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simecolModels log file (check_x86_64_linux)

Tue Jul 11 22:26:09 2017: Checking package simecolModels (SVN revision 268) ...
* using log directory ‘/mnt/building/build_2017-07-11-22-24/RF_PKG_CHECK/PKGS/simecolModels.Rcheck’
* using R version 3.4.1 Patched (2017-07-09 r72907)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘simecolModels/DESCRIPTION’ ... OK
* this is package ‘simecolModels’ version ‘0.3-1’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Thomas Petzoldt ’

New submission

No package encoding and non-ASCII characters in the following R files:
  R/NPZD.R
    41:               ksPAR              =140,       # Einst/m2/s
  R/SiDia.R
    67:        bwDSi    = 150         # mol/l
  R/algaepH.R
    67:               ksPAR     =100,   #Einst/m2/s   Half-saturation ct for light-limited growth
    71:               parDay    =250.,  #Einst/m2/s   PAR during the light phase
  R/aquaphy.R
    73:               alpha          =-0.125/150, #Einst/m2/s/hr    Light dependency factor
    88:               parMean        =250.,       #molPhot/m2/s     PAR during the light phase
  R/daphnia_deb.R
    73:       t.kelvin  = 20 + 273.15,  # 20C
  R/daphnia_deb_lifeequations.R
    83:   ## hatch ohne Rckhalt der Eier
    90:     # nach hatch werden neue Eier und Eialter rckgesetzt
  R/daphnia_deb_phyto.R
    28:       mort            = -0.05,         #background mortality rate in EBT (d_b; Hlsmann2002)
  R/daphnia_tefi.R
    50:       T   = 20,  # temperature, 20C
  R/mcyst_batch.R
    1: ### Jhnichen, S.; Ihle, T. and Petzoldt, T. (2008)
  R/mcyst_batch_mc.R
    1: ### Jhnichen, S.; Ihle, T. and Petzoldt, T. (2008)
  R/mcyst_chemostat.R
    1: ### Jhnichen, S.; Ihle, T. and Petzoldt, T. (2008)
  R/slight.R
    11: #    Modellierung limnischer kosysteme. 
    111:         toptx   = 20,    # optimal temp. for photosynthesis (C) [SALMO Diat]
    114:         rxtmin = 0.02,   # T dependence of resp (1/C) [SALMO, Diat]
    117:         momin = 0.015,   # Zooplankton mortality near 0C (1/d) [SALMO]
    118:         mot = 0.006,     # temperature dependence of zooplankton mortality (C/d) [SALMO]
    120:         dtb = 0.3720601, # inverse of egg development time at 20C (d) [BOTTRELL]
    122:         tref = 293.15,   # reference temperature 20C (K)

The Title field should be in title case, current version then in title case:
‘Model collection for the simecol package’
‘Model Collection for the Simecol Package’

The Description field should not start with the package name,
  'This package' or similar.
* 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 whether package ‘simecolModels’ can be installed ... [2s/2s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NPZriver : : no visible global function definition for
  ‘steady.1D’
OmexDia : : no visible global function definition for
  ‘steady.1D’
SiDia : : no visible global function definition for
  ‘steady.1D’
StreamIron : : no visible global function definition for
  ‘steady.1D’
UvasCreek : : no visible global function definition for
  ‘steady.1D’
UvasCreek : : no visible global function definition for
  ‘ode.1D’
Undefined global functions or variables:
  ode.1D steady.1D
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
File ‘simecolModels/libs/simecolModels.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 installed files from ‘inst/doc’ ... OK
* checking examples ... [20s/20s] NOTE
Examples with CPU or elapsed time > 5s
           user system elapsed
UvasCreek 5.908  0.136   6.045
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/mnt/building/build_2017-07-11-22-24/RF_PKG_CHECK/PKGS/simecolModels.Rcheck/00check.log’
for details.


Run time: 63.98 seconds.