89) shuffleDirectShortArray(org.xerial.snappy.BitShuffleTest) java.lang.NoClassDefFoundError: Could not initialize class org.xerial.snappy.BitShuffle at org.xerial.snappy.BitShuffleTest.shuffleDirectShortArray(BitShuffleTest.java:161) ... 32 trimmed Caused by: java.lang.ExceptionInInitializerError: Exception java.lang.UnsatisfiedLinkError: /var/tmp/portage/dev-java/snappy-1.1.10.1/temp/snappy-1.1.10-76757304-c94a-401d-9f13-5a64b0da38c1-libsnappyjava.so: /usr/lib64/libbitshuffle.so.0: undefined symbol: LZ4_compressBound [in thread "main"] at java.base/jdk.internal.loader.NativeLibraries.load(Native Method) at java.base/jdk.internal.loader.NativeLibraries$NativeLibraryImpl.open(NativeLibraries.java:388) at java.base/jdk.internal.loader.NativeLibraries.loadLibrary(NativeLibraries.java:232) at java.base/jdk.internal.loader.NativeLibraries.loadLibrary(NativeLibraries.java:174) at java.base/java.lang.ClassLoader.loadLibrary(ClassLoader.java:2394) at java.base/java.lang.Runtime.load0(Runtime.java:755) at java.base/java.lang.System.load(System.java:1953) at org.xerial.snappy.SnappyLoader.loadNativeLibrary(SnappyLoader.java:182) at org.xerial.snappy.SnappyLoader.loadBitShuffleApi(SnappyLoader.java:167) at org.xerial.snappy.BitShuffle.<clinit>(BitShuffle.java:34) at org.xerial.snappy.SnappyTest.isValidArrayInputLengthForBitShuffleShuffle(SnappyTest.java:461) ... 33 more FAILURES!!! Tests run: 101, Failures: 89 * ERROR: dev-java/snappy-1.1.10.1::gentoo failed (test phase): * Running junit failed * * Call stack: * ebuild.sh, line 136: Called src_test * environment, line 3322: Called java-pkg-simple_src_test * environment, line 1683: Called ejunit4 '-classpath' 'target/test-classes:snappy.jar:/var/tmp/portage/dev-java/snappy-1.1.10.1/distdir/hadoop-common-3.3.5.jar:/usr/share/commons-io-1/lib/commons-io.jar:/usr/share/commons-lang-2.1/lib/commons-lang.jar:/usr/share/junit-4/lib/junit.jar:/usr/share/hamcrest-core-1.3/lib/hamcrest-core.jar:/usr/share/plexus-classworlds/lib/plexus-classworlds.jar:/usr/share/xerial-core/lib/xerial-core.jar:/usr/share/osgi-core/lib/osgi-core.jar' 'org.xerial.snappy.SnappyOutputStreamTest' 'org.xerial.snappy.pool.CachingBufferPoolTest' 'org.xerial.snappy.SnappyTest' 'org.xerial.snappy.SnappyLoaderTest' 'org.xerial.snappy.SnappyInputStreamTest' 'org.xerial.snappy.SnappyHadoopCompatibleOutputStreamTest' 'org.xerial.snappy.SnappyFramedStreamTest' 'org.xerial.snappy.OSInfoTest' 'org.xerial.snappy.CalgaryTest' 'org.xerial.snappy.BitShuffleTest' * environment, line 999: Called ejunit_ 'junit-4' '-classpath' 'target/test-classes:snappy.jar:/var/tmp/portage/dev-java/snappy-1.1.10.1/distdir/hadoop-common-3.3.5.jar:/usr/share/commons-io-1/lib/commons-io.jar:/usr/share/commons-lang-2.1/lib/commons-lang.jar:/usr/share/junit-4/lib/junit.jar:/usr/share/hamcrest-core-1.3/lib/hamcrest-core.jar:/usr/share/plexus-classworlds/lib/plexus-classworlds.jar:/usr/share/xerial-core/lib/xerial-core.jar:/usr/share/osgi-core/lib/osgi-core.jar' 'org.xerial.snappy.SnappyOutputStreamTest' 'org.xerial.snappy.pool.CachingBufferPoolTest' 'org.xerial.snappy.SnappyTest' 'org.xerial.snappy.SnappyLoaderTest' 'org.xerial.snappy.SnappyInputStreamTest' 'org.xerial.snappy.SnappyHadoopCompatibleOutputStreamTest' 'org.xerial.snappy.SnappyFramedStreamTest' 'org.xerial.snappy.OSInfoTest' 'org.xerial.snappy.CalgaryTest' 'org.xerial.snappy.BitShuffleTest' * environment, line 1026: Called die * The specific snippet of code: * java "${args[@]}" || die "Running junit failed" * * If you need support, post the output of `emerge --info '=dev-java/snappy-1.1.10.1::gentoo'`, * the complete build log and the output of `emerge -pqv '=dev-java/snappy-1.1.10.1::gentoo'`. !!! When you file a bug report, please include the following information: GENTOO_VM=openjdk-17 CLASSPATH="" JAVA_HOME="/usr/lib64/openjdk-17" JAVACFLAGS="-source 1.8 -target 1.8" COMPILER="" and of course, the output of emerge --info =snappy-1.1.10.1 * The complete build log is located at '/var/tmp/portage/dev-java/snappy-1.1.10.1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/dev-java/snappy-1.1.10.1/temp/environment'. * Working directory: '/var/tmp/portage/dev-java/snappy-1.1.10.1/work/snappy-java-1.1.10.1' * S: '/var/tmp/portage/dev-java/snappy-1.1.10.1/work/snappy-java-1.1.10.1' Reproducible: Always
Created attachment 871189 [details] build.log # emerge -pqv '=dev-java/snappy-1.1.10.1::gentoo' [ebuild U ] dev-java/snappy-1.1.10.1 [1.1.7.8-r1] USE="test* -doc -source" # emerge --info '=dev-java/snappy-1.1.10.1::gentoo' Portage 3.0.51 (python 3.11.5-final-0, default/linux/amd64/17.1/no-multilib/hardened, gcc-13, glibc-2.38-r2, 6.5.5 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-6.5.5-x86_64-Intel-R-_Core-TM-_i7-4810MQ_CPU_@_2.80GHz-with-glibc2.38 KiB Mem: 16282872 total, 8228520 free KiB Swap: 20971516 total, 20971516 free Timestamp of repository gentoo: Sat, 23 Sep 2023 10:00:01 +0000 Head commit of repository gentoo: 9acaae3e1a70ec6bd72e3c324b115bae1a05ed5f sh bash 5.2_p15-r6 ld GNU ld (Gentoo 2.41 p2) 2.41.0 app-misc/pax-utils: 1.3.7::gentoo app-shells/bash: 5.2_p15-r6::gentoo dev-java/java-config: 2.3.1-r1::gentoo dev-lang/perl: 5.38.0-r1::gentoo dev-lang/python: 3.11.5::gentoo, 3.12.0_rc3::gentoo dev-lang/rust: 1.72.0::gentoo dev-util/cmake: 3.27.6-r1::gentoo dev-util/meson: 1.2.1-r1::gentoo sys-apps/baselayout: 2.14::gentoo sys-apps/openrc: 0.50::gentoo sys-apps/sandbox: 2.38::gentoo sys-devel/autoconf: 2.13-r8::gentoo, 2.71-r7::gentoo sys-devel/automake: 1.16.5-r1::gentoo sys-devel/binutils: 2.41-r1::gentoo sys-devel/binutils-config: 5.5::gentoo sys-devel/clang: 16.0.6::gentoo, 17.0.1::gentoo sys-devel/gcc: 13.2.1_p20230826::gentoo sys-devel/gcc-config: 2.11::gentoo sys-devel/libtool: 2.4.7-r1::gentoo sys-devel/lld: 16.0.6::gentoo sys-devel/llvm: 16.0.6::gentoo, 17.0.1::gentoo sys-devel/make: 4.4.1-r1::gentoo sys-kernel/linux-headers: 6.5::gentoo (virtual/os-headers) sys-libs/glibc: 2.38-r2::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 volatile: True sync-rsync-verify-metamanifest: yes sync-rsync-extra-opts: --new-compress sync-rsync-verify-max-age: 24 sync-rsync-verify-jobs: 1 local location: /var/lib/portage-local/local masters: gentoo priority: 0 volatile: True ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="@FREE" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -mtune=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /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 -mtune=native -O2 -pipe" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--with-bdeps=y" ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GDK_PIXBUF_MODULE_FILE GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR XDG_STATE_HOME" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg-live collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu" LEX="flex" LINGUAS="" MAKEOPTS="-j8" PKGDIR="/var/cache/binpkgs" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_EXTRA_OPTS="--new-compress" 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" SHELL="/bin/bash" USE="X a52 acl acpi alsa amd64 avx bzip2 cairo caps cdda cddb cdparanoia cli crypt cups dbus dri dts dvd elogind fam ffmpeg fftw flac fontconfig gdbm gif gimp gmp gnutls gtk hardened iconv icu idn ipv6 jpeg lame lcms libnotify libtirpc lzma mad matroska mmap mmx mmxext mp3 mpeg ncurses networkmanager nptl ogg opengl openmp pam pcre pie png policykit ppds readline sasl sdl seccomp split-usr sse sse2 sse3 sse4 sse4_1 sse4_2 ssl ssp ssse3 startup-notification svg test test-rust theora threads tiff truetype udev udisks unicode upower vaapi verify-sig vorbis wayland x264 xattr xcb xinerama xml xtpax xv xvid zlib" ABI_X86="64" ADA_TARGET="gnat_2021" 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 sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt rdrand sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" GRUB_PLATFORMS="efi-64" INPUT_DEVICES="evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php8-1" POSTGRES_TARGETS="postgres15" PYTHON_SINGLE_TARGET="python3_11" PYTHON_TARGETS="python3_11" RUBY_TARGETS="ruby31" VIDEO_CARDS="crocus intel nouveau" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq proto steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LANG, LC_ALL, LD, LFLAGS, LIBTOOL, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS
Created attachment 871190 [details] environment
The problem in all cases is the undefined symbol "LZ4_compressBound" in /usr/lib64/libbitshuffle.so.0: java.lang.UnsatisfiedLinkError: /var/tmp/portage/dev-java/snappy-1.1.10.1/temp/snappy-1.1.10-ad349fa5-a39e-4636-94ee-ca2a5047a8a4-libsnappyjava.so: /usr/lib64/libbitshuffle.so.0: undefined symbol: LZ4_compressBound
# equery belongs /usr/lib64/libbitshuffle.so.0 * Searching for /usr/lib64/libbitshuffle.so.0 ... dev-libs/bitshuffle-0.3.5 (/usr/lib64/libbitshuffle.so.0.3.5) dev-libs/bitshuffle-0.3.5 (/usr/lib64/libbitshuffle.so.0 -> libbitshuffle.so.0.3.5) # emerge -qpv dev-libs/bitshuffle [ebuild R ] dev-libs/bitshuffle-0.3.5
Created attachment 873421 [details] build log with all tests passing Those test failures are not always reproducible and did not even affect stabilization, see commit #3294f5d7da. I am attaching a build log where all tests pass.
Created attachment 873422 [details] "emerge --info" where all tests pass
The ebuild for bitshuffle seems off. It only DEPENDs on lz4, no RDEPEND, and the custom Makefile we use doesn't link against lz4 at all? Note that the guix Makefile it's based on _does_ use the bundled copy of lz4 so it doesn't suffer from this problem.
(In reply to Sam James from comment #7) > The ebuild for bitshuffle seems off. > > It only DEPENDs on lz4, no RDEPEND, and the custom Makefile we use doesn't > link against lz4 at all? > > Note that the guix Makefile it's based on _does_ use the bundled copy of lz4 > so it doesn't suffer from this problem. Are you saying the solution is adding RDEPEND to bitshuffle-0.3.5.ebuild? How could we be sure it would change anything without being able to reproduce that error?
(In reply to Volkmar W. Pogatzki from comment #8) > (In reply to Sam James from comment #7) > > The ebuild for bitshuffle seems off. > > > > It only DEPENDs on lz4, no RDEPEND, and the custom Makefile we use doesn't > > link against lz4 at all? > > > > Note that the guix Makefile it's based on _does_ use the bundled copy of lz4 > > so it doesn't suffer from this problem. > > Are you saying the solution is adding RDEPEND to bitshuffle-0.3.5.ebuild? > How could we be sure it would change anything without being able to > reproduce that error? No, the main issue is the Makefile is broken. But RDEPEND is also wrong.
Reproduced with dev-java/snappy-1.1.10.5-r1
Created attachment 899839 [details] bitshuffle-0.3.5 build log (In reply to Sam James from comment #9) > [...] > No, the main issue is the Makefile is broken. But RDEPEND is also wrong. Even if I add 'LIBS := -llz4' to that custom Makefile it runs on error, logfile attached. files/bitshuffle-0.3.5-Makefile 29,30d28 < LIBS := -llz4 < 32c30 < $(CC) $(CFLAGS) -o $@ -shared $(LDFLAGS) -Wl,-z,defs -Wl,-soname,$(SONAME) $^ --- > $(CC) $(CFLAGS) -o $@ -shared $(LDFLAGS) -Wl,-soname,$(SONAME) $^
> x86_64-pc-linux-gnu-gcc -O3 -ffast-math -std=c99 -fPIC -march=native -O2 -pipe -o libbitshuffle.so.0.3.5 -shared -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,defs -Wl,-soname,libbitshuffle.so.0 src/bitshuffle.o src/bitshuffle_core.o src/iochain.o Indeed, -lz4 isn't there. Try adding $(LIBS) after $^.
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d4bba0ecd6f6e00a6cb031268320a8c9c7e0adbc commit d4bba0ecd6f6e00a6cb031268320a8c9c7e0adbc Author: Volkmar W. Pogatzki <gentoo@pogatzki.net> AuthorDate: 2024-08-12 05:29:35 +0000 Commit: Miroslav Šulc <fordfrog@gentoo.org> CommitDate: 2024-08-29 10:48:37 +0000 dev-libs/bitshuffle: fix underlinked error Bug: https://bugs.gentoo.org/914570 Signed-off-by: Volkmar W. Pogatzki <gentoo@pogatzki.net> Closes: https://github.com/gentoo/gentoo/pull/38110 Signed-off-by: Miroslav Šulc <fordfrog@gentoo.org> .../{bitshuffle-0.3.5.ebuild => bitshuffle-0.3.5-r1.ebuild} | 6 +++++- dev-libs/bitshuffle/files/bitshuffle-0.3.5-Makefile | 4 +++- 2 files changed, 8 insertions(+), 2 deletions(-)
