• using R version 3.0.0 RC (2013-03-31 r62463)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘MeDiChI/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘MeDiChI’ version ‘0.4.0’
• 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 ‘MeDiChI’ 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 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 ‘MeDiChI/R/chip.deconv.pkg.R’:
  .onLoad calls:
  cat("Loading MeDiChI, version ", VERSION, " (", DATE, ")\n", sep = "")
  
  Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
  See section ‘Good practice’ in '?.onAttach'.
  
  chip.deconv: warning in mget(names(formals()), env =
  as.environment(-1)): partial argument match of 'env' to 'envir'
  chip.deconv: warning in solve.QP(Dmat, t(t(cnts) %*% tmp.xx), A =
  t(diag(ncol(tmp.xx))), b = rep(0, ncol(tmp.xx)), meq = 0): partial
  argument match of 'A' to 'Amat'
  chip.deconv: warning in solve.QP(Dmat, t(t(cnts) %*% tmp.xx), A =
  t(diag(ncol(tmp.xx))), b = rep(0, ncol(tmp.xx)), meq = 0): partial
  argument match of 'b' to 'bvec'
  fit.peak.profile: warning in mget(names(formals()), env =
  as.environment(-1)): partial argument match of 'env' to 'envir'
  fit.peak.profile : get.fit.score: warning in deconv.entire.genome(data
  = orig.data, kern = best.kernel, plot = F, verbose = F, no.multicore
  = no.multicore, ...): partial argument match of 'kern' to 'kernel'
  fit.peak.profile : get.fit.score : <anonymous>: warning in
  chip.deconv(data = dat, fit.res = 30, window = NA, max.steps =
  max.steps.2, where = NA, center = NA, kernel = kernel, verbose = F,
  trace = F, n.boot = 1, tile.distance = tile.size, max.npeak = 1,
  min.npeak = 1, quant.cutoff = q.cutoff): partial argument match of
  'min.npeak' to 'min.npeaks'
  fit.peak.profile : get.fit.score : <anonymous>: warning in
  chip.deconv(data = dat, fit.res = 30, window = NA, max.steps =
  max.steps.2, where = NA, center = NA, kernel = kernel, verbose = F,
  trace = F, n.boot = 1, tile.distance = tile.size, max.npeak = 1,
  min.npeak = 1, quant.cutoff = q.cutoff): partial argument match of
  'max.npeak' to 'max.npeaks'
  fit.peak.profile: warning in deconv.entire.genome(data = orig.data,
  kern = in.kernel, plot = F, verbose = F, no.multicore = no.multicore,
  ...): partial argument match of 'kern' to 'kernel'
  plot.chip.deconv: warning in mget(names(formals()), env =
  as.environment(-1)): partial argument match of 'env' to 'envir'
  plot.genes.in.window: warning in exists("gene.coords", env =
  .GlobalEnv): partial argument match of 'env' to 'envir'
  plot.genes.in.window: warning in get("gene.coords", env = .GlobalEnv):
  partial argument match of 'env' to 'envir'
  deconv.entire.genome : apply.func: no visible binding for global
  variable ‘l’
  deconv.entire.genome : <anonymous>: no visible binding for global
  variable ‘ind’
  generate.binding.profile : apply.func: no visible binding for global
  variable ‘l’
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... NOTE
  S3 methods shown with full name in documentation object 'chip.deconv':
  ‘plot.chip.deconv’ ‘print.chip.deconv’ ‘coef.chip.deconv’
  
  S3 methods shown with full name in documentation object 'deconv.entire.genome':
  ‘print.chip.deconv.entire.genome’ ‘plot.chip.deconv.entire.genome’
  ‘coef.chip.deconv.entire.genome’
  
  S3 methods shown with full name in documentation object 'fit.peak.profile':
  ‘plot.fit.peak.profile’
  
  The \usage entries for S3 methods should use the \method markup and not
  their full name.
  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 sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking examples ... [29s/30s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [16s/16s] OK
• checking re-building of vignette PDFs ... [16s/16s] OK
• checking PDF version of manual ... OK
  NOTE: There were 2 notes.
  See
  ‘/home/hornik/tmp/R.check/r-prerel-ng/Work/PKGS/MeDiChI.Rcheck/00check.log’
  for details.