Package: mscalib

Version: 1.3.0

Command: /loc/biocbuild/1.9d/R/bin/R CMD check mscalib_1.3.0.tar.gz

RetCode: 1

Time: 115.8 seconds

Status: ERROR

CheckDir: mscalib.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/1.9d/Rpacks/mscalib.Rcheck'
* using R version 2.4.0 Under development (unstable) (2006-06-04 r38279)
* checking for file 'mscalib/DESCRIPTION' ... OK
* this is package 'mscalib' version '1.3.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'mscalib' can be installed ... OK
* 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 syntax errors ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking Rd files ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  pepruleFilterX
Undocumented S4 methods:
  generic pepruleFilterX and siglist Massvector
  generic pepruleFilterX and siglist Massvectorlist
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating mscalib-Ex.R ... OK
* checking examples ... ERROR
Running examples in mscalib-Ex.R failed.
The error most likely occurred in:

> ### * Cpf
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: Cpf
> ### Title: Number of cleavages per protein
> ### Aliases: Cpf
> ### Keywords: misc
> 
> ### ** Examples
> 
> Cpf(avgProtlength = 350, cleavagesites = c("K", "R"), AAfrequencies = get(data("frlist", 
+     package = "mscalib"))[[1]]) 
Warning in data("frlist", package = "mscalib") : 
	 data set 'frlist' not found
Error in get(x, envir, mode, inherits) : variable "frlist" was not found
Execution halted

* Installing *source* package 'mscalib' ...
** R
** data
** inst
** help
 >>> Building/Updating help pages for package 'mscalib'
     Formats: text html latex example 
  CSKrig-class                      text    html    latex   example
  CSTps-methods                     text    html    latex   example
  CSsurf-class                      text    html    latex   example
  CSsurf.gls-methods                text    html    latex   example
  CSsurf.ls-methods                 text    html    latex
  CalibPRstat-class                 text    html    latex   example
  Calibextstat-class                text    html    latex   example
  Calibintlist-class                text    html    latex   example
  Calibintstat-class                text    html    latex   example
  Caliblist-class                   text    html    latex   example
  Calibprelist-class                text    html    latex   example
  Calibprestat-class                text    html    latex   example
  Calibstat-class                   text    html    latex   example
  Cpf                               text    html    latex   example
  DATA                              text    html    latex   example
  DATA2                             text    html    latex   example
  DgetPRcalib                       text    html    latex
  Fcn                               text    html    latex   example
  Fmn                               text    html    latex   example
  Surf-class                        text    html    latex   example
  averageAAmass                     text    html    latex   example
  c0lambdaDBn                       text    html    latex   example
  c0lambdaDBnC                      text    html    latex   example
  correctinternal-methods           text    html    latex   example
  diffFilter-methods                text    html    latex   example
  distance3                         text    html    latex   example
  distance4                         text    html    latex   example
  frlist                            text    html    latex   example
  getLpepcalib-methods              text    html    latex   example
  getPPGmasses                      text    html    latex   example
  getPRcalib-methods                text    html    latex
  getdiff-methods                   text    html    latex   example
  getextcalib-methods               text    html    latex
  getglobalcalib-methods            text    html    latex
  getintcalib-methods               text    html    latex   example
  getmstCalib-methods               text    html    latex   example
  getpepcalib-methods               text    html    latex   example
  getprecalib-methods               text    html    latex
  globalcalib-methods               text    html    latex
  lambda.cleavagesite               text    html    latex   example
  lambda.none                       text    html    latex   example
  massFilter-methods                text    html    latex
  monoiso                           text    html    latex   example
  mstCalib-class                    text    html    latex   example
  nomina                            text    html    latex   example
  pepFilter-methods                 text    html    latex
  peproleFilter-methods             text    html    latex
  peprule                           text    html    latex   example
  pepruleFilter                     text    html    latex
  peprulecomp                       text    html    latex   example
  prAA                              text    html    latex   example
  residuals-methods                 text    html    latex
  restrictionenz                    text    html    latex   example
  undocument-internal               text    html    latex
  wsFilter-methods                  text    html    latex
** building package indices ...
* DONE (mscalib)