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Package 427/472HostnameOS / ArchBUILDCHECKBUILD BIN
snapCGH 1.23.0
John Marioni
Snapshot Date: 2011-06-21 19:21:48 -0700 (Tue, 21 Jun 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/snapCGH
Last Changed Rev: 54810 / Revision: 56351
Last Changed Date: 2011-04-13 18:14:51 -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 
moscato1 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: snapCGH
Version: 1.23.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch snapCGH_1.23.0.tar.gz
StartedAt: 2011-06-22 05:27:46 -0700 (Wed, 22 Jun 2011)
EndedAt: 2011-06-22 05:30:06 -0700 (Wed, 22 Jun 2011)
EllapsedTime: 140.3 seconds
RetCode: 0
Status:  OK 
CheckDir: snapCGH.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/snapCGH.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘snapCGH/DESCRIPTION’ ... OK
* this is package ‘snapCGH’ version ‘1.23.0’
* 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 installed package size ... 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 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
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’
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 ... NOTE
prepare_Rd: genomePlot.Rd:51-57: Dropping empty section \examples
prepare_Rd: heatmapGenome.Rd:76-77: Dropping empty section \examples
prepare_Rd: plotSegmentedGenome.Rd:52-58: Dropping empty section \examples
prepare_Rd: sim.structure.Rd:57-58: Dropping empty section \examples
* 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 sizes of PDF files under ‘inst/doc’ ... 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

snapCGH.Rcheck/00install.out:

* installing *source* package ‘snapCGH’ ...
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -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’
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o snapCGH.so optimizer.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/snapCGH.Rcheck/snapCGH/libs/i386
** R
** data
** inst
** preparing package for lazy loading

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



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



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.


** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘snapCGHguide.Rnw’ 
** testing if installed package can be loaded

* DONE (snapCGH)

snapCGH.Rcheck/snapCGH-Ex.timings:

nameusersystemelapsed
LargeDataObject0.0000.0010.000
convert.output0.0080.0000.008
dim0.0060.0000.007