[MacPorts] #46786: R changes broke rNMR package

MacPorts noreply at macports.org
Wed Feb 11 15:11:42 PST 2015

#46786: R changes broke rNMR package
  Reporter:  howarth.at.macports@…  |      Owner:  kjell.konis@…
      Type:  defect                 |     Status:  new
  Priority:  Normal                 |  Milestone:
 Component:  ports                  |    Version:  2.3.3
Resolution:                         |   Keywords:
      Port:  R                      |

Comment (by kjell.konis@…):

 Your example works fine for me:

 Prompty$ R CMD INSTALL rNMR_1.1.7.tar.gz
 * installing to library ‘/Users/kjellk/Library/R/3.1/library’
 * installing *source* package ‘rNMR’ ...
 ** R
 ** inst
 ** preparing package for lazy loading
 ** help
 *** installing help indices
 ** building package indices
 ** testing if installed package can be loaded
 * DONE (rNMR)
 Prompty$ R

 R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-apple-darwin14.1.0 (64-bit)

 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
 Type 'license()' or 'licence()' for distribution details.

   Natural language support but running in an English locale

 R is a collaborative project with many contributors.
 Type 'contributors()' for more information and
 'citation()' on how to cite R or R packages in publications.

 Type 'demo()' for some demos, 'help()' for on-line help, or
 'help.start()' for an HTML browser interface to help.
 Type 'q()' to quit R.

 > library(rNMR)
 Loading required package: tcltk

  rNMR version 1.1.7 (2011-08-03)
  Copyright (C) 2009 Ian A. Lewis and Seth C. Schommer
  rNMR is free software and comes with ABSOLUTELY NO WARRANTY.
  rNMR may be modified and redistributed under certain conditions.
  Go to http://www.r-project.org/Licenses/GPL-3 for more details.

  Lewis, I. A., Schommer, S. C., Markley, J. L.
  Magn. Reson. Chem. 47, S123-S126 (2009).

 > [1] 0 Hrs a.hsqc
 [1] 0 Hrs b.hsqc
 [1] 0 Hrs c.hsqc
 [1] 1.5 Hrs a.hsqc
 [1] 1.5 Hrs b.hsqc
 [1] 1.5 Hrs c.hsqc
 [1] 12 Hrs a.hsqc
 [1] 12 Hrs b.hsqc
 [1] 12 Hrs c.hsqc
 [1] 3 Hrs a.hsqc
 [1] 3 Hrs b.hsqc
 [1] 3 Hrs c.hsqc
 [1] 6 Hrs a.hsqc
 [1] 6 Hrs b.hsqc
 [1] 6 Hrs c.hsqc
 [1] Alanine.hsqc
 [1] BPG.hsqc
 [1] Glucose.hsqc
 [1] HEPES.hsqc
 [1] Lactate.hsqc
 [1] Pyruvate.hsqc

 Performing automatic backup . . . complete


 I get a ''Main Plot Window'', a ''Files'' browser (showing the hsqc files
 in your example), and a ''Menus'' bar.

 The problem appears to only manifest itself when you install the rNMR R
 package through the rNMR port.

 Replying to [comment:5 howarth.at.macports@…]:
 > The attached patch solves the startup problem with rNMR. There still is
 a later problem when testing the program on the test data set related to
 recent tcl/tk changes.
 > http://rnmr.nmrfam.wisc.edu/pages/data/files/rNMR_HSQC_Example.zip
 > If you follow the instructions on
 > cd rNMR_HSQC_Example
 > rRNMR
 > <select open menu item in Menus window  from rNMR>
 > <select rNMR_HSQC_Example directory in Open dialog from rNMR>
 > <shift click to select all of the *.hsqc files in the Open dialog from
 > <click the Open button in the Open dialog from rNMR>
 > This produces an error message...
 > Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") :
 >   [tcl] invalid command name "tablelist::tablelist".
 > which wasn't present until the recent R/tcl/tk revisions in MacPorts.
 > Currently I have...
 > tk @8.6.3_0+x11 (active)
 > tcl @8.6.3_0+threads
 > which always worked in the past.

Ticket URL: <https://trac.macports.org/ticket/46786#comment:7>
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