Notes.txt

OpenVnmrJ Release Notes.

March 2025
    Parameter values can use multi-byte characters such as
      umlauts.
    Installation of java on AlmaLinux 9 could fail in some cases.
    Compiling imaging sequences with seqgen gave warnings.
    Link for Spinsights Community Help Site fixed.
    Compiling OVJ with gcc 14 failed.
    Added ascii option to writespectrum. See manual/writespectrum.
    ll2d command has new 'peakno' keyword. See manual/ll2d.
    atcmd active keyword re-defined to mean any currently active OVJ.
    readspectrum can import complex 1D spectra. See manual/readspectrum
    write, copystr, and appendstr support writing to multiple files
    BUG: The copy command could fail if the file being written to
      does not exist.
    BUG: findLinks was failing on Ubuntu. Only an issue when Locator
      is in use. Bug reported in SpinSights
    Updates to gradient shimming macros from Bert Heise.
    BUG: Error during Edit Probe when adding solvent factors.
      Fixed by Bert Heise.
    Eliminate an unnecessary constant from pboxpulse.h. Also improved
      error messaging. Thanks to Barry DeZonia.
    getfile on MacOS could fail when used with alphasort. Could return
      pathnames prefaced with a /.
    Added dc1d parameters to change the default behavior for FID drift
      correction. See manual/ft
    BUG: setacq / setNIC could fail on Ubuntu 24.
    pl('side') would truncate negative peaks.
    pscharsize parameter was not functional for write('plotter',...)

September 2024 *****************
    OpenVnmrJ 3.2A release 

September 2024
    Updated IUPAC referencing standard to the 2008 version
      Thanks to David Vander Velde
    Appdir pathnames use USERDIR as keyword in any path name
      It will expand to the value of the userdir parameter.
    Added H2('lk') under Other Nuclei in the Experiment menu
      Often used for debugging. (Thanks to Bert Heise)
    cexp will make maclib directory if needed
    Added mechanism to not start Locator during installation
      By doing "touch LocatorOff" in the dvdimageOVJ[MI] directory,
      load.nmr will not try to start postgres aka Locator.
    OVJ now works in Windows 10 and 11. Thanks to Jessi Baughman for
      writing a script that installs the MicroSoft WSL tool and OVJ.
    Solids pulse sequences could give error about ""effective dmf too high..."
    Updated ovjGetpipe to install OS packages required by NMRPipe
      Run ovjGetpipe -h for usage information.
    Added tools to build a patch to support ARM architecture.
      See src/arm/README
    pageview could fail on MacOS due to missing ps2pdf script.
      Added ovjMacTools script to install it. It will also install
      ImageMagick and xterm. For help information, run
      ovjMacTools -h
    ArrayedSpectra vertical panel could reset display to a full array when
      a partial set of array elements had been selected (Thanks to Bert Heise).
    Documented how to set fonts in a dialog popup (see manual/dialog).
    load.nmr will run a non-interactive config to reset values to those from
      a previous installation.
    When double clicking the carbon experiment in the study queue to adjust any
      Carbon parameters, the window usually opens to the Acquisition parameter
      window instead of the Default C13. It now works like everything else.
    Removed CRAFT and ChemPack information from getversion
    Added unit 't' for 'msec'
    Help Overlay no longer is displayed by default
      It is still available from the Help menu.
    Added a button to mtune interface to toggle normal and wide line widths
      Suggestion from Ken Knott
    Fix some typos in  solidspack PSG error messages
    Additions from Bert Heise.
      new centerprobe macro and corresponding button on the gmapz panel
      Autotest calibration does Hdec and Cobs in addition to Hobs & Cdec.
      The Edit Probe popup window had overlapping widgets making it difficult
        to click/select the widgets in the top row (Add/Delete Nucleus etc.)
      LkGmap creates a z5 shimmap even for db-style probes while lkZ0 checks
        for the probe style and (correctly so) creates a z4 map only.
        Changed lkGmap to do the same style check and z4 map making.
      3D gradshim log file reading & writing of temporary best shims fails
        on widebore shim sets because
        (A) Wide-Bore shims (shimset=12) is unnecessarily excluded from writing
            the power dissipation into the log file
        (B) the latter creates a second "NA" entry into the log file which is
            then later being searched for (to determine the first word in each
            data line which is a poor way to read the second column via
            lookup('seekcs','NA','read') because there MIGHT be a number in
            Linewidth column whereupon the lookup will completely fail
            or the second NA entry lets the lookup fall over as well, leading
            to an "expected REAL value" error because the next column behind
            the "NA" power is a name, not a number
      Added INADEQUATE experiment for Mercury
      Added DbppLED DOSY experiment for all consoles
        Longitudinal eddy current compensation (may greatly improve phase behaviour)
      Veripulse now has faster 3D gradient shimming with doped ASTM
    Added tools to build a patch for ARM architecture. Change into patch directory and run
      scons -f SConstructpath_arm
    makeuser no longer removes files from psg, seqlib, or
      persistence user directories. These operations are now
      performed by the fixuser script.
    Added fixuser script to fix potential problems with a
      user account. (see manual/fixuser)
    Fixed several bugs and some enhancements. Added satellite definitions
      (Thanks to Krish Krishnamurthy)
      cfpmult     -  Quiet option with a return variable
      CPwtmenu    -  bug fixed and two functions added
      dodigfilt   -  minor improvement
      dsnmax      -  similar to dsn, returns two values
      dssi        -  potential bug fixed
      dssnoni     -  potential bug fixed
      fixarraydim -  simple utility macro
      invertphase -  simple utility macro
      loadcolors  -  potential bug fixed
      NUSproc     -  returns a value of 0/1
      randomize   -  utility macro
      rtvfs       -  minor edit
      setLP       -  bug fixed
      writetrace  -  works with spectra created with spadd
      xmhaha      -  supports calling craft_xmhaha for .par files
      ovjhostname - sets the instrument parameter in conpar
    
      templates/layout/toolPanels:
      VpLayout.xml -  bug fixed.
    
      satellites:
      DSS  -  Fiddle definition for DSS
      TMSc -  Fiddle definition for TMS, without using 13C satellites
      DSSc -  Fiddle definition for DSS, without using 13C satellites
    getfile on MacOS could fail when used with -R. The returned pathnames
      could be prefaced with a /
    Compile Vnmrbg on MacOS for both x86_64 and arm64 architectures
    Added several macros. Manual entries give additional information
      (Thanks to Jessi Baughman)
      autoh2cal - Automatically process speactra and run h2cal
      autosave - Setup future actions (wbs/wnt/wexp) for auto-saving data
      beep - Play an alert sound
      btime - Set/Display the length of time for one block size
      catfp - Display output from fp command in Text Output
      cattext - Append Text Output (alphatext) to Comment text
      ccr - Move cursor location to the center of the plot
      ctime - Display the total elapsed experiment time
      dsnpeak  - Display maximum signal-to-noise for selected peak
      dsnpeaks - Display maximum S/N for all peaks in linelist
      fa - Display future actions on line 3
      fdc - Performs a drift correction on all the spectra of an array
      fixsq - Fix Study Queue blank display
      fp2csv - Save peak frequencies and amplitudes to a comma-separated file
      fpi2fp - Convert fpi.out to fp.out in the current experiment
      hightemp - Process data and display temperature for ethylene glycol
              temperature calibration sample
      plhightemp - Plot processed hightemp spectrum, scale, and temperature text
      lowtemp    - Process data and display temperature for MeOH
      pllowtemp  - Plot processed lowtemp spectrum, scale, and temperature text
      autoh2cal - Automatically process speactra and run h2cal
      jact - Join active experiment
      logtempspin - Log current spin and temperature status to explog
      plres - Plot the line widths at half-height, 0.55, and 0.11 levels
      rosy - Display T1 or T2 relaxation data in a DOSY-like plot
      rotortemp - Estimate temperature change from spinning at a given rate
      setloc - Reassign current sample location
      vph - Set vertical position to middle of display
    Bug fixes to several macros (Thanks to Bert Heise)
      PWRcalib - may have problems with autocalibration
      cplog - errors with StudyQMimic
      checkplotter - issues with plotter names (kept the " " leading to errors)
      plh - problems not printing integrals
    Made imaging pulse elements putvalue, putarray, and putstring
      standard PSG elements
    Added command svdfit for singular value decomposition of a set
      of linear equations (see manual/svdfit)
    Some solids sequences could have controller timing errors
      (Thanks to Barry DeZonia for this fix)
    Bug fix: add / sub did not handle lvl / tlt correctly
    fidproc has an 'dofpmult' option to apply the fpmult correction
      (see manual/ft)
    Enforces active / not active parameter protection bit. off and
      on commands provide 'force' option to override (see manual/off)
    Parameter vpt controls position of trace above dconi plots.
      See manual/dconi
    Plot1D.xml gave syntax errors on some versions of java.
    Added support for parentheses "()" in filenames
    Updated installpkgs to support Ubuntu ARM architecture
    Updated build documentation for Macs. See ovjTools/OSX.md.
    Vnmr.jar was failing to compile with java 22.
    Updates to support compiling on Mac Silicon systems.
    upgrade.nmr should not replace loggingParamList
    Install failed on PC with preloaded Ubuntu due to directory
      permission problems.
    Updates to support Ubuntu 24
    ROI drawing caused OVJ to crash on Ubuntu but not CentOS
    Removed debugging messages from some macros
    Rounding error for negative numbers. If a number has a step size
      greater than one, negative numbers may be rounded incorrectly.
      For example, setlimit('rnd',50,-50,2) rnd=-16 returns rnd set
      to -18. Bug reported in SpinSights
    Updated ovjBuild. It supports a -c (--codeonly) option to just
      clone the repositories.
    Veripulse did not save default shims. Bug reported in SpinSights.
    Updated Acquisition Communication panel. Now has separate buttons
      to start and stop the acquisition communications
    Converting accounting log to XML failed with java 11.
    Added fiddlecf command (see manual/fiddle)
    Added sample loc to accounting logs (request from SpinSights)
    Infostat could fail if compiled with newer gcc versions (eg gcc 8).
    Made usage of PI value consistent (Thanks to Barry DeZonia)
    Added probeConnect macro to test the validity, and optionally
      to set, the probeConnect parameter (see manual probeConnect)
      (Thanks to Barry DeZonia)
    Supports AlmaLinux 9
    datafit of exponential could fail if used with a file as input.
    Made degree to radian conversions more accurate (Thanks to Barry DeZonia)
    dfs would fail if called immediately after bootup
    showarrays would not always show all elements
    added options to makefid (see manual/makefid)
    accounting package was failing in Canada
    The write and mkdir commands allow spaces in path names
    Imaging fdf files were not being converted to DICOM (aipOut)
    Added DbppADled experiment (thanks to Bert Heise)
    Added 'replace' option to svf and svp (see manual/svf)
    No longer sets LD_LIBRARY_PATH. This was overriding a local
      PSG library when using psggen and seqgen.
    Imaging pulse sequences could fail if nt or tr were arrayed.
    Imaging tool panel Colormap was blank.
    copyf could fail if 'tail' and '|wc w' options were used.
    Typo in rtpipe macro (pipePar should be PipePar)
    Now checks if automation file name is too long
    water_ES andwater_WG experiments could fail with the
      suselfrq macro aborting. Bug reported in SpinSights.
    Fixed several problems in solidspack and biosolidspack
      PSG and psglib (Thanks to Barry DeZonia of the
      Chad Rienstra group)
    Allow XY positioning of popup windows
    Added manual page for the fidarea command.
    Added manual page for the cmdHistory command.
    Operator password changes would not take effect until
      OpenVnmrJ was exited and restarted.
    Bug fix: spExec failed with a write error
      added 'isfinite' option to format (see manual/format)
      to handle case where values may be 'inf' or '-inf'
    can set axis label with fn_label parameter
    Bug fix: cat command may not show entire file written by Vnmrbg
      It requires a call to sync to write memory to the disk.
    added silencing option to listenoff
      Corrected the man page for listenon
    ping could fail on some systems. It was using IPv6.
    autocalibration macro could fail by using
      uninitialized variables.
    ft3d was failing on Linux systems.
    The ArrayedSpectra side panel may not show all array values.
    The shimbutton widget could show overlapping labels.
    VeriPulse was failing with some probeID systems. Allows setting
      probe serial number in the VeriPulse interface.
    Some PPC boards were failing to boot. Also updated tftp
      directories where bootpd searches for files.
    Added Imaging protocols that were in VJ 4.2 but missing from OVJ.
    Image display was failing on Ubuntu, causing OVJ to crash.
      It worked on CentOS. 
    the rm command with 'regex' would fail if the directory did
      not exist.
    makefid failure gave misleading error messages and caused
      subsequent df and dscale to hang.
    setpage supports header positioning options
      (see manual/setpage)
    Bug fix: fixgrd does not calculate negative gradients
    Bug fix: tancpx pulse sequence could cause a core dump
    Added tools to query ROIs (see manual/aspRoi)
    Bug fix: $e expected REAL return value
    Tray display for ASM100 can select order of zones
    Bug fix: Saved FID files did not respect umask or ACLs.
    Improved interactive creation of box and oval annotations.
    Supports Ubuntu 22.
    Bug fix: The loadcolors macro could fail if called from
      multiple background Vnmrbgs.
    readstr now handle either local or experiment parameters
      (see manual/readstr)
    Added T1rho experiment (thanks to Bert Heise)
    Bug fix: setacq was not starting tftp on Inova and Mercury
    Added last and an effective "all" option to teststr (see
      manual/teststr)
    dc command allows selection of number of points to use
      for lvl / tlt calculation (see manual/dc)
    Added newtrace option to spadd (see manual/spadd)
    ppcal on Mercury and Inova were not working correctly
      power was being set too late in pulse sequence
    Added regexpath option to getfile (see manual/getfile)
    Implemented probeConnect for Inova systems.
    makeuser no longer configures a user for the csh shell.
      It also removes the "CPpatch" appdir if it is defined.
    Bug fix: getparam failed on a datastation if a third parameter
      was not passwd
    Bug fix: could not process NUS data with IST
    Bug fix: foldflg not used during NUS processing
    Bug fix: seqgen was not working on MacOS
    Bug fix: aspAnno may not return values to a macro. It caused the ds_1
      menu to fail
    Bug fix: datafit returned incorrect R2 value. Needed to be squared.
    Bug fix: if called from background, the full command set wc and wc2 to -inf.
      Added '1d' and '2d' options to full command.
    Bug fix: The NOE mixing times displayed 1 ms for 1000 ms
      Bug reported in SpinSights
    Bug fix: Clicking the Auto Plot Preview button caused OVJ to crash
      Bug reported in SpinSights
    Fixed overlap in "System settings" popup
      Bug reported in SpinSights
    In automation, the HOME environmental parameter was being set to /root.
    Bug fix: psggen on Inova gave warning about wetfuncs.c
      Bug reported in SpinSights

Oct 2021 *****************
    OpenVnmrJ 3.1A release 

Feb 2020 - Oct 2021
    Added viewman and viewmacro macros (see manual/viewman and
      manual/viewmacro. Thanks to Eugenio Alvarado)
    macrocat now searches appdirs to find macro to display
    macrosyscat and macrosysrm commands removed
    Added command execexp (see manual/execexp)
    Added command macroLine (see manual/macroLine)
    config can configure Com1 or Com2 as the "Sample Changer Port"
    Bug fix: array indexes or values were not displayed for dss displays
    fileowner -g <file> will return group id of the <file>
    svf defaults to 'nodb' if Locator is turned off
    Bug fix: dconi menus will rotate annotations
    Added ovjGetFidlib script to install VnmrJ 4.2 fidlib
    Added command readstr (see manual/readstr)
    The files solvents, solventppm, and solventlist now respect
      the appdirs hierarchy.
    Updates to fiddle (see manual/fiddle  Thanks to Gareth Morris)
       - fix endian conversion in writecf/readcf (looks as though readcf
         hasn’t worked since the migration to Linux!)
       - fix halving of first point of corrected FID (corrected data
         sometimes had baseline offsets)
       - correct for the auto phasing of the reference region when
         writing out correction function (so that arrayed data are
         handled correctly when reading in correction functions)
       - implement a new option readsinglecf to apply the same correction
         function to all array elements.
    Bug fix: piv and dpiv aborted
      Bug reported in SpinSights
    Bug fix: Undesirable block size set by AgileNT macro.
      Bug reported in SpinSights
    Bug fix: trtune may show tuning dips in the wrong place
      Bug reported in SpinSights
    Bug fix: VJ admin won't set operator password
      Bug reported in SpinSights
    Improved ovjDiag to check /etc/hosts file
    added new annotation options (see manual/aspAnno)
    ovjBuild script will make OpenVnmrJ directly from sources
       on github (see manual/ovjBuild)
    The plot preview failed on MacOS 16 (Big Sur).
    protune only tunes channels that are used. For PROTON, this
       means the decoupler is no longer tuned to C13.
    Support for RedHat 8.3 as an acquisition system
    Support for Ubuntu 20.04 as an acquisition system
    Add relative symbolic link option to cp (see manual/cp)
    verifyCntrlsFlash failed on CentOS 8, which uses python3.
    prg_dec_on could use wrong pw_90 values when doing an array
       of pw_90
    exists has new options for the 'file' and 'directory' cases
       (see manual/exists)
    The plfit macro will plot to a file (see manual/plfit)
    Bug fix: noPing option was not working for ovjGetpipe and
       ovjGetManuals
    The global parameters psfont and psfont2 set the font and
       pscharsize sets the font character size used when plotting.
       (see manual/write and manual/setpage)
    Setting wtfile='noCtScaling' turns off scaling of the FID
       by the number of transients (ct) acquired for that FID
       (see manual/ft, manual/ft2d, manual/wtfile)
    ddf can return data values to a macro (see manual/ddf)
    Added upgrade.nmr script for upgrading an existing OpenVnmrJ
       installation. See the Install.md file for details.
    Bug fix: gHMBCmeAD may not work on systems with Performa 1 gradients
    Added commands copyf and copystr, similar to append and
       appendstr (see manual/copyf)
    Added new command appendstr and new options for append (see manual/append)
    Critical PSG errors show in error/hardware bar and line3/log file
    Gradient shimming will create homospoil shimmap if gradient
       is 'n' in probefile (thanks to Bert Heise)
    When gradient shimming with echo sequence, try cutting off
       spikes that may appear on both sides of gradient profile (thanks to Bert Heise)
    Bug fix: lock/gmap calibration had an unnecessary tuning step (thanks to Bert Heise)
    Bug fix: srate maximum value was wrong (thanks to Bert Heise)
    Bug fixes and improvements to 3D gradient shimming - some bugs and calculation errors
       prominent with shim coils of small gcalx/y like WB shims, 18 & 26-Ch WB shims are
       now supported (crashed VJ before) (thanks to Bert Heise)
    Bug fix: mtune could show an incorrect axis
    Veripulse: integration of "atb" probe type (will not ask to tune probe for each sample)
    Veripulse: Additional probe specs and corrections to existing probe specs
    Several improvements to the user interface (thanks to Bert Heise)
       Added buttons for "Add lk pars" and "Add SF/SP pars" (Solvent Factors) to Probe
         Edit popup.
       Help menu was not working on Centos7 and later OSes. Also changed
         spinsights reference to IVAN-Spinsights link
       Tools menu shows "trtune" for VNMRS-type consoles
       Lock panel adds an "Optimize Phase" button
       Inova config allows setting up the global "hdwshimlist" parameter to
         allow more than just z1 hdwshim
       For target S/N values used by agileNT, several experiments were missing
         like CRISIS2 and some newer exps
       Fixed header fonts for gmapz panels.
       Removed obsolete/old-style "Parameters" panel for all hetero2Ds
         added X pulse params to Acquisition2D panel
    jmol, jchempaint, and jdesign were not running on MacOS version
      Bug reported in SpinSights
    dpir and pir could show the wrong value for normalized integrals.
      Bug reported in SpinSights
    pulsetool was not handling .DEC shapes correctly
      Bug reported in SpinSights
    cryo_noisetest was failing
    spadd would crash if given incorrect arguments
    Improved the OpenVnmrJ installer to avoid installing for the wrong instrument type
    setacq could fail on Inova and Mercury systems
    clradd and fiddle were not handling integer data correctly
    graphics screen would not refresh after changing Linux desktops
    New 'basename' and 'nuc' options for substr (see manual/substr)
    fortran library missing on CentOS 8
    vnmrj adm was not autofilling user name when making a new user
    OpenVnmrJ could fail to start on CentOS 8 due to large PID values.
    New 'regex' option for rm (see manual/rm)
    3D Gradient shim "Set from cursors" sets wrong lsfrq.
      Bug reported in SpinSights
    Fixed some bugs with annotations.
    Added acqcomm script which is an alternative to "su acqproc" (see manual/acqcomm)
      Also added Operator Rights and Tools menu entry for this
    Added support for user-defined axis (axis='S') (see manual/axis and manual/saxis)
    Added 'axisonly' option to dpcon (see manual/dpcon)
    Added 'add' option to setenumeral (see manual/setenumeral)
    Added 'csv' option to the "find" case of substr (see manual/substr)
    Added new command datafit (see manual/datafit)
    New options for using ranges of traces for maxpeak (see manual/maxpeak)
    ovjUpdate makes a patch to transfer system files to a newly
      installed OpenVnmrJ (see manual/ovjUpdate)
    Support for CentOS 8.1 and 8.2 as an acquisition system.
    New options for proj (see manual/proj)
    New 'pos' and 'neg' options for peak and maxpeak (see manual/peak)
    gxyzmapsys could fail if previous map does not exist
    Add warning messages to gradient shim and lock prescans if tn='lk'
    pulsetool and accounting added to MacOS version
    Console software updates from versions of VnmrJ 2.1C and older failed
      due to missing NDDS libraries

Jan 2020 *****************
    OpenVnmrJ 2.1A release 

Aug 2018 - Jan 2020
    Support for CentOS 7 systems
    Support for the "new" ethernet naming scheme (alternative to eth0 and eth1)
    Includes console software. This means that it is not necessary to
      first install VnmrJ 4.2 and the "110" patch.
    An installpkgs script to install required CentOS packages. This means
      that a "CentOS kickstart" is not needed. It will also install required
      Ubuntu packages.
    The ovjGetRepo script in the dvdImage will collect the required
      packages for CentOS / RHEL and Ubuntu. These can then be transferred
      to a system without network access. The ovjUseRepo script will then
      cause installpkgs to use the previously downloaded packages.
    MacOS version is 64-bit
    As a datastation, OpenVnmrJ can be installed on Ubuntu 14, 16, and 18
      and MacOS 10.10 (Yosemite) to 10.15 (Catalina)
    Added new command paramcopy (see manual/paramcopy)
    Added new command flush2 (see manual/flush2)
    Added new command append (see manual/append)
    Added new command sortCmd (see manual/sortCmd)
    Added new command touch (see manual/touch)
    Added new command chmod (see manual/chmod)
    New 'link' and 'symlink' options to the cp command (see manual/cp)
    New options for readfile (see manual/readfile)
    New options for getfile (see manual/getfile)
    New 'parfile' option for exists (see manual/exists)
    New 'expand' option for format (see manual/format)
    New 'tr' option for substr (see manual/substr)
    New '-R' option for rm (see manual/rm)
    New phasing option for ds (see manual/ds)
    New output options for flush (see manual/flush)
    Toggle and Button XML widgets support label justification
    Configuration script ovjWallPaper to set background on PC.
    Added ovjGetManuals script to install VnmrJ 4.2 manuals
    Added ovjDiag script to help diagnose vnmrj startup problems
    Replaced VnmrJ icons with OpenVnmrJ icons (thanks to Hari Natarajan)
    NOESY pulse sequence could  not be used for 'NOESY 1st Increment' setup
       (improved solvent suppression, often used in metabolomics) when used
       with multi-frequency PRESAT - the shaped PRESAT during mixing time is
       unnecessarily split 70:30 even if the gradient and gstab delays are
       (typically) removed. (thanks to Bert Heise)
    A graphical interface for the mref command, which is available from
       the "Edit" menu.  (thanks to Bert Heise)
    Band-selective EXSIDE (bsEXSIDE) to quickly (on concentrated samples)
       measure specific C-H coupling constants without having to acquire
       a crazy number of increments (which normal EXSIDE requires).
       (thanks to Bert Heise)
    Fixed bugs and feature requests from SpinSights: (thanks to Bert Heise)
       trtune could fail due to expanded spectral region (require f command)
       Hdec calibration may plot WALTZ profile with wrong phases
       Fobs_Hdec doesn't work (makeFHdecshape)
       VeriPulse may produce text-only report
       Ndec autocalibration may not work
       mtune enhancement
       Could not set FTS to negative temperture
       dssl: with arrays displayed vertically, the position of the numbers
          was wrong
       showarrays: while acquiring arrays, spectra were overlapping
       process_dosy2D: missing 'full' and 'dssh'
       VeriPulse may fail gradient profile test due to rounding errors
       Fixed many experiment panels for consistent use of fonts
       Proshim may stop with error in spShimVals
       fixgrd may set gradient level to zero if gcal is large
    Added new macro catPlot (see manual/catPlot) (thanks to Hari Natarajan)
    Added dialog popup feature (see manual/dialog)
    Added new macro dsnf1max (see manual/dsnf1max)
    Added new options to ll2d command (see manual/ll2d)
    Added new options to aspAnno command (see manual/aspAnno)
    Added new option to peak2d command (see manual/peak2d)
    Added new probe type to VeriPulse that skips all probe tuning

Mar - Dec 2018
    Fixed several bugs reported in SpinSights:
       Hononuclear sw1 shows wrong ppm value in "Acquisition" panel.
       For T1 and T2 experiments. The "ProcPlotAdv" panel is missing.
       psGshim did not call gmapsolv
       mz did not work between spectrometers
       mtune and trtune could fail due to missing hfmode parameter
       addprobe gives an error if probe name not supplied as an argument.
       For the "Calibrate pw90" function,  it supports an optional
         userpw90proc macro to allow for additional parameter adjustments.
       pw90proc could fail with a division by zero.
       VeriPulse was missing P31 pw calibrations for ID probes.
       protune could cause automation to stop even if the "Skip sample
         if protune fails" is set to "no"
    New options to the makefid command (see manual/makefid)
    New sendMessage macro to control a background OpenVnmrJ
      process (see manual/sendMessage)
    Updated with ChemPack 8 bug fixes and improvements.
    Updated with ChemPack 8 new experiments:
       PSG includes watergate and flipsy support.
       Added bsgHSQCADTOXY, bsHSQCADTOXY, bsPSYCHE, bsPSYCHE_zTOCSY, water_WG
    Updated with ChemPack 8 new or improved macros:
       addarray - includes FID and spectrum add options
       dndNUS - reacts to 'doprocess' flag appropriately
       makeXdecshape - see manual/makeXdecshape (Thanks to Hari Natarajan)
       psGshim - pre-scan supports  gradient shimming with shaped pulse
                 (selective signal selection)
       vs2dadj - see manual/vs2sadj analogous to vsadj except for 2D data
    The SE option would always create datdirxxx directories in the REC
      directory.  Bug reported in SpinSights
    The SE option had problems saving a secure copy if the template for
      the 2nd copy contained a parameter.  Bug and work-around reported
      in SpinSights
    Added options to clradd command (see manual/clradd)
    Added options to add command (see manual/add)
    Added sleep command (see manual/sleep)
    Added nocase, starts, and startsNocase options to teststr (see
      manual/teststr)
    Added options to accounting so that it can be used in a non-interactive
      mode. Added doAcct that uses these options. (see manual/vnmr_accounting)
    Non-Uniform Sampling (NUS) implemented for Mercury systems.
    makefid could fail if called many times, such as when creating a 2D or
      arrayed 1D data set.
    dpcon can now be cancelled.
    fidmax could fail if makefid is used to make a new fid.
    seqgen could generate many warnings from "dps extensions"
    Added scalefid command (see manual/scalefid)
    Added ovjGetpipe to download and install NMRPipe
      ovjGetpipe -h 
      will display a manual
    Added ovjPasswd to generate "operator" passwords. 
    Converted nextexp into a command and documented it.
    Added icon and hide options to vnmrj (see manual/vnmrj)
    Added writespectrum and readspectrum commands (see manual/writespectrum)
    CPMG preparation option in all liquids sequences (Thanks to John Ryan).
    The dousermacro now supports return values
    Bug fixed in vjreplaceQ (the “buggy” version did not maintain the
      automation time when a nightQ is removed from an errored location
      – Thanks to Ken Knott for reporting this bug).
    cft2da/cft1da macros are included. They allow processing of craft2D results
      outside of craft tools.
    Posted the native MacOS version of OpenVnmrJ on the OpenVnmrJ github site at
      https://github.com/OpenVnmrJ/OpenVnmrJ/releases . This version was built
      for java version 1.8. With small modifications, it also will run with
      java version 1.6 and java version 9.
    Added "group option" to fread (see manual/fread)
    convertbru could fail on 2D data sets where only a single increment is
      collected. It could also fail if np (TD) is not a multiple of 64.
    Study queue errors fixed

Jan - Oct 2017
    Fixed some faults discussed in SpinSights.
      3D gradient shimming can fail with an uninitialized $isvnmrj variable
    Fixed some faults discussed in SpinSights.
      improved atcmd 'active' option documentation
      Print Screen to a file would fail if no plotter is defined.
      BioPack calibrations failed if VT unit is switched off.
      Added chainProshim (see manual/chainProshim)
      Added menu feature to UserPrefs (see manual/UserPrefs)
      Fixed svpdp to follow operator rights when making changes
    Fixed scripts used to install OpenVnmrJ. The standard sudo is now
      used. Linux obsoleted kudzu so we no longer need to deal with it.
      Also copy some rpms to the dvd for installation (tcl and tk)
    Add ovjUser script to add user information to OVJ's user admin
      files in /vnmr/adm. This can be used in lieu of the OVJ admin
      interface.  See the comments in the /vnmr/bin/ovjUser script.
    Include Bayes programs with CRAFT, courtesy of Joe Ackerman
      and Larry Bretthorst of Washington University.
    Added source code for FdfToDcm (FDF to Dicom) imaging program.
    makefid now has a 'rev' option to reverse the spectrum.
    chkname can now expand to 511 characters instead of 255.
    Updated with ChemPack 8 bug fixes and improvements.
    Updated with ChemPack 8 including new macros that:
       addarray - allows multiple arrayed FIDs to be added
       dndNUS - similar to dndfid for NUS data
       pi3ssb, pi4ssb, pi6ssb - shifted sine bell weighting functions
       pi3ssbsq, pi4ssbsq, pi6ssbsq - shifted sine bell squared functions
    Plot preview could cause OpenVnmrJ to exit with
      an "environment nesting" error
    Two macros would report errors when starting in background mode.
      One error was about system not being an acquisition system.
      The other error was that the file enterQ did not exist
    The  makefid, ddf, noise, getdatadim, and ilfid programs would fail
      if the length of the pathname was larger than 128 characters.
      Increased length limit to 256 characters, which is what most
      other programs use.
    If Vnmrbg was running in server mode, it would exit after receiving
      its first message on its server listening socket.
    Could not safely abort a background Vnmrbg. Now, kill -2 <pid>
      or a Cntrl-C will do it.
    Problem with numeric operators names
    If an operators name is a number, loading a ".rec" file
      resulted in "can't compare STRING with REAL" error.
      Bug and work-around reported in SpinSights
    ds program may show the wrong spectrum
    If an arrayed data set has more than nine traces
      and the  vertical scale (vs) or vertical position (vp)
      is interactively updated, alternating traces will be
      displayed. The integral could also be wrong.
    makeuser creates menujlib instead of obsolete menulib in user accounts
      The menulib was phased out several years ago. Graphics menus are
      now held in menujlib
    Solids PSG error in solidmpseqs.h
    Pulse sequences using Lee-Goldburg decoupling, as in a t1rho array,
      fail to start. They give a segmentation violation. There was an
      uninitialized variable. Bug reported in SpinSights.
    Linear prediction error with large number of increments
    Data with a large number of increments may not process correctly.
      One gets a lpext1<1 or lpext2<1 error. Bug reported in SpinSights.
    sread could fail to convert parameters whose name is more than
      eight characters.

Oct - Dec 2016
    The vnmrj startup script failed on Ubuntu systems. A sh script
      does not support the "source" feature supported by bash scripts.
    Some Linux packages required in the Ubuntu environment were not
      being installed.

Sep 2016 *****************
    OpenVnmrJ 1.1A release 

July - Sep 2016
    Added ovjapps and ovjsubmit features to enable retrieving and submitting
      appdirs to the OpenVnmrJ software package. See
      /vnmr/openvnmrj-utils/manual/ovjapps and
      /vnmr/openvnmrj-utils/manual/ovjsubmit
    Additional improvements for building OpenVnmrJ on MacOS systems.
    The OpenVnmrJ build process includes the git commit ID and checksums
      of all the files. These are stored in the /vnmr/adm/sha1 directory.
    go('check') was failing on MacOS
    Incorporated the VnmrJ 4.2A "110" patch corrections into OpenVnmrJ
    Installation of OpenVnmrJ on Ubuntu 14.04.2 LTS could fail.
    This was tracked down to some file permissions issues for items
      in maclib.
    Automation runs could fail. Autoproc was not removing entries from psgQ
      autofuncs.c used the tail command to remove lines from psgQ. However,
      without the -n option, the +12 was interpreted as a file name, causing
      tail to add a filename to psgQ. This bug may affect VnmrJ 4.2A when
      it is installed on newer Linux versions.
    Use dynamic libraries for MacOS psglib programs. This simplifies
      updating PSG on MacOS systems and significantly reduces the size
      of the PSG programs.
    Use clang compiler for MacOS builds.
    Incorporated VnmrJ 4.2A at the "109" patch level.