Maybe similar issue to https://bugs.gentoo.org/show_bug.cgi?id=289025#c1 ? x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform -I../../src -D_GNU_SOURCE -D_POSIX_C_SOURCE=200112L -DNDEBUG -UH5_DEBUG_API -I/apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/src -I/apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/test -I/apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/lib -std=c99 -pedantic -Wall -W -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 -O -finline-functions -O2 -mavx -c -o overhead.o /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c In file included from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c:37:0: /apps/gentoo/usr/include/io.h:22:6: error: nested redefinition of 'enum bigWigFile_type_enum' enum bigWigFile_type_enum { ^~~~~~~~~~~~~~~~~~~~ /apps/gentoo/usr/include/io.h:22:6: error: redeclaration of 'enum bigWigFile_type_enum' In file included from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/src/H5private.h:149:0, from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c:26: /apps/gentoo/usr/include/io.h:22:6: note: originally defined here enum bigWigFile_type_enum { ^~~~~~~~~~~~~~~~~~~~ In file included from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c:37:0: /apps/gentoo/usr/include/io.h:23:5: error: redeclaration of enumerator 'BWG_FILE' BWG_FILE = 0, ^~~~~~~~ In file included from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/src/H5private.h:149:0, from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c:26: /apps/gentoo/usr/include/io.h:23:5: note: previous definition of 'BWG_FILE' was here BWG_FILE = 0, ^~~~~~~~ In file included from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c:37:0: /apps/gentoo/usr/include/io.h:24:5: error: redeclaration of enumerator 'BWG_HTTP' BWG_HTTP = 1, ^~~~~~~~ In file included from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/src/H5private.h:149:0, from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c:26: /apps/gentoo/usr/include/io.h:24:5: note: previous definition of 'BWG_HTTP' was here BWG_HTTP = 1, ^~~~~~~~ In file included from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c:37:0: /apps/gentoo/usr/include/io.h:25:5: error: redeclaration of enumerator 'BWG_HTTPS' BWG_HTTPS = 2, ^~~~~~~~~ In file included from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/src/H5private.h:149:0, from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c:26: /apps/gentoo/usr/include/io.h:25:5: note: previous definition of 'BWG_HTTPS' was here BWG_HTTPS = 2, ^~~~~~~~~ In file included from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c:37:0: /apps/gentoo/usr/include/io.h:26:5: error: redeclaration of enumerator 'BWG_FTP' BWG_FTP = 3 ^~~~~~~ In file included from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/src/H5private.h:149:0, from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c:26: /apps/gentoo/usr/include/io.h:26:5: note: previous definition of 'BWG_FTP' was here BWG_FTP = 3 ^~~~~~~ In file included from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c:37:0: /apps/gentoo/usr/include/io.h:47:3: error: conflicting types for 'URL_t' } URL_t; ^~~~~ In file included from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/src/H5private.h:149:0, from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c:26: /apps/gentoo/usr/include/io.h:47:3: note: previous declaration of 'URL_t' was here } URL_t; ^~~~~ In file included from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c:37:0: /apps/gentoo/usr/include/io.h:62:8: error: conflicting types for 'urlRead' size_t urlRead(URL_t *URL, void *buf, size_t bufSize); ^~~~~~~ In file included from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/src/H5private.h:149:0, from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c:26: /apps/gentoo/usr/include/io.h:62:8: note: previous declaration of 'urlRead' was here size_t urlRead(URL_t *URL, void *buf, size_t bufSize); ^~~~~~~ In file included from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c:37:0: /apps/gentoo/usr/include/io.h:74:10: error: conflicting types for 'urlSeek' CURLcode urlSeek(URL_t *URL, size_t pos); ^~~~~~~ In file included from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/src/H5private.h:149:0, from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c:26: /apps/gentoo/usr/include/io.h:74:10: note: previous declaration of 'urlSeek' was here CURLcode urlSeek(URL_t *URL, size_t pos); ^~~~~~~ In file included from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c:37:0: /apps/gentoo/usr/include/io.h:91:8: error: conflicting types for 'urlOpen' URL_t *urlOpen(char *fname, CURLcode (*callBack)(CURL*), const char* mode); ^~~~~~~ In file included from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/src/H5private.h:149:0, from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c:26: /apps/gentoo/usr/include/io.h:91:8: note: previous declaration of 'urlOpen' was here URL_t *urlOpen(char *fname, CURLcode (*callBack)(CURL*), const char* mode); ^~~~~~~ In file included from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c:37:0: /apps/gentoo/usr/include/io.h:102:6: error: conflicting types for 'urlClose' void urlClose(URL_t *URL); ^~~~~~~~ In file included from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/src/H5private.h:149:0, from /apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18/tools/perform/overhead.c:26: /apps/gentoo/usr/include/io.h:102:6: note: previous declaration of 'urlClose' was here void urlClose(URL_t *URL); ^~~~~~~~ make[2]: *** [Makefile:911: overhead.o] Error 1 make[2]: Leaving directory '/apps/gentoo/var/tmp/portage/sci-libs/hdf5-1.8.18/work/hdf5-1.8.18_build/tools/perform' $ emerge --info '=sci-libs/hdf5-1.8.18::gentoo' Portage 2.3.5 (python 2.7.13-final-0, prefix/linux-standalone/amd64, gcc-4.9.4, glibc-2.24-r1, 2.6.32-573.12.1.el6.noc0w.x86_64 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-2.6.32-573.12.1.el6.noc0w.x86_64-x86_64-Intel-R-_Xeon-R-_CPU_E5-2695_v3_@_2.30GHz-with-centos-6.7-Final KiB Mem: 131927460 total, 15829280 free KiB Swap: 2097148 total, 2096500 free Timestamp of repository gentoo: Fri, 12 May 2017 09:00:01 +0000 sh bash 4.4_p12 ld GNU ld (Gentoo 2.27 p1.0) 2.27 app-shells/bash: 4.4_p12::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.24.1-r1::gentoo dev-lang/python: 2.7.13::gentoo, 3.4.6::gentoo, 3.5.3::gentoo, 3.6.1::gentoo dev-util/cmake: 3.8.0::gentoo dev-util/pkgconfig: 0.29.2::gentoo sys-apps/baselayout: 2.3::gentoo sys-apps/sandbox: 2.10-r4::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r2::gentoo sys-devel/automake: 1.14.1-r1::gentoo, 1.15-r2::gentoo sys-devel/binutils: 2.27::gentoo sys-devel/gcc: 3.4.6-r2::gentoo, 4.1.2::gentoo, 4.2.4-r1::gentoo, 4.4.7::gentoo, 4.5.4::gentoo, 4.7.4::gentoo, 4.8.5::gentoo, 4.9.3::gentoo, 4.9.4::gentoo, 5.4.0-r3::gentoo, 6.3.0::gentoo, 7.1.0-r1::gentoo sys-devel/gcc-config: 1.8_p20160608::rap sys-devel/libtool: 2.4.6-r4::gentoo sys-devel/make: 4.2.1::gentoo sys-kernel/linux-headers: 4.10::gentoo (virtual/os-headers) sys-libs/glibc: 2.24-r1::gentoo Repositories: gentoo location: /apps/gentoo/usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 eclass-overrides: rap rap location: /apps/gentoo/usr/portage-stage sync-type: git sync-uri: https://anongit.gentoo.org/git/proj/android.git masters: gentoo eclass-overrides: rap x-portage location: /apps/gentoo/usr/local/portage masters: gentoo priority: 0 eclass-overrides: rap haskell location: /apps/gentoo/var/lib/layman/haskell masters: gentoo priority: 50 eclass-overrides: rap science location: /apps/gentoo/var/lib/layman/science masters: gentoo priority: 50 eclass-overrides: rap ACCEPT_KEYWORDS="amd64 ~amd64 ~amd64-linux" ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE IBM-J1.6 skype-eula Nero-EULA-US AdobeFlash-10.3 skype-4.0.0.7-copyright AdobeFlash-11.x Intel-SDP OPERA-2014" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -mavx" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.3/conf" 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 -mavx" DISTDIR="/apps/gentoo/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles force-prefix merge-sync news nostrip parallel-fetch preserve-libs protect-owned sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans unprivileged" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://ftp.fi.muni.cz/pub/linux/gentoo/ http://gentoo.mirror.web4u.cz/ rsync://gentoo.mirror.dkm.cz/gentoo/ ftp://gentoo.mirror.web4u.cz/" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j24" PKGDIR="/apps/gentoo/usr/portage/packages" PORTAGE_CONFIGROOT="/apps/gentoo/" 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 --exclude=/.git" PORTAGE_TMPDIR="/apps/gentoo/var/tmp" USE="X alsa amd64 apache apache2 avx avx2 berkdb boost bzip2 cairo cgi cli coin cracklib crypt cryptlib cxx dbus device-mapper dhcp dri emboss encode fax fbcon ffmpeg fontconfig fortran gbm gd gdbm gimp glpk gnutls gtk hal hwdb iconv imaging innodb ithreads java javafx javascript jce jpeg jpg js jscript keymap ladspa lapack lcms libnotify lm_sensors mad mmx modules mpi mpich2 mysql ncurses nfs nls nptl nptlonly nscd objc openmp openssl pcre pdf perl php png policykit polkit ppds pppd prefix python qt3support readline resolvconf seccomp server session slideshow sndfile sqlite sse sse2 sse3 sse4_1 sse4_2 ssl ssse3 suexec svg syslog tcl tcpd threads tiff tk truetype unicode usb v4l v4l2 vim-syntax vnc wavpack wifi x11 xcb xml xorg xrandr xv xvid xvmc 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" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="avx avx2 fma3 mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en_US en_GB en cs" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python3_4" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby21 ruby22" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" 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: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Created attachment 472444 [details] build.log.bz2
$ equery belongs /apps/gentoo/usr/include/io.h * Searching for /apps/gentoo/usr/include/io.h ... sci-biology/libBigWig-9999 (/apps/gentoo/usr/include/io.h) $
(In reply to Martin Mokrejš from comment #2) > $ equery belongs /apps/gentoo/usr/include/io.h > * Searching for /apps/gentoo/usr/include/io.h ... > sci-biology/libBigWig-9999 (/apps/gentoo/usr/include/io.h) > $ It looks like sci-biology/libBigWig-9999 should be fixed.
I had an old version installed under -9999. Installing a fresh copy helped. Here is my past relevant commit in science overlay: commit 433b969988cb9547d03206170c24f750b01560e8 Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> Date: Fri Jul 28 22:13:07 2017 +0200 sci-biology/libBigWig: remove old version with conflicting io.h
