* using log directory 'd:/Rcompile/CRANpkg/local/2.15/caMassClass.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 'caMassClass/DESCRIPTION' ... OK
* this is package 'caMassClass' version '1.9'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... NOTE
As from R 2.14.0 all packages need a namespace.
One will be generated on installation, but it is better to handcraft a
NAMESPACE file: R CMD build will produce a suitable starting point.
CRAN requires a NAMESPACE file for all submissions.
* checking whether package 'caMassClass' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.0Mb
  sub-directories of 1Mb or more:
    Test   7.3Mb
* 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
* 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 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
msc.biomarkers.read.csv: warning in digest(fname, alg = "sha1", file =
  TRUE): partial argument match of 'alg' to 'algo'
msc.peaks.read.csv: warning in digest(fname, alg = "sha1", file =
  TRUE): partial argument match of 'alg' to 'algo'
msc.rawMS.read.csv : file.conn: warning in unz(file.path(path, sg[1]),
  file = sg[2]): partial argument match of 'file' to 'filename'
msc.rawMS.read.csv: warning in digest(out, alg = "sha1"): partial
  argument match of 'alg' to 'algo'
msc.rawMS.read.csv: warning in digest(fname, alg = "sha1", file =
  TRUE): partial argument match of 'alg' to 'algo'
* 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 ... WARNING
Assignments in \usage in documentation object 'msc.biomarkers.read.csv & msc.biomarkers.write.csv':
  X = msc.biomarkers.read.csv(fname, mzXML.record = FALSE)

Assignments in \usage in documentation object 'msc.peaks.read.csv & msc.peaks.write.csv':
  X = msc.peaks.read.csv(fname, mzXML.record = FALSE)

Assignments in \usage in documentation object 'read.mzXML & write.mzXML':
  mzXML = new.mzXML()
  mzXML = read.mzXML(filename)

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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 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 PDF version of manual ... OK
WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  'd:/Rcompile/CRANpkg/local/2.15/caMassClass.Rcheck/00check.log'
for details.