Created attachment 540156 [details] build log of sci-chemistry/vmd-1.9.3 Similar to a previous bug 406737, VMD doesn't build netcdfplugin.so even though it pulls in sci-libs/netcdf as a dependency and ebuild is setting the necessary environmental variables. The reason can be observed in the following line from the build log: make -j21 TCLINC=-I/usr/include TCLLIB=-L/usr/lib64 TCLLDFLAGS=-shared NETCDFLIB= /usr/lib64/libnetcdf.so NETCDFINC= /usr/include NETCDFLDFLAGS=-lnetcdf NETCDFDYNAMIC=1 EXPATINC=-I/usr/include EXPATLIB=-lexpat EXPATLDFLAGS=-shared EXPATDYNAMIC=1 LINUX It appears that NETCDFLIB and NETCDFINC do not get quoted properly when the are passed to make, and become effectively unset because their values contain a leading space. netcdfplugin.so got properly compiled once I've removed the leading spaces from NETCDFLIB and NETCDFINC. I've only checked sci-chemistry/vmd-1.9.3, but sci-chemistry/vmd-1.9.2 probably has the same problem. Just in case, I've attached my build log from unmodified ebuild. emerge --info: Portage 2.3.40 (python 3.5.5-final-0, default/linux/amd64/17.0/desktop, gcc-7.3.0, glibc-2.26-r7, 4.14.52-gentoo x86_64) ================================================================= System uname: Linux-4.14.52-gentoo-x86_64-Intel-R-_Core-TM-_i9-7900X_CPU_@_3.30GHz-with-gentoo-2.4.1 KiB Mem: 32566044 total, 212172 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Thu, 19 Jul 2018 06:30:01 +0000 Head commit of repository gentoo: 4ba06b5ba1fef6cbd2d1c120f84b09c06932a13f sh bash 4.4_p12 ld GNU ld (Gentoo 2.30 p2) 2.30.0 distcc 3.2rc1 x86_64-pc-linux-gnu [disabled] app-shells/bash: 4.4_p12::gentoo dev-lang/perl: 5.24.3-r1::gentoo dev-lang/python: 2.7.14-r1::gentoo, 3.5.5::gentoo dev-util/cmake: 3.9.6::gentoo dev-util/pkgconfig: 0.29.2::gentoo sys-apps/baselayout: 2.4.1-r2::gentoo sys-apps/openrc: 0.34.11::gentoo sys-apps/sandbox: 2.13::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r4::gentoo sys-devel/automake: 1.11.6-r3::gentoo, 1.15.1-r2::gentoo sys-devel/binutils: 2.30-r2::gentoo sys-devel/gcc: 6.4.0-r1::gentoo, 7.3.0-r3::gentoo sys-devel/gcc-config: 1.8-r1::gentoo sys-devel/libtool: 2.4.6-r3::gentoo sys-devel/make: 4.2.1::gentoo sys-kernel/linux-headers: 4.13::gentoo (virtual/os-headers) sys-libs/glibc: 2.26-r7::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-metamanifest: no sync-rsync-verify-max-age: 24 sync-rsync-extra-opts: sync-rsync-verify-jobs: 1 localrepo location: /usr/local/portage masters: gentoo ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -fomit-frame-pointer -fno-stack-protector -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /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="-march=native -fomit-frame-pointer -fno-stack-protector -O2 -pipe" DISTDIR="/usr/portage/distfiles" ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs candy config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync multilib-strict news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="rsync://ftp.iij.ad.jp/pub/linux/gentoo/ ftp://ftp.iij.ad.jp/pub/linux/gentoo/ http://ftp.iij.ad.jp/pub/linux/gentoo/ http://ftp.jaist.ac.jp/pub/Linux/Gentoo/ rsync://ftp.jaist.ac.jp/pub/Linux/Gentoo/ ftp://ftp.jaist.ac.jp/pub/Linux/Gentoo/" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j21" 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 --exclude=/.git" PORTAGE_TMPDIR="/var/tmp" USE="X a52 aac acl acpi alsa amd64 berkdb branding bzip2 cairo cdda cdr cjk cli consolekit crypt cups cxx dbus dri dts dvd dvdr emboss encode exif fam flac fortran gdbm gif glamor gpm gtk iconv icu ipv6 javafx jpeg lcms ldap libnotify libtirpc mad mng modules mp3 mp4 mpeg multilib ncurses nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppds pulseaudio qt5 readline sdl seccomp spell ssl startup-notification svg tcpd tiff truetype udev udisks unicode upower usb vorbis wxwidgets x264 xattr xcb xml 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="karbon plan sheets stage words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 avx512f avx512dq avx512cd avx512bw avx512vl f16c fma3 mmx mmxext pclmul 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" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6 php7-0" POSTGRES_TARGETS="postgres9_5 postgres10" PYTHON_SINGLE_TARGET="python3_5" PYTHON_TARGETS="python2_7 python3_5" RUBY_TARGETS="ruby23" SANE_BACKENDS="fujitsu" 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: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3e2a2a3baebbc26bdcd1ee23a765bf04ebed7ee3 commit 3e2a2a3baebbc26bdcd1ee23a765bf04ebed7ee3 Author: Pacho Ramos <pacho@gentoo.org> AuthorDate: 2019-05-30 11:14:56 +0000 Commit: Pacho Ramos <pacho@gentoo.org> CommitDate: 2019-05-30 11:14:56 +0000 sci-chemistry/vmd: Multiple fixes and update ebuild - Longer explanation to download sources files (#640440) - Fix tachyon support (#644122) - Install netcdf plugin (#661636) Bug: https://bugs.gentoo.org/640440 Closes: https://bugs.gentoo.org/644122 Closes: https://bugs.gentoo.org/661636 Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Pacho Ramos <pacho@gentoo.org> .../vmd/files/vmd-1.9.1-cuda-device_ptr.patch | 8 +- .../vmd/files/vmd-1.9.3-configure-libtachyon.patch | 13 + sci-chemistry/vmd/vmd-1.9.3-r1.ebuild | 262 +++++++++++++++++++++ 3 files changed, 279 insertions(+), 4 deletions(-)
