R Development Page

RHydro log file (check_x86_64_linux)

Thu Mar  9 17:25:31 2017: Checking package RHydro (SVN revision 185) ...
* using log directory ‘/mnt/building/build_2017-03-09-17-23/RF_PKG_CHECK/PKGS/RHydro.Rcheck’
* using R version 3.3.3 Patched (2017-03-06 r72315)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘RHydro/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RHydro’ version ‘2014-04.1’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Dominik Reusser , Wouter Buytaert , Claudia Vitolo , Till Francke ’

New submission

Version contains leading zeroes (2014-04.1)
Version contains large components (2014-04.1)

Unknown, possibly mis-spelled, fields in DESCRIPTION:
  ‘#Suggests’

No package encoding and non-ASCII characters in the following R files:
  R/abc.R
    17: 	  # Rekursionsvorschrift fr Gt: Gt = G0*(1-c)^t + Summe_von_i=1_bis_t_ber(a*Pi*(1-c)^(n-t))
    18: 	#  # die Zeitreihe fr G wird um einen Zeitindex nach "rechts" verschoben (also G[1]=G0)
  R/long.wave.radiation.balance.R
    1: long.wave.radiation.balance <- function(t.air, t.atm = t.air, t.snow=NULL, sigma= 4.9*10^-9 #MJ * 1/m*1/day*1/K^4
  R/wasim.read.Run.R
    26:            #Datenreihen aufspalten und fr RhydroModel-Objekt vorbereiten

The Title field should be in title case, current version then in title case:
‘Classes and methods for hydrological modelling and analysis’
‘Classes and Methods for Hydrological Modelling and Analysis’

The Description field should not start with the package name,
  'This package' or similar.

The Date field is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘xts’ ‘sp’ ‘lhs’ ‘deSolve’ ‘XML’ ‘qualV’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 whether package ‘RHydro’ can be installed ... [4s/5s] 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 ... NOTE
'library' or 'require' call to ‘segmented’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘XML’ ‘deSolve’ ‘lhs’ ‘qualV’ ‘sp’ ‘xts’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
HydroModel: no visible global function definition for ‘try.xts’
array2xml: no visible global function definition for ‘newXMLNode’
array2xml: no visible global function definition for ‘saveXML’
array2xml: no visible global function definition for
  ‘xmlInternalTreeParse’
array2xml: no visible global function definition for ‘xmlOutputDOM’
fft_fit: no visible global function definition for ‘segmented’
fft_fit: no visible global function definition for ‘seg.control’
fft_fit: no visible global function definition for ‘lines’
fft_fit: no visible global function definition for ‘points’
fft_fit: no visible global function definition for ‘legend’
fft_fit: no visible global function definition for ‘slope’
fuserouting.sim: no visible global function definition for ‘coredata’
fusesma.sim: no visible global function definition for ‘coredata’
fusesma.sim: no visible global function definition for ‘ode’
get.stations: no visible global function definition for ‘coordinates’
hydro.plot: no visible global function definition for ‘par’
hydro.plot: no visible global function definition for ‘matplot’
hydro.plot: no visible global function definition for ‘colors’
hydro.plot: no visible global function definition for ‘axis’
hydro.plot: no visible global function definition for ‘mtext’
lhs: no visible global function definition for ‘randomLHS’
lhs.abc: no visible global function definition for ‘randomLHS’
lhs.hbv: no visible global function definition for ‘randomLHS’
long.wave.radiation.balance: no visible global function definition for
  ‘coredata’
perfindices: no visible global function definition for ‘MAOE’
perfindices: no visible global function definition for ‘EF’
plot_rainfall.runoff: no visible global function definition for ‘index’
plot_rainfall.runoff: no visible global function definition for ‘par’
plot_rainfall.runoff: no visible global function definition for ‘lines’
plot_rainfall.runoff: no visible global function definition for
  ‘plot.window’
plot_rainfall.runoff: no visible global function definition for ‘axis’
plot_rainfall.runoff: no visible global function definition for ‘mtext’
plot_rainfall.runoff: no visible global function definition for
  ‘legend’
readmd: no visible global function definition for ‘data’
readmd: no visible binding for global variable ‘modlist’
topmodel: no visible global function definition for ‘try.xts’
topmodel: no visible global function definition for ‘as.zooreg’
topmodel: no visible global function definition for ‘zoo’
wasim.file2HydroRun: no visible global function definition for ‘zoo’
wasim.file2HydroRun: no visible global function definition for
  ‘SpatialPoints’
wasim.head2spatial: no visible global function definition for
  ‘SpatialPoints’
wasim.read.table: no visible global function definition for
  ‘count.fields’
wasim.read.table: no visible global function definition for
  ‘read.table’
wasim.read.table: no visible global function definition for ‘zoo’
merge,HydroRun-HydroRun: no visible global function definition for
  ‘coordinates’
plot,HydroModelParameters-ANY: no visible global function definition
  for ‘par’
plot,HydroModelParameters-ANY: no visible global function definition
  for ‘hist’
plot,HydroRun-ANY: no visible global function definition for ‘legend’
plot,HydroRun-ANY: no visible global function definition for ‘index’
plot,HydroRun-ANY: no visible global function definition for ‘lines’
predict,HydroModel: no visible global function definition for ‘try.xts’
predict,HydroModel: no visible global function definition for ‘xts’
predict,HydroModel: no visible global function definition for ‘index’
subset,HydroRun: no visible global function definition for
  ‘coordinates’
Undefined global functions or variables:
  EF MAOE SpatialPoints as.zooreg axis colors coordinates coredata
  count.fields data hist index legend lines matplot modlist mtext
  newXMLNode ode par plot.window points randomLHS read.table saveXML
  seg.control segmented slope try.xts xmlInternalTreeParse xmlOutputDOM
  xts zoo
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "axis", "hist", "legend", "lines", "matplot",
             "mtext", "par", "plot.window", "points")
  importFrom("utils", "count.fields", "data", "read.table")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘RHydro/R/readmd.R’:
  data(modlist)
See section ‘Good practice’ in ‘?data’.
* checking Rd files ... WARNING
baseflow_sep.Rd: non-ASCII input and no declared encoding
hydro_metrics.Rd: non-ASCII input and no declared encoding
problems found in ‘baseflow_sep.Rd’, ‘hydro_metrics.Rd’
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'baseflow_sep.Rd':
  \usage lines wider than 90 characters:
     baseflow_sep(runoff, method="DFM", parms=c(c=0.925, c_slope=diff(range(runoff))/length(runoff)/2, window_size=10, f_lowess=0.1))

Rd file 'hbv.Rd':
  \usage lines wider than 90 characters:
     hbv.prerun(init=NULL, prec, max_pre_runs=20, storage_tolerance=0.1, prerun_length=(365*24*60/5), verbose=TRUE,...)

Rd file 'hydro_metrics.Rd':
  \examples lines wider than 100 characters:
     time_of_conc   (rainfall, runoff) #apparently, this series is too short in relation to its storage effects

Rd file 'long.wave.radiation.balance.Rd':
  \usage lines wider than 90 characters:
     long.wave.radiation.balance(t.air, t.atm = t.air, t.snow = NULL, sigma = 4.9 * 10^-9, vap.pres, cloud.cover = 0, sky.view = 0, emiss.sn ... [TRUNCATED]

Rd file 'plot_rainfall.runoff.Rd':
  \examples lines wider than 100 characters:
     plot_rainfall.runoff(rain = zoo(inputs$P), q.model=zoo(inputs$Q), q.units = "mm/ 15min", p.units = "mm/15min")

Rd file 'topmodel.Rd':
  \usage lines wider than 90 characters:
     topmodel(parameters, data, delay, topidx, pm= c("NS"), return.simulations=TRUE, verbose = FALSE)

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘fuserouting.ranges’ ‘fusesma.ranges’ ‘huagrahumaP’
Undocumented data sets:
  ‘huagrahumaP’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'baseflow_sep':
baseflow_sep
  Code: function(runoff, method = "DFM", parms = c(c = 0.925,
                 window_size = 10, f_lowess = 0.1))
  Docs: function(runoff, method = "DFM", parms = c(c = 0.925, c_slope =
                 diff(range(runoff))/length(runoff)/2, window_size =
                 10, f_lowess = 0.1))
  Mismatches in argument default values:
    Name: 'parms'
    Code: c(c = 0.925, window_size = 10, f_lowess = 0.1)
    Docs: c(c = 0.925, c_slope = diff(range(runoff))/length(runoff)/2, 
          window_size = 10, f_lowess = 0.1)

Codoc mismatches from documentation object 'fuserouting.sim':
fuserouting.sim
  Code: function(U, mid, modlist, timedelay, deltim = 1, trace = FALSE)
  Docs: function(U, mid, modlist, timedelay, deltim)
  Argument names in code not in docs:
    trace
  Mismatches in argument default values:
    Name: 'deltim' Code: 1 Docs: 

Codoc mismatches from documentation object 'fusesma.sim':
fusesma.sim
  Code: function(DATA, mid, modlist, deltim = 1, states = FALSE, fluxes
                 = FALSE, fracstate0 = 0.25, rferr_add = 0, rferr_mlt =
                 1, frchzne, fracten, maxwatr_1, percfrac, fprimqb,
                 qbrate_2a, qbrate_2b, qb_prms, maxwatr_2, baserte,
                 rtfrac1, percrte, percexp, sacpmlt, sacpexp, iflwrte,
                 axv_bexp, sareamax, loglamb, tishape, qb_powr, trace =
                 FALSE)
  Docs: function(DATA, mid, modlist, deltim, states, fluxes,
                 fracstate0, rferr_add, rferr_mlt, frchzne, fracten,
                 maxwatr_1, percfrac, fprimqb, qbrate_2a, qbrate_2b,
                 qb_prms, maxwatr_2, baserte, rtfrac1, percrte,
                 percexp, sacpmlt, sacpexp, iflwrte, axv_bexp,
                 sareamax, loglamb, tishape, qb_powr)
  Argument names in code not in docs:
    trace
  Mismatches in argument default values (first 3):
    Name: 'deltim' Code: 1 Docs: 
    Name: 'states' Code: FALSE Docs: 
    Name: 'fluxes' Code: FALSE Docs: 

Codoc mismatches from documentation object 'topidx':
topidx
  Code: function(DEM, river = NA)
  Docs: function(DEM, res, river = NA)
  Argument names in docs not in code:
    res
  Mismatches in argument names:
    Position: 2 Code: river Docs: res

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking examples ... [22s/23s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
abc             6.604  0.092    6.70
fuserouting.sim 5.104  0.016    5.14
perfindices     5.100  0.000    5.10
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 5 NOTEs
See
  ‘/mnt/building/build_2017-03-09-17-23/RF_PKG_CHECK/PKGS/RHydro.Rcheck/00check.log’
for details.


Run time: 70.89 seconds.