Installation of RStudio fails

Hello All,

I am trying to install RStudio into the current and up-to-date Calculate Linux (LXQt). I am getting the following error:

[ 47%] Generating moc_DesktopNetworkReply.cxx
cd /var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/work/rstudio-0.98.490_build/src/cpp/desktop && /usr/lib64/qt4/bin/moc @/var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/work/rstudio-0.98.490_build/src/cpp/desktop/moc_DesktopNetworkReply.cxx_parameters
usr/include/boost/type_traits/detail/has_binary_operator.hp:50: Parse error at "BOOST_JOIN"
make[2]: *** [src/cpp/desktop/CMakeFiles/rstudio.dir/build.make:133: src/cpp/desktop/moc_DesktopNetworkReply.cxx] Error 1
make[2]: Leaving directory '/var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/work/rstudio-0.98.490_build'
make[1]: *** [CMakeFiles/Makefile2:586: src/cpp/desktop/CMakeFiles/rstudio.dir/all] Error 2
make[1]: Leaving directory '/var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/work/rstudio-0.98.490_build'
make: *** [Makefile:150: all] Error 2
 * ERROR: sci-mathematics/rstudio-0.98.490-r1::gentoo failed (compile phase):
 *   emake failed

Various logs copied below:

 # emerge --info '=sci-mathematics/rstudio-0.98.490-r1::gentoo'

Portage 2.3.3 (python 3.4.5-final-0, !../../var/lib/layman/distros/profiles/CLDL/amd64, gcc-4.9.4, glibc-2.23-r3, 4.9.17-calculate x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.9.17-calculate-x86_64-Intel-R-_Core-TM-_i5-3320M_CPU_@_2.60GHz-with-gentoo-17
KiB Mem:     6106668 total,   2549404 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Thu, 13 Apr 2017 11:30:01 +0000
sh bash 4.3_p48-r1
ld GNU ld (Gentoo 2.26.1 p1.0) 2.26.1
app-shells/bash:          4.3_p48-r1::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.22.3_rc4::gentoo
dev-lang/python:          2.7.12::gentoo, 3.4.5::gentoo
dev-util/cmake:           3.7.2::gentoo
dev-util/pkgconfig:       0.28-r2::gentoo
sys-apps/baselayout:      2.3::gentoo
sys-apps/openrc:          0.23.2::gentoo
sys-apps/sandbox:         2.10-r3::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69::gentoo
sys-devel/automake:       1.11.6-r1::gentoo, 1.15::gentoo
sys-devel/binutils:       2.26.1::gentoo
sys-devel/gcc:            4.9.4::gentoo
sys-devel/gcc-config:     1.7.3::gentoo
sys-devel/libtool:        2.4.6-r3::gentoo
sys-devel/make:           4.2.1::gentoo
sys-kernel/linux-headers: 4.9::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r3::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: git
    sync-uri: git://git.calculate-linux.org/repo/gentoo.git
    priority: -1000

calculate
    location: /var/lib/layman/calculate
    sync-type: laymansync
    sync-uri: git://github.com/calculatelinux/calculate.git
    masters: gentoo
    priority: 50

distros
    location: /var/lib/layman/distros
    sync-type: laymansync
    sync-uri: git://github.com/calculatelinux/distros.git
    masters: calculate gentoo
    priority: 50

Installed sets: @autodeps, @custom
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -march=x86-64 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /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/splash /etc/terminfo"
CXXFLAGS="-O2 -march=x86-64 -pipe"
DISTDIR="/var/calculate/remote/distfiles"
EMERGE_DEFAULT_OPTS=" --binpkg-changed-deps=n --quiet-build=n --binpkg-respect-use=y --jobs=4"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles getbinpkg merge-sync news parallel-fetch parallel-install preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://mirror.yandex.ru/gentoo-distfiles http://distfiles.gentoo.org"
INSTALL_MASK="/etc/systemd /usr/lib*/systemd"
LANG="en_AU.utf8"
LDFLAGS="-Wl,--as-needed"
MAKEOPTS="-j1"
PKGDIR="/var/calculate/packages/x86_64"
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/calculate/tmp"
USE="3dnow 3dnowext X a52 aac acl acpi aes alsa amd64 amr audiofile avi avx berkdb bittorrent bluetooth box bzip2 cairo caps cdda cddb cdparanoia cdr cgroups chm cli consolekit cpudetection cracklib crypt css cue cups cxx dbus dftk djvu dri dv dvd dvdr dvdread ebook encode exif faac fexif ffmpeg flac flash fma3 fma4 foomaticdb fortran ftp gd gdbm gif gphoto2 gpm gstreamer gtk hunspell iconv id3tag idn ieee1394 imagemagick imap introspection ios ipod ipv6 irc jabber jpeg jpeg2k libnotify libwww lm_sensors logrotate lzo mad matroska mikmod mimap mmx mmxext modules mp3 mpeg mplayer multilib musepack ncurses networkmanager nfs nls nptl nsplugin ogg oggvorbis openal opencore-amr openexr opengl openmp opus oscar padlock pam pcre pdf pm-utils png policykit popcnt portaudio ppp pulseaudio qt3support quicktime raw rdesktop readline real samba sasl scanner sdl seccomp semantic-desktop session smp smtp speex spell srt sse sse2 sse3 sse4_1 sse4_2 sse4a ssl ssse3 svg taglib tcpd tga theora threads tiff truetype udev udisks unicode upnp upower usb userlocales v4l v4l2 vaapi vcd vdpau vhosts vorbis vpx wavpack webkit webp wimax win32codecs wmf wxwindows x264 x265 xanim xattr xcomposite xinerama xmp xop xv xvid xvmc 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="*" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="3dnow 3dnowext mmx sse sse2 * mmxext" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" GRUB_PLATFORMS="efi-64 efi-32 pc" INPUT_DEVICES="libinput evdev mutouch synaptics keyboard mouse" KERNEL="linux" L10N="en be be_BY bg bg_BG bs cs cs_CZ da da_DK de de_DE en_GB es es_AR es_ES es_LA es_UY es_VE et et_EE fi fi_FI fr fr_CA fr_FR hr hr_HR hu hu_HU it it_IT kk kk_KZ lt lt_LT lv lv_LV nl nl_NL pl pl_PL pt pt_BR pt_PT ro ro_RO ru ru_RU sk sk_SK sl sl_SI sq sq_AL sr sr_RS sv sv_SE uk uk_UA de-1901 en-GB pt-BR" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en be be_BY bg bg_BG bs cs cs_CZ da da_DK de de_DE en_GB es es_AR es_ES es_LA es_UY es_VE et et_EE fi fi_FI fr fr_CA fr_FR hr hr_HR hu hu_HU it it_IT kk kk_KZ lt lt_LT lv lv_LV nl nl_NL pl pl_PL pt pt_BR pt_PT ro ro_RO ru ru_RU sk sk_SK sl sl_SI sq sq_AL sr sr_RS sv sv_SE uk uk_UA" LIRC_DEVICES="devinput" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby21" THEMES="CLD" USERLAND="GNU" VIDEO_CARDS="amdgpu i915 i965 intel nouveau nv nvidia r100 r200 r300 r600 radeon radeonsi vesa via" 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, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

 # emerge -pqv '=sci-mathematics/rstudio-0.98.490-r1::gentoo'

Local copy of remote index is up-to-date and will be used.
[ebuild  N    ] sci-mathematics/rstudio-0.98.490-r1 

 * IMPORTANT: 1 news items need reading for repository 'gentoo'.
 * Use eselect news read to view new items.

 # cat /var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/temp/build.log

....

[ 46%] Generating moc_DesktopGwtWindow.cxx
cd /var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/work/rstudio-0.98.490_build/src/cpp/desktop && /usr/lib64/qt4/bin/moc @/var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/work/rstudio-0.98.490_build/src/cpp/desktop/moc_DesktopGwtWindow.cxx_parameters
[ 46%] Generating moc_DesktopInputDialog.cxx
cd /var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/work/rstudio-0.98.490_build/src/cpp/desktop && /usr/lib64/qt4/bin/moc @/var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/work/rstudio-0.98.490_build/src/cpp/desktop/moc_DesktopInputDialog.cxx_parameters
[ 46%] Generating moc_DesktopMainWindow.cxx
cd /var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/work/rstudio-0.98.490_build/src/cpp/desktop && /usr/lib64/qt4/bin/moc @/var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/work/rstudio-0.98.490_build/src/cpp/desktop/moc_DesktopMainWindow.cxx_parameters
[ 46%] Generating moc_DesktopMenuCallback.cxx
cd /var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/work/rstudio-0.98.490_build/src/cpp/desktop && /usr/lib64/qt4/bin/moc @/var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/work/rstudio-0.98.490_build/src/cpp/desktop/moc_DesktopMenuCallback.cxx_parameters
[ 47%] Generating moc_DesktopNetworkAccessManager.cxx
cd /var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/work/rstudio-0.98.490_build/src/cpp/desktop && /usr/lib64/qt4/bin/moc @/var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/work/rstudio-0.98.490_build/src/cpp/desktop/moc_DesktopNetworkAccessManager.cxx_parameters
[ 47%] Generating moc_DesktopNetworkReply.cxx
cd /var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/work/rstudio-0.98.490_build/src/cpp/desktop && /usr/lib64/qt4/bin/moc @/var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/work/rstudio-0.98.490_build/src/cpp/desktop/moc_DesktopNetworkReply.cxx_parameters
usr/include/boost/type_traits/detail/has_binary_operator.hp:50: Parse error at "BOOST_JOIN"
make[2]: *** [src/cpp/desktop/CMakeFiles/rstudio.dir/build.make:133: src/cpp/desktop/moc_DesktopNetworkReply.cxx] Error 1
make[2]: Leaving directory '/var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/work/rstudio-0.98.490_build'
make[1]: *** [CMakeFiles/Makefile2:586: src/cpp/desktop/CMakeFiles/rstudio.dir/all] Error 2
make[1]: Leaving directory '/var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/work/rstudio-0.98.490_build'
make: *** [Makefile:150: all] Error 2
 * ERROR: sci-mathematics/rstudio-0.98.490-r1::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-mathematics/rstudio-0.98.490-r1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-mathematics/rstudio-0.98.490-r1::gentoo'`.
 * The complete build log is located at '/var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/temp/environment'.
 * Working directory: '/var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/work/rstudio-0.98.490_build'
 * S: '/var/calculate/tmp/portage/sci-mathematics/rstudio-0.98.490-r1/work/rstudio-0.98.490'
!!! When you file a bug report, please include the following information:
GENTOO_VM=icedtea-bin-8  CLASSPATH="" JAVA_HOME="/opt/icedtea-bin-3.3.0"
JAVACFLAGS="-source 1.5 -target 1.5" COMPILER=""
and of course, the output of emerge --info =rstudio-0.98.490

Of course I could just use a vim/tmux environment, but I wanted to try RStudio with my students. Any help would be most welcome!

Thanks, Bill

Hi Bill,
Try to update and install the package now.

cl-upate
emerge sci-mathematics/rstudio

Thanks Alexander, that works now and RStudio is installed! Thank you for the great support, I am really enjoying using Calculate Linux, I have been using it for over a year on my second machine and I am just this week building it on my primary daily driver.

Now that RStudio installs, it pulls down over 100 Haskell packages as dependencies. This problem has been discussed before (eg. https://forums.gentoo.org/viewtopic-t-994886-start-0.html), it seems that support in RStudio for Rmarkdown requires app-text/pandoc and dev-haskell/pandoc* and these pull down most of Haskell. Not ideal, but nothing to do with Calculate Linux specifically of course! I am building an iso for my students using the Calculate Linux tools and I will include RStudio.

A further question: RStudio v0.98.490 did not have these Haskall dependencies. I tried to specify and fix this version by adding

=sci-mathematics/rstudio-0.98.490

to /etc/portage/package.mask/custom but this did not work, emerge still tries to install the latest version. What am I doing wrong here?

Thanks, and thanks again for your quick resolution of the initial problem,

Cheers, Bill

Hi Bill,
I also failed to compile RStudio v0.98.490. Unlike it, the more recent version is compiled without errors. I do not see any problems in additional packages. They are (now) binary and their availability does not affect performance. As soon as the mantlers react, cl-update will remove the unused dependencies.

P.S. To mask the version in file /etc/portage/package.mask/custom, you should specify it: “=sci-mathematics/rstudio-1.0.136”.

Thanks Alexander,

The only problem with all these Haskall packages is for UNIX purists like me who try to build a minimal system! Anyway thanks for your help, much appreciated.

Cheers, Bill