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Bug 804909 - sci-libs/gdal-3.2.2[java]: gdalconst_wrap.c:154:10: fatal error: jni.h: No such file or directory
Summary: sci-libs/gdal-3.2.2[java]: gdalconst_wrap.c:154:10: fatal error: jni.h: No su...
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Sci-geo Project
Depends on:
Reported: 2021-07-28 20:31 UTC by Gary E. Miller
Modified: 2021-08-02 16:47 UTC (History)
4 users (show)

See Also:
Package list:
Runtime testing required: ---

Build Log gzipped (sci-libs:gdal-3.2.2:20210728-200812.log.gz,72.18 KB, text/plain)
2021-07-28 20:32 UTC, Gary E. Miller

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Description Gary E. Miller 2021-07-28 20:31:17 UTC
gdalconst_wrap.c:154:10: fatal error: jni.h: No such file or directory
  154 | #include <jni.h>
      |          ^~~~~~~
compilation terminated.
make: *** [GNUmakefile:125: gdalconst_wrap.lo] Error 1

Reproducible: Always

Steps to Reproduce:
1. emerge gdal

spidey ~ # emerge --info =gdal-3.2.2
Portage 3.0.20 (python 3.9.6-final-0, default/linux/amd64/17.1, gcc-11.1.0, glibc-2.33-r1, 5.12.13-gentoo x86_64)
                         System Settings
System uname: Linux-5.12.13-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_E5-1620_v3_@_3.50GHz-with-glibc2.33
KiB Mem:    16274400 total,  12577648 free
KiB Swap:   33554428 total,  33554428 free
Timestamp of repository gentoo: Wed, 28 Jul 2021 17:15:01 +0000
Head commit of repository gentoo: b13c1f48dc220976064484be869f51d71763f259
sh bash 5.1_p8
ld GNU ld (Gentoo 2.35.2 p1) 2.35.2
distcc[5183] (dcc_trace_version) distcc 3.4 x86_64-pc-linux-gnu; built Jul  5 2021 11:11:18 [disabled]
ccache version 4.3 [disabled]
app-shells/bash:          5.1_p8::gentoo
dev-java/java-config:     2.3.1::gentoo
dev-lang/perl:            5.34.0::gentoo
dev-lang/python:          2.7.18_p11::gentoo, 3.8.11::gentoo, 3.9.6::gentoo
dev-lang/rust:            1.53.0::gentoo
dev-util/ccache:          4.3-r2::gentoo
dev-util/cmake:           3.18.5::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.7::gentoo
sys-apps/openrc:          0.42.1-r1::gentoo
sys-apps/sandbox:         2.24::gentoo
sys-devel/autoconf:       2.13-r1::gentoo, 2.69-r5::gentoo
sys-devel/automake:       1.13.4-r2::gentoo, 1.16.3-r1::gentoo
sys-devel/binutils:       2.35.2::gentoo
sys-devel/gcc:            11.1.0-r2::gentoo
sys-devel/gcc-config:     2.4::gentoo
sys-devel/libtool:        2.4.6-r6::gentoo
sys-devel/make:           4.3::gentoo
sys-kernel/linux-headers: 5.13::gentoo (virtual/os-headers)
sys-libs/glibc:           2.33-r1::gentoo

    location: /var/db/repos/gentoo
    sync-type: rsync
    sync-uri: rsync://
    priority: -1000
    sync-rsync-verify-jobs: 1
    sync-rsync-extra-opts: --exclude ChangeLog* --delete-excluded
    sync-rsync-verify-max-age: 24
    sync-rsync-verify-metamanifest: yes

    location: /var/lib/layman/brother-overlay
    sync-type: laymansync
    masters: gentoo
    priority: 50

CFLAGS="-O2 -pipe -march=haswell -fcommon"
CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0 /var/bind"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php7.3/ext-active/ /etc/php/apache2-php7.4/ext-active/ /etc/php/apache2-php8.0/ext-active/ /etc/php/cgi-php7.3/ext-active/ /etc/php/cgi-php7.4/ext-active/ /etc/php/cgi-php8.0/ext-active/ /etc/php/cli-php7.3/ext-active/ /etc/php/cli-php7.4/ext-active/ /etc/php/cli-php8.0/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-O2 -pipe -march=haswell -fcommon"
EMERGE_DEFAULT_OPTS="--keep-going --with-bdeps=y --backtrack=15"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs cgroup 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 sfperms splitdebug unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS=" rsync://"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,-O1,--hash-style=gnu,--enable-new-dtags"
LINGUAS="en en_US"
MAKEOPTS="-j5 -l6"
PORTAGE_RSYNC_EXTRA_OPTS="--exclude ChangeLog* --delete-excluded"
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"
USE="X a52 aac aacplus aacs aalib acl adns aesicm aften aio alaw alsa amd64 amr ao archive ares aspell avahi avresample avx bash-completion bcmath binfilter bluray bzip2 cacert cairo calendar caps cdda cgi cgroup cli community corefonts cron crypt cscope cups curl daap dane dav1d dbi dbus dirac dlna dri drm dvb dvbcsa dvben50221 dvd ecwj2k egl elogind enca encode examples exif exit exiv2 extraengine faac faad fdk ffmpeg ffmpegthumbnailer fftw firmware flac fontconfig fontforge foomaticdb fortran fping fpm fpx g722 g729 gbm gcrypt gd gdbm geoip geos gif gimp git glamor glib gml gmp gmplayer gnome-keyring gnuplot gnutls gpg gphoto2 gps gs gsm gtk gtk3 gui hardened harfbuzz hddtemp hdf hdf5 hdri highlight http http2 hwdb iconv icu id3tag ilbc imagemagick imap infinality inifile inotify introspection ipmi iproute2 ipv6 jack java javascript jbig jce jemalloc jpeg jpeg2k json lcms libass libedit libextractor libglvnd liblockfile libnotify libsamplerate libsecret libsoxr libtirpc lmdb lto lxc lz4 lzma lzo mad magic managesieve matroska mbox memcached mhash mjpeg mmap mmx mmxext mng mp3 mp4 mpeg mtp multilib mysql ncurses netcdf netlink network nfs nfsv4 nfsv41 nginx nodrm nptl nsplugin offensive ogdi ogg openal openexr opengl openmp openssl openvg opus osmesa pam pango pcap pch pcntl pcre pdf pdfimport pdo pgo pkcs7 plotutils plugins png policykit postproc ppds printsupport pth pulseaudio python q32 q8 qt4 qt5 rar raw readline realtime rle romio rpc rpz rrl rtmp scanner schroedinger scrypt sctp seccomp server sharedmem slp smi smime smp sndfile snmp sockets spamassassin speex spell sphinx split-usr sqlite sqlite3 sse sse2 sse3 sse4_1 ssh ssl ssse3 stats subtitles svg syslog szip t1lib taglib tcpd theora thin-splines threads threadsafe thumbnail tiff tk tokudb tools truetype twolame udev uefi ulaw unbound unicode upcall update_drivedb urandom usb utils v4l2 vaapi vhosts vim-syntax vlc vorbis vorbix vpx wav wavpack webkit webkit2 webp wg-quick widgets wikipedia winbind wmf x264 xattr xcb xface xine xinerama xml xmp xmpp xorg xpm xslt xvfb xvid xz zeroconf zip zlib zstd" ABI_X86="64" ADA_TARGET="gnat_2018" 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="actions alias auth_basic authn_alias authn_anon authn_core authn_dbm authn_file authz_core authz_dbm authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir env expires ext_filter file_cache filter headers include info log_config logio mime mime_magic negotiation rewrite setenvif socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias http2 proxy proxy_fcgi" APACHE2_MPMS="worker" 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 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" INPUT_DEVICES="libinput" KERNEL="linux" L10N="en en-US" 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" NGINX_MODULES_HTTP="auth_pam mp4 access auth_basic autoindex browser charset empty_gif fastcgi geo grpc gzip limit_conn limit_req map memcached mirror proxy referer rewrite scgi split_clients ssi upstream_hash upstream_ip_hash upstream_keepalive upstream_least_conn upstream_zone userid uwsgi" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-3 php7-4" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_9" PYTHON_TARGETS="python3_9 python3_8" RUBY_TARGETS="ruby26 ruby27" USERLAND="GNU" VIDEO_CARDS="vesa" VOICEMAIL_STORAGE="file imap" 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"

                        Package Settings

sci-libs/gdal-3.2.2::gentoo was built with the following:
USE="aux-xml curl geos gif gml hdf5 java jpeg jpeg2k lzma mysql netcdf ogdi pdf png python sqlite threads webp zstd -armadillo -debug (-doc) -fits (-mdb) -odbc -opencl -oracle -perl -postgres -spatialite -xls" ABI_X86="(64)" CPU_FLAGS_X86="avx sse ssse3" PYTHON_TARGETS="python3_8 python3_9"
CFLAGS="-O2 -pipe -march=haswell -fcommon -I/usr/include/tirpc"
CXXFLAGS="-O2 -pipe -march=haswell -fcommon -I/usr/include/tirpc"

spidey ~ # emerge -pqv '=sci-libs/gdal-3.2.2::gentoo'
[ebuild   R   ] sci-libs/gdal-3.2.2  USE="aux-xml curl geos gif gml hdf5 java jpeg jpeg2k lzma mysql netcdf ogdi pdf png python sqlite threads webp zstd -armadillo -debug (-doc) -fits (-mdb) -odbc -opencl -oracle -perl -postgres -spatialite -xls" CPU_FLAGS_X86="avx sse ssse3" PYTHON_TARGETS="python3_8 python3_9"
Comment 1 Gary E. Miller 2021-07-28 20:32:45 UTC
Created attachment 727557 [details]
Build Log gzipped

Build Log gzipped
Comment 2 Sam James archtester gentoo-dev Security 2021-08-01 05:50:11 UTC
For now, turn off USE=java.
Comment 3 Volkmar W. Pogatzki 2021-08-01 08:13:21 UTC
Looks similar to bug #776910
Adding the author of
Comment 4 Sam James archtester gentoo-dev Security 2021-08-01 08:14:50 UTC Comment hidden (obsolete)
Comment 5 Sam James archtester gentoo-dev Security 2021-08-01 08:14:57 UTC
(In reply to Volkmar W. Pogatzki from comment #3)
> Looks similar to bug #776910
> Adding the author of
> ?id=16b7cf5e72b6255564733656746c76421b776b0a

Good spot!
Comment 6 "Leo" Y. Liao 2021-08-01 15:22:29 UTC
(In reply to Volkmar W. Pogatzki from comment #3)
> Looks similar to bug #776910
> Adding the author of
> ?id=16b7cf5e72b6255564733656746c76421b776b0a

Thanks! Will take a look when I have time
Comment 7 "Leo" Y. Liao 2021-08-02 16:47:05 UTC
I was not able to reproduce this bug, unless I had deliberately unset my system-vm preference.

Could you run 'eselect java-vm show' and ensure a system-vm has been selected?