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snapCGH 1.6.0
John Marioni
Last Changed Date: 2007-10-02 17:41:09 -0700
Last Changed Rev: 27709
lamb1 Linux (SUSE 10.1) x86_64  OK  OK 
wellington Linux (SUSE 9.2) i686  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) x64  OK  OK  OK 
pitt Mac OS X (10.4.10) i386  OK  OK  OK 
Package: snapCGH
Version: 1.6.0
Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check snapCGH_1.6.0.tar.gz
RetCode: 0
Time: 510.7 seconds
Status: OK
CheckDir: snapCGH.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/snapCGH.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'snapCGH/DESCRIPTION' ... OK
* this is package 'snapCGH' version '1.6.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'snapCGH' 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 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 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
generate.data: no visible binding for global variable
  'zero.length.distr.non.tiled'
generate.data: no visible binding for global variable
  'non.zero.length.distr.non.tiled'
generate.data: no visible binding for global variable
  'zero.length.distr.tiled'
generate.data: no visible binding for global variable
  'non.zero.length.distr.tiled'
processCGH: no visible binding for global variable 'RG'
readPositionalInfo: no visible binding for global variable 'RGList'
runPicard: possible error in segment(log2ratios, maxk =
  length(log2ratios), maxseg = min(length(log2ratios), maxSeg)): unused
  argument(s) (maxk = length(log2ratios), maxseg =
  min(length(log2ratios), maxSeg))
simulateData: no visible binding for global variable
  'zero.length.distr.non.tiled'
simulateData: no visible binding for global variable
  'zero.length.distr.tiled'
simulateData: no visible binding for global variable
  'non.zero.length.distr.non.tiled'
simulateData: no visible binding for global variable
  'non.zero.length.distr.tiled'
Found possibly global 'T' or 'F' in the following functions:
  read.clonesinfo readPositionalInfo simulateData
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating snapCGH-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating snapCGH-manual.tex ... OK
* checking snapCGH-manual.tex ... OK

snapCGH.Rcheck/00install.out:

* Installing *source* package 'snapCGH' ...
** libs
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c optimizer.c -o optimizer.o
gcc -std=gnu99 -shared -L/usr/local/lib -o snapCGH.so optimizer.o   -L/loc/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Loading required package: limma
Loading required package: tilingArray
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: affy
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: RColorBrewer
Loading required package: grid
Loading required package: strucchange
Loading required package: zoo

Attaching package: 'zoo'


	The following object(s) are masked from package:base :

	 rapply 

Loading required package: sandwich
Loading required package: vsn
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: geneplotter
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: xtable
Loading required package: lattice
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: pixmap
Loading required package: DNAcopy

Attaching package: 'DNAcopy'


	The following object(s) are masked from package:tilingArray :

	 segment 

Loading required package: GLAD
Loading required package: aws
Loading required package: tcltk
Loading Tcl/Tk interface ... done
[1] "Have fun with GLAD"
Loading required package: cluster
Loading required package: aCGH
Loading required package: multtest
Loading required package: sma

Attaching package: 'aCGH'


	The following object(s) are masked from package:stats :

	 heatmap 

** help
Note: unmatched right brace in 'SegList' on or after line 30
Note: unmatched right brace in 'find.param.one' on or after line 18
Note: unmatched right brace in 'non.zero.length.distr.non.tiled' on or after line 9
Note: unmatched right brace in 'processCGH' on or after line 44
 >>> Building/Updating help pages for package 'snapCGH'
     Formats: text html latex example 
  IDProbes                          text    html    latex
  LargeDataObject                   text    html    latex   example
  SegList                           text    html    latex
  Viterbi.five                      text    html    latex
  Viterbi.four                      text    html    latex
  Viterbi.three                     text    html    latex
  Viterbi.two                       text    html    latex
  cbind                             text    html    latex
  chrominfo.Mb                      text    html    latex
  compareSegmentations              text    html    latex
  convert.output                    text    html    latex   example
  dim                               text    html    latex   example
  dimnames                          text    html    latex
  filter                            text    html    latex
  find.param.five                   text    html    latex
  find.param.four                   text    html    latex
  find.param.one                    text    html    latex
  find.param.three                  text    html    latex
  find.param.two                    text    html    latex
  findBreakPoints                   text    html    latex
  fit.model                         text    html    latex
  genomePlot                        text    html    latex   example
  heatmapGenome                     text    html    latex   example
  imputeMissingValues               text    html    latex
  log2ratios                        text    html    latex
  mergeStates                       text    html    latex
  non.zero.length.distr.non.tiled   text    html    latex
  non.zero.length.distr.tiled       text    html    latex
  nudSegmentation                   text    html    latex
  plotSegmentedGenome               text    html    latex   example
  processCGH                        text    html    latex
  read.clonesinfo                   text    html    latex
  readPositionalInfo                text    html    latex
  removeByWeights                   text    html    latex
  runBioHMM                         text    html    latex
  runDNAcopy                        text    html    latex
  runGLAD                           text    html    latex
  runHMM                            text    html    latex
  runPicard                         text    html    latex
  sim.structure                     text    html    latex   example
  zero.length.distr.non.tiled       text    html    latex
  zero.length.distr.tiled           text    html    latex
  zoomChromosome                    text    html    latex
  zoomGenome                        text    html    latex
** building package indices ...
* DONE (snapCGH)