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plantbreeding log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2014-12-15-05-24/RF_PKG_CHECK/PKGS/plantbreeding.Rcheck'
* using R version 3.1.2 Patched (2014-12-11 r67162)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'plantbreeding/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'plantbreeding' version '1.1.1'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Umesh R. Rosyara '
New submission
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'plantbreeding' can be installed ... 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 dependencies in R code ... WARNING
'library' or 'require' call not declared from: 'lattice'
'library' or 'require' call to 'reshape' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'plyr' 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ammi.full: no visible global function definition for 'melt'
stability: no visible global function definition for 'wireframe'
stability: no visible global function definition for 'melt'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'manhatton.plot.rd':
  \usage lines wider than 90 characters:
     manhatton.plot(dataframe, SNPname, chromosome, position, pvcol, ylabel = "pvalue", pconv= "-log10", ymax = "maximum",
  \examples lines wider than 100 characters:
                                                                                                                                             ... [TRUNCATED]
     manhatton.plot(dataframe = data13, pconv= "NULL", ylabel = "R-square", SNPname = "snp", chromosome = "chr", 

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'gencor.lm'
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'manhatton.plot'
  'pconv'

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 the 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 ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
manhatton.plot 9.97   0.05   10.13
* checking PDF version of manual ... OK
* DONE

WARNING: There were 3 warnings.
NOTE: There were 4 notes.
See
  'R:/run/building/build_2014-12-15-05-24/RF_PKG_CHECK/PKGS/plantbreeding.Rcheck/00check.log'
for details.

Run time: 52.03 seconds.