* using log directory 'd:/Rcompile/CRANpkg/local/2.15/MeDiChI.Rcheck'
* using R version 2.15.0 (2012-03-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ... NOTE
Packages suggested but not available for checking:
  'multicore' 'doMC'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'MeDiChI' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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'
deconv.entire.genome : apply.func: no visible global function
  definition for '%dopar%'
deconv.entire.genome : apply.func: no visible global function
  definition for 'foreach'
deconv.entire.genome : apply.func: no visible binding for global
  variable 'l'
deconv.entire.genome : <anonymous>: no visible binding for global
  variable 'ind'
fit.peak.profile: warning in mget(names(formals()), env =
  as.environment(-1)): partial argument match of 'env' to 'envir'
fit.peak.profile: no visible binding for global variable 'mclapply'
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'
generate.binding.profile : apply.func: no visible global function
  definition for '%dopar%'
generate.binding.profile : apply.func: no visible global function
  definition for 'foreach'
generate.binding.profile : apply.func: no visible binding for global
  variable 'l'
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'
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                  old_size new_size compress
  halo.hires.rda     1.1Mb    593Kb       xz
  halo.lowres.rda    356Kb    300Kb       xz
  yeast.gcn4.rda     1.1Mb    695Kb       xz
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... OK
* checking re-building of vignette PDFs ... OK
* checking PDF version of manual ... OK
WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  'd:/Rcompile/CRANpkg/local/2.15/MeDiChI.Rcheck/00check.log'
for details.