From edd@debian.org  Sun Dec  9 15:35:19 2001
From: edd@debian.org (edd@debian.org)
Date: Sun, 9 Dec 2001 16:35:19 +0100 (MET)
Subject: [Rd] Bug#123084: r-base: R documentatio search engine unusable with Mozilla 6 (OK with netscape 4.7x) (PR#1202)
Message-ID: <200112091535.QAA17520@pubhealth.ku.dk>


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.

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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[Rd] Bug#123084: r-base: R documentatio search engine unusable with Mozilla 6 (OK with netscape 4.7x) (PR#1202)
edd@debian.org