Bug 305641 – dev-lang/R: Cannot access docs from R

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Paulo da Silva 2010-02-17 19:43:29 UTC]

Cannot access documentation html pages from R except the first one.


Reproducible: Always

Steps to Reproduce:
1.cd foo
2.R
3.help.start()
This correctly starts the first html page but most (all?) links from that page are broken.

Actual Results:  
Links from first page are broken.


Expected Results:  
The links should refer to existent html pages/docs.


Example of a missing link:
file:///tmp/RtmpS7W39r/.R/doc/html/manual/R-intro.html

This page is, in fact,
/tmp/RtmpS7W39r/.R/doc/manual/R-intro.pdf

[Comment 1 Paulo da Silva 2010-02-18 03:37:50 UTC]

> ...
> Example of a missing link:
> file:///tmp/RtmpS7W39r/.R/doc/html/manual/R-intro.html
> 
> This page is, in fact,
> /tmp/RtmpS7W39r/.R/doc/manual/R-intro.pdf
> 
Of course I meant:
/tmp/RtmpS7W39r/.R/doc/manual/R-intro.html

BTW, I unmasked the last version (2.10.1) and it works fine i.e. as expected.

[Comment 2 Sébastien Fabbro (RETIRED) 2010-02-19 04:24:49 UTC]

Hi,

Could you try with enabling USE=doc?

Thanks

[Comment 3 Paulo da Silva 2010-02-19 17:15:17 UTC]

(In reply to comment #2)
> Hi,
> 
> Could you try with enabling USE=doc?
> 
> Thanks
> 

I have USE=doc globally set.
The docs are in /usr/share/doc/R-...
They also are created in /tmp/... when I issue the R command help.start() but, as I said, the html pages are in different subdirs than those referred in the first page links. See, pls., the example (Comment 1 with correction on comment 2).

[Comment 4 Sébastien Fabbro (RETIRED) 2010-02-19 17:27:37 UTC]

With R-2.10.1, the links are broken with USE=-doc, but work with USE=doc.
Which version of R are you referring? Also post your emerge --info.

Thanks.

[Comment 5 Paulo da Silva 2010-02-21 02:03:20 UTC]

(In reply to comment #4)
> With R-2.10.1, the links are broken with USE=-doc, but work with USE=doc.
Yes. That's what I said in comment 1.

> Which version of R are you referring? Also post your emerge --info.
The last stable version, i.e. 2.9.2.

As I said in comment 1, I unmasked 2.10.1 and now I am running it.
Everything is running fine so far with this version.

------------------------------------------------------
Portage 2.2_rc62 (default/linux/amd64/10.0/desktop, gcc-4.3.4, glibc-2.10.1-r1, 2.6.31-gentoo-r6 x86_64)
=================================================================
System uname: Linux-2.6.31-gentoo-r6-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T7700_@_2.40GHz-with-gentoo-1.12.13
Timestamp of tree: Tue, 16 Feb 2010 18:15:01 +0000
distcc 3.1 x86_64-pc-linux-gnu [enabled]
ccache version 2.4 [enabled]
app-shells/bash:     4.0_p35
dev-java/java-config: 2.1.10
dev-lang/python:     2.6.4
dev-util/ccache:     2.4-r7
dev-util/cmake:      2.6.4-r3
sys-apps/baselayout: 1.12.13
sys-apps/sandbox:    2.2
sys-devel/autoconf:  2.13, 2.63-r1
sys-devel/automake:  1.8.5-r3, 1.9.6-r2, 1.10.2
sys-devel/binutils:  2.18-r3
sys-devel/gcc:       4.3.4
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.6b
virtual/os-headers:  2.6.27-r2
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/sandbox.d /etc/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/udev/rules.d"
CXXFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer"
DISTDIR="/GentooPalma/PKGS/distfiles"
FEATURES="assume-digests ccache distcc distlocks fixpackages news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="pt_PT.UTF-8"
LDFLAGS="-Wl,-O1"
LINGUAS="pt pt_PT pt_BR en"
MAKEOPTS="-j9"
PKGDIR="/GentooPalma/PKGS/packages64"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="X Xaw3d a52 aac acpi alsa amd64 apm arts audiofile berkdb bidi bluetooth bzip2 cairo cdparanoia cdr cli consolekit cracklib crypt css cups curl cxx dbus dga doc dri dts dvd dvdr dvdread eds embedded emboss encode fam fbcon ffmpeg firefox flac foomaticdb fortran gdbm gif gphoto2 gpm gstreamer gtk hal iconv imagemagick imlib ipv6 java java5 java6 jpeg kde lcms libnotify libwww mad midi mikmod mmx mng modules motif mozilla mp3 mp4 mpeg mplayer msn mudflap multilib musepack mysql nas ncurses net nls nptl nptlonly nsplugin nvidia ogg opengl openmp pam pcmcia pcre pdf perl pic png ppds pppd python qt3 qt3support qt4 quicktime readline reflection rtc scanner sdl session snmp socks5 speex spell spl sqlite sqlite3 sse sse2 ssl startup-notification subversion svg sysfs tcl tcpd tetex threads thunar tiff tk truetype unicode usb userlocales v4l v4l2 vcd videos vorbis webkit wifi wxwindows x264 xcomposite xine xml xorg xprint xulrunner xv xvid zlib" 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" 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="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 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" ELIBC="glibc" INPUT_DEVICES="keyboard mouse synaptics evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="pt pt_PT pt_BR en" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nv nvidia vesa fbdev" 
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

[Comment 6 Sébastien Fabbro (RETIRED) 2010-05-25 16:38:33 UTC]

R-2.9.2 is now gone from the tree. closing.