snapCGH 1.10.0
Thomas Hardcastle
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/snapCGH | | Last Changed Rev: 34811 / Revision: 38965 | | Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008) |
| wilson2 | 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 (10.5.6) / i386 | [ OK ] | OK | OK |
* checking for file 'snapCGH/DESCRIPTION' ... OK
* preparing 'snapCGH':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'snapCGH' ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -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'
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
** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -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'
gcc-4.2 -arch ppc -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
** arch - ppc64
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -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'
gcc-4.2 -arch ppc64 -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 -L/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64 -lR -dylib_file libRblas.dylib:/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64/libRblas.dylib -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -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'
gcc-4.2 -arch x86_64 -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
** 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: 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 :
as.Date.numeric
Loading required package: sandwich
Loading required package: vsn
Loading required package: lattice
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: xtable
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Attaching package: 'geneplotter'
The following object(s) are masked from package:lattice :
panel.smoothScatter
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
[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
>>> Building/Updating help pages for package 'snapCGH'
Formats: text html latex example
IDProbes text html latex
LargeDataObject text html latex example
Note: unmatched right brace in file 'SegList.Rd' on or after line 31
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
Note: unmatched right brace in file 'find.param.one.Rd' on or after line 18
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
Note: unmatched right brace in file 'non.zero.length.distr.non.tiled.Rd' on or after line 9
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
Note: unmatched right brace in file 'processCGH.Rd' on or after line 44
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)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'snapCGH_1.10.0.tar.gz'