From ripley@stats.ox.ac.uk  Sun Dec  9 16:39:57 2001
From: ripley@stats.ox.ac.uk (ripley@stats.ox.ac.uk)
Date: Sun, 9 Dec 2001 17:39:57 +0100 (MET)
Subject: [Rd] Bug#123084: r-base: R documentatio search engine unusable (PR#1203)
Message-ID: <200112091639.RAA17749@pubhealth.ku.dk>

On Sun, 9 Dec 2001 edd@debian.org wrote:

>
> As there is nothing Debian-specific in this bug report (and the .deb of the
> JVW is not from Debian either), I am forwarding this to R-bugs. My
> recollection from recent discussions on the R mailing list is that currently
> /no/ browser other than Netscape supports the Java search engine -- is that
> correct or was there some Netscape derivative (galeon?) which does?
> Maybe the documentation should be enhanced in time for 1.4.0 to clarify this.

It's very far from correct!  The search engine works with Netscape 6.2 on
Linux (and Windows), and with Internet Explorer and Opera 5 on Windows.
(We were told it works with Internet Explorer on Linux too.) Opera uses
Sun's 1.3.1, as I recall, so I don't think this is a Java-1.1 vs 1.3
issue.  (I've just checked: Netscape 6.2 uses JRE 1.3.1.)

What BTW is `Mozilla 6'?  The current Mozilla is 0.9.6, so `6' seems a
decade or so away.

Which documentation do you suggest is altered and how?  Given that the
Mozilla-0.9.4-based Netscape 6.2 with JRE 1.3.1 works, the finger is
pointing pretty insistently at a problem in the installation of `Mozilla
6', whatever that is, and/or its JRE.

> Cheers, Dirk
> Debian maintainer for R
>
>   From: Emmanuel Charpentier <charpent@bacbuc.dyndns.org>
>   To: Debian Bug Tracking System <submit@bugs.debian.org>
>   Subject: Bug#123084: r-base: R documentatio search engine unusable with Mozilla 6 (OK with netscape 4.7x)
>   Date: Sun, 09 Dec 2001 16:04:49 +0100
>
>   Package: r-base
>   Version: 1.3.1-6
>   Severity: normal
>
>   The html-based doc system has problems with (the current builds of) Mozilla 6 :
>   while the Java search engine does work in Netscape 4.77, it does *not* with
>   Mozilla. The Netscape Java is, of course, 1.x, while Mozilla needs at least a
>   j2re virtualm machine (I use the Blackdown's debian package of j2re1.3.1 and
>   j2sdk :
>
>   charpent@yod:~$ dpkg -l | grep j2
>   ii  j2sdk1.3       1.3.1-1        Blackdown Java(TM) 2 SDK, Standard Edition
>   charpent@yod:~$
>
>   When I try to use the search engine (clicking the "Search engine" anchor on the
>   root page of the R documentation), I get a JVM error dialog box stating :
>
>   java.security.AccessControlException: access denied (java.io.FilePermission /home/charpent/.R/doc/html/search/SearchEngine.class read)
>   	at java.security.AccessControlContext.checkPermission(AccessControlContext.java:272)
>   	at java.security.AccessController.checkPermission(AccessController.java:399)
>   	at java.lang.SecurityManager.checkPermission(SecurityManager.java:545)
>   	at java.lang.SecurityManager.checkRead(SecurityManager.java:890)
>   	at java.io.File.isDirectory(File.java:567)
>   	at sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:65)
>   	at sun.net.www.protocol.file.FileURLConnection.initializeHeaders(FileURLConnection.java:82)
>   	at sun.net.www.protocol.file.FileURLConnection.getContentLength(FileURLConnection.java:113)
>   	at sun.applet.AppletClassLoader.getBytes(AppletClassLoader.java:223)
>   	at sun.applet.AppletClassLoader.access$100(AppletClassLoader.java:41)
>   	at sun.applet.AppletClassLoader$1.run(AppletClassLoader.java:137)
>   	at java.security.AccessController.doPrivileged(Native Method)
>   	at sun.applet.AppletClassLoader.findClass(AppletClassLoader.java:134)
>   	at sun.plugin.security.PluginClassLoader.findClass(PluginClassLoader.java:252)
>   	at java.lang.ClassLoader.loadClass(ClassLoader.java:297)
>   	at sun.applet.AppletClassLoader.loadClass(AppletClassLoader.java:108)
>   	at java.lang.ClassLoader.loadClass(ClassLoader.java:253)
>   	at sun.applet.AppletClassLoader.loadCode(AppletClassLoader.java:373)
>   	at sun.applet.AppletPanel.createApplet(AppletPanel.java:579)
>   	at sun.plugin.AppletViewer.createApplet(AppletViewer.java:1178)
>   	at sun.applet.AppletPanel.runLoader(AppletPanel.java:515)
>   	at sun.applet.AppletPanel.run(AppletPanel.java:293)
>   	at sun.plugin.navig.motif.MotifAppletViewer.maf_run(MotifAppletViewer.java:127)
>   	at sun.plugin.navig.motif.MotifAppletViewer.run(MotifAppletViewer.java:123)
>   	at java.lang.Thread.run(Thread.java:484)
>
>   However :
>
>   charpent@yod:~$ ls -l .R/doc/html/search/
>   total 656
>   lrwxrwxrwx    1 charpent charpent       43 Dec  9 15:14 IndexEntry.class -> /usr/lib/R/doc/html/search/IndexEntry.class
>   lrwxrwxrwx    1 charpent charpent       44 Dec  9 15:14 IndexStream.class -> /usr/lib/R/doc/html/search/IndexStream.class
>   lrwxrwxrwx    1 charpent charpent       43 Dec  9 15:14 IndexTable.class -> /usr/lib/R/doc/html/search/IndexTable.class
>   lrwxrwxrwx    1 charpent charpent       49 Dec  9 15:14 SearchEngine-foot.html -> /usr/lib/R/doc/html/search/SearchEngine-foot.html
>   lrwxrwxrwx    1 charpent charpent       49 Dec  9 15:14 SearchEngine-head.html -> /usr/lib/R/doc/html/search/SearchEngine-head.html
>   lrwxrwxrwx    1 charpent charpent       45 Dec  9 15:14 SearchEngine.class -> /usr/lib/R/doc/html/search/SearchEngine.class
>   lrwxrwxrwx    1 charpent charpent       44 Dec  9 15:14 SearchEngine.html -> /usr/lib/R/doc/html/search/SearchEngine.html
>   lrwxrwxrwx    1 charpent charpent       44 Dec  9 15:14 SearchObject.html -> /usr/lib/R/doc/html/search/SearchObject.html
>   lrwxrwxrwx    1 charpent charpent       39 Dec  9 15:14 Tracer.class -> /usr/lib/R/doc/html/search/Tracer.class
>   lrwxrwxrwx    1 charpent charpent       38 Dec  9 15:14 Value.class -> /usr/lib/R/doc/html/search/Value.class
>   -rw-r--r--    1 charpent charpent   663581 Dec  9 15:14 index.txt
>
>   and, of course :
>
>   charpent@yod:~$ ls -l /usr/lib/R/doc/html/search/
>   total 184
>   -rw-r--r--    1 root     root         1412 Dec  4 05:32 IndexEntry.class
>   -rw-r--r--    1 root     root         3125 Dec  4 05:32 IndexStream.class
>   -rw-r--r--    1 root     root          735 Dec  4 05:32 IndexTable.class
>   -rw-r--r--    1 root     root          163 Dec  4 05:32 SearchEngine-foot.html
>   -rw-r--r--    1 root     root         2239 Dec  4 05:32 SearchEngine-head.html
>   -rw-r--r--    1 root     root         4715 Dec  4 05:32 SearchEngine.class
>   -rw-r--r--    1 root     root         9650 Dec  4 05:32 SearchEngine.html
>   -rw-r--r--    1 root     root         1087 Dec  4 05:32 SearchObject.html
>   -rw-r--r--    1 root     root         1273 Dec  4 05:32 Tracer.class
>   -rw-r--r--    1 root     root          675 Dec  4 05:32 Value.class
>   -rw-r--r--    1 root     root       130263 Dec  4 05:32 index.txt
>   charpent@yod:~$
>
>   The very same installation works pperfectly with Netscape (I just have to lauch
>   Netscape before invoking help.start(), which launches Mozilla by default).
>
>   What am I missing ? Not much, as far as I can tell. Mozilla does not seem to
>   have problems with Java (but I may be mistaken : I'm not much of a "surfer").
>
>   Therefore, I suspect that the SearchEngine.class code is somewhat java-1.1x
>   specific.
>
>   -- System Information
>   Debian Release: 3.0
>   Architecture: i386
>   Kernel: Linux yod 2.4.13 #2 Wed Oct 31 15:09:05 CET 2001 i686
>   Locale: LANG=C, LC_CTYPE=
>
>   Versions of packages r-base depends on:
>   ii  atlas2-athlon [blas2]     3.2.1-12       Automatically Tuned Linear Algebra
>   ii  atlas2-base [blas2]       3.2.1l-2       Automatically Tuned Linear Algebra
>   ii  blas1 [blas2]             1.0-9          A set of building blocks for perfo
>   ii  libc6                     2.2.4-7        GNU C Library: Shared libraries an
>   ii  libjpeg62                 6b-4           The Independent JPEG Group's JPEG
>   ii  libncurses5               5.2.20010318-3 Shared libraries for terminal hand
>   ii  libpng2                   1.0.12-2       PNG library - runtime
>   ii  libreadline4              4.2a-2         GNU readline and history libraries
>   ii  perl                      5.6.1-6        Larry Wall's Practical Extraction
>   ii  tcl8.3                    8.3.3-4        The Tool Command Language (TCL) v8
>   ii  tk8.3                     8.3.3-6        The Tk toolkit for TCL and X11 v8.
>   ii  xlibs                     4.1.0-10       X Window System client libraries
>   ii  zlib-bin                  1:1.1.3-18     compression library - sample progr
>   ii  zlib1g                    1:1.1.3-18     compression library - runtime
>
> --please do not edit the information below--
>
> Version:
>  platform = i386-pc-linux-gnu
>  arch = i386
>  os = linux-gnu
>  system = i386, linux-gnu
>  status =
>  major = 1
>  minor = 3.1
>  year = 2001
>  month = 08
>  day = 31
>  language = R
>
> Search Path:
>  .GlobalEnv, package:ctest, Autoloads, package:base
>
>
> --
> Good judgment comes from experience; experience comes from bad judgment.
> 							    -- F. Brooks
>
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>

-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595


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[Rd] Bug#123084: r-base: R documentatio search engine unusable (PR#1203)
ripley@stats.ox.ac.uk