final documentation fixes for 1.2

svn path=/bioperl-live/trunk/; revision=5308

BUGS

@@ -1,7 +1,16 @@
-# $Id: BUGS,v 1.3 2001-11-19 17:34:08 jason Exp $
+# $Id: BUGS,v 1.4 2002-12-31 13:09:05 birney Exp $
 
 Known Bugs 
 
+Bioperl 1.2
+===========
+
+ * The searchio.t test is failing on cygwin installations (and
+   nowhere else). We need a developer who works with cygwin to
+   help us out here. We suspect something to do with temporary file
+   opening.
+
+
 Bioperl 0.9.0 
 =============
  * Bio::Tools::Blast continues to cause problems for some people.  As

Bio/AnnotatableI.pm

@@ -30,7 +30,9 @@ Bio::AnnotatableI - the base interface an annotatable object must implement
 
 =head1 DESCRIPTION
 
-This is the base interface that all annotatable objects must implement.
+This is the base interface that all annotatable objects must implement. A good
+example is Bio::Seq which is an AnnotableI object; if you are a little confused
+about what this module does, start a Bio::Seq.
 
 =head1 FEEDBACK
 
@@ -100,4 +102,6 @@ sub annotation{
     shift->throw_not_implemented();
 }
 
+
+
 1;

Bio/PrimarySeq.pm

@@ -54,7 +54,7 @@ PrimarySeq is a lightweight Sequence object, storing little more than
 the sequence, its name, a computer useful unique name. It does not
 contain sequence features or other information.  To have a sequence
 with sequence features you should use the Seq object which uses this
-object.
+object - go perldoc Bio::Seq
 
 Although newusers will use Bio::PrimarySeq alot, in general you will
 be using it from the Bio::Seq object. For more information on Bio::Seq

Bio/Seq.pm

@@ -73,7 +73,7 @@ Bio::Seq - Sequence object, with features
     my $trunc = $seqobj->trunc(100,200);
     my $rev   = $seqobj->revcom();
 
-    # there are many options to translate
+    # there are many options to translate - check out the docs
     my $trans = $seqobj->translate();
 
     # these functions can be chained together

PLATFORMS

@@ -1,8 +1,10 @@
-# $Id: PLATFORMS,v 1.19 2002-08-14 18:20:53 bosborne Exp $
+# $Id: PLATFORMS,v 1.20 2002-12-31 13:09:05 birney Exp $
 
 Perl general comments:
 
-	o Perl 5.00404 and lower often have problems with GDB.t
+	o Perl must be 5.005 or higher. We tend to test on
+          5.6 Perl. Perl 5.8 definitely works, but might have
+          small errors
 
 	o Perl on Digital Unix, WindowsNT, and MacOS has been reported
           to have problems with the Bio::DB::GDB on module (and
@@ -13,7 +15,7 @@ Perl general comments:
 	  likely cause tests 3 and/or 27 to fail).
 
 	o Index.t will fail if you have an out-of-date DBM file
-	  installation.
+	  installation or a bad DB_File installation
 
 
 Tested systems & OS Specific Comments or Warnings
@@ -58,28 +60,33 @@ Comments: Some warnings about <HANDLE> which can be safely
 	  IO::String cannot be installed on 5.004.  Bio::DB::GDB will
 	  not work on pre 5.005 versions of perl.
 
+          The makefile's should now work without shell modifications.
+          Let us know if that's an issue
+
 Machine : Win32, WinNT i386
 Compiler: --
 Perl    : ActiveState Perl 5.6, 5.5.1
 Comments: Be sure that the module DB_File is installed and up-to-date 
 	  to allow Bio::Index modules to work properly. 
-          File::Temp potentially broken (causing at least BPpsilite to fail)
 	  Installing ppm's IO-stringy and IO-String and File-Temp are 
 	  necessary as well.
-	  See http://bioperl.org/Core/windows-bioperl.html for more info on 
-	  installing on Windows.
+  
+          See INSTALL.WIN for more information
 
 Machine : CygWin NT_5 v. 1.3.10 on Windows 2000 5.00
 Compiler: gcc
 Perl    : 5.6.1
 Comments: Recommend that blastall app be obtained from NCBI
           (blast/executables/blastz.exe). expat is part of Cygwin.
+          Cygwin has an error in the SearchIO test, possibly due to some
+          temporary file issues
 
 Machine : MacOS
 Compiler: --
 Perl    : MacPerl
 Comments: Issues and possible ways to fix them summarized by Todd Richmond
-          on the bioperl.org Wiki.
+          on the bioperl.org Wiki. We don't recommend using Bioperl on
+          MacOS 9 systems
 
 Machine : MacOS X
 Compiler: gcc
@@ -106,3 +113,6 @@ Comments: Tested by (dag@sonsorol.org) on a barebones 4-cpu system without the
           working on getting 100% pass rate. Thanks due to HP for providing 
           the OBF with an Itanium workstation plus internet access to other 
           HP test platforms. Feedback from HP-UX users is appreciated.
+
+
+

bioperl.PL

@@ -86,16 +86,18 @@ documentation.
 
 The Bioperl modules are distributed as a tar file that expands into a
 standard perl CPAN distribution.  Detailed installation directions 
-can be found in the distribution INSTALL file.
+can be found in the distribution INSTALL file. Installing on windows
+using ActiveState Perl is covered in the INSTALL.WIN file.
 
 The Bioperl modules can now interact with local flat file and relational
 databases. To learn how to set this up, look at the biodatabases.pod
 documentation ('perldoc biodatabases.pod' should work once Bioperl has
 been installed).
 
-The bioperl-db, bioperl-gui, corba-server, bioperl-pipeline and 
-corba-client packages are installed separately from Bioperl. Please
-refer to their respective documentation for more information.
+The bioperl-db, bioperl-run, bioperl-gui, corba-server,
+bioperl-pipeline and corba-client packages are installed separately
+from Bioperl. Please refer to their respective documentation for more
+information.
 
 
 =head1 GETTING STARTED
@@ -211,16 +213,18 @@ part of 2002. We also participated in the 1st Bio-Hackathon that
 February which drew developers from several Open-Bio projects to
 lovely Cape Town, South Africa and the hospitality of the co-sponsor
 Electric Genetics (O'Reilly and Associates also co-sponsored the
-event).  In early May we released bioperl 1.0 as an effort to put a
-stamp of completeness on the toolkit and submitted a paper detailing
-the efforts thus far (see the FAQ).  In late 2002 we released a
-developer release 1.1 for testing purposes and released bioperl 1.2 at
-the beginning of 2003.
+event, and AstraZeneca contributed to the sponorship).  In early May
+we released bioperl 1.0 as an effort to put a stamp of completeness on
+the toolkit and submitted a paper detailing the efforts thus far (see
+the FAQ).  In late 2002 we released a developer release 1.1 for
+testing purposes and released bioperl 1.2 at the beginning of 2003.
+
 
 Current server hardware for bioperl.org (and other open-bio.org hosted
-projects) was provided by Compaq Computer Corporation.  The donation 
-was facilitated by both the Pharmaceutical Sales and High Performance 
-Technical Computing (HPTC) groups.
+projects) is provided by Sun. A previous server was provided by Compaq
+Computer Corporation.  The compaq donation was facilitated by both the
+Pharmaceutical Sales and High Performance Technical Computing (HPTC)
+groups. 
 
 The Bioperl servers reside in Cambridge, Massachusetts USA with
 colocation facilities and Internet bandwidth donated by Genetics