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HITXML log file (check_x86_64_linux)

Mon Nov 26 12:30:10 2018: Checking package HITXML (SVN revision 74) ...
* using log directory ‘/srv/rf/building/build_2018-11-26-12-28/RF_PKG_CHECK/PKGS/HITXML.Rcheck’
* using R version 3.5.1 Patched (2018-11-24 r75665)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘HITXML/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HITXML’ version ‘0.9.12’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Steffen Greilich ’

New submission

No package encoding and non-ASCII characters in the following R files:
  R/HX.RBE.LEM.R
    2: # Krmer et al. (2000) using statistical sampling

The Title field should be in title case, current version then in title case:
‘Planning tools for ion beam therapy’
‘Planning Tools for Ion Beam Therapy’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘HITXML’ can be installed ... [9s/9s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
  ‘stringr’ ‘tidyr’
'library' or 'require' call not declared from: ‘lattice’
'library' or 'require' call to ‘lattice’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
package 'methods' is used but not declared
* checking S3 generic/method consistency ... WARNING
plot:
  function(x, ...)
plot.SOBP:
  function(plot.ddds, plot.depths.g.cm2, plot.weights, add.comment,
           start.depth.cm, end.depth.cm)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  plot.SOBP
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
  .C("AT_SPC_get_number_of_bins_from_filename_fast_R", ..., PACKAGE = "libamtrack")
  .C("AT_SPC_read_data_from_filename_fast_R", ..., PACKAGE = "libamtrack")
  .C("AT_SPC_read_header_from_filename_fast_R", ..., PACKAGE = "libamtrack")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [10s/10s] NOTE
File ‘HITXML/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("HITXML package loaded.\n")

See section ‘Good practice’ in '?.onAttach'.

HX.construct.field: no visible global function definition for ‘sd’
HX.construct.field.circle : get.segments: no visible global function
  definition for ‘tail’
HX.construct.field.shells : get.segments: no visible global function
  definition for ‘tail’
HX.correct.user.input: no visible binding for global variable
  ‘energy.idx’
HX.get.BP.depth: no visible global function definition for ‘read.table’
HX.optimize.field: no visible global function definition for ‘optim’
HX.optimize.field: multiple local function definitions for
  ‘custom.panel’ with different formal arguments
HX.read.defaults: no visible global function definition for
  ‘read.table’
HX.save.defaults: no visible global function definition for
  ‘write.table’
RBE.LEM.single: no visible global function definition for ‘rpois’
RBE.LEM.single: no visible global function definition for ‘sd’
RBE.initial: no visible global function definition for ‘approx’
SPC.read: no visible global function definition for ‘unzip’
clan.txtplot: no visible global function definition for ‘par’
clan.txtplot: no visible global function definition for ‘text’
dataDDD: no visible global function definition for ‘read.table’
dataDDD: no visible global function definition for ‘new’
dataDDDset: no visible global function definition for ‘new’
dataRBE: no visible global function definition for ‘new’
dataSIS: no visible global function definition for ‘read.table’
dataSIS: no visible global function definition for ‘new’
dataSPC: no visible global function definition for ‘new’
dataSPCset: no visible global function definition for ‘new’
dataSpectrum : : no visible global function definition for
  ‘new’
get.RBE.from.set: no visible global function definition for ‘mclapply’
get.RBE.from.set: no visible global function definition for ‘approx’
get.alpha.ion.Gy: no visible global function definition for ‘approx’
get.beta.ion.Gy2: no visible global function definition for ‘approx’
get.dose.Gy: no visible global function definition for ‘approx’
get.dose.Gy.from.set: no visible global function definition for
  ‘mclapply’
get.spc: no visible global function definition for ‘head’
plot.SOBP : : no visible binding for global variable
  ‘ddds.sub’
plot.SOBP: no visible binding for global variable ‘ddds.sub’
read.FLUKA.phase.space : : no visible global function
  definition for ‘read.table’
redistribute.spc : : no visible global function definition
  for ‘approx’
redistribute.spc: no visible global function definition for ‘new’
spectrum.at.depth.g.cm2: no visible global function definition for
  ‘approx’
*,dataDDD-numeric: no visible global function definition for ‘new’
*,dataSpectrum-numeric: no visible global function definition for ‘new’
+,dataSpectrum-dataSpectrum: no visible global function definition for
  ‘new’
[,dataDDDset: no visible global function definition for ‘new’
[,dataSPCset: no visible global function definition for ‘new’
Undefined global functions or variables:
  approx ddds.sub energy.idx head mclapply new optim par read.table
  rpois sd tail text unzip write.table
Consider adding
  importFrom("graphics", "par", "text")
  importFrom("methods", "new")
  importFrom("stats", "approx", "optim", "rpois", "sd")
  importFrom("utils", "head", "read.table", "tail", "unzip",
             "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... WARNING
prepare_Rd: dataSPC.Rd:7-9: Dropping empty section \description
prepare_Rd: dataSPC.Rd:19-21: Dropping empty section \details
prepare_Rd: dataSPC.Rd:22-28: Dropping empty section \value
prepare_Rd: dataSPC.Rd:35-37: Dropping empty section \note
prepare_Rd: dataSPC.Rd:32-34: Dropping empty section \author
prepare_Rd: dataSPC.Rd:29-31: Dropping empty section \references
prepare_Rd: dataSPC.Rd:41-43: Dropping empty section \seealso
checkRd: (5) dataSPC.Rd:0-58: Must have a \description
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'HT.optimize.field.Rd':
  \usage lines wider than 90 characters:
     HX.optimize.field( focus.FWHM.mm, field.size.mm, fluence.cm2, N.min, d.start.mm, plot = FALSE)

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘D.cut.Gy’ ‘HX.RBE.LEM’ ‘HX.construct.field’
  ‘HX.construct.field.circle’ ‘HX.construct.field.shells’
  ‘HX.construct.field.square’ ‘HX.correct.user.input’ ‘HX.custom.menu’
  ‘HX.get.BP.depth’ ‘HX.get.available.energies’ ‘HX.get.user.input.IES’
  ‘HX.get.user.input.basic’ ‘HX.getMinAndMax’ ‘HX.prompt.user’
  ‘HX.read.PBR’ ‘HX.read.defaults’ ‘HX.save.defaults’ ‘RBE.LEM.single’
  ‘RBE.initial’ ‘SPC.interpolate’ ‘SPC.read’ ‘SPC.tapply’ ‘alpha.X’
  ‘alpha.ion’ ‘beta.X’ ‘beta.ion’ ‘clan.create.latex.table’
  ‘clan.txtplot’ ‘dataDDD’ ‘dataDDDset’ ‘dataRBE’ ‘dataSIS’ ‘dataSPC’
  ‘dataSPCset’ ‘depth.dose’ ‘get.IES.index’ ‘get.RBE.from.set’
  ‘get.alpha.ion.Gy’ ‘get.beta.ion.Gy2’
  ‘get.clostest.beam.energy.MeV.u’ ‘get.data.table’ ‘get.ddd’
  ‘get.dose.Gy’ ‘get.dose.Gy.from.set’ ‘get.foci’ ‘get.focus.FWHM.mm’
  ‘get.intensities’ ‘get.intensity.N.s’ ‘get.spc’ ‘leading.blanks’
  ‘plot.SOBP’ ‘r.nucleus.um’ ‘read.item.character’ ‘read.item.numeric’
  ‘redistribute.spc’ ‘s.max’ ‘spectra’
  ‘spectrum.Mass.Stopping.Power.MeV.cm2.g’ ‘spectrum.dLET’
  ‘spectrum.dose.Gy’ ‘spectrum.fLET’ ‘spectrum.get.depth.g.cm2’
  ‘spectrum.total.n.particles’ ‘writeDDD’
Undocumented S4 classes:
  ‘dataSPCset’ ‘dataDDDset’ ‘dataRBE’ ‘dataSPC’ ‘dataDDD’
Undocumented S4 methods:
  generic '*' and siglist 'dataDDD,numeric'
  generic '*' and siglist 'dataSpectrum,numeric'
  generic '+' and siglist 'dataSpectrum,dataSpectrum'
  generic '[' and siglist 'dataDDDset'
  generic '[' and siglist 'dataSPCset'
  generic 'plot' and siglist 'dataDDD'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'Mass.Stopping.Power.MeV.cm2.g' but not in code:
  Mass.Stopping.Power.MeV.cm2.g

Functions or methods with usage in documentation object 'dddSPC' but not in code:
  dddSPC

Functions or methods with usage in documentation object 'dose.Gy' but not in code:
  dose.Gy

Functions or methods with usage in documentation object 'total.n.particles' but not in code:
  total.n.particles

Codoc mismatches from documentation object 'HX.cost.function':
HX.cost.function
  Code: function(field.shape, par, focus.FWHM.mm, fluence.cm2,
                 field.par, N.min, resolution.mm)
  Docs: function(d.mm, focus.FWHM.mm, fluence.cm2, field.size.mm,
                 N.min)
  Argument names in code not in docs:
    field.shape par field.par resolution.mm
  Argument names in docs not in code:
    d.mm field.size.mm
  Mismatches in argument names (first 3):
    Position: 1 Code: field.shape Docs: d.mm
    Position: 2 Code: par Docs: focus.FWHM.mm
    Position: 3 Code: focus.FWHM.mm Docs: fluence.cm2

Codoc mismatches from documentation object 'HX.optimize.field':
HX.optimize.field
  Code: function(par.start, focus.FWHM.mm, fluence.cm2, N.min,
                 field.shape, field.par, n.IES, resolution.mm = 1,
                 spot.distance.mm, plot = FALSE)
  Docs: function(focus.FWHM.mm, field.size.mm, fluence.cm2, N.min,
                 d.start.mm, plot = FALSE)
  Argument names in code not in docs:
    par.start field.shape field.par n.IES resolution.mm
    spot.distance.mm
  Argument names in docs not in code:
    field.size.mm d.start.mm
  Mismatches in argument names (first 3):
    Position: 1 Code: par.start Docs: focus.FWHM.mm
    Position: 2 Code: focus.FWHM.mm Docs: field.size.mm
    Position: 5 Code: field.shape Docs: d.start.mm

Codoc mismatches from documentation object 'HX.compute.field':
HX.compute.field
  Code: function(beam.spot.grid, field.mm = NULL, resolution.mm, method
                 = "old")
  Docs: function(beam.spot.grid, field.mm = NULL, resolution.mm)
  Argument names in code not in docs:
    method

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'HX.optimize.field'
  ‘plot’

Undocumented arguments in documentation object 'get.multivariate.weighted.histogram'
  ‘n.x.bins’
Documented arguments not in \usage in documentation object 'get.multivariate.weighted.histogram':
  ‘n.x.bin’

Undocumented arguments in documentation object 'plot,dataSpectrum-method'
  ‘x’

Undocumented arguments in documentation object 'read.FLUKA.phase.space'
  ‘region.name.prefix’

Undocumented arguments in documentation object 'spectrum.at.depth.g.cm2'
  ‘spectra’ ‘depth.g.cm2’ ‘interpolate’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File ‘HITXML/libs/HITXML.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... [1s/1s] OK
* checking PDF version of manual ... OK
* DONE

Status: 6 WARNINGs, 5 NOTEs
See
  ‘/srv/rf/building/build_2018-11-26-12-28/RF_PKG_CHECK/PKGS/HITXML.Rcheck/00check.log’
for details.


Run time: 84.7 seconds.

Additional Logs:   00install.out
Thanks to:
Vienna University of Economics and Business University of Wisconsin - Madison Powered By FusionForge