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icav log file (check_x86_64_linux)

Wed Feb 19 16:30:46 2014: Checking package icav (SVN revision 42) ...
* using log directory ‘/mnt/building/build_2014-02-19-16-14/RF_PKG_CHECK/PKGS/icav.Rcheck’
* using R version 3.0.2 Patched (2014-02-18 r65029)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘icav/DESCRIPTION’ ... OK
* this is package ‘icav’ version ‘0.2-3’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Ariel E. Baya ’
New submission
Uses the superseded package: ‘multicore’
* 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 ‘icav’ can be installed ... [3s/8s] 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 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
gapStat.mc : foo.null: warning in matrix(unlist(lapply(1:NCOL,
  do.rand.matrix, NData, Min.x, Max.x)), nc = NCOL, nr = NData):
  partial argument match of 'nr' to 'nrow'
gapStat.mc : foo.null: warning in matrix(unlist(lapply(1:NCOL,
  do.rand.matrix, NData, Min.x, Max.x)), nc = NCOL, nr = NData):
  partial argument match of 'nc' to 'ncol'
icav.gap.mc : foo: warning in matrix(unlist(lapply(1:length(min.x),
  do.rand.matrix, N, min.x, max.x)), nc = length(min.x), nr = N):
  partial argument match of 'nr' to 'nrow'
icav.gap.mc : foo: warning in matrix(unlist(lapply(1:length(min.x),
  do.rand.matrix, N, min.x, max.x)), nc = length(min.x), nr = N):
  partial argument match of 'nc' to 'ncol'
icav.gap.mc: warning in matrix(unlist(clust.null), nc = M, nr = k.max):
  partial argument match of 'nr' to 'nrow'
icav.gap.mc: warning in matrix(unlist(clust.null), nc = M, nr = k.max):
  partial argument match of 'nc' to 'ncol'
icav.gap.mc: no visible binding for global variable ‘kmax’
* checking Rd files ... WARNING
prepare_Rd: mst2Path.Diss.Rd:5-8: Dropping empty section \description
checkRd: (5) mst2Path.Diss.Rd:0-33: Must have a \description
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘Gap.plot’ ‘do.means’ ‘eucmetric’ ‘gapStat.mc’ ‘icav.Matrix.chunk’
  ‘icav.Matrix.sort’ ‘icav.estimator’ ‘icav.estimator.apply’ ‘icav.gap’
  ‘icav.gap.mc’ ‘plot.GapStat’ ‘plot.clusterGap’ ‘sil’ ‘withinSum’
Undocumented data sets:
  ‘datos’ ‘datos.class’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... WARNING
Non-portable flags in variable ‘PKG_CFLAGS’:
  -fopenmp -std=gnu99 -fgnu89-inline
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... [2s/4s] OK
* checking PDF version of manual ... OK

WARNING: There were 3 warnings.
NOTE: There were 2 notes.
See
  ‘/mnt/building/build_2014-02-19-16-14/RF_PKG_CHECK/PKGS/icav.Rcheck/00check.log’
for details.

Run time: 92.01 seconds.