cc -DHAVE_CONFIG_H -I../../src/util -I../../src/matrices -I. -I. -pthread -c -O2 -g -ggdb -pipe matrixio.c -o matrixio.o matrixio.c: In function ‘write_attr’: matrixio.c:91: error: too few arguments to function ‘H5Dcreate2’ matrixio.c:97: error: too few arguments to function ‘H5Acreate2’ matrixio.c: In function ‘open_attr’: matrixio.c:112: warning: passing argument 1 of ‘H5Eget_auto2’ makes integer from pointer without a cast /usr/include/H5Epublic.h:173: note: expected ‘hid_t’ but argument is of type ‘herr_t (**)(hid_t, void *)’ matrixio.c:112: warning: passing argument 2 of ‘H5Eget_auto2’ from incompatible pointer type /usr/include/H5Epublic.h:173: note: expected ‘herr_t (**)(hid_t, void *)’ but argument is of type ‘void **’ matrixio.c:112: error: too few arguments to function ‘H5Eget_auto2’ matrixio.c:112: warning: passing argument 1 of ‘H5Eset_auto2’ makes integer from pointer without a cast /usr/include/H5Epublic.h:174: note: expected ‘hid_t’ but argument is of type ‘void *’ matrixio.c:112: error: too few arguments to function ‘H5Eset_auto2’ matrixio.c:112: error: too few arguments to function ‘H5Dopen2’ matrixio.c:112: warning: passing argument 1 of ‘H5Eset_auto2’ makes integer from pointer without a cast /usr/include/H5Epublic.h:174: note: expected ‘hid_t’ but argument is of type ‘H5E_auto2_t’ matrixio.c:112: error: too few arguments to function ‘H5Eset_auto2’ matrixio.c:119: warning: passing argument 1 of ‘H5Eget_auto2’ makes integer from pointer without a cast /usr/include/H5Epublic.h:173: note: expected ‘hid_t’ but argument is of type ‘herr_t (**)(hid_t, void *)’ matrixio.c:119: warning: passing argument 2 of ‘H5Eget_auto2’ from incompatible pointer type /usr/include/H5Epublic.h:173: note: expected ‘herr_t (**)(hid_t, void *)’ but argument is of type ‘void **’ matrixio.c:119: error: too few arguments to function ‘H5Eget_auto2’ matrixio.c:119: warning: passing argument 1 of ‘H5Eset_auto2’ makes integer from pointer without a cast /usr/include/H5Epublic.h:174: note: expected ‘hid_t’ but argument is of type ‘void *’ matrixio.c:119: error: too few arguments to function ‘H5Eset_auto2’ matrixio.c:119: warning: passing argument 1 of ‘H5Eset_auto2’ makes integer from pointer without a cast /usr/include/H5Epublic.h:174: note: expected ‘hid_t’ but argument is of type ‘H5E_auto2_t’ matrixio.c:119: error: too few arguments to function ‘H5Eset_auto2’ matrixio.c: In function ‘matrixio_create_sub’: matrixio.c:419: error: too few arguments to function ‘H5Gcreate2’ matrixio.c:429: error: too few arguments to function ‘H5Gopen2’ matrixio.c: In function ‘matrixio_open_dataset’: matrixio.c:456: error: too few arguments to function ‘H5Dopen2’ matrixio.c:458: error: too few arguments to function ‘H5Dopen2’ matrixio.c: In function ‘matrixio_create_dataset’: matrixio.c:523: error: too few arguments to function ‘H5Dcreate2’ matrixio.c:523: error: too few arguments to function ‘H5Dopen2’ matrixio.c: In function ‘matrixio_dataset_exists’: matrixio.c:551: warning: passing argument 1 of ‘H5Eget_auto2’ makes integer from pointer without a cast /usr/include/H5Epublic.h:173: note: expected ‘hid_t’ but argument is of type ‘herr_t (**)(hid_t, void *)’ matrixio.c:551: warning: passing argument 2 of ‘H5Eget_auto2’ from incompatible pointer type /usr/include/H5Epublic.h:173: note: expected ‘herr_t (**)(hid_t, void *)’ but argument is of type ‘void **’ matrixio.c:551: error: too few arguments to function ‘H5Eget_auto2’ matrixio.c:551: warning: passing argument 1 of ‘H5Eset_auto2’ makes integer from pointer without a cast /usr/include/H5Epublic.h:174: note: expected ‘hid_t’ but argument is of type ‘void *’ matrixio.c:551: error: too few arguments to function ‘H5Eset_auto2’ matrixio.c:551: error: too few arguments to function ‘H5Dopen2’ matrixio.c:551: warning: passing argument 1 of ‘H5Eset_auto2’ makes integer from pointer without a cast /usr/include/H5Epublic.h:174: note: expected ‘hid_t’ but argument is of type ‘H5E_auto2_t’ matrixio.c:551: error: too few arguments to function ‘H5Eset_auto2’ matrixio.c: In function ‘matrixio_read_real_data’: matrixio.c:754: warning: passing argument 1 of ‘H5Eget_auto2’ makes integer from pointer without a cast /usr/include/H5Epublic.h:173: note: expected ‘hid_t’ but argument is of type ‘herr_t (**)(hid_t, void *)’ matrixio.c:754: warning: passing argument 2 of ‘H5Eget_auto2’ from incompatible pointer type /usr/include/H5Epublic.h:173: note: expected ‘herr_t (**)(hid_t, void *)’ but argument is of type ‘void **’ matrixio.c:754: error: too few arguments to function ‘H5Eget_auto2’ matrixio.c:754: warning: passing argument 1 of ‘H5Eset_auto2’ makes integer from pointer without a cast /usr/include/H5Epublic.h:174: note: expected ‘hid_t’ but argument is of type ‘void *’ matrixio.c:754: error: too few arguments to function ‘H5Eset_auto2’ matrixio.c:754: error: too few arguments to function ‘H5Dopen2’ matrixio.c:754: warning: passing argument 1 of ‘H5Eset_auto2’ makes integer from pointer without a cast /usr/include/H5Epublic.h:174: note: expected ‘hid_t’ but argument is of type ‘H5E_auto2_ matrixio.c:754: error: too few arguments to function‘H5Eset_auto2’ make[1]: *** [matrixio.o] Error 1 Reproducible: Always Steps to Reproduce: 1. Be ~amd64 2. Try emerge sci-physics/mpb-1.4.2-r2 with sci-libs/hdf5-1.8.3 installed with USE flag hdf5 set. 3. Actual Results: Fails to compile due to new/different API. Expected Results: Compiles fine. Portage 2.1.6.13 (default/linux/amd64/2008.0/desktop, gcc-4.4.1, glibc-2.10.1-r0, 2.6.30-gentoo-r4-4d x86_64) ================================================================= System uname: Linux-2.6.30-gentoo-r4-4d-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9300_@_2.50GHz-with-gentoo-2.0.1 Timestamp of tree: Fri, 21 Aug 2009 10:00:01 +0000 app-shells/bash: 4.0_p28 dev-java/java-config: 2.1.8-r1 dev-lang/python: 2.6.2-r1, 3.1.1 dev-util/cmake: 2.6.4-r2 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.4.3-r3 sys-apps/sandbox: 2.0 sys-devel/autoconf: 2.13, 2.63-r1 sys-devel/automake: 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2, 1.11 sys-devel/binutils: 2.19.1-r1 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6a virtual/os-headers: 2.6.30-r1 ACCEPT_KEYWORDS="amd64 ~amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -g -ggdb -pipe" 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/bind" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /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 -g -ggdb -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks fixpackages nostrip parallel-fetch protect-owned sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="ftp://gentoo.inode.at/source/ ftp://ftp.fi.muni.cz/pub/linux/gentoo/ ftp://gentoo.mirror.web4u.cz/ " LANG="cs_CZ.UTF-8" LC_ALL="cs_CZ.UTF-8" LDFLAGS="-Wl,-O1" LINGUAS="cs en" MAKEOPTS="-j5" PKGDIR="/usr/portage/packages" PORTAGE_COMPRESS="echo" 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" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X a52 aac accessibility acl acpi alsa amd64 arts avahi berkdb bluetooth branding bzip2 cairo cdr cli cracklib crypt cups dbus directfb djvu doc dri dts dvd dvdr eds emacs emboss encode esd evo examples exif fam firefox flac fontconfig fortran freetds gcj gd gdbm gedit geoip gif gimp glep gmp gnome gnome-keyring gpm gstreamer gtk guile hal htmlhandbook iconv idn ieee1394 isdnlog ithreads jadetex java jpeg jpeg2k kde kdehiddenvisibility kerberos lapack latex lcms ldap libedit libffi libnotify lzma lzo mad mikmod mmx mono mp3 mp4 mpeg mudflap multilib mysql nautilus ncurses nls nptl nptlonly objc objc++ objc-gc odbc ogg openexr opengl openmp pam pch pcre pdf perl png policykit portaudio ppds pppd pulseaudio python qt3 qt3support qt4 quicktime readline reflection ruby samba sasl sdl session slang soundex source spell spl sqlite sse sse2 sse3 ssl startup-notification svg sysfs tcl tcpd threads tiff tk truetype unicode usb v4l v4l2 vorbis wmf x264 xinerama xml xorg xpm xulrunner xv xvid 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 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="evdev keyboard mouse joystick" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="cs en" LIRC_DEVICES="inputlirc" USERLAND="GNU" VIDEO_CARDS="nvidia nv vesa v4l" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
Probably needs the CPPFLAGS to contain "-DH5_USE_16_API". Or adapted upstreem sources.
Created attachment 201926 [details, diff] checking for HDF5 version
Created attachment 201927 [details, diff] Fixing API Alternatively problem can be solved by using -DH5_USE_16_API with hdf5-1.8
Thanks much for the note! I've just fixed this in portage cvs by enabling the hdf5-1.6 legacy API via -DH5_USE_16_API. cheers, Markus
