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qtl.outbred log file (check_x86_64_linux)

Fri Sep 20 16:40:46 2013: Checking package qtl.outbred (SVN revision 27) ...
* using log directory ‘/mnt/building/build_2013-09-20-16-04/RF_PKG_CHECK/PKGS/qtl.outbred.Rcheck’
* using R version 3.0.1 Patched (2013-08-27 r63742)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘qtl.outbred/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qtl.outbred’ version ‘2013.05.03’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Xia Shen ’
New submission
Version contains leading zeroes (2013.05.03)
* 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 ‘qtl.outbred’ can be installed ... [1s/2s] OK
* checking installed package size ... NOTE
  installed size is 11.8Mb
* 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 ... NOTE
‘library’ or ‘require’ call to ‘qtl’ which was already attached by Depends.
  Please remove these calls from your code.
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 ... WARNING
Found an obsolete/platform-specific call in the following function:
  ‘calc.prob’
Found the defunct/removed function:
  ‘zip.file.extract’

In addition to the above warning(s), found the following notes:

File ‘qtl.outbred/R/outbred.R’:
  .onLoad calls:
    require(qtl)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

calc.prob: no visible global function definition for ‘zip.file.extract’
plot.outbred: no visible global function definition for ‘plot.scanone’
plot.outbred: no visible global function definition for ‘plot.scantwo’
* 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 ... WARNING
Functions or methods with usage in documentation object 'Scanone' but not in code:
  Scanone

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

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files are already in R: ‘Sweave.sty’
Please remove them from your package.
The following files look like leftovers/mistakes:
  ‘pdfpages.ins’
Please remove them from your package.
* checking examples ... [1s/1s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
   ‘outbred.Rnw’ ... [0s/0s] OK
   ‘qtl.outbred.Rnw’ ... [0s/0s] OK
 [1s/1s] OK
* checking re-building of vignette outputs ... [1s/1s] OK
* checking PDF version of manual ... OK

WARNING: There were 2 warnings.
NOTE: There were 4 notes.
See
  ‘/mnt/building/build_2013-09-20-16-04/RF_PKG_CHECK/PKGS/qtl.outbred.Rcheck/00check.log’
for details.

Run time: 39.18 seconds.

Additional Logs:   00install.out
Thanks to:
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