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Package 287/319HostnameOS / ArchBUILDCHECKBUILD BIN
snapCGH 1.12.0
John Marioni
Bioconductor Changelog
Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/snapCGH
Last Changed Rev: 39013 / Revision: 42512
Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009)
wilson1 Linux (openSUSE 11.1) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
Package: snapCGH
Version: 1.12.0
Command: /home/biocbuild/bbs-2.4-bioc/R/bin/R CMD check --no-vignettes snapCGH_1.12.0.tar.gz
StartedAt: 2009-10-20 17:59:14 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 18:00:28 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 73.5 seconds
RetCode: 0
Status: OK
CheckDir: snapCGH.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.4-bioc/meat/snapCGH.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'snapCGH/DESCRIPTION' ... OK
* this is package 'snapCGH' version '1.12.0'
* checking package name space information ... OK
* 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 whether the name space 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'
heatmapGenome: no visible binding for global variable 'floor.func'
readPositionalInfo: no visible binding for global variable 'RGList'
runTilingArray: 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'
* checking Rd files ... OK
* checking Rd files against version 2 parser ... 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
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

snapCGH.Rcheck/00install.out:

* Installing *source* package 'snapCGH' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c optimizer.c -o optimizer.o
optimizer.c: In function 'fr_two':
optimizer.c:26: warning: unused variable 'temp3'
optimizer.c:26: warning: unused variable 'temp2'
optimizer.c:26: warning: unused variable 'denom'
optimizer.c: In function 'fr_three':
optimizer.c:195: warning: unused variable 'temp3'
optimizer.c:195: warning: unused variable 'temp2'
optimizer.c:195: warning: unused variable 'denom'
optimizer.c:194: warning: unused variable 'alphahat'
optimizer.c: In function 'fr_four':
optimizer.c:413: warning: unused variable 'temp3'
optimizer.c:413: warning: unused variable 'temp2'
optimizer.c:413: warning: unused variable 'denom'
optimizer.c:412: warning: unused variable 'alphahat'
optimizer.c: In function 'fr_five':
optimizer.c:687: warning: unused variable 'temp3'
optimizer.c:687: warning: unused variable 'temp2'
optimizer.c:687: warning: unused variable 'denom'
optimizer.c:686: warning: unused variable 'alphahat'
optimizer.c:943: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false
optimizer.c: In function 'fr_four':
optimizer.c:585: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false
gcc -std=gnu99 -shared -L/usr/local/lib64 -o snapCGH.so optimizer.o -L/home/biocbuild/bbs-2.4-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase

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: pixmap

Attaching package: 'DNAcopy'


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

	 segment 

[1] "Have fun with GLAD"
[1] "For smoothing it is possible to use either"
[1] "the AWS algorithm (Polzehl and Spokoiny, 2002)"
[1] "or the HaarSeg algorithm (Ben-Yaacov and Eldar, 2008)"
[1] ""
[1] "If you use the package with AWS, please cite:"
[1] "Hupe et al. (2004) and Polzehl and Spokoiny (2002)"
[1] ""
[1] "If you use the package with HaarSeg, please cite:"
[1] "Hupe et al. (2004) and (Ben-Yaacov and Eldar, 2008)"
Loading required package: survival
Loading required package: splines
Loading required package: multtest

Attaching package: 'aCGH'


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

	 heatmap 

** help
*** installing help indices
 >>> 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
Note: removing empty section \examples in file 'genomePlot.Rd'
  genomePlot                        text    html    latex
Note: removing empty section \examples in file 'heatmapGenome.Rd'
  heatmapGenome                     text    html    latex
  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
Note: removing empty section \examples in file 'plotSegmentedGenome.Rd'
  plotSegmentedGenome               text    html    latex
  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
  runTilingArray                    text    html    latex
Note: removing empty section \examples in file 'sim.structure.Rd'
  sim.structure                     text    html    latex
  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)