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ithir log file (check_x86_64_linux)

Mon Feb 22 12:05:32 2016: Checking package ithir (SVN revision 126) ...
* using log directory ‘/mnt/building/build_2016-02-22-12-04/RF_PKG_CHECK/PKGS/ithir.Rcheck’
* using R version 3.2.3 Patched (2016-02-20 r70194)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘ithir/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ithir’ version ‘1.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Brendan Malone ’
New submission

Package has a FOSS license but eventually depends on the following
package which restricts use:
  tripack

Uses the superseded package: ‘snow’

The Date field is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* 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 ‘ithir’ can be installed ... [9s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
goof: no visible global function definition for ‘eqscplot’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'ea_spline.Rd':
  \usage lines wider than 90 characters:
     ea_spline(obj, var.name, lam = 0.1, d = t(c(0,5,15,30,60,100,200)), vlow = 0, vhigh = 1000, show.progress=TRUE)

Rd file 'plot_ea_spline.Rd':
  \usage lines wider than 90 characters:
     plot_ea_spline(splineOuts, d = t(c(0,5,15,30,60,100,200)), maxd, type = 1 , label = "", plot.which = 1)
  \examples lines wider than 100 characters:
     eaFit <- ea_spline(oneProfile, var.name="C.kg.m3.",d= t(c(0,5,15,30,60,100,200)),lam = 0.1, vlow=0, show.progress=FALSE )
     plot_ea_spline(splineOuts=eaFit, d= t(c(0,5,15,30,60,100,200)), maxd=200, type=1, label="carbon density") 

Rd file 'plot_soilProfile.Rd':
  \examples lines wider than 100 characters:
     plot_soilProfile(data = oneProfile, vals = oneProfile$C.kg.m3., depths = oneProfile[,2:3], label= names(oneProfile)[4])

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  ‘HV100’ ‘HV_dem’ ‘USYD_dIndex’ ‘USYD_soil1’ ‘elevation’ ‘landsat_b3’
  ‘landsat_b4’ ‘radK’ ‘twi’ ‘.Random.seed’ ‘hvGrid25m’ ‘hvPoints250’
  ‘oneProfile’
Undocumented S4 methods:
  generic 'dissever' and siglist 'RasterStack,RasterLayer'
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 ... OK
* checking Rd \usage sections ... WARNING
Bad \usage lines found in documentation object 'dissever':
  S4method{dissever}{r2 = "RasterStack", c.grid = "RasterLayer}(r2, c.grid, ss = 0.5, cores = 8, thresh = 0.01)

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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [12s/12s] OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 5 NOTEs
See
  ‘/mnt/building/build_2016-02-22-12-04/RF_PKG_CHECK/PKGS/ithir.Rcheck/00check.log’
for details.


Run time: 149.76 seconds.