S-PLUS Workbench User's Guide - Department of Mathematics and

S-PLUS Workbench User's Guide - Department of Mathematics and
the knowledge to act™
S-PLUS Workbench
User’s Guide
®
May 2007
Insightful Corporation
Seattle, Washington
Proprietary
Notice
Insightful Corporation owns both this software program and its
documentation. Both the program and documentation are
copyrighted with all rights reserved by Insightful Corporation.
The correct bibliographical reference for this document is as follows:
S-PLUS
®
Workbench User’s Guide, Insightful Corporation, Seattle, WA.
Printed in the United States.
Copyright Notice Copyright © 1987-2007, Insightful Corporation. All rights reserved.
Insightful Corporation
1700 Westlake Avenue N, Suite 500
Seattle, WA 98109-3044
USA
Trademarks
ii
Insightful, Insightful Corporation, the Insightful logo and tagline
"the Knowledge to Act," Insightful Miner, S+, S-PLUS, S+FinMetrics,
S+EnvironmentalStats, S+SeqTrial, S+SpatialStats, S+Wavelets,
S+ArrayAnalyzer, S-PLUS Graphlets, Graphlet, Trellis, and Trellis
Graphics are either trademarks or registered trademarks of Insightful
Corporation in the United States and/or other countries. Intel and
Pentium are trademarks or registered trademarks of Intel
Corporation or its subsidiaries in the United States and other
countries. Microsoft, Windows, MS-DOS and Windows NT are
either registered trademarks or trademarks of Microsoft Corporation
in the United States and/or other countries. Sun, Java and Solaris are
trademarks or registered trademarks of Sun Microsystems, Inc. in the
United States or other countries. UNIX is a registered trademark of
The Open Group. Linux is a registered trademark of Linus Torvalds
in the United States and other countries.
ACKNOWLEDGMENTS
S-PLUS would not exist without the pioneering research of the Bell
Labs S team at AT&T (now Lucent Technologies): John Chambers,
Richard A. Becker (now at AT&T Laboratories), Allan R. Wilks (now
at AT&T Laboratories), Duncan Temple Lang, and their colleagues in
the statistics research departments at Lucent: William S. Cleveland,
Trevor Hastie (now at Stanford University), Linda Clark, Anne
Freeny, Eric Grosse, David James, José Pinheiro, Daryl Pregibon, and
Ming Shyu.
Insightful Corporation thanks the following individuals for their
contributions to this and earlier releases of S-PLUS: Douglas M. Bates,
Leo Breiman, Dan Carr, Steve Dubnoff, Don Edwards, Jerome
Friedman, Kevin Goodman, Perry Haaland, David Hardesty, Frank
Harrell, Richard Heiberger, Mia Hubert, Richard Jones, Jennifer
Lasecki, W.Q. Meeker, Adrian Raftery, Brian Ripley, Peter
Rousseeuw, J.D. Spurrier, Anja Struyf, Terry Therneau, Rob
Tibshirani, Katrien Van Driessen, William Venables, and Judy Zeh.
iii
S-PLUS BOOKS
®
The S-PLUS documentation includes books to address your focus
and knowledge level. Review the following table to help you choose
the S-PLUS book that meets your needs. These books are available in
PDF format in the following locations:
•
In your S-PLUS installation directory (SHOME\help on
Windows, SHOME/doc on UNIX/Linux).
•
In the S-PLUS Workbench, from the Help 䉴 S-PLUS
Manuals menu item.
•
In Microsoft Windows , in the S-PLUS GUI, from the
Help 䉴 Online Manuals menu item.
®
®
S-PLUS documentation.
Information you need if you...
See the...
Are new to the S language and the S-PLUS GUI,
and you want an introduction to importing data,
producing simple graphs, applying statistical
Getting Started
Guide
®
models, and viewing data in Microsoft Excel .
iv
Are a system administrator or a licensed user and
you need guidance licensing your copy of S-PLUS
and/or any S-PLUS module.
S-PLUS licensing Web
site
keys.insightful.com/
Are a new S-PLUS user and need how to use
S-PLUS, primarily through the GUI.
User’s Guide
Are familiar with the S language and S-PLUS, and
you want to use the S-PLUS plug-in, or
customization, of the Eclipse Integrated
Development Environment (IDE).
S-PLUS Workbench
User’s Guide
Have used the S language and S-PLUS, and you
want to know how to write, debug, and program
functions from the Commands window.
Programmer’s Guide
S-PLUS documentation. (Continued)
Information you need if you...
See the...
Are familiar with the S language and S-PLUS, and
you want to extend its functionality in your own
application or within S-PLUS.
Application
Developer’s Guide
Are familiar with the S language and S-PLUS, and
you are looking for information about creating or
editing graphics, either from a Commands
window or the Windows GUI, or using S-PLUSsupported graphics devices.
Guide to Graphics
Are familiar with the S language and S-PLUS, and
you want to use the Big Data library to import and
manipulate very large data sets.
Big Data
User’s Guide
Want to download or create S-PLUS packages for
submission to the Comprehensive S Archival
Network (CSAN) site, and need to know the steps.
Guide to Packages
Are looking for categorized information about
individual S-PLUS functions.
Function Guide
If you are familiar with the S language and S-PLUS,
and you need a reference for the range of statistical
modelling and analysis techniques in S-PLUS.
Volume 1 includes information on specifying
models in S-PLUS, on probability, on estimation
and inference, on regression and smoothing, and
on analysis of variance.
Guide to Statistics,
Vol. 1
If you are familiar with the S language and S-PLUS,
and you need a reference for the range of statistical
modelling and analysis techniques in S-PLUS.
Volume 2 includes information on multivariate
techniques, time series analysis, survival analysis,
resampling techniques, and mathematical
computing in S-PLUS.
Guide to Statistics,
Vol. 2
v
vi
CONTENTS
S-PLUS Books
Chapter 1
The S-PLUS Workbench
iv
1
Introduction
2
Terms and Concepts
3
Finding Help for the Workbench
6
Starting the S-PLUS Workbench
9
Examining S-PLUS Preferences
12
Examining the S-PLUS Workbench GUI
23
Commonly-Used Features in Eclipse
48
Chapter 2
The S-PLUS Perspective
51
Introduction
52
S-PLUS Perspective Views
53
Chapter 3 S-PLUS Workbench Debug Perspective
65
Introduction
66
Debug Perspective Options and Preferences
68
Debug Perspective Views
74
Chapter 4 S-PLUS Workbench Tasks
99
Introduction
100
S-PLUS Workbench Projects
101
vii
Contents
Customized Perspective Views
120
Working Projects and Databases
123
S-PLUS Project Files and Views
128
S-PLUS Workbench Debugger Tasks
139
Chapter 5
153
Introduction
154
“Workspace in Use” Error
155
Working with Calls to S-PLUS GUI Functions
156
View is not visible
157
Debugging Using the Run Button
158
Subclipse Add-in error with Workbench
159
Index
viii
Troubleshooting
161
THE S-PLUS WORKBENCH
1
Introduction
2
Terms and Concepts
3
Finding Help for the Workbench
Getting Started Tutorial
Help for S-PLUS Functions
The S-PLUS Workbench PDF
6
6
7
8
Starting the S-PLUS Workbench
From Microsoft Windows
From Unix
The S-PLUS Workspace
9
9
10
10
Examining S-PLUS Preferences
File Associations
S-PLUS Workbench options
Console Options
Editor
Outline Options
Output Options
Task Options
12
12
14
16
17
20
21
22
Examining the S-PLUS Workbench GUI
S-PLUS New Project Wizard
Customized Menus, Toolbars, and Dialogs
S-PLUS Workbench Status Bar
S-PLUS Workbench Perspectives and Views
Default Shared Views
23
23
23
29
30
37
Commonly-Used Features in Eclipse
48
1
Chapter 1 The S-PLUS Workbench
INTRODUCTION
S-PLUS provides a plug-in, or customization, of the Eclipse Integrated
Development Environment (IDE) called the S-PLUS Workbench. You
can use the S-PLUS Workbench, the basic Eclipse IDE features, and
other third-party plug-ins for many tasks, including:
•
Manage your project files and tasks.
•
Edit your code.
•
Run S-PLUS commands.
•
Examine S-PLUS objects.
•
Debug your code.
•
Track resource use, functions, variables, and expressions.
•
Troubleshoot problems with S-PLUS code.
•
Provide source control for shared project files.
The S-PLUS Workbench is a stand-alone application that runs the
S-PLUS engine. When you run the S-PLUS Workbench, you do not
need to run any other version of S-PLUS (for example, the console or
traditional Windows or Java GUI).
Caution
If you run two or more simultaneous sessions of S-PLUS (including one or more in the S-PLUS
Workbench), take care to use different working directories. To use the same working directory
for multiple sessions can cause conflicts, and possibly even data corruption.
This chapter introduces the S-PLUS Workbench and provides
important conceptual information and definitions of terms you need
to know to use the S-PLUS Workbench most effectively.
2
•
Chapter 2 provides reference for the S-PLUS perspective.
•
Chapter 3 provides reference for the Debug perspective.
•
Chapter 4 provides tasks for learning to use the S-PLUS
Workbench.
Terms and Concepts
TERMS AND CONCEPTS
Before you start using the S-PLUS Workbench, you should understand
key terms and concepts that vary from the traditional S-PLUS for
Windows GUI and S-PLUS for UNIX Java GUI.
Note
If you are using the Eclipse IDE on a UNIX platform from a Windows machine using a
Windows X-server software package, you might notice that Eclipse runs slowly, similar to the
S-PLUS Java GUI. See the Release Notes for more information and recommendations for
improving UI performance.
Note
Eclipse version 3.2 or later does not support SPARC/Motif for Solaris. If you are using a version
of Solaris prior to version 10, you must install the GTK (version 2.2.4 or greater) library. For
more information about finding this library, see http://www.sun.com/software/solaris/. (This
library is included in Solaris 10.)
Table 1.1: Important terms and concepts.
Term
Definition
Perspective
Defines the preferences, settings, and views for working with
Eclipse projects.
• The S-PLUS perspective is conceptually equivalent to the
traditional S-PLUS Windows GUI or UNIX Java GUI. Use
the S-PLUS perspective as the primary perspective for
interactive S-PLUS command line use. For an example of
changing the perspective, see the section Customized
Perspective Views on page 120.
• The Debug perspective provides an integrated debugging
and profiling environment, with customized views, menu
options, and behavior. For more information about using
the Debug perspective, see Chapter 3, S-PLUS Workbench
Debug Perspective.
3
Chapter 1 The S-PLUS Workbench
Table 1.1: Important terms and concepts. (Continued)
Term
Definition
Workspace
A physical directory on your machine that manages S-PLUS
Workbench resources such as projects and other options. On
your machine's hard drive, the workspace directory contains
a single S-PLUS .Data database and the Eclipse .metadata
database. (You should never touch these resources.) This
design is different from the association you notice when you
work in S-PLUS in other environments. When you start the
S-PLUS Workbench, you are prompted to create or identify
the workspace. See the section The S-PLUS Workspace on
page 10.
Project
A resource containing text files, scripts, and associated files.
The S-PLUS Workbench project is used for build and version
management, sharing, and resource management. Before you
begin working with any files in the S-PLUS Workbench,
create a project. You can create a new project by:
•
Specifying a project name and allowing Eclipse to
locate the project in the workspace directory, and
then selecting an existing directory containing
project files at an alternate location (that is, work
with the files at the specified location).
•
Specifying a project name and selecting an existing
directory containing project files.
Another important concept is that of the working project. Set a
project as the working project, which changes the working
directory to the project’s directory in your workspace and
stores data objects in the project’s .Data database. See the
section Setting the Working Project on page 123 for more
information.
Important: If you select an existing S-PLUS project directory
for your Workbench project, you must set that project to be
the working project to write data objects to its .Data directory.
See the section Working Projects and Databases on page 123
for a detailed discussion. See the section Creating a Project
on page 102.
4
Terms and Concepts
Table 1.1: Important terms and concepts. (Continued)
Term
Definition
View
A perspective’s integrated window, containing menus,
options, and commands, that display specific parts of your
data and projects and provide tools for data manipulation.
For descriptions of the S-PLUS perspective views, see the
section S-PLUS Perspective Views on page 53. For
descriptions of the Debug perspective views, see the section
Debug view on page 76. For practice exercises working with
views, see Chapter 4, S-PLUS Workbench Tasks.
Editor
An integrated code/text editor that includes support for
syntax coloring, text formatting, and integration with the
other views. Analogous to the Script Editor in the traditional
S-PLUS GUI. For more information, see the section S-PLUS
Workbench Script Editor on page 45. To practice using the
Script Editor, see the section Editing Code in the Script
Editor on page 129.
5
Chapter 1 The S-PLUS Workbench
FINDING HELP FOR THE WORKBENCH
The Eclipse IDE contains extensive, in-depth documentation for its
user interface. For information about basic Eclipse IDE functionality,
on the menu, see the Eclipse Workbench User Guide.
Getting
Started
Tutorial
If you are not familiar with the Eclipse IDE, after you start the S-PLUS
Workbench, take the first few minutes to learn the basic concepts and
IDE layout by working through the basic tutorial in the Workbench
User Guide.
To view the Eclipse Getting Started tutorial
1. From the S-PLUS Workbench main menu, click Help 䉴 Help
Contents.
Figure 1.1: Eclipse IDE Help menu.
2. In the left pane, expand the table of contents by clicking
Workbench User Guide.
3. Click Getting Started, and then click Basic tutorial.
6
Finding Help for the Workbench
Figure 1.2: The Eclipse basic tutorial.
The Workbench User Guide opens in a separate window; you can toggle
between the S-PLUS Workbench application and the Help browser.
Help for S-PLUS
Functions
The S-PLUS Workbench provides access to function help topics.
•
In
the
Console, type help(functionname) where
is the function for which you want help.
functionname
•
In the Script Editor, highlight the function for which you
want help, and then press F1.
•
Use the S-PLUS Workbench menu options. In the Script
Editor, select the function for which you want help, and
then, on the menu click either:
•
S-PLUS 䉴 Open S-PLUS Help File
•
Help 䉴 S-PLUS Help
or
7
Chapter 1 The S-PLUS Workbench
The S-PLUS
Workbench
PDF
If you browsed to and opened this document directly from the
installation directory, you might be interested to know how you can
open it directly from the S-PLUS Workbench user interface.
Note
®
®
Whether you are working in Windows or a UNIX platform, You must have access to a PDF
reader to open any of the PDFs shipped with S-PLUS.
On the S-PLUS Workbench menu, click Help 䉴 S-PLUS Manuals 䉴
S-PLUS Workbench Guide. (Note that all S-PLUS manuals are
available from the S-PLUS Manuals menu, including the Programmer’s
Guide, the Application Developer’s Guide, the Function Guide, the Big
Data User’s Guide, the Guide to Packages and the Guide to Graphics,
among others.)
To specify a PDF reader, on the S-PLUS Workbench menu, click
Window 䉴 Preferences, and then, in the S-PLUS page of the
Preferences dialog, set your PDF reader’s name and location.
For more information about setting preferences, see the following
documentation:
•
The section Examining S-PLUS Preferences on page 12.
•
The section Setting the S-PLUS Workbench Preferences on
page 110.
•
The Eclipse Workbench User Guide, available from the S-PLUS
Workbench menu item Help 䉴 Help Contents.
Note
To get information about using the S-PLUS Packages feature with the S-PLUS Workbench, see the
Guide to Packages.
8
Starting the S-PLUS Workbench
STARTING THE S-PLUS WORKBENCH
The S-PLUS Workbench user interface is the same in both Microsoft
Windows and UNIX platforms.
From Microsoft
Windows
In Microsoft Windows, click the Start menu 䉴 All Programs 䉴
S-PLUS 8.0 䉴 S-PLUS Workbench.
Note
When you start the S-PLUS Workbench from the Windows Start menu, it uses a shortcut that
starts a Java virtual machine ( JVM) immediately. This shortcut is defined to run a command with
the option to set memory heap size: -Xmx400m.
<SHOME>\eclipse\eclipse.exe ...various options... -Xmx400m
You can override this setting and increase the memory heap size by appending a different setting
at the end of the shortcut. (For example, change -Xmx400m to -Xmx600m at the end of the
command to set the memory heap size to 600mb.) See Figure 1.3 for an example.
Figure 1.3: S-PLUS Workbench Properties dialog.
9
Chapter 1 The S-PLUS Workbench
From Unix
In UNIX, at the command prompt, type
Splus -w
or type
Splus -workbench
Note
To extend the Java maximum memory heap size to 600MB, set the environment variable
JAVA_OPTIONS to -Xmx600m. For example, on Solaris or Linux, start the S-PLUS Workbench with:
env JAVA_OPTIONS="-Xmx600m" SPlus -w
The S-PLUS
Workspace
When you launch the S-PLUS Workbench, you see the Workspace
Launcher dialog. You must indicate the location of the workspace.
Figure 1.4: The Workspace Launcher dialog.
The S-PLUS workspace is the directory where the S-PLUS workspace
.Data and Eclipse .metadata databases are stored. (You should never
touch these files.) Optionally, the workspace directory can also store
your project directories. The S-PLUS workspace is the default
directory specified for the project's directory in the New Project
wizard. See the section S-PLUS New Project Wizard on page 23 for
more information. (For instruction on creating a workspace, see the
section Setting the Workspace on page 101.)
Important
In the S-PLUS Workbench, you have two options for storing data
objects:
10
Starting the S-PLUS Workbench
•
Using the S-PLUS Workbench model, where the S-PLUS
workspace contains a .Data directory, not individual projects.
The .Data directory can store objects for projects to share in
the workspace.
•
Using the familiar S-PLUS model, the working S-PLUS project
stores its data objects to its .Data directory and replaces the
first entry in the Search Path with the project's location. It is
also the location to which relative paths are resolved.
Working projects are marked by an arrow icon, and by the
cue (working) in the navigator:
Figure 1.5: The working project.
For more information about setting the S-PLUS working project, see
the section Setting the Working Project on page 123.
Figure 1.6: Workspace directory (in Windows) showing .Data directory,
.metadata directory, and project directories.
Notes
When you work with S-PLUS Workbench projects, avoid nesting projects (that is, create one
project in a subdirectory of another project).
To avoid conflicts, never work on S-PLUS files in the S-PLUS Workbench and another S-PLUS
interface at the same time.
11
Chapter 1 The S-PLUS Workbench
EXAMINING S-PLUS PREFERENCES
The S-PLUS Workbench IDE defaults are set to the S-PLUS
perspective. The preferences include project type, window
appearance, editor preferences, menu options, and file associations.
Use the Preferences dialog to change these preferences and any
other default Eclipse preferences. To display the Preferences dialog,
on the main menu, click Window 䉴 Preferences.
You can also display the Preferences dialog for the following S-PLUS
Workbench views by clicking the drop-down button (
selecting Preferences from the control menu:
•
Tasks view.
•
Outline view.
•
Output view.
•
Console view.
) and
You can display the Preferences dialog for the S-PLUS Workbench
Script editor from the right-click menu (that is, right-click the Script
Editor, and from the menu, click Preferences).
Hint
The Eclipse Workbench User Guide includes descriptions of the Eclipse options in the
Preferences dialog.
For instruction on setting S-PLUS preferences, see the section Setting
the S-PLUS Workbench Preferences on page 110.
The S-PLUS Workbench sets defaults for the following preferences.
File
Associations
12
S-PLUS recognized file types include *.q, *.r, *.ssc, and *.t. Any of
these files, associated with the S-PLUS Script editor, are checked for
syntax errors and scanned for task tags.
Examining S-PLUS Preferences
Note that when you select the file type, its associated editors are
displayed in the Associated editors box. You can add or remove
both file types and associated editors.
Figure 1.7: The File Associations page of the Preferences dialog.
13
Chapter 1 The S-PLUS Workbench
S-PLUS
Workbench
options
These options control general settings for the S-PLUS Workbench.
Figure 1.8: The S-PLUS Workbench Options page of the Preferences dialog.
Run code on
startup
Select this option, and then provide any code that you want the
S-PLUS Workbench to run when it starts up. Note that this box is
selected by default, and the Big Data library is loaded by default.
Note
If you clear the Run code on startup box, or if you remove the option to load the Big Data
library on startup, and then later open a project that uses the Big Data library, you could see
unexpected results when you try to perform actions. If your typical projects include large data
sets, select this option to always load the Big Data library when you start the S-PLUS Workbench.
Set PDF Viewer
Location
14
Provide the name and path to your PDF viewer. This is used to open
documents from the Help menu. (Most S-PLUS documentation is
provided in PDF format, so you must have a PDF viewer to read the
S-PLUS documentation.) If you leave this box blank, the S-PLUS
Workbench attempts to use the default PDF file viewer on your
system, if one is available.
Examining S-PLUS Preferences
Integrate Java
Graphs into the
S-PLUS
Workbench
This option is selected by default. Clear this option if you do not want
Java graphs embedded in the S-PLUS Workbench.
Note
java.graph is the default device for the S-PLUS Workbench.
With this option selected, any Java graphs created as part of your
script appear embedded in a view to the right of the folder containing
the console view by default.
Figure 1.9 shows the a Java graph from the Census sample,
embedded in the S-PLUS Workbench.
Figure 1.9: Java graph embedded in the S-PLUS Workbench.
15
Chapter 1 The S-PLUS Workbench
Console
Options
The Console page controls settings for the S-PLUS Workbench
Console.
Figure 1.10: Console page of the Preferences dialog.
Store Console
History Between
Sessions
By default, this option is selected. It persists the commands you issue
in the Console (which then appear in the History), between sessions.
When you re-start the S-PLUS Workbench, click History to display
the stored entries. Entries you select in the History then appear in the
Console. Also, you can scroll up and down in the History to display
items in the Console. For more information about using the History,
see the section Examining the History view on page 136. For
information about setting options for the Output view, see section
Output Options on page 21.
Font Settings
By default, the Console displays input and output text using the
default system font as blue and red, respectively. You can change
both the font and the color.
•
16
To set the font, click Change, and then, in the Font dialog,
select from Font, Font style, Size, and any additional font
properties to use. Note that the font changes for both input
and the output displayed in the Console.
Examining S-PLUS Preferences
•
To set a custom font color, click the Input Color or Output
Color button, and then, in the Color picker, select a color for
the input or output.
Background
Settings
By default, the S-PLUS Console uses the system default. Select
Custom Color, and then click the color button to display the Color
picker and choose a different background color.
Include Prompts
in Copy action
Select if you want to include prompts (> and +) when you copy code
from either the Console.
Editor
These options control settings for the S-PLUS Workbench Script
Editor.
Figure 1.11: The Editor page of the Preferences dialog.
17
Chapter 1 The S-PLUS Workbench
Syntax
Highlighting
Specifies the colors for text and defined syntax appearing in the Script
Editor. To change the default color for any of the items listed, click
Choose Color and, from the color picker dialog, select a color.
Note
To set background color, in the Preferences dialog, select General 䉴 Editors 䉴 Text Editors,
and, in the Appearance color options box, select Background color. See the Workbench User
Guide for more information about setting general options.
User Tokens
Lists items specified for user-defined syntax highlighting.
By default, no user-defined highlighted terms are defined. Any term
you define using this option appears in the S-PLUS Script Editor in the
color you define in Syntax Highlighting for the option User. To
add a user-defined token, click New, and then, in the Add Desired
S-PLUS Text dialog, provide the term or source.
Figure 1.12: Add Desired S-PLUS Text dialog.
In the Add Desired S-PLUS Text dialog, you can provide:
•
Individual terms, separated by commas.
•
The contents of a comma-separated file.
•
The results of an S-PLUS command. (Note that Figure 1.11
shows the results of the S-PLUS command objects(), which
adds all objects in the current working project to the User
Token list.
For more information about adding user tokens, see the section
S-PLUS View Preferences on page 111.
Hover
18
Displays a tooltip when the mouse hovers over an expression. The
tooltip displays the value of the expression, if the engine is available.
Examining S-PLUS Preferences
S-PLUS Format
Options
Provides control over the S-PLUS Workbench’s automatic code layout
and formatting style.
Note
Changes you make to the S-PLUS Format Options do not affect your code until you select from
the menu S-PLUS 䉴 Format.
Table 1.2: S-PLUS Format Options.
Format Option
Description
Margin Column
Sets the right-hand margin to the specified
character column, counting from the leftmost character. By default, set to 60, making
the editing space 59 characters wide.
Use Spaces for
Indentation
By default, cleared. If selected, the default
value is 4. If you leave this cleared, the autoformatting feature uses tab indents, rather
than character spaces.
Encapsulate all scope
blocks with {}
Select to enclose all of your scope blocks
with curly brackets ({}). Selected by default.
Start each scope block
on a new line
Inserts a line break before the first line of a
scope block.
The read-only text box appearing at the bottom of the S-PLUS
Format Options area provides an preview of your choices.
19
Chapter 1 The S-PLUS Workbench
Outline
Options
Lists the options to display anonymous functions and functions to
watch.
Figure 1.13: The Outline page of the Preferences dialog.
Show Anonymous By default, the S-PLUS Script Editor shows anonymous functions in
the outline.
Functions in
Outline
Functions to
Watch
20
Contains a predefined list of S-PLUS functions to identify in the
Outline view. You can add your own functions to this list using the
New button. You can also remove functions from the list or reorder
the list.
Examining S-PLUS Preferences
Output
Options
The Output page controls settings for the S-PLUS Workbench
Output view.
Figure 1.14: Output page of the Preferences dialog.
Font Settings
Background
Settings
By default, the Output view displays output text using the default
system font as red. You can change both the font and the color.
•
To set the font, click Change, and then, in the Font dialog,
select from Font, Font style, Size, and any additional font
properties.
•
To set a custom font color, click the Output Color button,
and then, in the Color picker, select a color for the output.
By default, the Output view uses the system default. Select Custom
Color, and then click the color button to display the Color picker
and choose a different background color.
21
Chapter 1 The S-PLUS Workbench
Task Options
Lists the three pre-defined default task tags. See the section Tasks
view on page 61 for more information.
Figure 1.15: The Task Tags page of the Preferences dialog.
22
Examining the S-PLUS Workbench GUI
EXAMINING THE S-PLUS WORKBENCH GUI
After the S-PLUS Workbench GUI opens, and you set preferences,
spend a moment examining the user interface, including the toolbars,
menus, perspectives, and views.
•
For more information about perspectives, see the section
S-PLUS Workbench Perspectives and Views on page 30.
•
For more information about views, see the section Examining
the Views on page 32.
S-PLUS New
Project Wizard
When you start a new S-PLUS project in the S-PLUS Workbench, you
see the New Project wizard, where you specify the location of your
project files. See the section Creating a Project on page 102 for more
information about specifying the project file location.
Working with
Files External to
the Project
You can use the Eclipse editor to edit non-project files in the S-PLUS
Workbench. To open a non-project file, on the File menu, click
Open File, and then browse to the location of the file to edit. For
more information about editing files in Eclipse, see the Eclipse
Workbench User Guide.
Customized
Menus,
Toolbars, and
Dialogs
The S-PLUS Workbench includes in the Eclipse GUI:
Customized
menus
S-PLUS customizes the basic Eclipse menu to provide easy access to
global S-PLUS control and to control debugging options.
•
Customized top-level menu items.
•
Customized top-level toolbar.
•
Customized view-specific toolbars and view menus. (See the
section Control and Right-Click Menus on page 34 for more
information about the menus.)
23
Chapter 1 The S-PLUS Workbench
S-PLUS Menu
The S-PLUS menu contains the following options:
Table 1.3: S-PLUS menu options.
S-PLUS Menu Option
Description
Format
Applies S-PLUS consistent formatting and line
indentation to the entire script.
Toggle Comment
Designates the selected text in the Script
editor as a comment, or, if the selected text
already is a comment, removes the comment
designation
Shift Right
Moves the selected text to the right.
Shift Left
Moves the selected text to the left.
Define Folding Region
In the S-PLUS Script Editor, sets the currentlyselected code block as a collapsible block. A
collapsible region is indicated by the icon
in the left margin, and a vertical line, marking
the region to collapse. A collapsed region is
indicated by the icon
.
In Windows, you can hover the mouse
pointer over the collapsed region to display
the contents of the region in a tooltip.
Run Selection
Runs the code that is currently selected. If
nothing is selected, the current editor contents
are run.
This menu item also appears in the right-click
menu of the S-PLUS Script Editor and is
represented by the Run S-PLUS Code button
on the main S-PLUS Workbench toolbar.
Run Current File
24
Runs the entire contents of the script
currently open in the S-PLUS Script Editor.
Examining the S-PLUS Workbench GUI
Table 1.3: S-PLUS menu options. (Continued)
S-PLUS Menu Option
Description
Find “function”
Finds the selected function definition and
opens it for editing.
Find looks first in files currently open in an
editor, then it looks through your workspace.
Finally, it searches the S-PLUS database.
If the function is not found in an editor and
multiple definitions exist in the workspace,
use the resulting dialog to indicate the proper
source.
Note: Highlighting a function and typing
click also opens the selected
function definition for editing.
CTRL+mouse
See the section To edit a function definition
on page 130 for more information
Find References
Locates and highlights all instances of a
function call in a workspace. Find References
opens the Search view and displays the
number of times in a workspace where the
selected function is called. You can See the
Eclipse Workbench User Guide for more
information about the Search view.
See the section To find all references to a
function on page 131 for more information.
Copy to Console
Copies the selected code and pastes it into the
Console view. See the section Copying Script
Code to the Console on page 135
Open S-PLUS Help File
Opens the S-PLUS Language Reference to the
topic for the selected function. If you have no
documented function selected, the help
function topic is displayed.
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Chapter 1 The S-PLUS Workbench
Run Menu
The Run menu varies, depending on the perspective selected. In both
the S-PLUS and Debug perspective, the following S-PLUS Workbench
options are available. (See the corresponding descriptions for the
toolbar buttons in the section The S-PLUS Workbench Toolbar on
page 27 for more information.)
•
Run S-PLUS Code
•
Run Next S-PLUS Command
•
Stop S-PLUS Code
•
Toggle S-PLUS Debugger
•
Toggle S-PLUS Profiler
•
Toggle S-PLUS Warning Breakpoint
•
Toggle S-PLUS Error Breakpoint
For more information about the Run menu options available only in
the Debug perspective, see the section Debug Run Menu Options on
page 70.
Window Menu
The S-PLUS Workbench preferences are available from the Window
䉴 Preferences menu option. See the section Examining S-PLUS
Preferences on page 12 for more information.
Help Menu
Reference help, conceptual help, books, and user-interface guidance
are available from the Help menu.
Customized
Toolbars
26
•
Click S-PLUS Help from the Help menu to display the
S-PLUS Language Reference topic for the help function.
•
Click S-PLUS Manuals for a list of the PDFs that are installed
by default with your S-PLUS installation.
Both S-PLUS perspectives in the Workbench provide customizations
to the Eclipse toolbar and to view-specific toolbars.
Examining the S-PLUS Workbench GUI
The S-PLUS Workbench Toolbar
Regardless of the displayed perspective, the S-PLUS Workbench
toolbar appears in the IDE.
Figure 1.16: The S-PLUS Workbench toolbar.
Note
Eclipse implements a Run menu item that is different from that of S-PLUS Workbench
implementation. Use the S-PLUS Workbench Run menu item.
Use the S-PLUS Workbench toolbar to control running, debugging,
breaking, and profiling your code.
Table 1.4: S-PLUS Workbench toolbar.
Button
Description
Run S-PLUS Code. Click in either the Debug or the S-PLUS
perspective to run code that appears in the editor. (To view
the output, select the Output.)
27
Chapter 1 The S-PLUS Workbench
Table 1.4: S-PLUS Workbench toolbar. (Continued)
Button
Description
Run Next S-PLUS Command. Looks for the current
selection and runs the top-level S expression found at that
location.
If the cursor location does not match an expression exactly,
the next expression is evaluated (rather than the first one).
The output is routed to the Output, and the next expression is
selected automatically (or the first expression in the script is
selected automatically, if the expression that was just run was
the last one).
Stop S-PLUS Code. Click in either the Debug or the S-PLUS
perspective to stop running code.
Toggle S-PLUS Debugger. Engages the S-PLUS debugger.
(You can engage the S-PLUS debugger in either the S-PLUS or
the Debug perspectives; however, by default, the views
displaying debugging information are visible in the Debug
perspective.)
After you engage the S-PLUS debugger, any expression you
type in the Console, or that you run by clicking Run S-PLUS
Code on the toolbar, invokes the S-PLUS debugger.
Toggle S-PLUS Profiler. Engages the S-PLUS Profiler. (You
can engage the S-PLUS Profiler in either the S-PLUS or the
Debug perspectives; however, by default, the views displaying
profiling information are visible in the Debug perspective.)
You do not need to engage the S-PLUS debugger in order to
engage the Profiler. See the section Profiler on page 96 for
more information.
Toggle S-PLUS Warning Breakpoint. Requires that the
S-PLUS debugger be toggled on. Stops execution if S-PLUS
encounters a warning. See Table 3.7 in the section
Breakpoints view on page 89 for more information about
warning breakpoints.
28
Examining the S-PLUS Workbench GUI
Table 1.4: S-PLUS Workbench toolbar. (Continued)
Button
Description
Toggle S-PLUS Error Breakpoint. Requires that the S-PLUS
debugger be toggled on. Stops execution if S-PLUS encounters
an error. See Table 3.7 in the section Breakpoints view on
page 89 for more information about error breakpoints.
View toolbars
For more information about individual views’ toolbars, see the
individual views’ descriptions. See the section Examining the Views
on page 32 for more information.
S-PLUS
Workbench
Status Bar
The Workbench features a status bar that provides important
information about the working project and the current view.
Figure 1.17: Status bar.
Table 1.5: S-PLUS Workbench status bar.
Status Item
Description
Show View as Fast View. An Eclipse feature.
•
Click to display a list of available views,
and then select a view to maximize it and
add its icon to the status bar.
•
Click the view’s icon in the status bar to
minimize the view. (Alternatively, click the
view’s minimize icon, in its upper right
corner, to minimize it.)
For more information, see the Eclipse Workbench
User Guide.
Current working directory and file. When the
Script Editor has focus, this section of the status bar
displays the current file.
29
Chapter 1 The S-PLUS Workbench
Table 1.5: S-PLUS Workbench status bar. (Continued)
Status Item
Description
Working project. Displays the name of the project
that is currently set as the working project. For more
information about the working project, see the
section Working Projects and Databases on page
123.
Status indicator. When the box is labeled Busy,
and the status indicator is filling, then code is
currently running. When the box is clear and reads
Ready, no code is running.
File attribute. Indicates whether the file is readonly or writable.
Smart Insert. Toggles the insert mode. To toggle
this view, type CTRL+SHIFT+INSERT. When Smart
Insert mode is toggled off, typing aids like
automatic indentation, closing of brackets, and so
on, are not available. Smart Insert is an Eclipse
feature.
Cursor position. Indicates the line and column
position of the cursor.
S-PLUS
Workbench
Perspectives
and Views
The S-PLUS Workbench plug-in for Eclipse includes two customized
perspectives:
•
The S-PLUS perspective
•
The Debug perspective.
(See Table 1.1 for a short description of the perspectives.) By default,
each perspective includes Eclipse views and customized S-PLUS
Workbench views.
30
Examining the S-PLUS Workbench GUI
Changing the
S-PLUS
Workbench
Perspective
You can change the perspective to suit your development style by
moving, hiding, or closing views. For more information about
customizing the views within the perspective, see the section
Customizing the S-PLUS Perspective Views on page 54. For practice
exercises customizing the perspective, see the section Customized
Perspective Views on page 120.
•
To customize the default S-PLUS perspective, on the menu,
click Window 䉴 Customize Perspective. The Customize
Perspective dialog has two pages: Shortcuts and
Commands. Each of these pages describes global changes
you can make to the perspective.
•
To save a changed perspective, click Window 䉴 Save
Perspective As.
•
To restore an unsaved perspective’s default settings, click
Window 䉴 Reset Perspective.
•
To open another perspective, click Window 䉴 Open
Perspective, and then select a perspective from the Select
Perspective dialog.
Figure 1.18 shows the S-PLUS perspective with the views set at their
default positions.
Figure 1.18: S-PLUS Workbench window, S-PLUS perspective.
31
Chapter 1 The S-PLUS Workbench
Examining the
Views
A view is a visual component in the workbench. Views support the
script editor by providing alternate means of navigating through,
working with, and examining the elements of the project.
Using the standard Eclipse IDE features, you can:
•
Close a view by clicking the X icon on the view tab.
•
Reposition a view by clicking its tab and dragging it to
another part of the UI.
•
Set a selected view to “Fast View.” This option hides the view
to free space in the Workbench window and places a
minimized icon, which you can click to open the view, on the
status bar.
•
Change the views you see in the perspective. See the section
To change the displayed views on page 121.
Most views have their own control menus. (See the section Control
and Right-Click Menus on page 34 for more information.)
Saving views items changed in views
When you modify an item in a view, it is saved immediately.
Normally, only one instance of a particular type of view can exist in
the Workbench window.
32
Examining the S-PLUS Workbench GUI
Perspective views
The following table lists the views shown by default in each
perspective and indicates which views are shared by both
perspectives. This section includes descriptions for the views shared
across S-PLUS Workbench perspectives.
Table 1.6: Default views in the S-PLUS Workbench perspectives.
View Name
S-PLUS
Workbench
Perspective
Debug
Perspective
Description
reference
Allocations
view
x
page 98
Breakpoints
view
x
page 89
x
page 37
Debug view
x
page 76
Expressions
view
x
page 87
Function Calls
view
x
page 97
Console view
x
History view
x
page 54
Navigator
x
Objects view
x
Outline view
x
x
page 41
Output view
x
x
page 43
Problems view
x
x
Eclipse Workbench
User Guide
page 56
page 59
33
Chapter 1 The S-PLUS Workbench
Table 1.6: Default views in the S-PLUS Workbench perspectives. (Continued)
View Name
S-PLUS
Workbench
Perspective
Script Editor
x
Search Path
view
x
Tasks view
x
Variables view
Debug
Perspective
x
Description
reference
page 44
page 60
x
page 61
x
page 82
Hint
Change the view layout by moving views around the IDE, or control the views displayed using
the Show View dialog. For more information, see the section To change the displayed views on
page 121.
Control and
Right-Click
Menus
Views contain their own control and/or right-click menus, with menu
items that act on the view display or on the type of data displayed in
the view. Menus are displayed either when you click the drop-down
button ( ), located in the upper right corner of each view, or when
you right click the body of the view.
34
Examining the S-PLUS Workbench GUI
The following two images show the two types of menus in the
Navigator view. For more information about the Navigator, see the
section Navigator on page 39.
Figure 1.19: Control menu, available via drop-down button.
Figure 1.20: Context-sensitive menu, available via right-click in the view.
35
Chapter 1 The S-PLUS Workbench
•
The Script Editor has only a context-sensitive menu, available
via a right-click action. Its available options depend on the
current selection in the editor. For example, if you select text
and right-click, you have the option to cut or copy the
selection. If you select an S-PLUS function, you have the
option to open the S-PLUS Help file for that function.
The options on the Script Editor’s context-sensitive menu are
a selection of options that appear on the main menu.
•
The Outline view and the Allocations view have only the
control drop-down menu.
In the following views, the right-click (context-sensitive) menu and
the control drop-down menu are identical. The control menu for each
view is described in this document in the section describing its view.
See the section Examining the Views on page 32 for more
information:
•
Console view.
•
Function Calls view.
•
History view.
•
Objects view.
•
Output view.
•
Search Path view.
The following views each contain two different menus:
36
•
The control menu, available from the drop-down button.
•
The context-sensitive menu, available via right-click in the
body of the view. The options available on the right-click
menu vary according to the item selected in the view (for
Examining the S-PLUS Workbench GUI
example, removing a selection, copying a selection, and so
on.) For more information about where each view appears,
see the section Perspective views on page 33.
Table 1.7: Views with different control and right-click menus.
View
Location of more menu information
Navigator
page 39
Tasks view
page 63
Problems view
page 59
Debug view
page 78
Variables view
page 84
Expressions view
page 84
Breakpoints view
page 89
Each view action also has a quick-key sequence to perform an action.
(For example, to clear the text in the console, with the Console
active, type CTRL+L.)
Default Shared
Views
The following sections describe the views that are shown, by default,
in both the S-PLUS perspective and the Debug perspective.
S-PLUS
Workbench
Console
The S-PLUS Workbench Console is an editable view, analogous to
the Commands window in the S-PLUS GUI. Using the Console, you
can:
•
Run individual S-PLUS commands by typing them and
pressing ENTER.
•
Scroll through previous commands by pressing the
DOWN arrow on the keyboard.
UP
or
37
Chapter 1 The S-PLUS Workbench
•
Copy an individual command or blocks of commands from
the Script Editor, using the Copy to Console menu item, to
run them in the Console. (Note that you do not need to select
Paste; Copy to Console copies your selected text in the
Script Editor and pastes it into the Console.)
Figure 1.21: S-PLUS Workbench Console.
•
Copy from the console to a script file. (You can also copy the
command prompts. To set this option, on the menu, click
Window 䉴 Preferences, and on the Console/Output page,
select Include Prompts in Copy action.)
Console control and right-click menus
The Console controls include these Eclipse options:
•
Pin the view in place (
).
•
Toggle between open Console views (
•
Open a new Console (
).
).
The Console control menu and right-click menu are the same. You
can use the Console control menu (click
or right-click the body of
the Console) to perform the following tasks:
38
•
Clear the contents of the console.
•
Copy the selected text.
•
Cut the selected text.
•
Paste text from the clipboard to the console.
•
Find a string.
•
Select all text.
•
Save the console contents to a file.
Examining the S-PLUS Workbench GUI
•
Print the console contents.
•
Open the Preferences dialog to set such options as font color
and style, among others.
For exercises using the S-PLUS Workbench Console, see the section
Copying Script Code to the Console on page 135. For more
information about the S-PLUS Commands window, see Chapter 10,
Using the Commands Window in the S-PLUS User’s Guide.
Navigator
The Navigator is a standard Eclipse view. Its drop-down ( ) control
menu is standard to Eclipse, while its right-click menu contains three
S-PLUS-specific items, described in the following section. For
information about using the Navigator, see the Eclipse Workbench
User Guide, available from the Help 䉴 Help Contents menu.
Navigator control and right-click menus
In addition to having a drop-down control menu, the Navigator has
a right-click menu containing three S-PLUS-specific options:
Table 1.8: Navigator S-PLUS-specific right-click menu options.
Menu option
Description
Source S-PLUS
Files
Parses and then evaluates each expression in the
selected project or file. (Note that if you have selected
the project, every file in that project is sourced.)
Format S-PLUS
Files
Applies S-PLUS consistent formatting and line
indentation to all scripts in the working project.
To customize the formatting options, on the main
menu, click Window 䉴 Preferences, in the left pane,
click S-PLUS to expand the view, and then click
Editor. Use the Editor page to customize formatting
options. See the section To change the code formatting
options on page 117 for more instruction.
39
Chapter 1 The S-PLUS Workbench
Table 1.8: Navigator S-PLUS-specific right-click menu options. (Continued)
Menu option
Description
Toggle
Working
S-PLUS Project
Available when you select a project in the Navigator.
The project that you set as working becomes the
current working directory, or the root to which all
relative paths are resolved.
The working project also becomes the first position (in
the search path, which you can see in the Search Path.
This path contains the .Data database. All objects
created as a result of running code in the S-PLUS
Workbench are written to that .Data database
(regardless of the project the code is in).
When you toggle off (that is, clear) the selection and
have no working project, the .Data database is set to
the current workspace, and the Search Path shows the
workspace in the first position. In this case, all objects
created in any project are written to the .Data database
in the workspace and are available to any project in the
workspace.
See Figure 1.22 for an illustration. For more
information about working projects and the current
working directory, see the section Setting the Working
Project on page 123.
40
Examining the S-PLUS Workbench GUI
Figure 1.22: Toggle Working S-PLUS Project shows current working project at
the top of the Search Path.
Outline view
The Outline view displays an outline of the elements in the script
open in the script editor. In the S-PLUS Workbench, Outline view
displays functions and objects in the order they appear in the script
editor. Items that you have identified to “watch” in the Functions to
41
Chapter 1 The S-PLUS Workbench
Watch text box of the Preferences dialog appear in the Outline
view with an arrow. You can jump to the definition of a function or
object (or other structure element) by clicking it in Outline view.
Figure 1.23: S-PLUS Workbench Outline view.
Note
The Outline view updates only after you save changes to its associated file, displayed in the
Script Editor.
42
Examining the S-PLUS Workbench GUI
Outline view toolbar
The Outline view contains a toolbar that displays the following
toggle buttons:
Table 1.9: Outline view buttons.
Button
Description
Hides all standard functions displayed in the Outline view.
Click again to display standard functions.
Hides all functions that you have designated to watch
displayed in the Outline view. Click again to display the
functions.
Hides all anonymous functions displayed in the Outline
view. Click again to display the functions.
Hides all variables in the Outline view. Click again to
display the variables.
Sorts items displayed the Outline view alphabetically. Click
again to return the items to the order in which they appear
in the script.
Displays a menu showing all buttons available on the button
bar. (You can toggle these selections either using the menu,
or on the button bar.)
Outline view control menu
The Outline view control menu provides menu access to the buttons
visible on the Outline view toolbar, and to the Preferences dialog.
See the descriptions in Figure 1.9 for more information. (The Outline
view contains no right-click menu.)
Output
The Output displays the code you run (and the results of the code
you run) when you click either Run S-PLUS Code on the toolbar, or
when you press F9. The text displayed in the Output is replaced each
43
Chapter 1 The S-PLUS Workbench
time you click Run S-PLUS Code or press F9. That is, unlike the
Console, the Output does not store and display previously-run
commands. Also unlike the Console, the Output is not editable;
however, you can select and copy lines of text in the Output. You
can also print or clear the entire contents of the Output.
Figure 1.24: S-PLUS Workbench Output.
Output control and right-click menus
You can use the Output control menu (click
following tasks:
) to perform the
•
Clear the contents of the view.
•
Copy the selected text.
•
Find a string.
•
Select all text.
•
Save the view contents to a file.
•
Print the view contents.
•
Display the Preferences dialog to change the font color and
style.
The drop-down control menu and the right-click context-sensitive
menu are identical in the Output.
44
Examining the S-PLUS Workbench GUI
S-PLUS
Workbench
Script Editor
The S-PLUS Workbench Script Editor is a text editor displayed in
both the S-PLUS perspective and the Debug perspective. The S-PLUS
Workbench Script Editor is similar to the Script Editor in S-PLUS;
however, it contains additional script-authoring features such as
syntax coloring and integration with the other views in the IDE.
Figure 1.25: S-PLUS Workbench Script Editor.
You can run code in the S-PLUS Workbench Script Editor by
highlighting the code and clicking Run S-PLUS Code (
toolbar.
) on the
Note
To interrupt code that you run from the Script Editor, either click Stop S-PLUS Code (on the
toolbar) or press ESC.
Text Editing Assistance
To help you write efficient, easy-to-follow scripts, the Script Editor
provides the following features:
•
Displays keywords, user-defined text, and function arguments
in customizable colors. See the section Setting the S-PLUS
Workbench Preferences on page 110.
•
Displays code line numbers in a column adjacent to the code.
45
Chapter 1 The S-PLUS Workbench
•
Provides automatic code indentation and parenthesis
matching. (See the Eclipse documentation for more
information on the editor’s standard features.)
Note
To indent selected text, first highlight the text to be indented, and then press TAB or CTRL+TAB
to shift the selected text right or left, respectively.
•
Activates the Script Outline view when you edit a script.
•
Displays task and breakpoint markers in the left margin, and a
task marker “thumb” in the right margin.
•
Displays the help topic for documented functions when you
select the function name, and then type F1.
Note
You can use the Eclipse editor to edit non-project files in the S-PLUS Workbench. To open a nonproject file, on the File menu, click Open File, and then browse to the location of the file to edit.
For more information about editing files in Eclipse, see the Eclipse Workbench User Guide.
View integration
The Script Editor is closely integrated with the views in both the
S-PLUS perspective and Debug perspective. This integration includes
the following:
46
•
When you type a task keyword in the editor, it is
automatically added to the Tasks view after you save the file.
See the section Tasks view on page 61 for more information.
•
When you set a breakpoint, the breakpoint appears in the
margin of the Script Editor both in the Debug perspective and
the S-PLUS perspective. (You can also set a breakpoint in the
margin of the Script Editor in both perspectives. See the
section Setting breakpoints on page 141.)
•
When you make an error and save your script file, the error
shows in the Problems view. See the section To examine
problems on page 137 for more information.
Examining the S-PLUS Workbench GUI
•
When you create a new object in the script, it appears in the
Outline view. To make it appear in the Objects view, you
must run the script and refresh the Objects view.
Script Editor right-click menu
The right-click menu in the Script Editor combines actions from the
Eclipse main menu, including the options available from the S-PLUS
menu, and the Preferences dialog.
See the section S-PLUS Menu on page 24 for information about the
S-PLUS options.
See section Setting the S-PLUS Workbench Preferences on page 110
for information about setting Preferences options.
(The Script Editor has no drop-down control menu.)
47
Chapter 1 The S-PLUS Workbench
COMMONLY-USED FEATURES IN ECLIPSE
The core Eclipse IDE contains many additional features that you
might find helpful in managing your projects. The following table lists
a few of these features, along with references to the Eclipse Workbench
User Guide to help you learn how to use them effectively.
Table 1.10: Eclipse Tasks and Features.
Task
Eclipse Feature Description
Comparing files with
previous versions.
The Compare With Local History menu item
is available from the control menu in Navigator
view. Using this feature, you can compare the
current version of the selected file with
previously-stored local versions. For more
information, see the topic “Local history” in the
Eclipse Workbench User Guide.
Replacing files with a
previous version.
The Replace With Local History and Replace
With Previous from Local History menu
items are available from the control menu in
Navigator view. Using these features, you can
replace the current version of the selected file
with one of the previously-stored local versions.
Replace With Previous from Local History
displays no selection dialog; it just replaces the
file. To choose a previous state in the Local
History list, use Replace With Local History.
For more information, see the topic “Replacing a
resource with local history” in the Eclipse
Workbench User Guide.
Finding a word in a
project or a term in a
Help topic.
48
Using the Search 䉴 File menu item, you can
find all occurrences of a word in a project or
Help topic. For more information, see the topic
“File search” in the Eclipse Workbench User Guide.
Commonly-Used Features in Eclipse
Table 1.10: Eclipse Tasks and Features. (Continued)
Task
Eclipse Feature Description
Filter files in the
Navigator view.
Using the Working Sets menu option on the
control menu in Navigator view, you can create
subsets of files to display or hide. For more
information, see the topics “Working Sets” and
“Showing or hiding files in the Navigator view”
in the Eclipse Workbench User Guide.
View a file that is not
part of your project.
Use the File 䉴 Open File menu item to open a
file that is not part of your project.
49
Chapter 1 The S-PLUS Workbench
50
THE S-PLUS PERSPECTIVE
2
Introduction
52
S-PLUS Perspective Views
Customizing the S-PLUS Perspective Views
History view
Objects view
Problems view
Search Path view
Tasks view
53
54
54
56
59
60
61
51
Chapter 2 The S-PLUS Perspective
INTRODUCTION
S-PLUS Workbench perspectives define the appearance and behavior
of the S-PLUS Workbench Eclipse plug-in, including the S-PLUS Script
Editor, views, menus, and toolbars. The S-PLUS perspective combines
S-PLUS Workbench views and options so you can accomplish specific
types of tasks and work with specific types of resources.
•
For more information about the S-PLUS Debugger perspective
options and views, see Chapter 3.
•
For practice instruction using the features in the S-PLUS
perspective, as well as the S-PLUS Workbench and Debug
perspective, see Chapter 4, S-PLUS Workbench Tasks.
Note
You can change a perspective to suit your development style by moving, hiding, or closing views.
For more information about customizing the views within the perspective, see the section
Changing the S-PLUS Workbench Perspective on page 31, or see the section Customized
Perspective Views on page 120.
Figure 2.1: The S-PLUS perspective.
52
S-PLUS Perspective Views
S-PLUS PERSPECTIVE VIEWS
The S-PLUS Workbench includes views shared across perspectives.
For a list of all views and their default perspectives, see Table 1.6 in
Chapter 1. (Chapter 1 also includes descriptions of the shared views.)
The S-PLUS perspective includes default Eclipse views and
customized views. Customized views in the S-PLUS perspective
include the following:
Table 2.1: S-PLUS perspective views and exercise references.
View
Descriptions
Practice exercises
Console view
Shared view. For a
description, see the section
S-PLUS Workbench Console
on page 37.
"To run copied script
code" on page 136
History view
For a description, see the
section History view on
page 54.
"To examine the history"
on page 137
Objects view
For a description, see the
section Objects view on
page 56.
"To examine the
objects" on page 132
Outline view
Shared view. For a
description, see the section
Outline view on page 41.
"To examine the
outline" on page 131
Output view
Shared view. For a
description, see the section
Output on page 43.
"To run code" on page
137
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Chapter 2 The S-PLUS Perspective
Table 2.1: S-PLUS perspective views and exercise references. (Continued)
View
Descriptions
Practice exercises
Problems
view
For a description, see the
section Problems view on
page 59.
"To examine problems"
on page 137
Search Path
view
For a description, see the
section Search Path view on
page 60.
"Adding a Database" on
page 125 and
"Detaching a Database"
on page 126
Tasks view
Shared view. For a
description, see the section
Tasks view on page 61.
"To add a task in the
script file" on page 134
and "To add a task
directly to the Tasks
view." on page 133
Both the S-PLUS perspective and the Debug perspective also display
the default Eclipse Navigator view, which displays project directories
and all files associated with each project. The Navigator view and
other Eclipse IDE views are described in the Eclipse Workbench User
Guide.
Customizing
the S-PLUS
Perspective
Views
The default S-PLUS perspective settings control the views that open by
default in preset locations; however, you can customize the view
appearance, and then save the resulting perspective. See the section
Customized Perspective Views on page 120 for more information.
History view
The History view is similar to the Commands History dialog in
S-PLUS for Windows. The History view is a scrollable list of
commands that have previously been run in the Console.
(Commands that you run by clicking Run S-PLUS Code or pressing
F9 do not appear in the History view. See the section Output on page
43.)
54
The following sections describe only the views that appear by default
in only the S-PLUS perspective.
S-PLUS Perspective Views
•
When you select a command in the History view, the
pending text in the Console changes to the selected text. You
can then press ENTER, or you can double-click the text in the
History view to execute the command. You can select only
one line at a time in the History view.
•
When you scroll up or down through previously-run
commands in the Console, the corresponding command is
highlighted in the History view.
Note
In Windows, S-PLUS uses the key F10 to run a selected command. The S-PLUS Workbench uses
the key F9 to run a selected command in all platforms.
Figure 2.2: S-PLUS Workbench History view
History view control and right-click menus
You can use the History view control menu (click
) to:
•
Select input displayed in the History view and copy it to the
Console.
•
Clear the History view.
55
Chapter 2 The S-PLUS Perspective
Note
In the Preferences dialog, you can set the option to persist entries in the History view between
sessions. For more information about this option, see the section Store Console History Between
Sessions on page 16. The History view holds up to 150,000 lines of commands.
The drop-down control menu and the right-click context-sensitive
menu are identical in the History view.
Objects view
The Objects view is similar to the Object Explorer in the S-PLUS
GUI. It displays all objects for projects associated with the workspace
in two panes: a table view and an expandable tree view (the
Workbench Object Explorer).
The two panes of the Objects view are linked: when the Objects
view table pane has focus, items you select in the table are highlighted
in the tree pane. When the tree pane has focus, objects you select in
the tree are also highlighted in the table pane. (If you select an object
member in the tree pane, its corresponding object is highlighted in
the table pane.)
Figure 2.3: S-PLUS Workbench Objects view.
Objects view control and right-click menus
You can use the Objects view control menu (click
following tasks:
56
) to perform the
•
Select another database.
•
Refresh the view on the currently-active database.
S-PLUS Perspective Views
•
Remove the selected object from the currently-active
database.
•
Show or hide S-PLUS system objects, such as .Last.value,
.Data, and .Random.seed. (These objects are hidden by
default.)
•
Change the number of items displayed in the tree view
members.
The drop-down control menu and the right-click context-sensitive
menu are identical in the Objects view.
Note
When you run code that creates objects in an S-PLUS script, the Objects view is not
automatically refreshed to display the new objects. To refresh Objects view and display newlycreated objects, right-click the Objects view (or click the control menu button
from the menu, click Refresh.
), and then
Warning
If you select a large database, such as splus, in the Objects view, it can take a long time to
display the contents in the table and tree view panes.
Objects view
table pane
The Objects view includes a table pane displaying a list of the names
and types of objects in S-PLUS databases. The Objects view table
includes the following information about each object:
•
name
•
data class
•
storage mode
•
extent
•
size
•
creation or change date.
By default, the S-PLUS system objects, such as .Random.seed and
.Last.value are hidden. You can display these objects by toggling the
option on the Objects view control menu.
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Chapter 2 The S-PLUS Perspective
Object Explorer
(tree view pane)
The Objects view includes an expandable tree view, the Object
Explorer. (See Figure 2.4.) Objects listed in the Object Explorer
correspond to objects in the Objects view table pane.
The Object Explorer displays icons representing the type of object
or object member, along with its name as a label. (These icons are the
same icons used in the standard S-PLUS GUI.)
You can expand the objects to display each objects’ members. By
default, the Object Explorer displays up to 25 object members at
each expandable level. You can change this default using the Objects
view context-sensitive menu item, Set Max Children.
Figure 2.4: The S-PLUS Workbench Object Explorer.
•
Display the Set Max Children dialog to indicate the number
of object members to display in the Object Explorer. By
default, this option is set to 25.
Figure 2.5: Set Max Children dialog.
58
S-PLUS Perspective Views
Problems view
The Problems view is a standard Eclipse view that displays errors as
you edit and save code. For example, if you forget a bracket or a
quotation mark, and then save your work, the description appears as
a syntax error in the Problems view.
Note
Syntax problems appear in the Problems view only after you save the file.
If your code has a problem that is displayed in the Problems view,
and the view is not the active view, the Problems view tab title
appears as bold text.
To open the Script editor at the location of the problem, double-click
the error in the Problems view.
Figure 2.6: S-PLUS Workbench Problems view showing the right-click contextsensitive menu.
Problems view control and right-click menus
You can use the Problems view control menu (click
the following tasks:
) to perform
•
Display the Sorting dialog to sort the problems displayed in
the view, either in ascending or descending order, and
according to the problems’ characteristics.
•
Display the Filters dialog to specify properties for filtering
problems.
For more information about using these dialogs, see the Eclipse
Workbench User Guide.
59
Chapter 2 The S-PLUS Perspective
You can use the Problems view right-click context-sensitive menu
(see Figure 2.6) to perform the following tasks:
•
Jump to the location in the file containing the problem.
•
Display the file name containing the problem in the
Navigator. (This action opens an instance of the Navigator.)
•
Copy the Problems view table to the clipboard.
•
Select all entries in the table.
•
View the properties of the problem.
These menu items are standard to the Eclipse GUI. For more
information, see the Eclipse Workbench User Guide.
Search Path
view
The Search Path view displays the names and search path position of
all the attached S-PLUS databases.
Figure 2.7: S-PLUS Workbench Search Path view.
The databases that are in your search path determine the objects that
are displayed in Objects view. That is, if a database is in your search
path, the objects in that database appear in the Objects view. See the
section Examining Objects on page 132. For more information about
working with the Search Path view, see the section Changing
Attached Databases on page 125.
The first position in the Search Path view shows the current working
directory, which can be either the workspace or the current path. You
can set a project to be the working project by right-clicking its name
in the Navigator, and then clicking Toggle Working S-PLUS
Project. See the section Navigator on page 39, and the section Setting
the Working Project on page 123.
60
S-PLUS Perspective Views
Search Path view control and right-click menus
You can use the Search Path view control menu (click
) to:
•
Attach a library.
•
Attach a module.
•
Attach a directory.
•
Detach the currently-selected database in the view.
•
Refresh the current view.
The drop-down control menu and the right-click context-sensitive
menu are identical in the Search Path view.
Note
When you use the control menu to add to (or remove from) the Search Path view a library,
module, or directory, the view automatically refreshes. When you run code to add or remove a
library, module, or directory, the view is not automatically refreshed. To refresh the view, rightclick the Search Path view (or click the control menu button, and then from the menu, click
Refresh.
Tasks view
The Tasks view is a standard Eclipse IDE view, which is customized
in S-PLUS to provide three levels of tasks:
Table 2.2: S-PLUS Workbench Tasks.
Task
Description
FIXME
Defines high-priority tasks. The
task appears with an
exclamation mark in the Tasks
view.
TODO
Defines medium-priority tasks.
XXX
Defines low-priority tasks.
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Chapter 2 The S-PLUS Perspective
You can change these tasks, or you can add your own custom tasks.
For more information about changing task settings, see section Task
Options on page 22, and the section To set the S-PLUS preferences
on page 111.
Figure 2.8: S-PLUS Workbench Tasks view showing the right-click context-sensitive
menu.
Tasks view toolbar
The Tasks view also contains a toolbar that displays the following
buttons:
Table 2.3: Tasks view buttons.
Button
Description
Click to display the Add Task dialog to add a custom task.
Click to delete the selected custom task. (Note that you
cannot use this button to delete tasks identified in the script.)
Click to display the Filters dialog to specify properties for
filtering the tasks.
62
S-PLUS Perspective Views
Tasks view control and right-click menus
You can use the Tasks view control menu (click
following tasks:
) to perform the
•
Display the Sorting dialog to sort the tasks displayed in the
view, either in ascending or descending order, and according
to the tasks’ characteristics.
•
Display the Filters dialog to specify properties for filtering
tasks.
You can use the standard Eclipse Tasks view right click contextsensitive menu to:
•
Add a task to the list that is not linked to a file (Displays the
Eclipse Add Task dialog).
•
Open a file and display the location of a linked task in the
Script Editor.
•
Display the location of a linked task in the Navigator (opens
an instance of the Navigator).
•
Copy the Tasks view table to the clipboard.
•
Select all entries in the table.
•
Delete all tasks marked as completed (that is, containing a
check mark in the first column).
•
View the properties of the task.
For more information about the basic Eclipse Tasks view, see the
Eclipse Workbench User Guide.
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Chapter 2 The S-PLUS Perspective
64
S-PLUS WORKBENCH DEBUG
PERSPECTIVE
3
Introduction
66
Debug Perspective Options and Preferences
Setting Preferences
Debug Mode
Debug Run Menu Options
68
69
69
70
Debug Perspective Views
Profiler
Profiler views
74
96
97
65
Chapter 3 S-PLUS Workbench Debug Perspective
INTRODUCTION
The S-PLUS Workbench includes the Debug perspective, which is
based on the Eclipse standard debugging perspective.
From the Debug perspective, you can observe the run-time behavior
of your program and determine the location of semantic errors. The
S-PLUS debugger understands features that are built into the S-PLUS
programming language and its associated libraries. With the S-PLUS
debugger, you can break (suspend) execution of your program to
examine your code and evaluate variables.
After you have written your code and resolved any syntax errors, you
can use the S-PLUS debugger to correct any logic errors that keep your
code from running correctly. Using the S-PLUS debugger, you can:
66
•
Control your code testing by setting break points, stepping
into, though, and out of code, and pausing or terminating the
process at any point using the S-PLUS debugger features.
•
Set, disable, enable, or remove breakpoints while you are
debugging.
•
View variable and expression values at breakpoints while
stepping through your code.
•
Track resource allocation and function use.
Introduction
Figure 3.1 shows the Debug perspective’s views. This chapter
describes the options, features, and views included in the Debug
perspective.
Figure 3.1: The Debug perspective.
The Debug perspective also includes a profiler, which you can use to
inspect allocated memory and functions called, including call count
and duration. For more information about the S-PLUS Profiler, see the
section Profiler on page 96.
•
For tasks that walk you through using the S-PLUS debugger
and profiler, see the section Chapter 4, S-PLUS Workbench
Tasks.
•
For information about the S-PLUS perspective, see Chapter 2,
The S-PLUS Perspective.
Note
You can create your own perspective that displays a combination of views from the perspectives,
or you can change the Debug perspective to suit your development style by adding, moving,
hiding, or closing views. For more information about customizing the views within the
perspective, see the section Changing the S-PLUS Workbench Perspective on page 31, or see the
section Customized Perspective Views on page 120.
67
Chapter 3 S-PLUS Workbench Debug Perspective
DEBUG PERSPECTIVE OPTIONS AND PREFERENCES
When you examine the Debug perspective, examine the S-PLUS
Workbench toolbars, menus, default options, and preferences in the
IDE.
Note that the S-PLUS Workbench toolbar includes the S-PLUS
debugger buttons (as well as the Profiler button). These buttons are
described in greater detail in Table 1.4.
Figure 3.2: The S-PLUS Workbench toolbar.
Note
When you are in the Debug perspective, notice that the Eclipse environment displays a generic
toolbar that includes a Run button, a Debug button, and an External Tools button. These
buttons might work with other Eclipse plug-ins, but they are not intended to be used with
S-PLUS. You can set breakpoints from the Debug view toolbar, or from several menus, and you
can run code using the Run S-PLUS Code button on the S-PLUS toolbar or from the console.
68
Debug Perspective Options and Preferences
Setting
Preferences
From the menu, click Window 䉴 Preferences to open the
Preferences dialog and examine the options. (For more information
about setting preferences, see the section Examining S-PLUS
Preferences on page 12. For more information about Eclipse
preferences, see the Eclipse Workbench User’s Guide, available from the
Help 䉴 Help Contents menu in the IDE.)
Most options in the S-PLUS pages of the Preferences dialog apply to
global settings in the S-PLUS Workbench. For example, options
controlling editor or Console view text colors apply to both
perspectives. Only the Profiler page under S-PLUS controls S-PLUS
debugger behavior, and that controls only the refresh rate for system
allocations and function calls. See section Examining S-PLUS
Preferences on page 12 for more information.
Debug Mode
To start debugging, first activate the debugger using one of the
following methods:
•
On the toolbar, click Toggle S-PLUS Debugger
.
•
On the menu, click the Run 䉴 Toggle S-PLUS Debugger.
•
On the keyboard, press CTRL+ALT+D.
After you activate the S-PLUS debugger, any expression you type in
the Console view, or that you run by clicking Run S-PLUS Code ( )
on the toolbar, invokes the S-PLUS debugger.
Note
You can set Eclipse an option to be notified that a debug session is about to begin (that is, if you
click Debug ( ) and try to run a function in the Console view that encounters any
breakpoints).
1. From the main menu, click Windows 䉴 Preferences.
2. Expand Run/Debug and select Perspectives.
3. In the Perspectives dialog, in the Open the associated perspective when
launching group, select Prompt. Click OK.
Using this Eclipse option, you are prompted to change to the Debug perspective with the
message box shown in Figure 3.3. Clicking Yes displays the Debug perspective with the Debug
view open and the debugging started.
69
Chapter 3 S-PLUS Workbench Debug Perspective
Figure 3.3: The Confirm Perspective Switch message box.
Debug Run
Menu Options
When you switch to the Debug perspective, the S-PLUS Workbench
Run menu changes to list all of the code control actions specific to
that perspective. Note that many of the options listed in this menu are
default Eclipse debugging options. For more information about those
options, see the Eclipse Workbench User Guide. The Debugger actions
are available in the Debug perspective views.
Table 3.1: Debug perspective Run menu.
70
Menu item
Description
Run S-PLUS Code
Runs the code in the currently-active file,
or runs the selected code.
Run Next S-PLUS
Command
Runs the next available S-PLUS command.
Toggle S-PLUS Debugger
When toggled on, engages the S-PLUS
debugger. (You can engage the Debugger
in either the S-PLUS or the Debug
perspectives; however, by default, the
views displaying debugging information
are visible in the Debug perspective.)
Debug Perspective Options and Preferences
Table 3.1: Debug perspective Run menu. (Continued)
Menu item
Description
Toggle S-PLUS Profiler
When toggled on, engages the S-PLUS
Profiler. (You can engage the S-PLUS
Profiler in either the S-PLUS or the Debug
perspectives; however, by default, the
views displaying profiling information are
visible in the Debug perspective.)
You do not need to engage the debugger
in order to engage the Profiler. See the
section Profiler on page 96 for more
information.
Resume
Resumes debugging when the debugger is
paused.
Suspend
Suspends debugging.
Terminate
Terminates debugging.
Step Into
Steps into the current function by one
level
Step Over
Stays at the same expression level but
steps to the next expression.
Step Return
Steps out of the current function by
one level.
Run to Line
Core Eclipse debugger option; not
implemented in S-PLUS.
Use Step Filters
Core Eclipse debugger option; not
implemented in S-PLUS.
Run Last Launched
Core Eclipse debugger option; not
implemented in S-PLUS.
71
Chapter 3 S-PLUS Workbench Debug Perspective
Table 3.1: Debug perspective Run menu. (Continued)
72
Menu item
Description
Debug Last Launched
Core Eclipse debugger option; not
implemented in S-PLUS.
Run Last Launched
Core Eclipse debugger option; not
implemented in S-PLUS.
Debug Last Launched
Core Eclipse debugger option; not
implemented in S-PLUS.
Run History
Core Eclipse debugger option; not
implemented in S-PLUS.
Run As
Core Eclipse debugger option; not
implemented in S-PLUS.
Run
Core Eclipse debugger option; not
implemented in S-PLUS. (Use the Run
S-PLUS Code option at the top of the
main menu, F9, the Debug view contextsensitive menu, or on the Debugger
toolbar.)
Debug History
In its submenu, lists the previouslylaunched debugging actions. From this
list, you can select a previous
Debug As
Core Eclipse debugger option; not
implemented in S-PLUS.
Debug
Core Eclipse debugger option; not
implemented in S-PLUS.
External Tools
Core Eclipse debugger option; not
implemented in S-PLUS.
Debug Perspective Options and Preferences
Table 3.1: Debug perspective Run menu. (Continued)
Menu item
Description
Toggle S-PLUS Warning
Breakpoint
Requires that the S-PLUS debugger be
toggled on. When toggled on, stops
execution if S-PLUS encounters a warning.
See Table 3.7 in the section Breakpoints
view on page 89 for more information
about warning breakpoints.
Toggle S-PLUS Error
Breakpoint
Requires that the S-PLUS debugger be
toggled on. When toggled on, stops
execution if S-PLUS encounters an error.
See Table 3.7 in the section Breakpoints
view on page 89 for more information
about error breakpoints.
Toggle Line Breakpoint
When toggled on, removes the breakpoint
on the selected line.
Toggle Method
Breakpoint
Core Eclipse debugger option; not
implemented in S-PLUS.
Toggle Watchpoint
Not implemented in the debugger.
Skip All Breakpoints
When selected, disregards but maintain
(that is, does not remove or disable) all
breakpoints. When this button is toggled
on, all breakpoints appear with a diagonal
slash, as shown in the button.
Remove All Breakpoints
Removes every breakpoint from files in
open projects. (This item does not remove
breakpoints from files in closed projects.)
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Chapter 3 S-PLUS Workbench Debug Perspective
DEBUG PERSPECTIVE VIEWS
The Debug perspective includes views specific to using the debugger
and the profiler, as well as views shared across perspectives. For a list
of all views and their default perspectives, see Table 1.6 in Chapter 1.
(Chapter 1 also includes descriptions of the shared views.)
The Debug perspective includes the default Eclipse Navigator view
and customized views. Customized views in the Debug perspective
include the following:
Table 3.2: Debug perspective views and exercise references.
74
View
Descriptions and Practice exercises
Allocations
view
An S-PLUS Profiler view. For a description, see the
section Allocations view on page 98. For practice using
this view, see the exercise in the section Examining
Resource Usage on page 150. (The Profiler views are
discussed in more detail in the section Profiler Mode on
page 97.)
Breakpoints
view
For a description, see the section Breakpoints view on
page 89. For practice using this view, see the exercise in
the section Setting breakpoints on page 141.
Console view
Shared view. For a description, see the section S-PLUS
Workbench Console on page 37. For practice using this
view, see the exercise in the section To run copied script
code on page 136.
Debug view
For a description, see the section Debug view on page
76. For practice using this view, see the exercise in the
section Examining the call stack on page 144.
Expressions
view
For a description, see the section Expressions view on
page 87. For practice using this view, see the exercise in
the section Examining Variables and Expressions on
page 145
Debug Perspective Views
Table 3.2: Debug perspective views and exercise references. (Continued)
View
Descriptions and Practice exercises
Function
Calls view
An S-PLUS Profiler view. For a description, see the
section Function Calls view on page 97. For practice
using this view, see the exercise in the section
Examining Function Calls on page 150. (The Profiler
views are discussed in more detail in the section Profiler
Mode on page 97.)
Outline view
Shared view. For a description, see the section Outline
view on page 41. For practice using this view, see the
exercise in the section To examine the outline on page
131.
Output view
Shared view. For a description, see the section Output
on page 43. For practice using this view, see the exercise
in the section To run code on page 137.
Variables
view
For a description, see the section Variables view on
page 82. For practice using this view, see the exercise in
the section Examining Variables and Expressions on
page 145.
Tasks view
Shared view. For a description, see the section Tasks
view on page 61. For practice using this view, see the
exercise in the section Adding a Task to A Script on
page 132.
Additionally, the Debug perspective displays the Script Editor, which
is shared with the S-PLUS perspective. See the section Editor on page
79 for more information about using the Script Editor with the
Debugger. See the section S-PLUS Workbench Script Editor on page
45 for more general information about editing code in the Script
Editor.
From the Debug perspective, you can observe the run-time behavior
of your program and determine the location of semantic errors. The
Workbench debugger understands features that are built into the
75
Chapter 3 S-PLUS Workbench Debug Perspective
S-PLUS programming language and its associated libraries. With the
debugger, you can break (suspend) execution of your program to
examine your code and evaluate and edit variables.
Debug view
The Debug view displays the call stack of a currently-paused
expression. Clicking any level of the call stack displays in the Editor
the current function and/or the highlighted expression.
Figure 3.4 displays the Debug view, in its default position, displaying
the call stack for the kahanSum example.
Figure 3.4: The Debug view.
76
Debug Perspective Views
Debug view toolbar
The Debug view contains a toolbar with the following buttons for
evaluation control, in the order of their appearance, left to right:
Table 3.3: Debug view toolbar buttons.
Button
Description
Remove All Terminated Launches. Clears
the call stack of all debugging sessions that
ended with a termination.
Resume. Continues to the next breakpoint.
Suspend. Pauses the execution as though a
breakpoint had been hit.
Terminate. Stops the execution. Similar to
ESC functionality.
Disconnect. For remote debugging. Not
implemented for S-PLUS.
Step Into. Steps into the current function by
one level.
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Chapter 3 S-PLUS Workbench Debug Perspective
Table 3.3: Debug view toolbar buttons. (Continued)
Button
Description
Step Over. Stays at the same expression
level but steps to the next expression.
Step Return. Step out of the current function
level.
Use Step Filters/Step Debug. This feature is
not supported in the S-PLUS Workbench.
Note
The feature Drop to Frame is not implemented in the S-PLUS Workbench.
Debug view control and right-click menus
The Debug view contains a control drop-down ( ) menu with one
command: View Management, which displays the View
Management page of the Eclipse Preferences dialog, in which you
can set options to open and close views automatically. This dialog is
also available from the Windows 䉴 Preferences menu. For more
information about using this menu item, see the Eclipse Workbench
User’s Guide.
You can use the Debug view right-click menu (Figure 3.5) to perform
the following tasks:
78
•
Copy the contents of the stack.
•
Step into the code.
•
Step over the code.
•
Step one level out of the current function.
•
Resume debugging.
•
Suspend debugging.
Debug Perspective Views
•
Terminate the debugging session.
•
Terminate and restart the current debugging session.
•
Remove from the view all previously terminated debugging
sessions.
•
Terminate and remove the currently-active debugging session.
•
Restart the current debugging session.
•
Terminate all debugging.
These menu items are available on the toolbar, or from the main Run
menu. For more information, see the section Debug view toolbar on
page 77 or the section Debug Run Menu Options on page 70.
Figure 3.5: The Debug view right-click context-sensitive menu.
Editor
The Debugger perspective uses the existing S-PLUS Workbench
editor. You can set and remove breakpoints in the Script Editor by:
•
Double-clicking the margin on the left side of the screen (to
the left of the line numbers).
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Chapter 3 S-PLUS Workbench Debug Perspective
•
By right clicking the margin, and from the menu, select
Toggle Breakpoint.
•
By using the Run 䉴 Toggle Line Breakpoint menu option.
•
By pressing CTRL+SHIFT+B.
When you are debugging, if your functions call any functions in files
other than those in your workspace (including functions in a library),
you can double-click the expression in the Debug view and open a
temporary file that contains the called function. You can set
breakpoints in these functions, too.
Figure 1: A temporary file in the debugger.
You can view functions that are not defined in your workspace in one
of the following ways:
80
•
Double-click the Debug view.
•
Press CTRL+click in the S-PLUS Script Editor.
•
On the menu, click S-PLUS 䉴 Find
Debug Perspective Views
•
Press CTRL+SHIFT+F
Note
•
Breakpoints that you set in functions in your workspace are associated with function and
with the file. These breakpoints persist until you remove them.
•
Breakpoints that you set in functions outside of your workspace are associated with the
functions, and not with the temporary files. They persist until you remove them.
•
Setting breakpoints in code files in the S-PLUS Workbench does not affect the file if you
open it in the S-PLUS GUI in Windows. Breakpoints are evaluated only in the S-PLUS
Workbench, and only when the debugger is engaged.
•
Breakpoints can be set only on a line contained within a function definition. Lines not
contained within a function cannot have a breakpoint set.
If you close a temporary file containing a breakpoint, and then rerun your function, the functions
called by your code reopen in another temporary file, and any breakpoints you set persist.
Examining
Using the Hover feature, you can position the mouse over an
Expression Values expression in the Script Editor, and then examine the expression’s
value, which appears in a tooltip. This feature is available for all
in Tooltips
expressions in the Script Editor, not just those where a breakpoint
appears; however, examining the value of an expression at a
breakpoint can be very useful.
You can limit the size of the expression that the Hover feature
evaluates by using the following S-PLUS command:
options(workbenchMaxDims=c(rows, columns))
See the section Hover on page 18 for more information.
You can enable or disable the hover tooltip feature in the Editor
options dialog from the Windows 䉴 Preferences menu. This feature
is enabled by default.
Figure 3.6: Hover option in the Editor preferences dialog.
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For practice tasks on setting breakpoints, see the section Setting
breakpoints on page 141.
Figure 3.7: Breakpoints view and Editor.
Variables view
Displays all variables in the current frame. As you debug, at each
breakpoint or step, the debugger re-evaluates the variables. At any
breakpoint or stopping point, you can review, but not edit or alter, the
variables at the current frame.
Figure 3.8 shows the Variables view with the current variable
selected. The Details pane of this view contains variable information
that would result from calling print() on the selected variable or
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Debug Perspective Views
expression. The Details pane is editable; you can select, cut, or copy
the contents of this pane. Editing the Details pane does not affect the
value of a variable.
Figure 3.8: The Variables view.
Variables view and Expressions view toolbars
The Variables view and Expressions view contain similar toolbars to
control the view display and feature options.
Table 3.4: Variables view and Expressions view toolbar buttons.
Button
Description
Show Type Names. Select to
display the variables’ types.
Show Logical Structure. This
feature is currently not supported
in the S-PLUS Workbench.
Collapse All. Collapses the logical
structure display (which is currently
not supported in the S-PLUS
Workbench).
Remove Selected Expressions
(Expressions view only).
Remove All Expressions
(Expressions view only).
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Variables view control and right-click menus
The Variables view and Expressions view drop-down control
menus provide additional options to control the view’s display. The
respective menus are available from the down arrow button on the
Variables or Expressions view toolbar.
Figure 3.9: The Variables view control menu.
The Variables view and Expressions view control menus include
the following options:
Table 3.5: Variables view and Expressions view control menu options.
84
Menu item
Description
Vertical View Orientation
Tiles the Details pane of the view
vertically. That is, the Details pane
appears below the Variables or
Expressions pane.
Horizontal View Orientation
Tiles the Details pane of the view
horizontally. That is, the Details
pane appears beside the Variables
or Expressions pane.
Debug Perspective Views
Table 3.5: Variables view and Expressions view control menu options.
Menu item
Description
Variables View Only
Hides the Details pane of the
Variables or Expressions view.
Expressions View Only
Detail Pane
Displays the Configure Details
Area dialog, which controls the
maximum number of characters to
display in the Details pane. See
Figure 3.10.
Wrap Text in Details pane
Wraps the text that appears in the
Details pane.
Figure 3.10: Configure Details Area dialog.
Note
Figure 3.10 shows the Configure Details Area dialog, with which you can set the number of
characters to display. This option just controls the number displayed; it does not limit the number
of characters returned. To limit the number of text variables and expressions to return, use the
S-PLUS command options(workbenchMaxDims=c(rows, columns)). This option is useful if you
are working with a large number of text variables or expressions.
Setting this option also limits the size of the expression that the hover feature evaluates. For
example, if you are evaluating a large data object, and you hover the mouse over the expression,
if you do not set this option, S-PLUS tries to evaluate the expression on the spot.
The Variables view contains two right-click context-sensitive menus:
•
The Variables view (Figure 3.9).
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•
The Details pane (Figure 3.12).
You can use the Variables view right-click context-sensitive menu to
perform the following tasks:
•
Select all variables in the pane.
•
Copy the selected variable.
•
Find a specified variable.
•
Set an expression watch for the selected variable. (When you
select this option, the selected variable is added to the
Expressions view.)
Figure 3.11: Variables view showing the right-click menu.
You can use the right-click context-sensitive menu in the Variables
view Details pane to perform the following tasks:
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•
Cut the currently-selected text.
•
Copy the currently-selected text.
•
Paste the contents of the clipboard to the cursor location in
the pane.
•
Select all text in the pane.
Debug Perspective Views
•
Find a specified string in the pane. (The S-PLUS Workbench
does not support replacing strings in the Details pane using
the Find/Replace dialog.)
Figure 3.12: Variables view showing the right-click menu in the Details pane.
Expressions view The Expressions view displays the values of any S-PLUS expression.
Like the Variables view, it is re-evaluated at each evaluation pause
(breakpoint or step).
Note on Expressions
An expression is any syntactical interaction that S-PLUS can evaluate.
Expressions persist from session to session. S-PLUS recognizes a wide
variety of expressions, but in interactive use, the most common are
names, which return the current definition of the named data object,
and function calls, which carry out a specified computation. Any of
the following are S-PLUS expressions:
1:10
rnorm(5)
mean(1:10)
traceback()
If you were debugging a function, for example:
incrementByTwo <- function(x) {
* x + 2
}
you could have an expression that evaluated:
x + 2
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at the breakpoint (denoted with the * in the above function
definition).
Note
If you leave in the Expressions view expressions that are no longer in scope for your current
debugging session, you might notice that the debugger slows significantly to evaluate the
expression that is no longer in scope. To keep the debugger from slowing down, remove
expressions that are no longer in scope for your current debugging session.
For more information about expressions, see the Programmer’s Guide,
or see the S-PLUS Help topic ExpressionLanguage.
The Expressions view toolbar buttons are the same as those of the
Variables view, with the addition of the Remove and Remove All
buttons. See Table 3.4 for more information.
The Expressions view contains two right-click context-sensitive
menus:
•
The Expressions view (Figure 3.13)
•
The Details pane (Figure 3.12).
You can use the Expressions view right-click context-sensitive menu
to perform the following tasks:
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•
Select all expressions in the pane.
•
Copy the selected expression.
•
Remove the selected expression.
•
Remove all expressions in the view.
•
Add an expression to watch (opens the Add Watch
Expression dialog, in which you can provide an expression
and indicate whether to enable or disable it).
•
Re-evaluate the expressions.
•
Disable the currently-selected expression.
•
Enable the currently-selected expression (if it was previously
disabled).
Debug Perspective Views
•
Edit the currently-selected expression. (Opens the Edit
Watch Expression dialog, in which you can change
expression and indicate whether to enable or disable it.)
Figure 3.13: Expressions view showing the right-click menu.
The right-click context-sensitive menu for the Details pane in the
Expressions view is the same as that of the Variables view Details
pane. See Figure 3.12 and the section Variables view control and
right-click menus on page 84 for more information.
Find a specified string in the pane. (The S-PLUS Workbench does not
support replacing strings in the Details pane using the Find/Replace
dialog.)
Figure 3.14: Variables view showing the right-click menu in the Details pane.
Breakpoints view The Breakpoints view displays the currently set breakpoints, which
you can organize by resources, files, working sets, or just a simple list
or type. Each breakpoint displayed in the Breakpoints view shows
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the function name (e.g., kahanAddNext), the file name (e.g.,
kahanAddNext_func.q), and the line number (e.g., [line 7]) where
the breakpoint occurs.
In addition to setting general user interface options, you can use the
Breakpoints view to manage breakpoint working sets and group
breakpoints. See the Eclipse Workbench User’s Guide for more
information.
Selecting a breakpoint displays in the Editor the associated file,
highlighting the breakpoint line. You can activate, disable, or delete
breakpoints from this view.
Figure 3.15 displays the Breakpoints view with the file structure
shown, and all breakpoints activated.
Figure 3.15: Breakpoints view.
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Breakpoint types
Breakpoints are the best tools to stop an evaluation and inspect the
engine's state. The S-PLUS Workbench supports three types of
breakpoints.
Table 3.6: Types of breakpoints.
Breakpoint type
Description
Line breakpoints
Use line breakpoints to stop an evaluation at the
specified line number. To set line breakpoints,
from any perspective:
Double-click the left margin of the S-PLUS
Editor.
Right-click the left margin of the S-PLUS Editor.
From the Debug perspective, Click the Run 䉴
Toggle Line Breakpoint menu item.
After you set a line breakpoint, you can enable or
disable it in the Breakpoints view, or by rightclicking the breakpoint marker ( ) in the left
margin of the Editor.
(For more information about using the
Breakpoints view, see the section Breakpoints
view on page 89.)
Warning breakpoints
Warning breakpoints are triggered only if the
S-PLUS Debugger is toggled on.
Use warning breakpoints to stop an evaluation
when a warning is generated. You can activate
warning breakpoints from any perspective by
clicking Toggle S-PLUS Warning Breakpoint
( ) on the S-PLUS toolbar, or by clicking the
Run 䉴 Toggle S-PLUS Warning Breakpoint
menu item.
•
Warning breakpoints do not appear in
the Breakpoints view.
•
Warning breakpoints are not affected by
the option Skip All Breakpoints ( ).
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Table 3.6: Types of breakpoints. (Continued)
Breakpoint type
Description
Error breakpoints
Error breakpoints are triggered only if the S-PLUS
Debugger is toggled on.
Use error breakpoints to stop an evaluation when
an error is generated. You can activate error
breakpoints from any perspective by clicking
Toggle S-PLUS Error Breakpoint ( ) on the
S-PLUS toolbar, or by clicking the Run 䉴 Toggle
S-PLUS Error Breakpoint menu item.
•
Error breakpoints do not appear in the
Breakpoints view.
•
Error breakpoints are not affected by the
option Skip All Breakpoints ( ).
Breakpoints view toolbar
The Breakpoints view contains a toolbar to control the view’s
display and feature options.
Button
Description
Remove Selected Breakpoints. From the Breakpoints
view, click to remove the selected breakpoint from both the
Debug view and the Breakpoints view.
Remove All Breakpoints. From the Breakpoints
view, click to remove every breakpoint from both the
Debug view and the Breakpoints view.
Show Breakpoints Supported by Selected Target.
When toggled off, all breakpoints are displayed. When
toggled on, the Breakpoints view displays only breakpoints
applicable to the selected debug target. For example, if you
had installed a Java package for Eclipse (not included in the
S-PLUS Workbench), and you were running a Java debug
session and an S-PLUS debug session simultaneously, you
could filter using this feature.
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Button
Description
Go to File for Breakpoint. Click to jump to the file and
line number containing the breakpoint currently selected in
the Breakpoints view.
Skip All Breakpoints. Click to disregard but maintain
(that is, not remove or disable) all breakpoints. When this
button is toggled on, all breakpoints appear with a diagonal
slash, as shown in the button.
Expand All. If the Breakpoints view is set to display
breakpoints in groups such as files, working sets, projects,
resources, or breakpoint types, clicking this button expands
the tree to display the breakpoints in all groups. (See Table
3.7 for more information about the group display options.)
Collapse All. If the Breakpoints view is set to display
breakpoints in groups such as files, working sets, projects,
resources, or breakpoint types, clicking this button collapses
the tree to display only the top-level groups. (See Table 3.7
for more information about the group display options.)
Link With Debug View. As breakpoints are encountered,
they are selected in the Breakpoints view.
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Breakpoints view control and right-click menus
The Breakpoints view contains a control menu to control the types
and levels of resources displayed, and options for managing working
sets. See the Eclipse Workbench User’s Guide for more information
about managing working sets.
Figure 3.16: The Breakpoints view menu.
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Debug Perspective Views
The Breakpoints control menu includes the following options:
Table 3.7: Breakpoints view menu.
Menu Item
Description
Group By
Displays a submenu providing the following options:
•
Breakpoints. Displays only the breakpoints
in a flat list.
•
Breakpoint Types. Displays breakpoints
grouped by type ( Java, S-PLUS, and so on).
•
Breakpoint Working Sets. Displays
breakpoints grouped by identified working
sets. See (working sets section) for more
information.
•
Files. Displays breakpoints grouped by the
files containing them.
•
Projects. Displays breakpoints grouped by
the projects containing them.
•
Resource Working Sets. Displays
breakpoints by the resources to which they
belong.
•
Advanced. Displays the Group
Breakpoints dialog. See the Eclipse
Workbench User’s Guide for more information
about using working sets and groups.
Select Default
Working Set
Displays a dialog to create, select, or remove the
breakpoint working set that is your project’s default.
See the Eclipse Workbench User’s Guide for more
information about using working sets.
Deselect Default
Working Set
Clears the working set that you specified in the
Select Default Working Set dialog.
Working Sets
Displays the Select Working Set dialog.
You can use the Breakpoints right-click context-sensitive menu (see
Figure 3.17) for the following tasks:
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•
Open the file and location for the selected breakpoint.
•
Enable the selected disabled breakpoint.
•
Disable selected breakpoint.
•
Remove the selected breakpoint.
•
Remove all breakpoints in the view.
•
Select all breakpoints in the view.
•
Copy the breakpoints to the clipboard.
Figure 3.17: The Breakpoints view displaying the right-click menu.
Working with
Working Sets
The S-PLUS Workbench provides tools to group and manage project
files and resources using working sets. Working set menus are
available in several Eclipse views, including the Breakpoints view.
For general information about using working sets, see the Eclipse
Workbench User’s Guide.
Console, Output, The Debugger perspective shares the S-PLUS Workbench Console
view, Output view, and Outline view. For more information about
and Outline
using these views, see:
views
The section S-PLUS Workbench Console on page 37
The section S-PLUS Perspective Views on page 53.
Profiler
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The Workbench Profiler is composed of two views: the Function
Calls view and the Allocations view, which are available in the
Debug perspective. You can run the Profiler from either the Run
Debug Perspective Views
menu or from the Toggle S-PLUS Profiler button ( ), located next
to the Toggle S-PLUS Debugger button on the S-PLUS Workbench
toolbar. (See Figure 3.2.)
Profiler Mode
To start profiling, first activate the S-PLUS profiler by clicking Toggle
S-PLUS Profiler toolbar item, by typing CTRL+ALT+P, or by clicking
Run 䉴 Toggle S-PLUS Profiler on the menu. Once the Profiler is
activated, any expression you type in the Console view, or that you
enter by clicking Run S-PLUS Code, invokes the Profiler adds to the
Function Call and Allocation views.
Profiler views
The S-PLUS Workbench Profiler includes two views to monitor the
system performance:
•
Function Calls view
•
Allocations view
These views are described in this section.
Function Calls
view
By default, the Function Calls view displays a function call tree that
reflects the engine's activity.
Figure 3.18: Function Calls view, tree display.
Alternatively, you can display the information in a tabular view by
either of the following methods:
•
Right-click the view, and from the menu, toggle Show
Function Tree
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•
From the Function Call menu, toggle Show Function Tree.
Figure 3.19: Function Calls view, table display.
Function Calls menu
The Function Calls view menu displays the following options:
Table 3.8: Function Calls view menu options.
Allocations view
Menu option
Description
Show Function Tree
Toggle to show the function calls in a tree
view or in a tabular view. The tabular
format displays the total number of calls
and total duration of each function.
Refresh Function Calls
Forces an update of the function call tree or
table.
Reset Function Calls
Clears the function call tree or table.
Displays the number of allocations the engine has performed. It
breaks the allocations down into bytes and the basic S-PLUS data
types.
Allocations view menu
The Allocations view menu displays options to refresh or reset the
view, similar to the Function Calls view options. See Table 3.8 for
more information.
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4
Introduction
100
S-PLUS Workbench Projects
Setting the Workspace
Creating a Project
Setting the S-PLUS Workbench Preferences
101
101
102
110
Customized Perspective Views
120
Working Projects and Databases
Setting the Working Project
Changing Attached Databases
123
123
125
S-PLUS Project Files and Views
Creating a Script
Editing Code in the Script Editor
Running Code
Closing and Reopening the Project
128
128
129
134
138
S-PLUS Workbench Debugger Tasks
Kahan Example
Opening the Debug Perspective
Launching the debugger
Setting breakpoints
Starting execution
Examining the call stack
Examining Variables and Expressions
Setting a Watch Expression
Stepping into, over, and out of a function
Examining Resource Usage
Examining Function Calls
139
139
139
140
141
143
144
145
146
148
150
150
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Chapter 4 S-PLUS Workbench Tasks
INTRODUCTION
This chapter provides the basic tasks that demonstrate using the
S-PLUS Workbench. For information about basic Eclipse IDE tasks,
see the Eclipse Workbench User Guide.
This chapter includes:
General S-PLUS Workbench tasks, including:
•
Setting the Workspace, page 101
•
Creating a Project, page 102
•
Setting the S-PLUS Workbench Preferences, page 110
•
Customized Perspective Views, page 120
•
Specifying Working Projects and Databases, page 123
•
Working with S-PLUS Project Files and Views, page 128
This chapter also includes tasks that introduce you to using the views
and features in the S-PLUS perspective. For more information, see the
section S-PLUS Workbench Projects on page 101.
Finally, this chapter includes tasks that introduce you to using the
views and features in the Debug perspective. For more information,
see the section S-PLUS Workbench Debugger Tasks on page 139.
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S-PLUS WORKBENCH PROJECTS
Before you begin working with files in the S-PLUS Workbench, you
must set your workspace and then create a project.
Setting the
Workspace
When you first launch the S-PLUS Workbench, you are prompted to
supply the path to your S-PLUS workspace.
To set the workspace
1. In the Workspace Launcher dialog (Figure 4.1), specify the
directory location where the workspace .Data and .metadata
databases will be stored.
2. Indicate whether you want to be prompted in future sessions
to identify a workspace using this dialog.
Figure 4.1: The Workspace Launcher dialog.
Changing the
Workspace
You can switch to another workspace from within the S-PLUS
Workbench user interface.
To open a different workspace in S-PLUS Workbench
1. Save your work.
1. Click File 䉴 Switch Workspace.
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2. In the Workspace Launcher dialog, provide the new
workspace location.
Note
When you switch workspaces during an S-PLUS Workbench session, the current session closes,
and a new session of S-PLUS Workbench starts, using the new workspace location.
After you set the workspace, create the project.
Note
On Microsoft Vista™, you must be elevated to the role of administrator to specify the default
directory as C:\Program Files\Insightful\splus80\users\yourname; however, it is not
recommended that you use this directory
Creating a
Project
The S-PLUS Workbench project is a resource containing scripts and
other associated files. You can use the project to control build,
version, sharing, and resource management.
Understanding
Project Options
Before you create a new project, consider the following scenarios, and
then review the S-PLUS Workbench options.
Table 4.1: S-PLUS Workbench project scenarios.
Scenario
S-PLUS Workbench Option
You are starting an empty
project with no existing files.
In the New Project wizard, specify a
project name and accept the default
project directory location. Your project is
created as a subdirectory in the
workspace directory. (The Navigator
view displays the .project resource but no
existing project files.)
(Note: This is the only way
to create a project that is
stored in your workspace.)
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Table 4.1: S-PLUS Workbench project scenarios. (Continued)
Scenario
S-PLUS Workbench Option
You have one or more
project(s), and you want to
work with the files at their
existing location.
In the New Project wizard, specify a
project name, clear the Use default
check box, and then browse to the
location of the project files. S-PLUS
Workbench works with the files at the
specified location. (The Navigator view
displays the .project resource and all files
in the project directory.)
Note that the project cannot overlap other
projects and cannot be located under
your workspace.
You have an existing
project, and you want to
copy selected files to a
workspace directory (for
example, in the cases where
the files are kept at a remote
location, are read-only, or
where you do not want to
work with the original files).
In the New Project wizard, specify a
project name and accept the default
project directory location. An empty
project subdirectory is created in the
workspace directory. You can then import
your project files. See the section
Importing Files on page 104 for more
information.
Based on the scenario that applies to your project needs, In the
following sections, create an empty project, and then import the
Census project files (the third scenario described above).
To create the example census project
1. Click File 䉴 New䉴 Project.
2. In the New Project dialog, select S-PLUS Project. Click Next.
3. Provide the friendly project name, “Census.”
4. Accept the option Use default. This option creates the
project directory in the default workspace location.
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5. Click Finish to create the project.
Figure 4.2: New Project dialog.
Note
When you create a project, you see in the Navigator view the .project resource. This resource is
created by Eclipse and contains information that Eclipse uses to manage your project. You
should not edit this file.
Importing Files
In this exercise, import the Census example, one of the examples
provided with S-PLUS.
To import files
1. With the Census project selected in the Navigator view, click
File 䉴 Import.
2. In the Import Select dialog, select File system, and then
click Next.
3. In the Import File system dialog, browse to the location of
the census project (by default, in your installation directory at
SHOME/samples/bigdata/census.)
4. Select the directory, and then click OK. The directory name
appears in the left pane, and all of the project’s files appear in
the right pane.
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5. Select the folder name in the left pane to select all files, and
then click Finish to add the files to your project.
f
Figure 4.3: Import File System dialog for Census project.
Hint
You can select just the .ssc file to import if you prefer, because the script itself references the data
in these files. For the purposes of this part of the exercise, we import all files.
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Figure 4.4 shows the Navigator with the Census project and
all its files.
Figure 4.4: Navigator showing Census project.
Note
Alternatively, you can copy files from a different location to your project directory in your
workspace. If you simply copy files, you must refresh the Navigator view to include the files in
your project and display them in the project file list. To refresh the view, right-click the project
name, and from the menu, click Refresh.
Loading a Library You work with S-PLUS code in the Workbench the same way you
work with it in other environments, such as the Java GUI, the
command line, or the Windows GUI. To load a library, in the
Console view, simply call:
library(libraryname)
Where libraryname is the library to load.
For example, if you are working with S-PLUS packages, before you get
started, load the pkgutils library:
library(pkgutils)
Adding a Second
Project
In this exercise, create a project with the files for the Boston Housing
example at their existing location (the second scenario described
above), rather than importing the files into a workspace directory.
Boston Housing is an example provided in the S-PLUS sample files,
by default, in your installation directory at SHOME/samples/
bigdata/boston.
To add a project
1. Click File 䉴 New 䉴 Project.
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2. In the New Project wizard, select S-PLUS Project, and then
click Next.
3. In the Project name text box, type “Boston Housing,” and
then clear the Use default check box.
4. Browse to the location of the Boston Housing sample
directory, by default in the SHOME/samples/bigdata
directory of your S-PLUS installation. Select the boston
directory, and then click OK. Click Finish to add the project.
Figure 4.5: New Project dialog, using boston files at their installed location.
5. In the Navigator view, the Boston Housing project appears.
This directory contains all of the files in that sample directory
location.
Figure 4.6: Navigator containing two projects.
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6. You won't be using this project for the remainder of this
tutorial section, so right-click the directory, and then select
Delete.
7.
In the Confirm Delete Project dialog, select Do not delete
contents. (Otherwise, you will delete the sample from your
installation directory.)
8. Click Yes to remove the project.
Figure 4.7: Confirm Project Delete dialog--do not delete the contents.
Copying Files
You can copy files from an existing project to a working project by
Between Projects copying their .ssc files from the original project to the working
project’s directory. Note that to see these files in your project, you
must refresh the view. To refresh the Navigator view, right-click the
project, and from the menu, click Refresh. (Restarting the S-PLUS
Workbench does not automatically refresh the view.) Alternatively,
you can use the File 䉴 Import menu command: Specify a file
system, browse to the original location of the desired file, and then
select only that file to import. (Importing a file into a project from
another location copies that file to the project folder in your
workspace.)
Adding the
Sample
Debugging
Project
In this exercise, add another project, importing the sample files, as
you did in the section To create the example census project on page
103. This second project is the project you will use later in this
chapter to practice debugging tasks.
Follow the directions for creating a project on pages 103 to page 106,
but instead of importing the Census project, import the kahanSum
project, located in your installation directory at SHOME/samples/
kahanSum.
To add the kahanSum project
1. Click File 䉴 New 䉴 Project.
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2. In the New Project dialog, select S-PLUS Project. Click
Next.
3. Provide the friendly project name, “kahanSum.”
4. Accept the option Use default. This option creates the
project directory in the default workspace location.
5. Click Finish to create the project.
6. With the kahanSum project selected in the Navigator view,
click File 䉴 Import.
7.
In the Import Select dialog, select File system, and then
click Next.
8. In the Import File system dialog, browse to the location of
the census project (by default, in your installation directory at
/samples/kahanSum.)
9. Select the directory, and then click OK. The directory name
appears in the left pane, and all of the project’s files appear in
the right pane.
10. Click Select All, and then click Finish to add the files to your
project.
Figure 4.8 shows the Navigator with the kahanSum project
and all its files added to the workspace. (You will work with
this project later in this chapter.)
Figure 4.8: Navigator showing kahanSum project added to the workspace.
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Setting the
S-PLUS
Workbench
Preferences
General Options
S-PLUS provides customizations to the Eclipse IDE to accommodate
the specific needs of the S-PLUS programmer. You can change the
IDE to suit your development style, including adding, removing, and
repositioning the views, and setting the preferences.
•
To review the preference options in the Preferences dialog,
see the section Examining S-PLUS Preferences on page 13.
•
To review the views available in the S-PLUS Workbench, see
the section Examining the S-PLUS Workbench GUI on page
24.
•
To learn more about customizing the views in the S-PLUS
Workbench, see the section Customized Perspective Views
on page 120.
This section demonstrates setting specific preferences in the
Preferences dialog.
To set text editor options
1. On the Window menu, click Preferences.
2. In the Preferences dialog, select General, and then click
Editors 䉴 Text Editors.
3. Review the options, including tab width (by default 4), line
numbers (by default displayed), and appearance color options
(by default, the system colors). You can set additional options
in the S-PLUS 䉴 Editor options dialog. See Figure 4.13 for
an example.
To examine file association preferences
4. In the Preferences dialog, select General, and then click
Editors. Examine the dialog pages.
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S-PLUS Workbench Projects
5. Click File Associations and review the file types that the
Script Editor recognizes.
Figure 4.9: File Associations page.
S-PLUS View
Preferences
The previous section demonstrated setting Eclipse general
preferences that the S-PLUS Workbench takes advantage of. The
following sections demonstrate setting preferences specific to the
S-PLUS Workbench views. These preferences include general S-PLUS
preferences, preferences for the Console view and the Output view,
preferences for the Output view, and preferences for defining task
tags.
To set the S-PLUS preferences
1. Click S-PLUS.
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2. Review the options. Make sure the bigdata library loads on
startup: check the check box Run code on startup. (The
Census example demonstrated in this chapter uses the
bigdata library.)
Figure 4.10: S-PLUS Preferences page.
To store the console history between sessions
1. In the left pane tree view, click S-PLUS to expand, and then
click Console to display that page.
2. In the Console page, select Store Console History
between sessions. You can use this setting to persist the
contents of the History view to use later in the Console view.
For more information about storing the console history and
using it in the output, see the section Console Options on
page 17.
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S-PLUS Workbench Projects
3. Optionally, change the input and/or output color or font to a
color or font of your choice. For more information about
these options, see the section Font Settings on page 17.
Figure 4.11: Console page.
To add text with a user-defined highlight color
1. In the left pane tree view, under S-PLUS, click Editor to
display that page.
2. In the Editor dialog, in the Syntax Highlighting list box,
select User, and then click Choose Color.
3. In the Color dialog, select a color, and then click OK.
4. In the User Tokens area, click New.
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5. In the Add Desired S-PLUS Text dialog, select Comma
Separated Text. In the text box, type census, and then click
OK.
Figure 4.12: Add Desired S-PLUS Text dialog.
6. Note that census appears in the User Tokens list box. Click
Apply. In later exercises, when you manipulate the Census
project, you will see the string you selected highlighted in the
color you specified. You can add other user-defined terms,
including S-PLUS commands or the contents of a comma-
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S-PLUS Workbench Projects
separated file and see how it makes tracking these items
through your code easier. For more information about this
option, see the section Syntax Highlighting on page 19.
Figure 4.13: Editor page with census added as highlighted user text.
To add the contents of a comma-separated file
1. Open a text editor, such as Notepad.
2. Type some terms to highlight, separated by commas. For
example, if you want to highlight in your code every time the
data viewer or a graph opens, type bd.data.viewer, hist,
xyplot, bwplot, histogram, and so on.
3. Save the file with a convenient name and to a convenient
location (for example, C:\terms.txt).
4. Return to the S-PLUS Workbench Editor preferences dialog,
and, in the User Tokens area, click New.
5. In the Add Desired S-PLUS Text dialog, select Comma
Separated File.
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6. Either type the file path, or click Browse and browse to the
file location.
7.
Click OK, and notice that all of the terms in the file are added
to the User Tokens list. Figure 4.14 shows the User Tokens
list with the terms added from the file.
Figure 4.14: User Tokens list displaying the contents of a file.
To add an S-PLUS command to the User Token list
1. In the User Tokens area, click New.
2. In the Add Desired S-PLUS Text dialog, select S-PLUS
Command.
3. In the S-PLUS Text to Highlight box, type the S-PLUS
command objects().
4. Click OK, and notice that all of the objects in the working
project are added to the User Tokens list. Figure 4.15 shows
the updated User Tokens list.
Figure 4.15: User Tokens list displaying working project objects.
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S-PLUS Workbench Projects
To remove items from the User Tokens list, select them and click
Remove.
To change the code formatting options
1. In the S-PLUS Editor options page, review the S-PLUS
Format Options group.
2. Select Use spaces for indentation, and notice how the
example display changes to reflect the default 4. Clear this
option, if you choose, or change the default to add more or
fewer indentation spaces.
3. Change some of the other formatting options to suit your
programming style, and then click Apply to apply any
changes to the editor.
To add a function to watch
1. In the left pane tree view, click Outline to display that page.
2. Click New.
3. In the Add New Function to Watch dialog, add set.seed.
Click OK.
Figure 4.16: Add New Function to Watch dialog with set.seed .
4. Review the list in the Functions to Watch dialog. Note that
set.seed has been added to the list. (Later, when you are
working with a project that uses the set.seed function, you
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can see its display in the Outline view has a special icon.) For
more information about this option, see the section Functions
to Watch on page 21.
Figure 4.17: Outline page with set.seed added.
To add a task to the Task Tags options
1. In the left-pane tree view, click Task Tags.
2. Click New to display the Add New Task Type dialog.
3. In the Task Name box, type a name for a new task to watch.
Set the severity to your preference, and click OK to add the
task.
Figure 4.18: Add New Task Type dialog.
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S-PLUS Workbench Projects
4. Highlight the items to change in the S-PLUS Task Options
text box, or, using the New, Remove, Up, and Down
buttons, edit the available tasks. In the Script Editor, when
you type this term, prefaced with a comment character (#),
the line is added to the Tasks view with the severity you
indicate for the custom tag.
Figure 4.19: Task Tags page with a new task added.
5. Click OK or Apply to save your changes, or click Restore
Defaults to return the task options to their default state.
6. Click OK to save your changes.
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CUSTOMIZED PERSPECTIVE VIEWS
The default layout of the S-PLUS perspective presents the Navigator
view, Outline view, and History view on the left side of the window.
The Console view, Objects view, Search Path view, Output view,
Tasks view, and Problems view are tiled across the bottom of the
window. The Script Editor pane is empty.
To customize the S-PLUS perspective default perspective
1. Click the Outline view tab and drag the view beside the
Navigator view. The Outline view now tiles with the
Navigator view.
2. Click the History view tab and drag the view to the right; it
now tiles with the other views.
3. Right-click the Tasks view tab and select Fast View. The
Tasks view minimizes and appears as an icon in the window’s
status bar.
4. Click the Output view tab to select it.
Figure 4.20: Customized S-PLUS perspective.
5. Click Window 䉴 Save Perspective As.
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6. In the Name box, type “Sample Exercise,” and then click
OK.
The Sample Exercise perspective button appears on the toolbar:
Figure 4.21: Sample exercise perspective button.
To change the displayed views
1. To change the views, or to display the list of available views,
on the menu, click Window 䉴 Show View.
2. From the submenu, select the view to display.
Alternatively, if you do not see the view you want to display,
from the Show View menu, click Other, and then select a
view from the Show View dialog. For example, if you want
to display a view that is typically in the Debug perspective,
expand Debug, and then select a view from the list.
Figure 4.22: Show View dialog.
•
If the view is not currently visible in the UI, selecting it
displays the view and gives it focus in the UI.
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•
If the view is available, selecting it gives it focus in the UI.
Note
The S-PLUS (Deprecated) folder contains options to display S-PLUS views that are deprecated in
your current release. You can use these views; however, in the future, they will be unavailable.
Because of ongoing improvements and implementation changes, occasionally S-PLUS views
might change or become obsolete. If you use a workspace containing a deprecated view (that is,
created prior to the release in which it was deprecated), you see the (Deprecated) label in the
view’s tab, and the view is moved to the S-PLUS (Deprecated) folder in the view management
tool.
You can change your workspace to use the newer view. To change to a new view permanently:
•
Reset the perspective using the Windows 䉴 Reset Perspective menu option; or
•
Delete the following file from your workspace directory:
<WORKSPACE>/.metadata/.plugins/org.eclipse.ui.workbench/workbench.xml.
To return to the S-PLUS perspective default
1. Click the perspective button to the left of the Sample
Exercise button, and then click Other.
2. In the Select Perspective dialog, select S-PLUS (default),
and then click OK. The perspective returns to its previous
layout.
You can select other views to display in your perspective.
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Working Projects and Databases
WORKING PROJECTS AND DATABASES
This section describes setting working projects and changing
databases.
The S-PLUS Workbench provides the following ways you can store
your data objects:
•
In the working project .Data, where the objects are available
only to the project.
•
In the workspace .Data, where the objects are available to all
projects in the workspace.
You can change the .Data storage option at any time by setting any
project in the workspace as the working project, or toggling off the
working project option and writing data objects to the workspace
.Data database.
Setting the
Working
Project
When you create a workspace, a .Data database is created in the
workspace, and (after you refresh the view) the workspace path
appears in the first position in the Search Path view, as shown in
Figure 4.23. If you specify no working project, the S-PLUS
Workbench writes data objects to the workspace .Data database, and
the objects in that .Data database are available to all projects in the
workspace.
Figure 4.23: Search Path view with first position set to the workspace.
When you create a project and import project files, the S-PLUS
Workbench creates a .Data in the project, sets it as the working
project, and sets the project in the first position in the Search Path
view. Any objects created are added to the working project’s .Data
database.
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To set the working project
1. Select the project to set as the working project.
2. From the main menu, click File 䉴 Toggle Working S-PLUS
Project. (Alternatively, in the Navigator, right-click the
project that you want to set as the working project, and from
the context sensitive menu, click Toggle Working S-PLUS
Project.) Figure 4.24 shows the context menu.
Figure 4.24: Toggle Working S-PLUS Project on the Navigator context-sensitive
menu.
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The selected project is displayed as the working project. Any
objects you create are stored in the Census .Data database
until you choose another project as the working project, or
toggle off the working project, so the workspace .Data is the
database.
Figure 4.25: Census set as the working project.
Changing
Attached
Databases
Adding a
Database
S-PLUS recognizes libraries, modules, lists, and directories as
legitimate object databases. You can add and detach any of these
types of databases to the Search Path view.
By default, the Search Path view displays the full path of the working
database and all of the attached S-PLUS data libraries. Objects existing
in a recognized active database appear in the Objects view.
Objects in an added database appear in Objects view when you
refresh the view to that database. See the section Examining Objects
on page 132.
To add a library
1. Right-click the Search Path view.
2. From the right-click menu, click Add Library.
3. In the Attach Library dialog, type MASS. Clear the Attach
at top of search list check box to indicate that you want add
the library to the bottom position.
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4. Click OK and examine the Search Path view for the change.
Figure 4.26: Attach Library dialog.
To add a module
1. From the right-click Search Path view menu, click Add
Module.
2. In the Attach Module dialog, provide an installed module
name and indicate whether to add it to the first position.
3. Click OK and examine the Search Path view for the change.
To add a directory
1. Right-click the Search Path view.
2. From the menu, click Attach Directory.
3. In the Attach dialog, in the Directory to attach text box,
browse to the directory location.
4. In the Label text box, type Projects
5. In the Position text box, type 4.
6. Click OK and examine the Search Path view. The label you
provided should appear at position 4.
Detaching a
Database
From the Search Path view, you can detach a database from your
current session.
To detach a database
1. In the Search Path view, right-click bigdata.
2. In the right-click menu, select Detach.
3. Examine the Search Path view. The Big Data library is no
longer attached.
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Refreshing the
View
When you refresh the view, any changes to the Search Path view
that have not been reflected in a recent change are displayed. For
example, if you add a library by calling the load function in an S-PLUS
script, the change is not immediately displayed in the Search Path
view.
To refresh the view
1. Using the Console view, reattach the Big Data library. In the
Console view, type
library(bigdata, first = T)
2. Right-click the Search Path view.
3. In the right-click menu, click Refresh. Notice that the Big
Data library appears as attached in the first position (position
2).
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S-PLUS PROJECT FILES AND VIEWS
The S-PLUS Workbench recognizes *.ssc, *.q, *.r, and *.t files, all file
extensions common in S-PLUS code.
Creating a
Script
You can create a new S-PLUS script file, or you can import an existing
script file. The following two examples demonstrate both techniques.
To create a new script file
1. Click File 䉴 New 䉴 Other.
2. In the Select a wizard dialog, select S-PLUS Script. Click
Next.
3. In the New File dialog, select the parent directory (the
Census project directory)
4. In the File name text box, type Sample.ssc.
5. Click Finish to create the file.
We won’t work with this file for this exercise, so you can either
disregard the file, or delete it from your project. Alternatively, you
can open the file, add some S-PLUS code, and save it in the project.
Viewing Project
Files
The Navigator view displays the project files. In Windows, if you
have Microsoft Excel installed, you can open a CSV file in an
external window. In this project, only the files identified in Windows
䉴 Preferences in the File Extensions page open in the Script editor.
Removing files
from a project
Because the project script imports the data in the files from their
installation directory in S-PLUS, you don’t need to have them all in
the project. However, removing an imported file deletes it from your
project directory, so remove individual files with care.
To remove a file from the Census project
1. In the Navigator view, open the Census project and select all
files except the .project file and census.demo.ssc.
2. Right-click the selected files, and then click Delete.
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3. In the Confirm Multiple Resource Delete dialog, click Yes
to remove the files from the project. The Navigator view
should now just display the Census Project directory, the
project file, and census.demo.ssc:
Figure 4.27: Navigator view after deleting files
Editing Code in
the Script
Editor
The S-PLUS script is a text file that you can edit in the Script Editor. In
this exercise, just edit census.demo.ssc using the menu items
provided specifically for S-PLUS.
To edit script code
1. In the Navigator view, double-click the file census.demo.ssc
to open it in the Script Editor and examine the script. Note
that:
•
The comment text appears in the Script Editor as green.
(You can change this default color in the Preferences
dialog. See the Eclipse Workbench User Guide and the
section Setting the S-PLUS Workbench Preferences on
page 110 for more information.)
•
Note that the term census appears in the color you
specified in the section To add text with a user-defined
highlight color on page 113.
•
The line that has focus appears highlighted.
•
The line numbers appear to the left of the script text.
2. Scroll to line 17 and highlight the line and the next line:
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"/samples/bigdata/census/census.csv", sep=""),
stringsAsFactors=F, bigdata=T)
3. Click S-PLUS 䉴 Shift Left. The code shifts to the left.
4. Click S-PLUS 䉴 Format. This command formats the entire
script. Note that the formatting change you made in the
previous step has been reverted. Also note that the line
numbers for formatted functions are highlighted.
Hint
The line numbers for any line changed in your script are highlighted until the next time
you save your work.
5. Scroll to the line containing the code
graph.setup(Name="USA")
6. Click S-PLUS 䉴 Toggle Comment to add a comment
character. Notice that the script text color changes to indicate
that the line is no longer a comment.
7.
Repeat step 6, or type
comment.
CTRL+SHIFT+#
to remove the
To edit a function definition
1. In the Script Editor, select the function whose definition you
want to edit.
2. Press the ctrl key and click the function again.
3. The function definition opens in a temporary file in the Script
Editor.
Alternatively, you can right-click a function name, and from the
menu, click Find. Find searches files currently open in the Script
Editor, then files in the working project, and finally in the S-PLUS
database for the function definition.
Note
Any code changes you make in an editor are not recognized by S-PLUS until you source the
code.
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S-PLUS Project Files and Views
To find all references to a function
1. Right-click the function whose references you want to find.
2. From the menu, click Find References.
3. Review the results in the Search view. Figure 4.28 displays
the results of running Find References on the function hist
in the Census project.
Figure 4.28: The Search view after running Find References on hist.
Examining the
Outline
The Outline view displays all of the items (objects, functions, and so
on) that are contained in the open script. Outline view is not editable.
To examine the outline
1. Examine the objects that appear in the Outline view. Note
that set.seed appears with a yellow arrow next to it, because
in the section Setting the S-PLUS Workbench Preferences on
page 110, you indicated that set.seed was a function to
watch.
2. Scroll through the Outline view list and highlight an object.
Note that the Script Editor scrolls to, and highlights, the line
where the object appears.
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Examining
Objects
When you start a new workspace, the Objects view is not populated.
Details about your project’s objects (and all objects in your database)
will appear in the Objects view. Objects view is not editable;
however, you can refresh the contents, delete objects, or change the
view to another attached database. To refresh the view, right-click the
Objects view and click Refresh.
To examine the objects
1. Select the Objects view tab to display the objects and their
details. By default, the objects are displayed sorted by name.
2. Right-click the Objects view table pane and, in the contextsensitive menu, click bigdata. The Big Data library objects
are displayed in the Objects view. (It might take a few
moments to display all of the objects.)
3. Re-sort the objects by any property displayed in the Objects
view by clicking the property’s column title.
To display hidden objects
1. In the Objects view, right-click the table pane to display the
context-sensitive menu.
2. Examine the menu. Note that, by default the S-PLUS system
objects are hidden.
3. On the menu, click Hide S-PLUS System Objects to clear
the selection.
4. Examine the Objects view table pane and tree view pane to
see the S-PLUS system objects in your project.
To select another object database
1. Right-click the Objects view and, in the right-click menu,
click your current working directory (the directory at the top
of the list). The project objects are displayed in the Objects
view. (It might take a few seconds to display all of the objects.)
Adding a Task to The Tasks view displays outstanding project tasks. As discussed in
the section Setting the S-PLUS Workbench Preferences on page 110,
A Script
the indicators for task levels are stored in the Preferences dialog.
(Click Windows 䉴 Preferences to display them.) You can add a task
in one of two ways:
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•
Add the task directly to the Tasks view.
•
Add the task to the script file.
To add a task directly to the Tasks view.
1. Click the Tasks view tab to display its contents.
2. Right-click the view, and then click Add Task.
3. In the Add Task dialog, provide the description and priority
level of the task.
Figure 4.29: Add Task dialog.
4. Click OK to save and display the new task.
Figure 4.30: A generic task in the Tasks view.
A task added directly to the Tasks view displays a check box (for
marking the task complete) in the Tasks view’s first column. It does
not display a reference to a resource, a directory, or a location.
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To add a task in the script file
In the script file, select a blank line.
1. Type the following text:
#FIXME: Change this section.
2. Save the script file.
Note that the FIXME comment appears in the Tasks view as
a high-level task, with a red exclamation mark in its second
column. The task also displays information about its resource,
directory, and line location. You can go directly to any task in
your script by double-clicking it in the Tasks view.
Figure 4.31: A FIXME task in the Tasks view.
3. In the Script Editor, change the level of the task by changing
FIXME to TODO and save the file. Note that the
exclamation mark disappears, and the task becomes a normal
level task.
Running Code
134
You can run your S-PLUS script code directly from Eclipse in two
ways, which are described in the following section.
S-PLUS Project Files and Views
Script Running
Options
The S-PLUS Workbench provides the following customized solutions
for running your scripts from either the S-PLUS perspective or the
Debug perspective.
Table 4.2: Script Editor options for running code.
Copying Script
Code to the
Console
Option
Description
Copy to Console
Available from the right-click menu in the Script
Editor and from the S-PLUS menu, this option
copies the selected code and pastes it into the
Console view. See the section Copying Script
Code to the Console on page 135.
Run S-PLUS Code
Available from the Run menu, by pressing F9, on
the toolbar, and from the right-click menu in the
Script Editor. This option runs the selected code
(or all code, if none is selected), and then displays
output in the Output view. See the section
Running Code and Reviewing the Output on
page 137 for more information.
Run Current File
Available from the S-PLUS menu. This option runs
the file that is open.
Run Next S-Plus
Command
Available from the Run menu and from the
S-PLUS Workbench toolbar. This option runs the
currently selected S expression or, if the cursor is
not exactly on an expression, the next expression.
The Console view is an editable view (in other words, you can type
commands and run them by pressing ENTER); therefore, when you
copy script contents to the Console view using Copy and Paste
actions, you must include the line return, or the script will not run.
This behavior is consistent with the S-PLUS Commands window, in
the S-PLUS GUI, which also requires a line return to run code.
Also like the S-PLUS Commands window, the Console view
concatenates the code that runs throughout your S-PLUS Workbench
session, so you can review and save it.
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To run copied script code
1. From within the Census project’s script, select lines 1 - 13 in
the script. Be sure to select the line return at the end of line 13.
2. Right-click the code and click Copy to Console. The
selected code is copied immediately to the Console view and
runs. You do not need to paste it in the Console view.
3. Repeat steps 1 and 2 for lines 15-18.
4. Finally, repeat steps 1 and 2 for a few more lines.
(You can select all of the code, but if you do so, it appears in
the History view as one line. By following the steps above,
the History view reflects the three different calls to run the
code. See the section Examining the History view on page
136 for more information.)
Copying Script
Code from the
Console view
Examining the
History view
You can select and copy code from the Console view.
•
To copy just code, select the code in the console that you
want to copy, right-click the Console view, and from the
menu, click Copy.
•
To copy code and the prompts (> and +) in the Console view,
set the Window 䉴 Preferences option Include Prompts in
Copy action on the Console/Output page. After you set
this option, any lines you select and copy using the right-click
Copy action includes both code and prompts.
•
To copy the entire contents of the Console view, right-click
the view, and on the menu, click Select All, and then rightclick again and select Copy.
This exercise uses the script code run in the section Copying Script
Code to the Console on page 135.
The History view reflects the code run in the Console view. Note
that the History view displays each selection you make, even if it is
more than one command, on one line, and if the line extends beyond
about 50 characters, the History view displays an ellipse (...) to
indicate more code. To display each line of code in the History view,
you must run the lines individually.
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S-PLUS Project Files and Views
To examine the history
1. To examine and rerun code from the History view.
2. Click the History view tab to give it focus.
3. Right-click the first line of code, and click Select input. The
code is copied to the Console view. You must return to the
Console view and press ENTER to run the code.
(Alternatively, double-click the code in the History view to
copy it to the Console view and run it.)
You can scroll through the individual entries in the History view; as
you scroll, the selection appears in the Console view. To run a
selected item, switch from the History view to the Console view and
press ENTER at the end of the code line.
Running Code
and Reviewing
the Output
You can run code directly from the Script Editor by using the Run
S-PLUS Code feature.
To run code
1. Select the Output view tab.
2. In the Script Editor, select the code to run (or, to run the
whole script, select nothing), and press F9, or on the toolbar,
click RunS-PLUS Code.
The Output view displays the run code and any S-PLUS
messages.
To run the current expression
•
Fixing Problems
in the Code
On the S-PLUS toolbar, click Run Next S-PLUS Command.
The currently-selected S expression runs, and the next
expression is selected. (If the cursor location does not match
an expression exactly, the next expression is evaluated.
Introduce a programmatic problem in the script to examine the
results in the Problems view.
To examine problems
1. In the Script Editor, on line 13 of the script, remove the
closing parenthesis.
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Chapter 4 S-PLUS Workbench Tasks
2. Save the file. Note that the Problems view tab shows bold
text.
3. Click the Problems view tab to display the view.
4. Click the problem description. Note that the Script Editor
highlights the line where the code is broken.
5. In the Script Editor, replace the missing parenthesis and save
your file. Note that the problem disappears from the
Problems view.
Closing and
Reopening the
Project
The S-PLUS Workbench maintains a list of your projects in the
Navigator view, even after you close all associated files.
To close the project
1. Select the project to close.
2. Right-click the Navigator view and, from the menu, click
Close Project.
3. Examine the Objects view and note that it still displays
project or workspace objects.
To reopen the closed project
1. Select the project.
2. Right-click the Navigator view and, from the menu, click
Open Project.
In the next section, examine the Debug perspective using a different
example, creating a new project. You can close the Census project at
this point, if you choose.
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S-PLUS Workbench Debugger Tasks
S-PLUS WORKBENCH DEBUGGER TASKS
This section describes basic tasks you will want to know how to
perform on a simple file set.
Note
If you open a file using the File 䉴 Open File menu command, and that file is not in an S-PLUS
Workbench project, you cannot set a breakpoint in that file.
The following instruction works with the kahanSum example, located in your SHOME/
samples/directory. To create a kahanSum project, follow the steps to create a project (see the
section Creating a Project on page 102).
Kahan
Example
In numerical analysis, the Kahan summation algorithm minimizes the
error when adding a sequence of finite precision floating point
numbers. (It is also called compensated summation. This algorithm is
attributed to William Kahan.)
The S-PLUS Debugger example uses a simple Kahan summation
algorithm captured in two files. If you have not already done so,
create this project and import the example files. See the section
Adding the Sample Debugging Project on page 108.
The project’s two files are as follows:
Opening the
Debug
Perspective
•
kahanSum.q contains the function kahanSum.
•
kahanAddNext_func.q contains the function, kahanAddNext,
which is called by the function kahanSum.
Before using the Workbench Debugger and Profiler, you must open
the Debug perspective. If you have closed your project in the
previous exercise and want to continue practicing using the S-PLUS
Debugger, first re-open your project, and open the two files in the
Script Editor. Next, change to the Debug perspective.
For a more in-depth description of the Debug perspective, see the
section Debug Perspective Options and Preferences on page 68.
To open the Debug perspective
1.
On the perspective toolbar, click Open Perspective.
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Chapter 4 S-PLUS Workbench Tasks
2.
From the menu, select Debug.
Figure 4.32: The Open Perspective menu options.
The Debug perspective button appears to the left of the
S-PLUS perspective button, and the perspective changes to the
Debug perspective as shown in Figure 4.33.
Figure 4.33: Selecting the Debug perspective.
Now, you can toggle between the S-PLUS perspective and the Debug
perspective by clicking their respective buttons. The Debug
perspective button stays visible in this and future S-PLUS Workbench
sessions, unless you close it by right-clicking its button and clicking
Close.
Launching the
debugger
To start debugging, first activate the S-PLUS debugger using one of the
following methods:
•
140
On the toolbar, click Toggle S-Plus Debugger (
).
S-PLUS Workbench Debugger Tasks
•
On the menu, click the Run 䉴 Toggle S-PLUS Debugger.
•
On the keyboard, press CTRL+ALT+D.
After you activate the debugger, any expression you type in the
Console view, or that you run by clicking Run S-PLUS Code ( ) on
the toolbar, invokes the debugger.
Setting
breakpoints
One of the most basic debugging tasks is setting a breakpoint. Set
breakpoints at locations in your code where you want to evaluate
variables. In this exercise, set the breakpoints in the Script Editor. For
a more in-depth description of the Script Editor, see section S-PLUS
Workbench Script Editor on page 46.
To set the breakpoints
1. From the Project files, open the file kahanAddNext_func.q
in the Script Editor. (Note that to work with the debugger,
your
2. Find the line in the code that reads:
correctedX <- nextX + kahanValues[["correction"]].
3. In the left margin, right-click to display the menu, and then
select Toggle Breakpoint. (Double-clicking the left margin
next to the code line also adds the breakpoint.)
4. Open the file kahanSum.q in the Script Editor.
5. Find the line in the code that reads:
kahanValues <- kahanAddNext(x[i], kahanValues).
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Chapter 4 S-PLUS Workbench Tasks
6. Repeat step 3 to put a breakpoint at this line.
Figure 4.34: Breakpoint set in the kahanSum function.
Note
Setting breakpoints in code files the S-PLUS Workbench does not affect the file if you open it in
the S-PLUS GUI in Windows. Breakpoints are evaluated only in the S-PLUS Workbench, and
only when the debugger is engaged.
To examine your breakpoints
1. Click the Breakpoints view tab. Both breakpoints you set
appear in this view.
Figure 4.35: kahanSum breakpoints in Breakpoints view.
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S-PLUS Workbench Debugger Tasks
2. Right-click the breakpoint kahanAddNext, and from the
context-sensitive menu, click Go to File. Note that the
kahanAddNext_func.q file opens in the Script Editor, and
the line with the breakpoint is highlighted.
3. In the Breakpoints view, clear the check box next to the
kahanAddNext breakpoint. Note that the icon changes from a
solid circle to a blank circle in both the Breakpoints view
and in the Script file margin. This action disables the
breakpoint in future sessions but does not remove it.
4. Select the check box to enable the breakpoint.
5. On the Breakpoints view toolbar, click Skip All
Breakpoints ( ). Toggling this option disregards but
maintains (that is, does not remove or disable) all breakpoints
in the Breakpoints view.
6. Take some time manipulating the breakpoints using the menu
options and buttons in the Breakpoints view. For a more indepth description of the Breakpoints view, see section
Breakpoints view on page 89.
When you have finished, re-set the breakpoints in the files as
described in the section To set the breakpoints on page 141.
Starting
execution
Before you run the debugger, first initialize the objects and set the
output display option.
To initialize the objects
1. Open the file kahanAddNext_func.q in the Script Editor.
2. On the toolbar, click Run S-PLUS Code (
).
3. Repeat steps 2 and 3 for the file kahanSum.q.
4. In the Console view, at the prompt, type the following code:
options(digits=17)
To start the debugging session
1. Engage the debugger by clicking its toolbar button (
).
2. Click the Debug view tab to display its contents.
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Chapter 4 S-PLUS Workbench Tasks
3. In the Console view, at the prompt, type the following code:
kahanSum(rep(1000000000.1, 10))
Examining the
call stack
After you have started the debugging session, examine the UI:
Figure 4.36: At the first breakpoint in kahanSum.
To examine the call stack
1. Note that the Script Editor highlights the breakpoint line.
2. Note that the Debug view shows the contents of the call stack.
Figure 4.37: The Debug view containing the call stack.
To resume debugging
1. Resume debugging by clicking the Resume button (
144
).
S-PLUS Workbench Debugger Tasks
2. Re-examine the Debug view, and note that the debugger
stops at the next break point: the first breakpoint in the
kahanAddNext function.
For a more in-depth description of the Debug view, see the
section Debug view on page 76.
To remove a breakpoint mid-session and resume debugging
1. You don’t need the breakpoint in kahanAddNext, so remove it.
In the Breakpoints view, select the breakpoint for
kahanAddNext.
2. On the Breakpoints view toolbar, click Remove Selected
Breakpoints ( ).
3. Click the Resume button again to run the debugger to the
next breakpoint. The code runs the for loop and stops at the
kahanSum breakpoint again. Observe the results in the Debug
view.
4. Click Resume a few more times to continue debugging to the
first calculate correction. In the next section, examine the
results of the first calculated correction.
Examining
Variables and
Expressions
As you debug, at each breakpoint or step, the debugger re-evaluates
the variables and displays the results in the Variables view. At any
breakpoint or stopping point, you can review, but not edit or alter, the
variables at the current frame.
For a more in-depth description of the Variables view, see the
section Variables view on page 82.
To examine the variables
1. Click the Variables view to display its contents.
2. In the Debug view, highlight the last line in the call stack.
3. Note that the Variables view displays the variables resulting
from the code run so far.
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Chapter 4 S-PLUS Workbench Tasks
4. Highlight a variable in the Variables view and note that its
value is displayed in the Details pane.
Figure 4.38: Variables view during debugging session.
5. On the Variables view toolbar, click the Show Type Names
button ( ). Note that the Variables view now displays the
variable type information.
Figure 4.39: Variables view showing type names for the variables.
6. Take some time examining the variables using the menu
options and buttons in the Variables view, clicking Resume
in the Debug view and watching the variables change.
Setting a
Watch
Expression
You can track variable assignments in the Variables view, and you
can track variables and expressions in the Expressions view. This
section demonstrates how to track individual variable assignments
and interesting expressions.
Note on Expressions
An expression is any syntactical interaction that S-PLUS can evaluate.
Expressions persist from session to session. S-PLUS recognizes a wide
variety of expressions, but in interactive use the most common are
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S-PLUS Workbench Debugger Tasks
names, which return the current definition of the named data object,
and function calls, which carry out a specified computation. Any of
the following are S-PLUS expressions:
1:10
rnorm(5)
mean(1:10)
traceback()
If you were debugging a function, for example:
incrementByTwo <- function(x) {
* x + 2
}
you could have an expression that evaluated:
x + 2
at the breakpoint (denoted with the * in the above function
definition).
For more information about expressions, see the Programmer’s Guide,
or see the S-PLUS Help topic ExpressionLanguage.
To watch expressions
1. Right-click the Expressions view to display the contextsensitive menu.
2. From the menu, select Add Watch Expression.
3. In the Add Watch Expression dialog, type the following:
kahanValues[["sum"]]
Figure 4.40: Add Watch Expression dialog with expression added.
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Chapter 4 S-PLUS Workbench Tasks
4. Add a second expression to watch:
kahanValues[["correction"]]
5. Click the Variables view and right-click the variable x.
6. On the context-sensitive menu, click Create
Expressions.
7.
Watch
The debugger returns to the Expressions view. Note that the
variable X is now on the list.
8. Add the following two more expressions to watch:
sum(x)
sum(x)-kahanValues[["sum"]]
The first expression provides the sum of the variable x.
The second expression provides the difference between the
sum of x and the sum of kahanValues.
Optionally, restart debugging to start evaluating the expressions from
the start, pausing to see the results between the Variables view and
the Expressions view.
Figure 4.41: Evaluating expressions.
Stepping into,
over, and out
of a function
148
Other common debugging tasks include stepping through, over, and
out of a routine’s functions. When you step through a routine, the
debugger pauses at every function and function body, giving you the
opportunity to examine the results.This feature is also used to enter
if/else statements, for loops, while loops, and other routines.
S-PLUS Workbench Debugger Tasks
To step into a routine
1. Click the Step Into button (
into routines and their bodies.
). Repeat to continue to step
2. Note that as you click Step Into, the code being evaluated is
highlighted in the Script Editor and is evaluated in the call
stack.
3. Keep stepping into the code until you come to an internal
function. (See Figure 4.42).
Because this function is not in your project files, note that the
function is displayed in a temporary file. (You can set a
breakpoint in such a function, and continue to evaluate it in
future debugging sessions.)
Figure 4.42: Stepping into a function displayed in a temporary file.
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Chapter 4 S-PLUS Workbench Tasks
You can also step over a function (
function (
), or you can step out of a
), using the buttons on the Debug view toolbar.
Note
If you are debugging using the Run button, rather than running a function via the Console view,
when you reach the last expression, you can find yourself in internal S-PLUS code. To avoid this
situation, type the name of the function and parameters in the Console view instead. See the
section Debugging Using the Run Button on page 158 for more information.
Examining
Resource
Usage
You can track resource allocation usage by engaging the S-PLUS
Workbench Profiler.
To track resource usage
1. On the S-PLUS Workbench main menu, click the Profiler
button ( ) to toggle it on.
2. Click the Allocations view tab.
3. Examine the resource usage. Note that it is sorted
alphabetically by type. Click the Type column head; note
that the view is now sorted in reverse.
4. Click the Amount column head; note that the view is now
sorted by amount, smallest to largest.
5. Click Amount again; note that it re-sorts, largest to smallest.
6. Click the drop-down menu, and then
Allocations. Note that the table is cleared.
Examining
Function Calls
Reset
In the next section, examine the functions used in the example. You
can examine the functions either in an expandable tree view or in a
table view. (Make sure the Profiler is engaged by toggling on the
Profiler button on the main menu.)
To track functions used
1. Click the Function Calls view tab.
150
click
S-PLUS Workbench Debugger Tasks
2. Examine the tree. Note that after each function, in
parentheses, is the amount of time the function call took to
run.
3. Scroll down to the kahanAddNext function, expand the
selection, and examine the time values.
Figure 4.43: Tree view of the Function Calls view.
4. Right-click the Function
Function Tree to clear it.
Calls view and click Show
5. Examine the resulting table.
6.
Scroll down to the kahanAddNext function and review the call
count (that is, number of times called so far) and duration.
Figure 4.44: Table view of the Function Calls view.
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Chapter 4 S-PLUS Workbench Tasks
152
TROUBLESHOOTING
5
Introduction
154
“Workspace in Use” Error
155
Working with Calls to S-PLUS GUI Functions
156
View is not visible
157
Debugging Using the Run Button
158
Subclipse Add-in error with Workbench
159
153
Chapter 5 Troubleshooting
INTRODUCTION
This section provides information about using S-PLUS code in the
Workbench, and presents workarounds and solutions for special cases
you might encounter.
154
“Workspace in Use” Error
“WORKSPACE IN USE” ERROR
Occasionally, when you start the S-PLUS Workbench, you might see
an error that the workspace is already in use when you have not been
running a Workbench session.
This problem occurs when you switch computers or versions of
UNIX, and you have changes to absolute paths to a given directory.
1. Check your computer to ensure that the path listed in the
Workspace Selection dialog exists.
2. After you set the appropriate path to an existing workspace, if
the problem persists, check for a .lock file in the
WORKSPACE/.metadata directory. Delete this file.
3. If you do not find a .lock file, check the running processes to
see if old Eclipse processes are running that point to the
workspace. End the processes and try re-starting the S-PLUS
Workbench.
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Chapter 5 Troubleshooting
WORKING WITH CALLS TO S-PLUS GUI FUNCTIONS
While you are working with S-PLUS , you might encounter libraries or
sample code that include calls to S-PLUS GUI functions. For
example, the nSurvival library includes calls to guiCreate and
guiRemove functions in their .First.lib and .Last.lib objects,
respectively.
To solve this problem, in .First.lib and .Last.lib functions, wrap
the code that creates and removes Windows GUI elements in
conditional statements. For example:
if(interactive() && platform() == "WIN386" &&
getenv("S_ECLIPSE") == "") {
##...Code that creates or removes Windows GUI elements...##
}
156
View is Not Visible
VIEW IS NOT VISIBLE
If you accidentally close a view, or if the view you want to see is not
visible, on the Windows 䉴 Show View menu, select the view to
display. If the view to display is not on this list, click Other to display
the Show View dialog, and then select the folder, and then the view
to display.
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Chapter 5 Troubleshooting
DEBUGGING USING THE RUN BUTTON
When you use the Run button to invoke a debug session rather than
using the Console view, and you come to the last expression and
click Step, Step In, or Step Out, you can end up in internal S-PLUS
functions that are called by your code.
This behavior occurs because any time you click Run, the expression
that S-PLUS runs is wrapped in a complex S expression designed to
capture parse errors, syntax errors, and so on.
To avoid finding yourself in this internal code, run the function by
typing it in the Console view.
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Subclipse Add-in Error with Workbench
SUBCLIPSE ADD-IN ERROR WITH WORKBENCH
If you are running the Subclipse add-in while you run the S-PLUS
®
Workbench in Microsoft Windows , you might see the following
error when you switch between projects:
"Unknown problem executing expression (interrupt?)"
It is possible to remove this problem by performing an SVN Cleanup
operation in the Workbench.
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Chapter 5 Troubleshooting
160
INDEX
Symbols
C
.Data
working 40
.Data database 10
.metadata database 10
changing databases
adding a directory 126
adding a library 125
adding a module 126
clear History view 55
code indenting 46
code problems
locating 59
collapsing breakpoints 93
color options
user-defined 18
commands
persisting history 16
scroll through 37
comparing versions 48
console fonts 16, 21
Console view 33, 37, 53, 74
Console view menu 36, 38
copy
project files between projects
108
copy history to the Console view 55
copying code
from the Console view 136
copying from script to console 135
Copy to Console 25
create a Workbench project 101
current working directory 40
customized menus 23
customized toolbars 23
A
add a task
in script file 134
Allocations view 33, 74
anonymous functions
showing in outline 20
B
background color 18
background color in Console view
changing 17, 21
Breakpoint
types 91
breakpoints
Line 91
Breakpoints view 33, 74, 89
Breakpoints view menu
Deselect Default Working Set
95
Select Default Working Set 95
Working Sets 95
Breakpoints view toolbar 92
161
Index
D
databases
detaching 61
examining search path 60
manipulating 56
debugger 158
Debug perspective 66
Debug perspective views 74
Debug view 74
Debug view toolbar 77
Define Folding Region 24
defining color
user terms 18
deprecated 122
deselecting default working set
Breakpoints view menu 95
Details pane
Expressions view 89
Variables view 86
device
default 15
dialog
Filters 59, 63
Outline options 20
Preferences 12
Select Perspective 122
Show View 121
Sorting 59, 63
Task Tags 22
Workspace Launcher 101
directory
attaching 61
down arrow 37
E
Eclipse 2
edit code 129
editing
function definitions 130
editor 45
empty project
creating 102
existing files
162
creating a project for 102
existing project
importing files for 103
expanding breakpoints 93
expression evaluating
hovering 18, 81
expressions 146
limiting return 85
Expressions view 74
Details pane 89
Expressions view control menu 84
Expressions view toolbar 88
external files
opening 49
F
file associations 12
files
formatting 39
opening files not in your project
23
filtering files 49
Filters dialog 59, 63
find
function calls 25
FIXME
high-priority tasks 61
font settings
console and output 16, 21
format code 24
Format S-Plus Files 39
Function Calls view 75
function definition
editing 25, 130
function definitions
editing 130
function help 7
functions
watching 20
G
Go to File for Breakpoint 93
Group By 95
Index
H
help
displaying 46
help menu 26
high-priority tasks 61
history
persisting 16
History view 53, 54, 136
hover 85
hovering
evaluating expression 18, 81
I
IDE defaults
S-PLUS perspective 12
importing files 103
Import menu command 108
indenting
code 46
internal S-PLUS functions
in temporary files 158
interrupt code 45
J
Java graph 15
L
library
attaching 61
Line breakpoints 91
line limits
History view 56
line numbers 129, 130
displaying 45
low-priority tasks 61
M
medium-priority tasks 61
menu
Console view 36, 38
help 26
Objects view 56
Problems view 59, 60
Run 26
S-PLUS 24
Tasks view 63
Window 26
menus
customized 23
module
attaching 61
multiple projects 106
N
Navigator view 54, 128
New Project wizard 23
O
Object Explorer
Workbench 58
object members
changing number displayed in
Objects view 58
objects
examining 57
Objects view 53, 56
Objects view menu 56
opening external files 23, 46
Outline dialog 20
Outline view 41, 53, 75
Outline view toolbar 43
output fonts 16, 21
Output View 75
Output view 43, 53
P
PDF reader
specifying 8, 14
Perspective 3
perspective 31
Debug 66
reset 122
S-PLUS 52
163
Index
Preferences
debugging 69
preferences 12
setting 110
Preferences dialog 12
Problems view 54, 59, 137
Problems view menu 59, 60
profiler 67
project files
copying 108
removing 128
R
refreshing
Objects view 57
Problems view 59
Search Path view 61
views 127
Remove All Breakpoints 92
removing
project files 128
restoring files 48
reviewing objects 57
run 26
Run Current File 135
Run menu 26
run next command 26
running code 26, 45, 134, 135
on startup 14
running scripts 135
running S-PLUS code 27, 29
S
script
creating 128
Script Editor 45
in the Debug perspective 75
searching terms 48
Search Path View 60
Search Path view 54, 125
selecting the default working set
Breakpoints view menu 95
164
Select Perspective dialog 122
setting return limits
variables and expressions 85
shared views 33
show anonymous functions 20
Show Breakpoints Supported by
Selected Target 92
Show View dialog 121
simultaneous sessions 2
Skip All Breakpoints 93
Sorting dialog 59, 63
Source S-PLUS Files 39
specifying a PDF reader 8, 14
S-PLUS
internal functions 158
S-PLUS (Deprecated) 122
S-PLUS Debugger
toggling 28, 30
S-PLUS error breakpoint
toggling 29, 30
S-PLUS menu 24
Find 25
Find References 25
Format 24
Open S-PLUS Help File 25
Run Current File 24
Run Selection 24
Shift Left 24
Shift Right 24
Toggle Comment 24
S-PLUS Packages 8
S-PLUS perspective 52
S-PLUS perspective views 53
S-PLUS Profiler
toggling 28, 30
S-PLUS warning breakpoint
toggling 28, 30
S-PLUS Workbench 2
starting the Workbench 9
step into
internal S-PLUS code 158
stop 26
store console history 16
Index
T
V
table pane
Objects view 57
task levels 61
Tasks view 54
Tasks view menu 63
Tasks view toolbar 62
task tags
defining 22
Task Tags dialog 22
text variables
limiting return 85
TODO
medium-priority tasks 61
toggle Debug mode 26
toggle Profile mode 26
toggle S-PLUS error breakpoint 26
toggle S-PLUS warning breakpoint
26
Toggle Working S-PLUS Project 40
toggling comments 24
toggling S-PLUS Debugger 28, 30
toggling S-PLUS error breakpoint
29, 30
toggling S-PLUS Profiler 28, 30
toggling S-PLUS warning
breakpoint 28, 30
toolbar
Breakpoints 92
Debug view 77
Expressions view 88
Outline view 43
S-PLUS Workbench 27
Tasks view 62
toolbars
customized 23
tooltip 18, 81
tree view pane
Objects view 58
Variables view 75, 83
Details pane 86
Variables view control menu 84
view
Allocations 74
Breakpoints 74
Console 74
Debug 74
definition 32
display issues 122
Expressions 74
Function Calls 75
Outline 75
Output 75
refreshing 61
Search Path 60, 125
Variables 75
views
changing display 121
customizing 120
Debug perspective 74
shared 33
S-PLUS perspective 53
U
up arrow 37
W
watching functions 20
Window menu 26
Workbench Project 4
Workbench project
creating 101
Workbench Script Editor 5
Workbench User Guide 6
Workbench View 5
working directory
setting current 40
Working Sets
Breakpoints view menu 95
Workspace 4
workspace 10, 101
changing 101
Workspace Launcher dialog 101
165
Index
X
XXX 61
166
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