Notes.txt

OpenVnmrJ Release Notes.

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.