• using R Under development (unstable) (2012-05-19 r59366)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• 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 ... WARNING
  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 for executable files ... OK
• checking whether package ‘caMassClass’ can be installed ... OK
• checking installed package size ... NOTE
  installed size is 8.1Mb
  sub-directories of 1Mb or more:
  Test 7.4Mb
• checking package directory ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... 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
• 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 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
  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 ... NOTE
  Package(s) unavailable to check Rd xrefs: ‘xcms’
• 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 ... [83s/83s] OK
• checking PDF version of manual ... OK
  WARNING: There were 2 warnings.
  NOTE: There were 3 notes.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/caMassClass.Rcheck/00check.log’
  for details.