapack latex midi mmx mudflap ncurses nptl nptlonly nsplugin nvidia openmp pam pcre perl png pppd python qt4 readline realmedia reflection sasl session spl sse sse2 sse3 ssl svga sysfs tcpd tetex threads umfpack unicode wmp x86 xinerama xorg xvmc zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 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 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" ELIBC="glibc" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="nvidia" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS 3) glacier ~ # cat /var/log/portage/sci-libs:hdf5-1.8.3:20090624-195143.log >>> Unpacking source... >>> Unpacking hdf5-1.8.3.tar.gz to /var/tmp/portage/sci-libs/hdf5-1.8.3/work >>> Source unpacked in /var/tmp/portage/sci-libs/hdf5-1.8.3/work >>> Preparing source in /var/tmp/portage/sci-libs/hdf5-1.8.3/work/hdf5-1.8.3 ... * Applying hdf5-1.8.3-as-needed.patch ... [ ok ] * Applying hdf5-1.8.3-includes.patch ... [ ok ] * Applying hdf5-1.8.3-gnutools.patch ... [ ok ] * Applying hdf5-1.8.3-noreturn.patch ... [ ok ] * Applying hdf5-1.8.3-destdir.patch ... [ ok ] * Applying hdf5-1.8.3-signal.patch ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-libs/hdf5-1.8.3/work/hdf5-1.8.3' ... * Running aclocal ... [ ok ] * Running autoconf ... [ ok ] * Running autoheader ... [ ok ] * Running automake --add-missing --copy --foreign ... [ !! ] * Failed Running automake ! * * Include in your bugreport the contents of: * * /var/tmp/portage/sci-libs/hdf5-1.8.3/temp/automake.out * * ERROR: sci-libs/hdf5-1.8.3 failed. * Call stack: * ebuild.sh, line 49: Called src_prepare * environment, line 2681: Called eautoreconf * environment, line 869: Called eautomake * environment, line 842: Called autotools_run_tool 'automake' '--add-missing' '--copy' '--foreign' * environment, line 354: Called die * The specific snippet of code: * die "Failed Running $1 !"; * The die message: * Failed Running automake ! * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/log/portage/sci-libs:hdf5-1.8.3:20090624-195143.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/hdf5-1.8.3/temp/environment'. * This ebuild is from an overlay named 'science': '/usr/local/portage/layman/science/' THE REST IS CONTINUED IN THE NEXT COMMENT
(In reply to comment #20) > (In reply to comment #19) > > > THE REST IS CONTINUED IN THE NEXT COMMENT > CONTINUED FROM COMMENT #20 4) glacier ~ # cat /var/tmp/portage/sci-libs/hdf5-1.8.3/temp/automake.out ***** automake ***** ***** PWD: /var/tmp/portage/sci-libs/hdf5-1.8.3/work/hdf5-1.8.3 ***** automake --add-missing --copy --foreign configure.in:2684: warning: AC_CACHE_VAL(hdf5_mpi_complex_derived_datatype_works, ...): suspicious cache-id, must contain _cv_ to be cached ../../lib/autoconf/general.m4:1974: AC_CACHE_VAL is expanded from... configure.in:2684: the top level configure.in:2703: warning: AC_CACHE_VAL(hdf5_mpi_special_collective_io_works, ...): suspicious cache-id, must contain _cv_ to be cached configure.in:2703: the top level configure.in:2832: warning: AC_CACHE_VAL(hdf5_direct_io, ...): suspicious cache-id, must contain _cv_ to be cached configure.in:2832: the top level configure.in:2992: warning: AC_CACHE_VAL(hdf5_ldouble_to_integer_works, ...): suspicious cache-id, must contain _cv_ to be cached configure.in:2992: the top level configure.in:3142: warning: AC_CACHE_VAL(hdf5_fp_to_ullong_accurate, ...): suspicious cache-id, must contain _cv_ to be cached configure.in:3142: the top level configure.in:3179: warning: AC_CACHE_VAL(hdf5_fp_to_ullong_right_maximum, ...): suspicious cache-id, must contain _cv_ to be cached configure.in:3179: the top level configure.in:3224: warning: AC_CACHE_VAL(hdf5_ldouble_to_uint_accurate, ...): suspicious cache-id, must contain _cv_ to be cached configure.in:3224: the top level configure.in:3426: warning: AC_CACHE_VAL(hdf5_ldouble_to_llong_accurate, ...): suspicious cache-id, must contain _cv_ to be cached configure.in:3426: the top level configure.in:3487: warning: AC_CACHE_VAL(hdf5_llong_to_ldouble_correct, ...): suspicious cache-id, must contain _cv_ to be cached configure.in:3487: the top level c++/src/Makefile.am:28: Libtool library used but `LIBTOOL' is undefined c++/src/Makefile.am:28: The usual way to define `LIBTOOL' is to add `AC_PROG_LIBTOOL' c++/src/Makefile.am:28: to `configure.in' and run `aclocal' and `autoconf' again. c++/src/Makefile.am:28: If `AC_PROG_LIBTOOL' is in `configure.in', make sure c++/src/Makefile.am:28: its definition is in aclocal's search path. fortran/src/Makefile.am:32: Libtool library used but `LIBTOOL' is undefined fortran/src/Makefile.am:32: The usual way to define `LIBTOOL' is to add `AC_PROG_LIBTOOL' fortran/src/Makefile.am:32: to `configure.in' and run `aclocal' and `autoconf' again. fortran/src/Makefile.am:32: If `AC_PROG_LIBTOOL' is in `configure.in', make sure fortran/src/Makefile.am:32: its definition is in aclocal's search path. fortran/test/Makefile.am:28: Libtool library used but `LIBTOOL' is undefined fortran/test/Makefile.am:28: The usual way to define `LIBTOOL' is to add `AC_PROG_LIBTOOL' fortran/test/Makefile.am:28: to `configure.in' and run `aclocal' and `autoconf' again. fortran/test/Makefile.am:28: If `AC_PROG_LIBTOOL' is in `configure.in', make sure fortran/test/Makefile.am:28: its definition is in aclocal's search path. hl/c++/src/Makefile.am:28: Libtool library used but `LIBTOOL' is undefined hl/c++/src/Makefile.am:28: The usual way to define `LIBTOOL' is to add `AC_PROG_LIBTOOL' hl/c++/src/Makefile.am:28: to `configure.in' and run `aclocal' and `autoconf' again. hl/c++/src/Makefile.am:28: If `AC_PROG_LIBTOOL' is in `configure.in', make sure hl/c++/src/Makefile.am:28: its definition is in aclocal's search path. hl/fortran/src/Makefile.am:30: Libtool library used but `LIBTOOL' is undefined hl/fortran/src/Makefile.am:30: The usual way to define `LIBTOOL' is to add `AC_PROG_LIBTOOL' hl/fortran/src/Makefile.am:30: to `configure.in' and run `aclocal' and `autoconf' again. hl/fortran/src/Makefile.am:30: If `AC_PROG_LIBTOOL' is in `configure.in', make sure hl/fortran/src/Makefile.am:30: its definition is in aclocal's search path. hl/src/Makefile.am:28: Libtool library used but `LIBTOOL' is undefined hl/src/Makefile.am:28: The usual way to define `LIBTOOL' is to add `AC_PROG_LIBTOOL' hl/src/Makefile.am:28: to `configure.in' and run `aclocal' and `autoconf' again. hl/src/Makefile.am:28: If `AC_PROG_LIBTOOL' is in `configure.in', make sure hl/src/Makefile.am:28: its definition is in aclocal's search path. src/Makefile.am:33: Libtool library used but `LIBTOOL' is undefined src/Makefile.am:33: The usual way to define `LIBTOOL' is to add `AC_PROG_LIBTOOL' src/Makefile.am:33: to `configure.in' and run `aclocal' and `autoconf' again. src/Makefile.am:33: If `AC_PROG_LIBTOOL' is in `configure.in', make sure src/Makefile.am:33: its definition is in aclocal's search path. test/Makefile.am:71: Libtool library used but `LIBTOOL' is undefined test/Makefile.am:71: The usual way to define `LIBTOOL' is to add `AC_PROG_LIBTOOL' test/Makefile.am:71: to `configure.in' and run `aclocal' and `autoconf' again. test/Makefile.am:71: If `AC_PROG_LIBTOOL' is in `configure.in', make sure test/Makefile.am:71: its definition is in aclocal's search path. tools/lib/Makefile.am:27: Libtool library used but `LIBTOOL' is undefined tools/lib/Makefile.am:27: The usual way to define `LIBTOOL' is to add `AC_PROG_LIBTOOL' tools/lib/Makefile.am:27: to `configure.in' and run `aclocal' and `autoconf' again. tools/lib/Makefile.am:27: If `AC_PROG_LIBTOOL' is in `configure.in', make sure tools/lib/Makefile.am:27: its definition is in aclocal's search path.
(In reply to comment #20) > sys-devel/libtool: 1.5.26 seems to be the problem. Ebuild works for me (libtool-2.2.6a)
(In reply to comment #22) > (In reply to comment #20) > > > sys-devel/libtool: 1.5.26 > seems to be the problem. Ebuild works for me (libtool-2.2.6a) > Thank you. libtool-2.2.6a allowed me to build succesfully. I was able to use my custom CFLAGS/LDFLAGS with out problem.
(In reply to comment #19) Firstly, let me thank you for your effort of putting hdf5-1.8.3 to science overlay! As for the problems I have encountered so far: hdf5-1.8 needs >=szip-2. It fails with current stable version (1.1-r1), but compiles with szip-2.1.
emerge fails with the examples use flag enabled: make -j5 DESTDIR=/var/tmp/portage/sci-libs/hdf5-1.8.3/image/ install-examples + for d in examples + cd examples + make install-examples make[1]: Entering directory `/var/tmp/portage/sci-libs/hdf5-1.8.3/work/hdf5-1.8.3/examples' + /usr/bin/install -c -m 644 ./h5_write.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/. /usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory + exit 1 + /usr/bin/install -c -m 644 ./h5_read.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/. /usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory + exit 1 + /usr/bin/install -c -m 644 ./h5_extend_write.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/. /usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory + exit 1 + /usr/bin/install -c -m 644 ./h5_chunk_read.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/. /usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory + exit 1 + /usr/bin/install -c -m 644 ./h5_compound.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/. /usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory + exit 1 + /usr/bin/install -c -m 644 ./h5_group.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/. /usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory + exit 1 + /usr/bin/install -c -m 644 ./h5_select.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/. /usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory + exit 1 + /usr/bin/install -c -m 644 ./h5_attribute.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/. /usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory + exit 1 + /usr/bin/install -c -m 644 ./h5_mount.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/. /usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory + exit 1 + /usr/bin/install -c -m 644 ./h5_reference.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/. /usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory + exit 1 + /usr/bin/install -c -m 644 ./h5_drivers.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/. /usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory + exit 1 + /usr/bin/install -c -m 644 ./h5_extlink.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/. /usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory + exit 1 + /usr/bin/install -c -m 644 ./h5_elink_unix2win.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/. /usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory + exit 1 + /usr/bin/install -c -m 644 ./h5_ref2reg.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/. /usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory + exit 1 + /usr/bin/install -c -m 644 ./h5_shared_mesg.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/. /usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory + exit 1 + /usr/bin/install -c -m 644 ./ph5example.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/. /usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory + exit 1 make[1]: *** [install-examples] Error 1 make[1]: Leaving directory `/var/tmp/portage/sci-libs/hdf5-1.8.3/work/hdf5-1.8.3/examples' + exit 1 make: *** [install-examples] Error 1 * * ERROR: sci-libs/hdf5-1.8.3 failed. * Call stack: * ebuild.sh, line 49: Called src_install * environment, line 2793: Called die * The specific snippet of code: * emake DESTDIR="${D}" install-examples || die "emake install examples failed"; * The die message: * emake install examples failed If I disable the examples use flag, emerge is successful.
After emerging hdf5 on ~amd64 with gcc-4.4 and USE="szip threads zlib -cxx -examples -fortran -mpi", I installed h5py-1.2 and observed a number of test failures, all of the tests of h5py.h5d failed with the same DatatypeError, for example: ====================================================================== ERROR: test_create_offset (h5py.tests.test_h5d.TestH5D) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/share/packages/h5py-1.2.0/h5py/tests/test_h5d.py", line 41, in setUp self.dset = h5d.open(self.fid, "CompoundChunked") File "/home/share/packages/h5py-1.2.0/h5py/_sync.py", line 88, in wrap return func(*args, **kwds) File "h5d.pyx", line 78, in h5py.h5d.open (h5py/h5d.c:1391) DatatypeError: Incorrect array datatype version (Datatype: Wrong version number) I ran "emerge -C hdf5" and then installed hdf5-1.8.3 manually with: ./configure --prefix=/usr/local --enable-threadsafe --with-zlib=/usr --with-pthread=/usr make sudo make install Then I ran the h5py tests again and this time they all passed. Does anyone know what the ebuild is doing differently?
Now in portage tree.