| Summary: | sci-libs/proj-6.0.0 - org_proj4_PJ.h:2:10: fatal error: jni.h: No such file or directory | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Juergen Rose <rose> |
| Component: | Current packages | Assignee: | Sci-geo Project <sci-geosciences> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | CC: | aklhfex, atoth, conikost, francoisvalenduc, jstein, kripton, leonchik1976, lssndrbarbieri, M4rkusXXL, mark+gentoobugs, mmokrejs, randy-andy-, sandyvujakovicj, tb |
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Attachments: |
build.log
proj-6.0.0-r2.ebuild |
||
|
Description
Juergen Rose
2019-05-06 20:47:18 UTC
Found the reason: In the ebuild, change the line append-cflags "$(java-pkg_get-jni-cflags)" to append-cxxflags "$(java-pkg_get-jni-cflags)" (In reply to Bernd Feige from comment #1) > Found the reason: In the ebuild, change the line > append-cflags "$(java-pkg_get-jni-cflags)" > to > append-cxxflags "$(java-pkg_get-jni-cflags)" Works for me! Thanks! Which JDK are you using? I thought this now needed JDK 9: https://github.com/OSGeo/proj.4/pull/969 !!! All ebuilds that could satisfy "=virtual/jdk-11" have been masked. !!! One of the following masked packages is required to complete your request: - virtual/jdk-11::gentoo (masked by: package.mask) /var/db/repos/gentoo/profiles/package.mask: # James Le Cuirot <chewi@gentoo.org> (17 Dec 2017) # Java 9+ is not yet fully supported on Gentoo. Packages cannot depend # on it so these virtuals are not yet required. If you wish to use # Java 9+ then install oracle-(jdk|jre)-bin or openjdk(-bin) directly. Also does it actually install any Java bindings? I did get it working for proj 5.0.1 but needed to add the use of java-ant-2 eclass. (In reply to Chris Mayo from comment #3) > Which JDK are you using? dev-java/oracle-jdk-bin-1.8.0.202 here, virtual/jdk-1.8.0-r4. > I thought this now needed JDK 9: > https://github.com/OSGeo/proj.4/pull/969 Can't find the requirement in this request but it's written in proj-6.0.0/jniwrap/Readme.md. > !!! All ebuilds that could satisfy "=virtual/jdk-11" have been masked. > !!! One of the following masked packages is required to complete your > request: > - virtual/jdk-11::gentoo (masked by: package.mask) > ... > Also does it actually install any Java bindings? I did get it working for > proj 5.0.1 but needed to add the use of java-ant-2 eclass. No, only the main compilation with --with-jni is fixed by the suggested ebuild change but proj.jar is still not installed. Probably because the ant build is not started. (In reply to Bernd Feige from comment #1) > Found the reason: In the ebuild, change the line > append-cflags "$(java-pkg_get-jni-cflags)" > to > append-cxxflags "$(java-pkg_get-jni-cflags)" Works for me as well. (In reply to Juergen Rose from comment #5) > > Works for me as well. USE="-java" would be simpler and get the same files installed ;) N.B. the data files from DATUMGRID aren't being installed, they need unpacking in the data subdirectory. I've create a PR without Java and fixed data files plus some other fixes here: https://github.com/gentoo/gentoo/pull/11963 Created attachment 575978 [details]
proj-6.0.0-r2.ebuild
Attached is an ebuild which is my -r1 with added Java code taken from my previous 5.0.1 ebuild.
repoman blocks this from being added to the repository because of JDK 11. Hence my -r1 PR.
I haven't tested this with USE="java", it may well need the
append-cflags "$(java-pkg_get-jni-cflags)"
to
append-cxxflags "$(java-pkg_get-jni-cflags)"
(In reply to Chris Mayo from comment #3) > Which JDK are you using? > > I thought this now needed JDK 9: > https://github.com/OSGeo/proj.4/pull/969 > > !!! All ebuilds that could satisfy "=virtual/jdk-11" have been masked. > !!! One of the following masked packages is required to complete your > request: > - virtual/jdk-11::gentoo (masked by: package.mask) > /var/db/repos/gentoo/profiles/package.mask: > # James Le Cuirot <chewi@gentoo.org> (17 Dec 2017) > # Java 9+ is not yet fully supported on Gentoo. Packages cannot depend > # on it so these virtuals are not yet required. If you wish to use > # Java 9+ then install oracle-(jdk|jre)-bin or openjdk(-bin) directly. > > > Also does it actually install any Java bindings? I did get it working for > proj 5.0.1 but needed to add the use of java-ant-2 eclass. root@lynx:/home/rose(110)# qlist -Iv jdk virtual/jdk-1.8.0-r4 And: dev-java/icedtea-bin-3.12.0 Same problem here.
# emerge --info '=sci-libs/proj-6.0.0::gentoo'
Portage 2.3.66 (python 2.7.16-final-0, default/linux/amd64/17.0, gcc-9.1.0, glibc-2.29-r2, 5.0.18-default-pciehp x86_64)
=================================================================
System Settings
=================================================================
System uname: Linux-5.0.18-default-pciehp-x86_64-Intel-R-_Core-TM-_i7-2640M_CPU_@_2.80GHz-with-gentoo-2.6
KiB Mem: 16363428 total, 5164368 free
KiB Swap: 26853460 total, 26853460 free
Timestamp of repository gentoo: Sat, 29 Jun 2019 08:30:02 +0000
Head commit of repository gentoo: 4e2f9f3967bb4df72362aabc9bc6ba06cb72e876
sh bash 5.0_p7
ld GNU ld (Gentoo 2.30 p5) 2.30.0
app-shells/bash: 5.0_p7::gentoo
dev-java/java-config: 2.2.0-r4::gentoo
dev-lang/perl: 5.28.9999::gentoo
dev-lang/python: 2.7.16-r101::stefantalpalaru, 3.5.6::gentoo, 3.6.8::gentoo, 3.7.3::gentoo
dev-util/cmake: 3.14.0::gentoo
dev-util/pkgconfig: 0.29.2::gentoo
sys-apps/baselayout: 2.6-r1::gentoo
sys-apps/openrc: 0.41.2::gentoo
sys-apps/sandbox: 2.17::gentoo
sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r4::gentoo
sys-devel/automake: 1.11.6-r2::gentoo, 1.12.6-r1::gentoo, 1.13.4-r2::gentoo, 1.14.1-r1::gentoo, 1.15.1-r2::gentoo, 1.16.1-r1::gentoo
sys-devel/binutils: 2.30-r4::gentoo, 2.31.1-r4::gentoo, 2.32-r1::gentoo
sys-devel/gcc: 5.5.0::gentoo, 6.5.0::gentoo, 7.3.0-r6::gentoo, 8.3.0-r1::gentoo, 9.1.0::gentoo
sys-devel/gcc-config: 2.0::gentoo
sys-devel/libtool: 2.4.6-r5::gentoo
sys-devel/make: 4.2.1-r4::gentoo
sys-kernel/linux-headers: 5.1::gentoo (virtual/os-headers)
sys-libs/glibc: 2.29-r2::gentoo
Repositories:
gentoo
location: /scratch/usr/portage
sync-type: rsync
sync-uri: rsync://rsync.gentoo.org/gentoo-portage
priority: -1000
sync-rsync-verify-jobs: 1
sync-rsync-verify-metamanifest: yes
sync-rsync-extra-opts:
sync-rsync-verify-max-age: 24
science
location: /scratch/mmokrejs/proj/sci
masters: gentoo
priority: 0
layman
location: /var/lib/layman
masters: gentoo
priority: 1
x-portage
location: /usr/local/portage
masters: gentoo
priority: 2
haskell
location: /var/lib/layman/haskell
masters: gentoo
priority: 50
stefantalpalaru
location: /var/lib/layman/stefantalpalaru
masters: gentoo science
priority: 50
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="@FREE dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE IBM-J1.6 Nero-EULA-US AdobeFlash-10.3 AdobeFlash-11.x OPERA-2014 RAR Intel-SDP intel-ucode Skype-TOS vmware linux-firmware fasta vienna-rna unafold GRL MSttfEULA hplip-plugin meme mRNAmarkup ApE ICS ipw3945 finchtv modeller gmap master-pdf-editor abyss swiss-prot Aladdin AVASYS truecrypt-3.0 pyvcf Non-profit-OSL-3.0 estscan bcca_2010 oncotator Adobe blat staden CeCILL-1.1 phrap STRIDE cctbx-2.0 bh-luxi ARIADNE unRAR all-rights-reserved trf annovar_personal_only stampy-academic BSD-BroadInstitute UPennState freedist free-noncomm blasr sun-jlfgr FLI-Jena PSTT netperf sun-jsr67 xv vim.org OSGi-Specification-2.0 colt"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.2/conf /usr/share/maven-bin-3.3/conf /usr/share/maven-bin-3.6/conf /var/bind /var/lib/hsqldb /var/spool/torque"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.6/ext-active/ /etc/php/apache2-php7.1/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cgi-php7.1/ext-active/ /etc/php/cli-php5.6/ext-active/ /etc/php/cli-php7.1/ext-active/ /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 /etc/vmware-installer"
CXXFLAGS="-O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize"
DISTDIR="/scratch/usr/portage/distfiles"
ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN 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-docompress binpkg-dostrip binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news nostrip parallel-fetch pid-sandbox preserve-libs protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://gentoo.wheel.sk/ 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"
LINGUAS="en_US en_GB en cs"
MAKEOPTS="-j2"
PKGDIR="/var/cache/binpkgs"
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="/scratch/var/tmp"
USE="R X acpi alsa amd64 amr apache apache2 asm avx bcache berkdb bluetooth boost bzip2 cairo cgi cli coin connection-sharing consolekit cracklib crypt cryptlib cryptsetup cups cxx dbus device-mapper dhcp directfb dri drm dvd emboss encode fax fbcon ffmpeg flac fontconfig fortran fuse gbm gcrypt gd gdbm geoip geolocation gimp glib glpk gmp gpm gps gtk hal hpijs hwdb iconv id3tag imaging innodb inotify iproute2 java javafx javascript jce jpeg jpg js jscript keymap kmod ladspa lame lapack laptop lcms libev libevent libnotify libtirpc lm_sensors mad matroska mmx modemmanager mp3 multicore multilib multimedia mysql ncurses netpbm networkmanager nfs nls nptl nptlonly nscd ntfs ntfsdecrypt ntfsprogs objc ocr ogg opengl openmp openssl opus pam parport pcre pcre16 pdf pdfimport pdl perl php pkcs11 plplot png policykit polkit postproc postscript ppds ppp pppd pptx python qt3support qt4 qt5 readline rendering resolvconf samba scanner sctp seccomp server session sha512 slideshow smartcard sna sndfile sparsehash sqlite sse sse2 sse3 sse4_1 sse4_2 ssh ssh-agent ssl sslv2 sslv3 ssse3 startup-notification suexec svg syslog tcl tcpd tevent threads tiff tk truetype twolame udev unicode upower usb v4l v4l2 vim-syntax vnc wavpack wifi x11 xattr xcb xcomposite xft xinerama xml xorg xrandr xv xvid zlib" ABI_X86="64 32" 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="alias authz_host auth_basic auth_digest cgi cgid deflate dir env filter include info mem_cache mime mime_magic negotiation remoteip setenvif status userdir vhost_alias rewrite usertrack cache file_cache disk_cache charset_lite log_config log_forensic" CALLIGRA_FEATURES="karbon sheets words" 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="aivdm ashtech earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 navcom ntrip oceanserver oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 tnt tripmate tsip ublox fury geostar nmea0183 nmea2000 passthrough" GRUB_PLATFORMS="pc" INPUT_DEVICES="libinput keyboard mouse" KERNEL="linux" L10N="en-US en en-GB cs" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" NETBEANS_MODULES="apisupport cnd groovy gsf harness ide identity j2ee java mobility nb php profiler soa visualweb webcommon websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_6 python3_7" RUBY_TARGETS="ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="vesa vmware fbdev intel i915 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
# qlist -Iv jdk
dev-java/htsjdk-2.3.0
dev-java/oracle-jdk-bin-1.7.0.40
dev-java/oracle-jdk-bin-1.8.0.202
dev-java/oracle-jdk-bin-11.0.2
dev-java/oracle-jdk-bin-9.0.4-r2
java-virtuals/jdk-with-com-sun-20111111-r3
virtual/jdk-1.6.0-r2
virtual/jdk-1.7.0-r2
virtual/jdk-1.8.0-r4
#
# eselect java-vm list
Available Java Virtual Machines:
[1] oracle-jdk-bin-1.7
[2] oracle-jdk-bin-1.8 system-vm
[3] oracle-jre-bin-1.7
[4] oracle-jre-bin-1.8
#
(In reply to Bernd Feige from comment #1)
> Found the reason: In the ebuild, change the line
> append-cflags "$(java-pkg_get-jni-cflags)"
> to
> append-cxxflags "$(java-pkg_get-jni-cflags)"
Works for me too! Thanks!
I hit this on yet another host. I would like to know the location of ebuild, I couldn't find this file? thanks! JNI is hard-disabled for some time in ebuilds and now dropped in upstream >=7.0.0. |
