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patchworkCG log file (check_x86_64_linux)

Wed Jun  5 16:21:06 2013: Checking package patchworkCG (SVN revision 171) ...
* using log directory ‘/mnt/building/build_2013-06-05-16-04/RF_PKG_CHECK/PKGS/patchworkCG.Rcheck’
* using R version 3.0.1 Patched (2013-06-04 r62868)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘patchworkCG/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘patchworkCG’ version ‘2.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Markus Rasmussen ’
New submission
* 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 ‘patchworkCG’ can be installed ... [1s/3s] 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 for unstated 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
File ‘patchworkCG/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("\n")
    packageStartupMessage("Welcome to patchwork for CompleteGenomics data!")
    packageStartupMessage("\n")
    packageStartupMessage("Version: ", utils::packageDescription("patchworkCG")$Version)
    packageStartupMessage("\n")
    packageStartupMessage("If this is your first time, please see the documentation at the")
    packageStartupMessage("homepage (http://patchwork.r-forge.r-project.org/) or in ?patchworkCG.readme")
    packageStartupMessage("or the README file found at the install location of patchworkCG/example_plots/README")

See section ‘Good practice’ in '?.onAttach'.

CG_KaCh: no visible binding for global variable ‘ideogram’
CG_KaChCN: no visible binding for global variable ‘ideogram’
CG_karyotype: no visible binding for global variable ‘ideogram’
patchwork.CG.copynumbers: no visible binding for global variable
  ‘ideogram’
patchwork.CG.copynumbers: no visible binding for global variable ‘segm’
patchwork.CG.copynumbers: no visible binding for global variable
  ‘depcov’
patchwork.CG.copynumbers: no visible binding for global variable
  ‘mastervar’

Found the following calls to data() loading into the global environment:
File ‘patchworkCG/R/CG_KaCh.r’:
  data(ideogram, package = "patchworkCG")
File ‘patchworkCG/R/CG_KaChCN.r’:
  data(ideogram, package = "patchworkCG")
File ‘patchworkCG/R/CG_karyotype.r’:
  data(ideogram, package = "patchworkCG")
File ‘patchworkCG/R/patchwork.CG.copynumbers.r’:
  data(ideogram, package = "patchworkCG")
See section ‘Good practice’ in ‘?data’.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file ‘/mnt/building/build_2013-06-05-16-04/RF_PKG_CHECK/PKGS/patchworkCG.Rcheck/00_pkg_src/patchworkCG/man/CG_KaChCN.Rd’:
  \usage lines wider than 95 characters:
     CG_KaChCN(chr,start,end,int,ai,Cn,mCn,mchr,mpos,mval,sval,schr,spos,name=‘’,xlim=c(0,2.4),ylim=c(0,1),maxCn=8)

These lines will be truncated in the PDF manual.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [1s/1s] OK
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/mnt/building/build_2013-06-05-16-04/RF_PKG_CHECK/PKGS/patchworkCG.Rcheck/00check.log’
for details.

Run time: 60.41 seconds.