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astaines
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Joined: 18 Apr 2004
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PostPosted: Sat Feb 09, 2013 7:58 pm    Post subject: [[SOLVED]] Making rstudio work on gentoo - help!! Reply with quote

Rstudio http://www.rstudio.com/ is a really nice GUI for R http://www.r-project.org/, the preeminent statistical programming language. It is surprisingly hard to build from source, unless you really know what you are doing, which I do not. Fortunately some kind, but seemingly anonymous, person has created an ebuild for it on the Gentoo science overlay http://euscan.iksaif.net/package/sci-mathematics/rstudio/ . Whoever you are - thank you!!

Running the ebuild I get problems.

Using the latest sci-mathematics/rstudio ebuild from the Gentoo science overlay, I try to emerge rstudio.

The build process fails as follows


During the cmake configuration phase this appears

Code:
XXXXXXXXXXXXXX
 Could not find libR shared library.
-- Found LibR: WARNING: ignoring environment value of R_HOME
/usr/lib/R 
-- Found R: WARNING: ignoring environment value of R_HOME
/usr/lib/R
XXXXXXXXXXXXXX


The rest of the configuration output is unremarkable.
The next interesting piece is
Code:
XXXXXXXXXXXXXXXXX

>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-mathematics/rstudio-0.97.237/work/rstudio-0.97.237 ...
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-mathematics/rstudio-0.97.237/work/rstudio-0.97.237_build"
make -j2 VERBOSE=1
/usr/bin/cmake -H/var/tmp/portage/sci-mathematics/rstudio-0.97.237/work/rstudio-0.97.237 -B/var/tmp/portage/sci-mathematics/rstudio-0.97.237/work/rstudio-0.97.237_build --check-build-system CMakeFiles/Makefile.cmake 0
CMake Error: Parse error in cache file /var/tmp/portage/sci-mathematics/rstudio-0.97.237/work/rstudio-0.97.237_build/CMakeCache.txt. Offending entry: /usr/share/doc/R-2.15.2-r1
CMake Error: Parse error in cache file /var/tmp/portage/sci-mathematics/rstudio-0.97.237/work/rstudio-0.97.237_build/CMakeCache.txt. Offending entry: /usr/lib/R
CMake Error: Parse error in cache file /var/tmp/portage/sci-mathematics/rstudio-0.97.237/work/rstudio-0.97.237_build/CMakeCache.txt. Offending entry: /usr/lib/R/include
Re-run cmake error reading : CMakeFiles/Makefile.cmake
-- Boost version: 1.52.0
-- Found the following Boost libraries:
--   date_time
--   filesystem
--   iostreams
--   program_options
--   regex
--   signals
--   system
--   thread
--   chrono
-- Could not find libR shared library.
-- Found LibR: WARNING: ignoring environment value of R_HOME 
-- Found R: WARNING: ignoring environment value of R_HOME
-- <<< Gentoo configuration >>>
Build type      Gentoo
Install path    /usr
Compiler flags:
C               -O2 -march=i686 -pipe
C++             -O2 -march=i686 -pipe
Linker flags:
Executable       -Wl,-O1 -Wl,--as-needed
Module           -Wl,-O1 -Wl,--as-needed
Shared           -Wl,-O1 -Wl,--as-needed

-- Configuring incomplete, errors occurred!
make: *** [cmake_check_build_system] Error 1
XXXXXXXXXXXXXXXX

I tried reinstalling R 2.15.2 with the static-libs USE flag, to see if that makes the shared library, which did not help.

Following the lead of some other posts on the Rstudio forums -

Code:
HP astaines # which R
/usr/bin/R

HP astaines # cat /usr/bin/R
#!/bin/sh
# Shell wrapper for R executable.

R_HOME_DIR=/usr/lib/R

I am fairly sure that this is an RStudio issue, not a gentoo issue as such, but I will crosspost to here to seek advice.

All help gratefully accepted,
Anthony Staines

Code:
HP ~ # emerge --info
Portage 2.1.11.31 (default/linux/x86/10.0/desktop/kde, gcc-4.6.3, glibc-2.15-r3, 3.3.8-gentoo i686)
=================================================================
System uname: Linux-3.3.8-gentoo-i686-Intel-R-_Core-TM-2_Duo_CPU_P8700_@_2.53GHz-with-gentoo-2.1
Timestamp of tree: Thu, 07 Feb 2013 21:00:01 +0000
ld GNU ld (GNU Binutils) 2.22
app-shells/bash:          4.2_p37
dev-java/java-config:     2.1.12-r1
dev-lang/python:          2.7.3-r2, 3.2.3
dev-util/cmake:           2.8.9
dev-util/pkgconfig:       0.28
sys-apps/baselayout:      2.1-r1
sys-apps/openrc:          0.11.8
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.10.3, 1.11.6
sys-devel/binutils:       2.22-r1
sys-devel/gcc:            4.6.3
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.6 (virtual/os-headers)
sys-libs/glibc:           2.15-r3
Repositories: gentoo dberkholz sabayon zugaina science x-portage x-g-ctan
ACCEPT_KEYWORDS="x86"
ACCEPT_LICENSE="* -@EULA"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -march=i686 -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb"
CONFIG_PROTECT_MASK="${EPREFIX}/etc/gconf /etc/ca-certificates.conf /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="-O2 -march=i686 -pipe"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -march=i686 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS="-O2 -march=i686 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_IE.UTF8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j2"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/dberkholz /var/lib/layman/sabayon /var/lib/layman/zugaina /var/lib/layman/science /usr/local/portage /usr/local/portage/g-ctan"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X a52 aac acl acpi alsa berkdb bluetooth branding bzip2 cairo cdda cdr cleartype cli consolekit corefonts cracklib crypt cups cxx dbus declarative dri dts dvd dvdr emboss encode exif fam firefox flac fortran gdbm gif gpm iconv ipv6 jack jpeg kde kipi lcms ldap libnotify mad mng modules mp3 mp4 mpeg mudflap ncurses nls nptl ogg opengl openmp pam pango pcre pdf phonon plasma png policykit ppds pulseaudio qt3support qt4 readline sdl semantic-desktop session spell ssl startup-notification svg tcpd tiff truetype type1 udev udisks unicode upower usb vorbis wxwidgets x264 x86 xcb xcomposite xinerama xml xscreensaver xv xvid zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" 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" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" FOO2ZJS_DEVICES="hp1022" 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 ubx" INPUT_DEVICES="evdev keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en_GB en" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="intel vesa fbdev" 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:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON


Last edited by astaines on Sun Feb 17, 2013 7:59 pm; edited 2 times in total
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slackline
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PostPosted: Sat Feb 16, 2013 7:32 am    Post subject: Re: Making rstudio work on gentoo - help!! Reply with quote

It would really help if you used the BBCode to mark-up your posts (the buttons above the box where you type/paste).

astaines wrote:


During the cmake configuration phase this appears

Code:

 Could not find libR shared library.
-- Found LibR: WARNING: ignoring environment value of R_HOME
/usr/lib/R 
-- Found R: WARNING: ignoring environment value of R_HOME
/usr/lib/R



You don't indicate which ebuild of R you are using, but there have been two recent releases, one of which (dev-lang/R-2.15.2-r2) addresses issues introduced in the previous (dev-lang/R-2.15.2-r1) about R_HOME.

From the ChangeLog...

Code:

$ head /usr/portage/dev-lang/R/ChangeLog
# ChangeLog for dev-lang/R
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/ChangeLog,v 1.210 2013/02/13 19:16:31 calchan Exp $

*R-2.15.2-r2 (13 Feb 2013)

  13 Feb 2013; Denis Dupeyron <calchan@gentoo.org> -R-2.15.2-r1.ebuild,
  +R-2.15.2-r2.ebuild:
  Fix R_HOME warning when R is started up.


So try syncing portage, re-emerging R and then emerging RStudio, I've got the latest ebuild from the Science overlay installed and it runs fine...

Code:

$ eix rstudio
[I] sci-mathematics/rstudio [1]
     Available versions:  (~)0.96.316 (~)0.96.331 (~)0.97.237 {+desktop server test ELIBC="FreeBSD"}
     Installed versions:  0.97.237(12:42:09 28/01/13)(desktop -server -test ELIBC="-FreeBSD")
     Homepage:            http://www.rstudio.org
     Description:         IDE for the R language

[1] "science" /var/lib/layman/science


slack
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PostPosted: Sat Feb 16, 2013 6:10 pm    Post subject: Reply with quote

dev-lang/R is in gentoos official repository. i hate overlays.... so ill craft a from scratch compile instruction 4 u.....

https://github.com/rstudio/rstudio/tarball/v0.97.318 is the source tarball im nabbing.....

Code:

cd Downloads
tar -xf rstudio-rstudio-v0.97.318-0-gd528686.tar.gz
cd rstudio-rstudio-d528686/
mkdir build
cd build


this is the tricky part.... cmake

Code:

ccmake ..


press c to configure

(e to exit errors)

scroll down to "/usr/local" and hit enter... change it to just "/usr"

press c again to configure, then g to generate, then q to quit



annnndddd boostdir not found fatal critical error, find me the boostdir and it should compile and build and install and run just fine =D
_________________
cat /etc/*-release
Funtoo Linux - baselayout 2.2.0
consider this warning no. 1
https://wiki.gentoo.org/index.php?title=Special:Contributions/666threesixes666&offset=&limit=500&target=666threesixes666
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PostPosted: Sun Feb 17, 2013 9:00 am    Post subject: Reply with quote

666threesixes666 wrote:
dev-lang/R is in gentoos official repository. i hate overlays.... so ill craft a from scratch compile instruction 4 u.....


Useful to know (I used to do all that stuff when I used Slackware years ago), but kind of defeats the object of using a package management system which includes the overlays because if just one of the DEPEND or RDEPEND's aren't already installed/pulled by another package then they'll have to be installed too, either by hand or via portage, then you end up cluttering /var/lib/portage/world up with libraries/dependencies that have been explicitly emerged rather than pulled in as dependencies.
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PostPosted: Sun Feb 17, 2013 4:51 pm    Post subject: Reply with quote

im looking at it as linux from scratch with a bit of automation to speed things up, not week long gnome compile..... i learned slackware before i learned linux from scratch, then migrated to gentoo for automation on huge packages like KDE.... a little bit of ubuntu between that.... i let portage do the heavy lifting, then the little stuff i do on my own. boost dirs just a tiny detail holding up the entire process..... i dont like overlays calling for outdated and wrong packages....

for me

emerge-webrsync

then

emerge rstudio

does the trick.... latest portage snapshot rstudio ebuild works for me as of june 24 2013
_________________
cat /etc/*-release
Funtoo Linux - baselayout 2.2.0
consider this warning no. 1
https://wiki.gentoo.org/index.php?title=Special:Contributions/666threesixes666&offset=&limit=500&target=666threesixes666


Last edited by 666threesixes666 on Mon Jun 24, 2013 6:07 am; edited 1 time in total
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astaines
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Joined: 18 Apr 2004
Posts: 84
Location: Ireland

PostPosted: Sun Feb 17, 2013 7:58 pm    Post subject: Stacklines suggestion worked perfectly! Reply with quote

I re-emerged R as suggested, and R-Studio is now running perfectly,
Many thanks,
Anthony
PS - I also used the BB buttons!
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