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mGSZ log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2014-02-17-16-13/RF_PKG_CHECK/PKGS/mGSZ.Rcheck'
* using R version 3.0.2 Patched (2014-02-14 r65008)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'mGSZ/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mGSZ' version '1.0'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Pashupati Mishra '
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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'mGSZ' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard files found at top level:
  'mGSZ' 'mGSZ_1.0.tar.gz'
* 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 ... NOTE
Packages in Depends field not imported from:
  'Biobase' 'GSA' 'MASS' 'ismev' 'limma'
  These packages need to be imported from for the case when
  this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... WARNING
diff:
  function(x, ...)
diff.FC.perm:
  function(data, sample.labels, perm.number, is.log)

log:
  function(x, base)
log.ev.cdf:
  function(x, mu, sigma)

log:
  function(x, base)
log.norm.cdf:
  function(x, mu, sigma)

sum:
  function(..., na.rm)
sum.test.score:
  function(expr.data, gene.sets)

See section 'Generic functions and methods' of the 'Writing R
Extensions' manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'R:/run/building/build_2014-02-17-16-13/RF_PKG_CHECK/PKGS/mGSZ.Rcheck/00_pkg_src/mGSZ/man/mGSZ.Rd':
  \usage lines wider than 90 characters:
     mGSZ(expr.data, gene.sets, sample.labels, flip.gene.sets = FALSE, select= 'T-score', is.log = TRUE, gene.perm = FALSE,  min.cl.sz=5, ot ... [TRUNCATED]

Rd file 'R:/run/building/build_2014-02-17-16-13/RF_PKG_CHECK/PKGS/mGSZ.Rcheck/00_pkg_src/mGSZ/man/toTable.Rd':
  \usage lines wider than 90 characters:
     toTable(mGSZobj, sample.perm.table = FALSE, method = c("mGSZ", "mGSA", "mAllez", "WRS", "SS", "SUM", "KS", "wKS"), no.top.sets = 10)

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 examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
StabPlotData 14.73   0.22   15.01
mGSZ         13.72   0.09   13.81
plotProfile  13.53   0.19   13.72
toTable       7.14   0.19    7.34
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
  'R:/run/building/build_2014-02-17-16-13/RF_PKG_CHECK/PKGS/mGSZ.Rcheck/00check.log'
for details.

Run time: 159.3 seconds.