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Package 10/462HostnameOS / ArchBUILDCHECKBUILD BIN
ADaCGH2 1.3.0
Ramon Diaz-Uriarte
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ADaCGH2
Last Changed Rev: 54802 / Revision: 55359
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: ADaCGH2
Version: 1.3.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings ADaCGH2_1.3.0.tar.gz
StartedAt: 2011-05-09 12:04:41 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 12:07:11 -0700 (Mon, 09 May 2011)
EllapsedTime: 149.4 seconds
RetCode: 0
Status:  OK  
CheckDir: ADaCGH2.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/ADaCGH2.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ADaCGH2/DESCRIPTION' ... OK
* this is package 'ADaCGH2' version '1.3.0'
* checking package name space information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'Rmpi' 'multicore'
* checking if this is a source package ... OK
* checking whether package 'ADaCGH2' can be installed ... OK
* checking installed package size ... OK
* 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
* 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 whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
mpi.clean.quit.Web: no visible global function definition for
  'mpi.comm.size'
mpi.clean.quit.Web: no visible global function definition for
  'mpi.close.Rslaves'
mpi.clean.quit.Web: no visible global function definition for
  'mpi.exit'
snowfallInit: no visible global function definition for
  'mpi.universe.size'
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

ADaCGH2.Rcheck/00install.out:

* installing *source* package 'ADaCGH2' ...
** libs
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c r_haarseg.c -o r_haarseg.o
r_haarseg.c: In function 'ad_HaarConv':
r_haarseg.c:65:12: warning: unused variable 'totalNorm'
r_haarseg.c: In function 'ad_FindLocalPeaks':
r_haarseg.c:152:8: warning: "/*" within comment
r_haarseg.c:176:8: warning: "/*" within comment
r_haarseg.c:128:9: warning: unused variable 'j'
r_haarseg.c: In function 'ad_HaarConv':
r_haarseg.c:59:12: warning: 'lowWeightSum' may be used uninitialized in this function
r_haarseg.c:60:12: warning: 'highWeightSum' may be used uninitialized in this function
r_haarseg.c:63:12: warning: 'lowNonNormed' may be used uninitialized in this function
r_haarseg.c:64:12: warning: 'highNonNormed' may be used uninitialized in this function
gcc -shared -s -static-libgcc -o ADaCGH2.dll tmp.def r_haarseg.o -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/ADaCGH2.Rcheck/ADaCGH2/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

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

Loading required package: pixmap
Loading required package: cluster
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

Loading required package: limma
Loading required package: DNAcopy

**************************************************************************
   The plan to change the data format for CNA object has been postponed   
 in order to ensure backward compatibility with older versions of DNAcopy 
**************************************************************************


Attaching package: 'DNAcopy'

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

    segment



######################################################################################



Have fun with GLAD



For smoothing it is possible to use either

the AWS algorithm (Polzehl and Spokoiny, 2002)

or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics,  2008)



If you use the package with AWS, please cite:

Hupe et al. (Bioinformatics, 2004) and Polzehl and Spokoiny (2002)



If you use the package with HaarSeg, please cite:

Hupe et al. (Bioinformatics, 2004) and (Ben-Yaacov and Eldar, Bioinformatics, 2008)



For fast computation it is recommanded to use

the daglad function with smoothfunc=haarseg



######################################################################################



New options are available in daglad: see help for details.



Attaching package: 'snapCGH'

The following object(s) are masked from 'package:aCGH':

    prop.na

Loading required package: snow

Attaching package: 'snow'

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

    enquote

Loading required package: tools
Loading required package: bit
Loading package bit1.1-7

package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2)

creators: bit bitwhich

coercion: as.logical as.integer as.bit as.bitwhich which

operator: ! & | xor != == 

querying: print length any all min max range sum summary

bit access: length<- [ [<- [[ [[<-

for more help type ?bit


Attaching package: 'bit'

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

    xor

Loading package ff2.2-2
- getOption("fftempdir")=="E:/biocbld/bbs-2.9-bioc/tmpdir/RtmpBajZie"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16095641.6 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==804782080 -- consider a different value for tuning your system

Attaching package ff

Attaching package: 'ff'

The following object(s) are masked from 'package:utils':

    write.csv, write.csv2

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

    is.factor, is.ordered

Setting adacgh_changepoints to DNAcopy:::changepoints
Setting adacgh_trimmed.variance to DNAcopy:::trimmed.variance
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'ADaCGH2.Rnw' using 'latin1' 
** testing if installed package can be loaded

* DONE (ADaCGH2)

ADaCGH2.Rcheck/ADaCGH2-Ex.timings:

nameusersystemelapsed
inputDataToADaCGHData0.540.005.80
outputToCGHregions 1.13 0.0112.82
pChromPlot 0.51 0.0210.07
pSegment 1.02 0.0615.51
snowfallInit0.050.007.24