make[6]: Entering directory '/var/tmp/portage/sci-biology/rmblast-1.2-r1/work/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC530-ReleaseMTDLL64/build/corelib' Updating dependency information for /var/tmp/portage/sci-biology/rmblast-1.2-r1/work/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/src/corelib/test_boost.cpp. /var/tmp/portage/sci-biology/rmblast-1.2-r1/work/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/src/corelib/test_boost.cpp:60:40: fatal error: boost/test/test_observer.hpp: No such file or directory compilation terminated. FAILED COMMAND: ccache /usr/bin/x86_64-pc-linux-gnu-g++ -M -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/var/tmp/portage/sci-biology/rmblast-1.2-r1/work/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC530-ReleaseMTDLL64/inc -I/var/tmp/portage/sci-biology/rmblast-1.2-r1/work/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/include -I/usr/include/boost/include -DBOOST_DISABLE_THREADS /var/tmp/portage/sci-biology/rmblast-1.2-r1/work/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/src/corelib/test_boost.cpp | sed ... ccache /usr/bin/x86_64-pc-linux-gnu-g++ -c -Wall -Wno-format-y2k -pthread -march=native -O2 -pipe -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/var/tmp/portage/sci-biology/rmblast-1.2-r1/work/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/GCC530-ReleaseMTDLL64/inc -I/var/tmp/portage/sci-biology/rmblast-1.2-r1/work/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/include -I/usr/include/boost/include -DBOOST_DISABLE_THREADS /var/tmp/portage/sci-biology/rmblast-1.2-r1/work/rmblast-1.2-ncbi-blast-2.2.23+-src/c++/src/corelib/test_boost.cpp -o test_boost.o $ cat emerge-info.txt ----------------------------------------------------------------- This is an unstable amd64 chroot image (named amd64-desktop-unstable_20160326-172343) at a hardened host acting as a tinderbox. ----------------------------------------------------------------- make.conf: USE="mmx sse sse2 pax_kernel -cdinstall -oci8 -bindist apache2 -btrfs cgoups corefonts csc curl custom-cflags custom-optimization dec_av2 designer dnssec evdev extraengine ffmpeg -fontconfig fpm gif -gnome-keyring gnutls imap javafx javascript javaxml jpeg mbox mng mysql mysqli nss plasma png postproc -postscript -pulseaudio qt3support rendering scripts -sddm sdl sqlite ssh-askpass system-jpeg szip tls tools -ufed uml v4l wav webkit webstart xa xmlreader xscreensaver" ----------------------------------------------------------------- Portage 2.2.28 (python 3.4.3-final-0, default/linux/amd64/13.0/desktop, gcc-5.3.0, glibc-2.22-r4, 4.4.6-hardened-r1 x86_64) ================================================================= System uname: Linux-4.4.6-hardened-r1-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2 KiB Mem: 16157888 total, 1941784 free KiB Swap: 16777212 total, 16706996 free Timestamp of repository gentoo: Thu, 07 Apr 2016 10:05:51 +0000 sh bash 4.3_p42-r2 ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1 ccache version 3.2.4 [disabled] app-shells/bash: 4.3_p42-r2::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.22.1::gentoo dev-lang/python: 2.7.11-r2::gentoo, 3.3.5-r7::gentoo, 3.4.3-r7::gentoo, 3.5.1-r2::gentoo dev-util/ccache: 3.2.4::gentoo dev-util/cmake: 3.5.1::gentoo dev-util/pkgconfig: 0.29.1::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/openrc: 0.20.5::gentoo sys-apps/sandbox: 2.10-r2::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r2::gentoo sys-devel/automake: 1.9.6-r4::gentoo, 1.10.3-r2::gentoo, 1.11.6-r2::gentoo, 1.12.6-r1::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo sys-devel/binutils: 2.25.1-r1::gentoo sys-devel/gcc: 4.9.3::gentoo, 5.3.0::gentoo sys-devel/gcc-config: 1.8-r1::gentoo sys-devel/libtool: 2.4.6-r2::gentoo sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 4.5::gentoo (virtual/os-headers) sys-libs/glibc: 2.22-r4::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.de.gentoo.org/gentoo-portage/ priority: 1 local location: /usr/local/portage masters: gentoo priority: 2 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /etc/grs/systems.conf /etc/stunnel/stunnel.conf /usr/lib64/fax /usr/share/gnupg/qualified.txt /usr/share/qpsmtpd/plugins /var/rancid/.cloginrc /var/spool/fax/etc" 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 -O2 -pipe" DISTDIR="/var/tmp/distfiles" EMERGE_DEFAULT_OPTS="--deep --verbose-conflicts --color=n --nospinner --tree --quiet-build --accept-properties=-interactive --accept-restrict=-fetch" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox 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="http://ftp.uni-erlangen.de/pub/mirrors/gentoo rsync://mirror.netcologne.de/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gor.bytemark.co.uk/gentoo/ rsync://ftp.snt.utwente.nl/gentoo" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j1" 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 apache2 berkdb bluetooth branding bzip2 cairo cdda cdr cgoups cli consolekit corefonts cracklib crypt csc cups curl custom-cflags custom-optimization cxx dbus dec_av2 designer dnssec dri dts dvd dvdr emboss encode evdev exif extraengine fam ffmpeg firefox flac fortran fpm gdbm gif glamor gnutls gpm gtk iconv imap ipv6 javafx javascript javaxml jpeg lcms ldap libnotify mad mbox mmx mmxext mng modules mp3 mp4 mpeg multilib mysql mysqli ncurses nls nptl nss ogg opengl openmp pam pango pax_kernel pcre pdf plasma png policykit postproc ppds qt3support qt4 readline rendering scripts sdl seccomp session spell sqlite sse sse2 ssh-askpass ssl startup-notification svg system-jpeg szip tcpd tiff tls tools truetype udev udisks uml unicode upower usb v4l vorbis wav webkit webstart wxwidgets x264 xa xattr xcb xml xmlreader 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="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" 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" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en en_GB" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="intel i965" 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Created attachment 429840 [details] emerge-history.txt
Created attachment 429842 [details] environment
Created attachment 429844 [details] sci-biology:rmblast-1.2-r1:20160407-122050.log
I get the same here. I think the ebuild should inherit most of the logic used for sci-biology/ncbi-tools++::science, notably disable compilation of the test suite via ncbi-tools++/files/disable-testsuite-compilation.txt patch. ;-) I tried to help with ncbi-tools++ ebuilds a lot in he past but still lack some capibility to cleanup the ebuilds, and Justin is I guess overloaded.
(In reply to Martin Mokrejš from comment #4) > I get the same here. I think the ebuild should inherit most of the logic > used for sci-biology/ncbi-tools++::science, notably disable compilation of > the test suite via ncbi-tools++/files/disable-testsuite-compilation.txt > patch. ;-) Hmm, I just hit the same error with =sci-biology/ncbi-tools++-12.0.0::science so it is a different issue. I just emailed Aaron Ucko from NCBI for an advise.
I just added this to science overlay. Toralf, would you mind tetsing this? ;-) commit ef30e8a1e8ba6e56b365f8dbaddd1b4812306392 Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> Date: Sat Dec 3 00:27:56 2016 +0100 sci-biology/ncbi-tools++: fix bug #579248#c by disabling more tests This will likely also fix the #579248 bug in rmblast (untested). Our $FILESDIR/disable-testsuite-compilation.txt only excludes test applications from usingboost, not the support library. Hence the above bug. We could either add --without-boost to the configuration command line to disable the bosost-related code in support library or, which is the path we take in this commit, we disable building of the yet escaping unit_tests which needed boost. Upstream further said: The C++ Toolkit makes very little use of Boost outside of unit tests, but that's a fair question. The simplest fix preserving other uses of Boost would be to edit .../src/corelib/Makefile.in and remove test_boost from LIB_PROJ. (You'll still also need to exclude building the tests by adding '-.*/unit_tests' to the $FILESDIR/disable-testsuite-compilation.txt file.) Package-Manager: portage-2.3.2
(In reply to Martin Mokrejš from comment #6) will try, but FWIW : !!! Section 'sci' in repos.conf has name different from repository name 'science' set inside repository This seems not only a harmless warning. I had to rename ./sci to ./science and all identifiers in repos.conf/* too to convince emerge to make "Performing Global Updates" and so on: # emerge -up sci-biology/rmblast Performing Global Updates (Could take a couple of minutes if you have a lot of binary packages.) .='update pass' *='binary update' #='/var/db update' @='/var/db move' s='/var/db SLOT move' %='binary move' S='binary SLOT move' p='update /etc/portage/package.*' /usr/local/sci/profiles/updates/3Q-2009........................ /usr/local/sci/profiles/updates/1Q-2011...... /usr/local/sci/profiles/updates/2Q-2011..... /usr/local/sci/profiles/updates/1Q-2012. /usr/local/sci/profiles/updates/4Q-2013. /usr/local/sci/profiles/updates/1Q-2014. /usr/local/sci/profiles/updates/2Q-2014..
hhm, at an image with gcc-6 I do get : mr-fox repos.conf # emerge -au sci-biology/ncbi-tools++ These are the packages that would be merged, in reverse order: Calculating dependencies . ........... done! [blocks b ] sci-biology/ncbi-tools++ ("sci-biology/ncbi-tools++" is blocking sci-biology/update-blastdb-12.0.0) [uninstall ] sci-biology/update-blastdb-12.0.0::gentoo [ebuild N ] sci-biology/ncbi-tools++-12.0.0::science USE="X berkdb bzip2 gif jpeg opengl pcre png tiff wxwidgets xml xslt -boost -cppunit -curl -debug -expat -fastcgi -fltk -freetype -glut -gnutls -hdf5 -icu -lzo -mesa -muparser -mysql -odbc -pch -python -sablotron -sqlite -static -static-libs {-test} -threads -xalan -xerces -xpm" PYTHON_TARGETS="python2_7" 0 KiB [ebuild NS ] sys-libs/db-4.3.29_p1-r1:4.3::gentoo [4.8.30-r2:4.8::gentoo, 6.0.35:6.0::gentoo] USE="cxx -doc -examples -java -rpc -tcl {-test}" 5,962 KiB Total: 2 packages (1 new, 1 in new slot, 1 uninstall), Size of downloads: 5,962 KiB Conflict: 1 block ... checking for x86_64-pc-linux-gnu-gcc option to accept ANSI C... none needed checking whether we are using the GNU C++ compiler... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes adjusted C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc adjusted C++ compiler: /usr/bin/x86_64-pc-linux-gnu-g++ Compiler /usr/bin/x86_64-pc-linux-gnu-g++ 6.2.0 is not fully supported. Consult doc/config.html\#ref_Compilers for the list of fully supported platforms/compilers. Do you still want to proceed (at your own risk)? [y/N] configure: error: Configuration has been canceled by user. * ERROR: sci-biology/ncbi-tools++-12.0.0::science failed (configure phase): * (no error message) * * Call stack: * ebuild.sh, line 115: Called src_configure * environment, line 3409: Called die * The specific snippet of code: * bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 --with-flat-makefile ${myconf[@]} || die *
(In reply to Toralf Förster from comment #8) > [blocks b ] sci-biology/ncbi-tools++ ("sci-biology/ncbi-tools++" is > blocking sci-biology/update-blastdb-12.0.0) The blocker is correct, ncbi-tools++ is the complete bundle. $ equery files ncbi-tools++ | grep update_blastdb /usr/bin/update_blastdb.pl $ > > Compiler /usr/bin/x86_64-pc-linux-gnu-g++ 6.2.0 is not fully supported. > Consult doc/config.html\#ref_Compilers for the list of > fully supported platforms/compilers. > Do you still want to proceed (at your own risk)? [y/N] > configure: error: Configuration has been canceled by user. > * ERROR: sci-biology/ncbi-tools++-12.0.0::science failed (configure phase): > * (no error message) > * > * Call stack: > * ebuild.sh, line 115: Called src_configure > * environment, line 3409: Called die > * The specific snippet of code: > * bash ./src/build-system/configure --srcdir="${S}" > --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 --with-flat-makefile > ${myconf[@]} || die > * Hmm, I never saw the interactive question being spit out but nevertheless, myself I cannot even use gcc-5.4.0 and so I use 4.9.3 as a maximum. Once I poked over some ebuild which used some approach to automatically pick the proper gcc version but do not ask which it was. I can only add some info message to the ebuild is compilation failed proposing a different compiler. After using a supported gcc version due to openMP support test both USE=boost and USE=-boost attempts.
(In reply to Toralf Förster from comment #7) > (In reply to Martin Mokrejš from comment #6) > will try, but FWIW : > > !!! Section 'sci' in repos.conf has name different from repository name > 'science' set inside repository > > This seems not only a harmless warning. > > I had to rename ./sci to ./science and all identifiers in repos.conf/* too > to convince emerge to make "Performing Global Updates" and so on: sci was renamed to science some while ago but more importantly, the CVS moved to git and hostnames changed. I am not really knowledgeable of this but I would recommend: layman -d sci layman -d science layman -a science https://wiki.gentoo.org/wiki/Project:Science/Overlay https://wiki.gentoo.org/wiki/Project:Science Beware github-hosted https://github.com/gentoo-science/sci tree does not get backported commits going straight into https://gitweb.gentoo.org/proj/sci.git/ . However, they are cherry-picked form github to the gentoo.org git tree of course. layman should access the tree with merged commits.
(In reply to Martin Mokrejš from comment #10) > (In reply to Toralf Förster from comment #7) > > (In reply to Martin Mokrejš from comment #6) > > will try, but FWIW : > > > > !!! Section 'sci' in repos.conf has name different from repository name > > 'science' set inside repository > > > > This seems not only a harmless warning. > > > > I had to rename ./sci to ./science and all identifiers in repos.conf/* too > > to convince emerge to make "Performing Global Updates" and so on: > > sci was renamed to science some while ago but more importantly, the CVS > moved to git and hostnames changed. I am not really knowledgeable of this > but I would recommend: > > layman -d sci > layman -d science > layman -a science > > https://wiki.gentoo.org/wiki/Project:Science/Overlay > https://wiki.gentoo.org/wiki/Project:Science > > Beware github-hosted https://github.com/gentoo-science/sci tree does not get > backported commits going straight into > https://gitweb.gentoo.org/proj/sci.git/ . > However, they are cherry-picked form github to the gentoo.org git tree of > course. layman should access the tree with merged commits. Martin, Toralf only works on the main tree, and I don't see any reason for him to also tinderbox the overlays. Please submit fixes to the main tree via Github, instead of accumulating supposed fixes in the overlay. The overlay has no general QA guarantees, and only adding fixes there gains us little to nothing. We should strive to improve the quality of the main tree, and ultimately to us the overlay only has a staging ground, and not as a tree that is taking on a life of its own (which it currently does).
But sci-biology/ncbi-tools++ did not even land in the gentoo-x86 tree yet. But feel free to move current sci-biology/ncbi-tools++::science to it. The rmblast ebuild should somehow re-use the logic from sci-biology/ncbi-tools++ ebuild as they act on the same type of source tree from same authors.
Still in the wrong tree, but at least some improvement: commit b146dec4b74edfdcd3ada5b3784ae01c7e3b208b Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> Date: Mon Dec 19 22:21:26 2016 +0100 sci-biology/rmblast: fix bug #579248 by disabling testsuite compilation Also improve DESCRIPTION. rmblastn binary is also provided by ncbi-tools++-12.0.0 although repeatmasker probably needs the rmblastn based on BLAST 2.2.23+. Package-Manager: Portage-2.3.3, Repoman-2.3.1
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d5c451e59a806404de4c3a9428a10c04a4f77dfc commit d5c451e59a806404de4c3a9428a10c04a4f77dfc Author: Jakov Smolić <jsmolic@gentoo.org> AuthorDate: 2022-02-10 09:16:27 +0000 Commit: Jakov Smolić <jsmolic@gentoo.org> CommitDate: 2022-02-10 09:17:33 +0000 sci-biology/rmblast: treeclean Closes: https://bugs.gentoo.org/515962 Closes: https://bugs.gentoo.org/579248 Closes: https://bugs.gentoo.org/664518 Closes: https://bugs.gentoo.org/711246 Closes: https://bugs.gentoo.org/716172 Closes: https://bugs.gentoo.org/457972 Closes: https://bugs.gentoo.org/724466 Closes: https://bugs.gentoo.org/828706 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org> profiles/package.mask | 1 - sci-biology/rmblast/Manifest | 2 -- sci-biology/rmblast/metadata.xml | 8 ------ sci-biology/rmblast/rmblast-1.2-r1.ebuild | 47 ------------------------------- 4 files changed, 58 deletions(-)
