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TAPS log file (check_x86_64_linux)

Mon Nov 23 11:05:38 2015: Checking package TAPS (SVN revision 219) ...
* using log directory ‘/mnt/building/build_2015-11-23-11-04/RF_PKG_CHECK/PKGS/TAPS.Rcheck’
* using R version 3.2.2 Patched (2015-11-20 r69676)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘TAPS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TAPS’ version ‘2.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Sebastian DiLorenzo  #Markus Mayrhofer ’
New submission

Unknown, possibly mis-spelled, fields in DESCRIPTION:
  ‘#Imports’

No package encoding and non-ASCII characters in the following R files:
  R/TAPS.r
    1200:     ### berkna tumorcellshalt!!
    1202:     ## empirical delta-R for one copy in diploid sample: 0.63 for Cyto/SNP6 and 0.48 for Illu

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 ‘TAPS’ 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 ... WARNING
'library' or 'require' calls not declared from:
  ‘DNAcopy’ ‘affxparser’ ‘dataview’ ‘doMC’ ‘fields’ ‘foreach’ ‘jpeg’
  ‘tcltk’ ‘xlsx’
'library' or 'require' calls in package code:
  ‘DNAcopy’ ‘affxparser’ ‘dataview’ ‘doMC’ ‘fields’ ‘foreach’ ‘jpeg’
  ‘stats’ ‘tcltk’ ‘xlsx’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
File ‘TAPS/R/zzz.r’:
  .onLoad calls:
    packageStartupMessage("\n")
    packageStartupMessage("Welcome to TAPS")
    packageStartupMessage("\n")
    packageStartupMessage("Version: ", utils::packageDescription("TAPS")$Version)
    packageStartupMessage("\n")
    packageStartupMessage("If this is your first time running TAPS you should visit the")
    packageStartupMessage("homepage at (http://patchwork.r-forge.r-project.org/) or see ?TAPS.")
    packageStartupMessage("\n")
    packageStartupMessage("TAPS can now be used to summarize aberration frequencies and compare sample groups. Try ?TAPS_freq and ?TAPS_compare.")
    packageStartupMessage("\n")
    packageStartupMessage("Remember to keep TAPS up to date: update.packages(repos=\"http://R-Forge.R-project.org\")")

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

TAPS_call: no visible global function definition for ‘registerDoMC’
TAPS_call: no visible global function definition for ‘read.xlsx’
TAPS_call: no visible global function definition for ‘%dopar%’
TAPS_call: no visible global function definition for ‘foreach’
TAPS_call: no visible binding for global variable ‘i’
TAPS_call: no visible binding for global variable ‘probes.txt’
TAPS_call: no visible binding for global variable ‘snps.txt’
TAPS_call: no visible binding for global variable ‘localDir’
TAPS_call: no visible binding for global variable ‘regs’
TAPS_click: no visible global function definition for ‘%do%’
TAPS_click: no visible global function definition for ‘foreach’
TAPS_click: no visible global function definition for ‘tclServiceMode’
TAPS_estimates: no visible global function definition for ‘%do%’
TAPS_estimates: no visible global function definition for ‘foreach’
TAPS_estimates: no visible binding for global variable ‘regs’
TAPS_plot: no visible global function definition for ‘registerDoMC’
TAPS_plot: no visible global function definition for ‘%dopar%’
TAPS_plot: no visible global function definition for ‘foreach’
TAPS_plot: no visible global function definition for ‘readCcg’
TAPS_plot: no visible binding for global variable ‘probes.txt’
TAPS_plot: no visible binding for global variable ‘snps.txt’
TAPS_region: no visible binding for global variable ‘regs’
TAPS_region: no visible binding for global variable ‘Log2’
TAPS_region: no visible binding for global variable ‘alf’
drawImage: no visible global function definition for ‘readJPEG’
segment_DNAcopy: no visible global function definition for ‘segment’
segment_DNAcopy: no visible global function definition for ‘smooth.CNA’
segment_DNAcopy: no visible global function definition for ‘CNA’
subplot: no visible global function definition for ‘viewport’
vplayout: no visible global function definition for ‘grid.newpage’
vplayout: no visible global function definition for ‘pushViewport’
vplayout: no visible global function definition for ‘viewport’
vplayout: no visible global function definition for ‘grid.layout’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'TAPS_plot.Rd':
  \usage lines wider than 90 characters:
     TAPS_plot(directory=NULL,autoEstimate=FALSE,bin=400,cores=1,matched=FALSE,allelePeaks=FALSE)

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 ... WARNING
Codoc mismatches from documentation object 'TAPS_plot':
TAPS_plot
  Code: function(directory = NULL, autoEstimate = FALSE, bin = 250,
                 cores = 1, matched = FALSE, allelePeaks = FALSE)
  Docs: function(directory = NULL, autoEstimate = FALSE, bin = 400,
                 cores = 1, matched = FALSE, allelePeaks = FALSE)
  Mismatches in argument default values:
    Name: 'bin' Code: 250 Docs: 400

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking examples ... NONE
* checking PDF version of manual ... OK
* checking for code which exercises the package ... WARNING
No examples, no tests, no vignettes
* DONE

Status: 3 WARNINGs, 4 NOTEs
See
  ‘/mnt/building/build_2015-11-23-11-04/RF_PKG_CHECK/PKGS/TAPS.Rcheck/00check.log’
for details.


Run time: 29.34 seconds.

Additional Logs:   00install.out
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