Release Notes


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Version 1.1.9 (February 9, 2015)


New features:

  • The ROI table and peak list editing GUIs, re() and pe(), have been modified to update their respective tables and refresh the spectrum automatically. In addition, view buttons have been added to enable zooming to the selected ROI/peak, along with a Refresh (manually refresh spectrum) and a Restore button (restores ROI/peak lists to their state prior to their respective GUI being opened).
  • The auto ROI function, ra(), has been modified to append the current contour threshold level to the ROI table when ROIs are created.
  • Internal peak picking function, peakPick(), has been modified to append default labels to newly picked peaks.

Internal Modifications:

  • New function createTclImage(), used as a shortcut for creating Tcl images for use in rNMR GUIs.

Bug fixes:

  • Modified calls to function readLines() to avoid warnings regarding first line null values.
  • Modified function myTopLevel() to ensure new child windows may be created without error (issue introduced in R 3.1.2).

Version 1.1.8 (June 12, 2013)


New features:

  • New feature added to files GUI, fs(). Spectra stored in memory as a list object (same format as fileFolder) may now be opened and displayed as if the spectrum was being read from a UCSF format file.
  • New utility function writeUcsf(). This function is intended for advanced users and is used to write newly created/converted spectra out to file in UCSF format.
  • Internal function ascii2rnmr()has been modified to decrease the time and memory required to convert ASCII files to UCSF format.

Internal Modifications:

  • Modifications were made to internal functions ucsf1D(), ucsf2D(), and ucsf3D() to allow plotting spectra stored in memory.
  • Simplified and improved the way rNMR reads, checks, and writes the default settings. Affected functions include readDef(), checkDef(), writeDef(), createObj(), and the defaultSettings global.

Bug fixes:

  • Corrected installer related issues. rNMR installers are now functional on all platforms and are compatible with R 3.0.0. As a result of these changes, versions of R prior to 2.10.0 are no longer supported. The rNMR source package is now stored only on the rNMR website server and is downloaded during installation. The installers themselves are no longer versioned.
  • Corrected a bug in the ASCII conversion GUI, ca(), that prevented files from being removed from the conversion list.
  • Modified internal function parseProcpar() to allow for the proper conversion of certain 1D Varian spectra, which could not be converted due to a misinterpretation of the "ni" parameter.
  • Modified internal functions parseProcs() and parseAcqus() to correctly parse Bruker processing and acquisition parameter files that differ from the standard format.
  • Improved the functionality of internal functions writeDef(), readDef(), checkDef(), and createObj(), used for saving and loading rNMR's default settings.
  • Fixed error generated by the overlay GUI, ol(), when attempting to switch spectra from the file list by pressing the enter key.
  • Corrected a bug in internal function updater() that was causing the function to exit prematurely when run manually (auto=FALSE) if defaultSettings$update was set to FALSE.

Version 1.1.7 (August 3, 2011)


New features:

  • No new features, this is a patch release that fixes minor bugs.

Bug fixes:

  • Further corrections (see fix in version 1.1.5) have been made to internal function updateFiles().

Version 1.1.6 (July 29, 2011)


New features:

  • Improved interface for the ca(), cf(), and fs() functions.
  • The display of names of overlaid spectra in the main plot window may now be turned on or off from the ol() GUI. Also, overlaid spectra are no longer displayed in the file list.
  • Minor modifications that improve the rNMR interface when running R in MDI mode.

Internal modifications:

  • The fs(), fo(), patch() and plotting functions have been modified to accept the "user_title" field which has been added to the "file.par" heading of the fileFolder object. This field is displayed as the title in the main plot window and is modified when users edit spectrum names in fs() rather than the names of fileFolder.
  • The patch() function has been modified to add the "overlay.text" field to defaultSettings if missing.
  • The reset() function has been modified to ensure overlaid spectra are not displayed in the file list of the overlay gui.
  • An option has been added to the message dialog displayed by the sdiCheck() function to discontinue its display. If selected, the "sdi" field of defaultSettings is set to FALSE.
  • An "overlay.text" argument has been added to the setGraphics() and createObj() functions to support the overlay display feature mentioned above.
  • The ucsfHead() function has been modified to read the noise estimate if it is present at the end of the main file header of a UCSF file. In such cases, the noise estimate is not calculated. Also, file sizes are now expressed in bytes rather than kilobytes.
  • All GUIs containing file lists have been modified to scroll to the current spectrum in the file list when opened.
  • The .onLoad() function now modifies the tablelist widget options to alternate row colors by default. Similar code contained within functions that create tablelist widgets has been removed. Also, .onLoad() now forces the default background color for selected items in tablelist widgets to match the color for selected in items in listbox widgets. This should improve visibility.

Bug fixes:

  • The bringFocus()funciton is no longer called when R is running in MDI mode. This prevents Tk windows from disappearing behind the MDI console.
  • Resolved an issue with the createObj() function that prevented the addition of new fields to defaultSettings without overwriting other settings.
  • The draw2D() function has been modified to ensure correct plotting of data in memory (e.g. entries in fileFolder with w1, w2, and data sections).
  • The re() function now allows for NA values.
  • Added a "check" agrument to the readDef() funtion which may be set to FALSE (defaults to TRUE) to bypass the format check on defaultSettings. This allows previous settings to be carried over to new versions of rNMR that include changes to defaultSettings.
  • The rSum() function has been modified to run correctly on spectra with customized names and on ROIs that contain no visible signal.

Version 1.1.5 (February 14, 2011)


New features:

  • No new features, this is a patch release that fixes minor bugs.

Bug fixes:

  • Internal function updateFiles() has been modified to function correctly with changes implemented in version 1.1.4 (spectrum names do not need to match file paths).
  • The fs() function now updates overlayList when spectrum names are changed. Also, the GUI's close button has been modified to operate correctly on files that have been renamed.
  • The mySave() function now adds a ".", if it is not already included, to the "defaultextension" argument to correct an error encountered on non-Widows platforms.

Version 1.1.4 (January 12, 2011)


New features:

  • Spectrum names for files opened in rNMR may be edited using the fs() function.

Bug fixes:

  • The ASCII (plain text) spectrum conversion function, ca(), has been modified to ensure spectra are not reversed during conversion.
  • Additional columns may now be appended to ROI tables without causing errors.
  • The plot utilities help page has been updated to include additional low-level plotting functions which were not previously exported to the rNMR namespace.

Version 1.1.3 (October 15, 2010)


New features:

  • No new features, this is a patch release that fixes minor bugs.

Bug fixes:

  • Dead links to images in the rNMR manual have been resolved.
  • The Windows installer has been updated to work properly with the R version 2.12.

Version 1.1.2 (September 22, 2010)


New features:

  • No new features, this is a patch release that fixes minor bugs.

Bug fixes:

  • The import() function turns on the peak display when peak tables are imported.
  • Settings displayed in the plot settings GUI are updated when spectra are opened or closed.
  • Internal function showGui() has been modified to ensure GUIs do not remain hidden behind the R console.

Version 1.1.1 (August 15, 2010)


New features:

  • Added arguments to peakPick and findTiles() functions to support internal peak picking operations (without opening and displaying a file).
  • The myOpen() and mySave() funtions have been modified to allow the display of a specific file type by default.

Bug fixes:

  • The ws() function now prints out the correct file path to the newly saved workspace upon completion.
  • Internal function trans2peak() now returns ordered peak lists. This fix was implemented to ensure proper sorting and naming of ROIs when using ra().
  • The updater() function now performs automatic updates properly when rNMR loads.

Version 1.1.0 (July 15, 2010)


New features:

  • Improved interface.
  • Improved peak and ROI table editors.
  • Installation of rNMR no longer requires administrative permissions.
  • Automatic update feature enabled during start up, as well as manual update via the Help menu.
  • Added support for Varian arrayed 1D spectra conversion.
  • Overlay function, ol(), now supports one-dimensional overlays on 2D spectra.
  • Additional summary features included in rSum().
  • New function ca() ASCII (plain text) spectra to UCSF format.
  • New function rr() allows active ROIs to be renamed without calling the ROI table editor.
  • New function fs() provides an interface for sorting files.
  • New function ep() allows rNMR's default settings to be modified.
  • New function rb() restores a backup copy of the current workspace to prevent unsaved work from being lost.
  • Region option added to ROI selection function rs().
  • Region maximum option added to the "Get shifts" feature in the zoom GUI.
  • rNMR now requires TclTk 8.5.0 and above.

Bug fixes:

  • Resolved file conversion (cf() function) errors generated when trying to convert Bruker spectra with certain file structures, especially single experiments containing a large number of spectra.
  • Menus in the main plot window under Windows platforms no longer disappear or cause R to crash.
  • rNMR help() function has been renamed myHelp() to avoid conflicts with R's help() function.
  • NMRPipe converter ensures that selected files are valid NMRPipe files before preceding with conversion.
  • pz() function minimizes GUIs before executing to match behavior of other iterative functions (eg zz(), ph(), etc.).
  • Attempting to load an invalid R workspace using wl() function no longer crashes rNMR.
  • 1D ROI expansion and contraction behavior is now more functional and intuitive.
  • updateFiles() function is now capable of restoring shift referencing changes to updated files.

Version 1.00.8 (February 17, 2010)


New features:

  • No new features, this is a patch release that fixes minor bugs.

Bug fixes:

  • Resolved file conversion (cf() function) errors generated when trying to convert Bruker spectra with certain file structures, especially single experiments containing a large number of spectra.

Version 1.00.7 (February 10, 2010)


New features:

  • Expanded compatibility for Linux distributions (fo() function is now able to open multiple files on all systems tested, regardless of installed Tcl/Tk version).

Bug fixes:

  • X11 fix from version 1.00.6 inadvertently switched graphics engines on Mac OS X to Quartz causing intermittent crashes in R.

Version 1.00.6 (January 26, 2010)


New features:

  • A message is displayed in the main plot window instructing users to open files when the package is loaded.

Bug fixes:

  • X11 fix from version 1.00.4 slowed down graphics on Linux platforms due to the use of cairo when generating X11 devices. Cairo is now implemented only when necessary (see the R help page on X11 for more information).

Version 1.00.5 (December 15, 2009)


New features:

  • No new features, this is a patch release that fixes minor bugs.

Bug fixes:

  • Improved error handling in cf() function.
  • Processing parameters modified by the Vnmr export macro are now correctly exported along with the data.
  • Minor changes to default processing commands in Vnmr export macro.

Version 1.00.4 (November 24, 2009)


New features:

  • No new features, this is a patch release that fixes minor bugs.

Bug fixes:

  • X11 font issues that may have been present on non-Ubuntu linux platforms have now been resolved.
  • Help documentation missing from the previous release has been reintegrated.

Version 1.00.3 (November 17, 2009)


New features:

  • No new features, this is a patch release that fixes minor bugs.

Bug fixes:

  • Function cf() now looks for five possible decoupler nuclei ("dn" through "dn5") and only returns those that are present in the "procpar" file when converting Varian spectra.

Version 1.00.2 (November 11, 2009)


New features:

  • No new features, this is a patch release that fixes minor bugs.

Bug fixes:

  • The rNMR menu no longer comes up twice when old workspaces are loaded automatically when R starts on linux platforms.

Version 1.00.1 (November 2, 2009)


New features:

  • No new features, this is a patch release that addresses issues related to the release of R 2.10.0.

Bug fixes:

  • Help functions are now compatible with R 2.10.0.

Version 1.00.0 (October 13, 2009)


New features:

  • New function cf() released for beta testing; converts Bruker, NMRPipe, and Varian format spectra to UCSF format (the default file format for rNMR).
  • New function pm(); peak picks the maximum intensity within a region.
  • New function delta(); retrieves the chemical shift range between two user-defined points in a spectrum in Hz or PPM.
  • Developer's toolkit; utility functions for advanced rNMR users. These functions are provided as a convenience for the creation and integration of custom functions into the rNMR package.

Bug fixes:

  • Internal function updateFiles() used for checking the validity of file paths in "fileFolder" now updates "overlayList" in addition to "fileFolder" if changes are made.
  • Multiple fixes for regionMax() function used in shift referencing GUI sr().
  • Files with the same name but different file paths may now be opened without causing errors.
  • The context menu for the main plot window on Windows platforms now displays the correct items when switching between 1D and 2D spectra.
  • The perspective GUI, per(), can no longer be opened when the current spectrum is 1D (1D spectra can not be displayed as a 3D perspective plot).
  • Function export() now returns an error message from the peak picking GUI if their isn't a peak list for the current spectrum.
  • Internal function drawNMR() now passes the "type" argument to plot1D(), this gives the user the ability to change the plot type (line, points, or both) for 1D spectra.

Version 0.99.0 (May 31, 2009)


  • First official rNMR release.

Please refer to the rNMR manual for information on using rNMR.

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