If you start Bio7 a warning or error can occur because of the changes how Apple treats signatures! Please see this post for a solution (Go to System Preferences>Security & Privacy>General, set ‘Allow Apps etc’ to ‘Anywhere’. Change it back after you download and executed this app.).
In addition For MacOSX you have to install R and Rserve.
To install Rserve open the R shell and then execute the menu action “Options->Install Rserve (coop. mode)”. This will download an install Rserve in your default R library location, see video below (please make sure that your default MacOSX R library install location has writing permissions! – normally you don’t have to worry about this on MacOSX!).
A new release of Bio7 is available for Windows (64-bit) and Linux (64-bit).
The MacOSX version will be released soon, too. This release comes with a plethora of new functions for R.
Bio7 is now based on Eclipse 4.6.3
Redesigned all Bio7 icons and created new icons, too
Nearly all icons are now available for high dpi displays
Added a dark Theme for Bio7
Added the default Eclipse theme as optional to Bio7
Added a new action for Linux and MacOSX to download and install Rserve (see Video in R section)
Custom views are now entitled with the id of the view
Added a new „Document“ perspective for LaTeX, Sweave, knitr and rmarkdown documents
Added a new PDF viewer in the JavaFX browser to display PDF’s from LaTeX, knitr, rmarkdown and R plots („Display“)
Added options and actions to fullscreen a PDF on different monitors (press the key ‘t’ and the PDF will be centered and the toolbar will be removed)
Added several PDF options (scroll to selected page, etc.)
Added a new JavaFX browser for *.html and *.pdf files based on PDF.js
PDF files can be opened within the Navigator view with a double-click of the mouse device (also popular image types with ImageJ).
Added drag and drop support for the browser for *.html and *.pdf files
All editor fonts can now be scaled with the key combination ‘Ctlr +’
Added new global preferences for the editor fonts
Added preferences links for an improved navigation
Updated the default scientific Java libraries
Implemented a reload of the JavaFX Browser to avoid a cached display
Improved the resizing of the Quadgrid (Hexgrid) view
Added a new preference to disable the scrollbars of the Quadgrid (Hexgrid) view
Updated R to 3.3.3 on Windows
Added an action to download and install ‘Rserve cooperative mode’ for Linux and MacOSX
Improved the speed of the „Load packages“ dialog
Improved the speed of the „Install packages“ dialog.
Improved the speed of the refresh action in the R-Shell view
Added browser preferences to select the browser and the display
Added a new toolbar action for Sweave
Added an extra view for plots
Added the package install dialog as an view
Added an option to open a HTML package info for a selected package in the package install view (see video below).
Added a preference for a custom Rserve client connection port if you start the Rserve server with a different port
Added code completion in the R-Shell view for s3 and s4 methods (see video below)
Added an option to automatically open code completion when typing in the R-Shell
R-Shell R help now recognizes the selected browser
Added several actions to create, built, and test R packages to the context menu of the Navigator view (using the ‘devtools’ package)
Added a Shiny test action in the context menu of the Navigator view which opens a browser with the running shiny application (select a project folder with the server and ui files – to stop the server use the interrupt action in the R-Shell console or press ‘Strg c’ in the Console).
Improved the transfer of variables and sheet names from the Table view and LibreOffice
Improved the display of the R preferences (opening the default preferences structure)
Improved the code completion in general
Code completion dialogs are now synchronized with the other dialogs
Added code completion for
S3 objects (after $)
S4 object slots (after @)
the library function (library())
the data function (data())
Added new individual images to the code completion
Improved the close parentheses functions
Improved the visual appearence of the hoover dialog
Corrected the code completion images to match the Outline view images
Improved the display of markers
Added a popup display for the ‚str‘ function when hoovering over a workspace variable
Fonts can now be scaled with the key shortcuts ‘Strg +’
Added automatic indention after parentheses (loops, function, etc.)
Added preferences for the formatR package
Added an formatR action to format editor selections only
Added a refactor rename method for a selected scope
Added roxygen code completion in comments
Added an action to create roxygen templates from selected function, S3, S4, Reference and R6 classes (see video below)
In the popup menu added several actions of the devtools package to create, test and install R packages (select a project or regular folder)
Added plot preferences to open plot images individually and an option to execute an ImageJ macro after plot creation (e.g. to scale a plot after creation, etc.)
Added an ‘Open File’ and ‘Save File’ dialog to create file templates with selected files in the R editor and the R-Shell view (see video)
Added a new shortcut to create an assign operator (‘ALT _’)
Added a new shortcut to create a pipe operator (‘CTRL SHIFT M’)
Added simple editor templates for S3, S4, Reference and R6 classes
Improved the preferences navigation
Reorganized some preferences
Updated the parser to ANTLR 4.6
Improved the R markdown editor
Header and R chunks are now displayed in the Outline view
Added spell checking to the rmarkdown editor
Compiled documents are now displayed in a special custom view of Bio7 if enabled (by default enabled)
Added font and color preferences to the editor
Added new browser preferences (use of JavaFX webkit browser or system browser) and additional preferences for the control of the output
Added preferences to compile the document automatically after a specific time intervall (adjustable in the preferences – see video below)
Added code templates for popular markdown commands
Added an option to open word documents embedded in a custom view with Word (Windows only)
Added a key shortcut for the action to compile markdown documents
Improved the compile actions in the Bio7 toolbar (new icon) and removed the popup actions in the Navigator view
Added a key shortcut for the compilation
By default Latex documents are opened in the new PDF viewer (custom view)
Added new Bio7 LaTeX preferences to compile documents easily (without the need to create a LaTeX project with Texclipse)
Added new preferences to optional use XeLaTex and cleanup auxiliary files in the project folder
Added an option to compile BibTeX along with the *.tex file (several compilation iterations are performed)
Updated ImageJ to version1.51m
Improved the ImageJ menus to display all ImageJ menus correctly and nested (with key shortcuts and seperators)
ImageJ plugins now extend the respective SWT menu analogue to the ImageJ AWT menu.
Plugins, scripts and macros are now displayed in their defined menus or submenus.
Some popular image types can now be opened (double-click) directly from a Navigator folder (registered as a fake editor type)
Added two preferences to define the install location of plugins and macros (e.g external locations for teams).
Plugins now contribute to all ImageJ menus (SWT) like it is known from ImageJ
Dramatically improved the compatibility for ImageJ plugins (partially AWT)
Added a menu option to open images in a nested JavaFX panel (fullscreen on different monitors possible)
Added a ImageJ macro wizard action to create ImageJ macros
Updated WorldWind to version 2.1
Made improvements for the dark theme
Just download the *.zip distribution file from http://bio7.org and unzip it in your preferred location. Bio7 comes bundled with the latest Java Runtime Environment, R and Rserve distribution and works out of the box.
To install Rserve open the R shell and then execute the menu action “Options->Install Rserve (coop. mode)”. This will download an install Rserve in your default R library location, see video below (please make sure that your default Linux R library install location has writing permissions!).
The next release of Bio7 comes with many new R features and improvements which were integrated since the last release.
In this post I like to present a subset of some new R documentation features of the upcoming Bio7 2.5 release.
1. R Markdown Editor:
I improved the R markdown editor of Bio7 and integrated some code templates, font colors and dynamic font resizing, a default PDF viewer for all Operating Systems (pdf.js), an outline view, spell checking and some new preferences useful for a constant writing and preview of documents. For an improved writing and preview layout I added a new document perspective for Bio7 for the supported document types of Bio7 (LaTeX, rmarkdown, knitr, Sweave, etc.).
Bio7 comes shipped by default with a full featured LaTeX editor (TeXclipse).
However for an easier default compilation and document preview I integrated several new dynamic actions without the necessity to built LaTeX documents.
Thus it is now possible to preview LaTeX documents inside the new custom display of Bio7 and I added several preferences to improve the compilation process and font rendering of Bio7 (BibTeX, XeLaTeX compilation, etc.).
In addition it will be possible to create presentations with the Beamer package and fullscreen the pdf presentation on different selected monitors (you can remove the toolbar and center the created pdf with a special key shortcut).
For the next upcoming release of Bio7 a new dark skin will be available. Here are some screenshots for Linux and Windows. Some UI elements of Windows are controlled from the OS and can’t be skinned at the moment.
Beside many changes for the next release I was able to find the time to update the icons of Bio7 for the next release. The icons are a subset of the FontAwesome icons and some custom icons and were created with Inkscape. They will be made available for free, too. At the moment the icons are available in two resolutions (100%, 200%) and the larger icons will be used when working with a high DPI monitor (> x dpi). For the rules see: