Venkatraman E. Seshan
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/DNAcopy |
| Branch: RELEASE_3_7 |
| Last Commit: fe26579 |
| Last Changed Date: 2018-04-30 10:35:00 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:32:10 -0400 (Wed, 17 Oct 2018).
| Package 402/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DNAcopy 1.54.0 Venkatraman E. Seshan
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DNAcopy |
| Version: 1.54.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DNAcopy.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings DNAcopy_1.54.0.tar.gz |
| StartedAt: 2018-10-17 01:39:05 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 01:39:47 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 41.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DNAcopy.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DNAcopy.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings DNAcopy_1.54.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/DNAcopy.Rcheck' * using R version 3.5.1 Patched (2018-07-24 r75005) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'DNAcopy/DESCRIPTION' ... OK * this is package 'DNAcopy' version '1.54.0' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'DNAcopy' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over 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 * loading checks for arch 'i386' ** 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 namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * loading checks for arch 'x64' ** 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 namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * checking 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 ... OK * 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 compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/DNAcopy/libs/i386/DNAcopy.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'redundancy,20090610,segment.R' OK ** running tests for arch 'x64' ... Running 'redundancy,20090610,segment.R' 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 vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/DNAcopy.Rcheck/00check.log' for details.
DNAcopy.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/DNAcopy_1.54.0.tar.gz && rm -rf DNAcopy.buildbin-libdir && mkdir DNAcopy.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DNAcopy.buildbin-libdir DNAcopy_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL DNAcopy_1.54.0.zip && rm DNAcopy_1.54.0.tar.gz DNAcopy_1.54.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 114k 100 114k 0 0 1941k 0 --:--:-- --:--:-- --:--:-- 2169k
install for i386
* installing *source* package 'DNAcopy' ...
** libs
C:/Rtools/mingw_32/bin/gfortran -O3 -mtune=generic -c cbsWtstats.f -o cbsWtstats.o
C:/Rtools/mingw_32/bin/gfortran -O3 -mtune=generic -c cbststats.f -o cbststats.o
C:/Rtools/mingw_32/bin/gfortran -O3 -mtune=generic -c changepoints-wtd.f -o changepoints-wtd.o
C:/Rtools/mingw_32/bin/gfortran -O3 -mtune=generic -c changepoints.f -o changepoints.o
C:/Rtools/mingw_32/bin/gfortran -O3 -mtune=generic -c esegment.f -o esegment.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c flchoose.c -o flchoose.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c fphyper.c -o fphyper.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c fpnorm.c -o fpnorm.o
C:/Rtools/mingw_32/bin/gfortran -O3 -mtune=generic -c getbdry.f -o getbdry.o
C:/Rtools/mingw_32/bin/gfortran -O3 -mtune=generic -c prune.f -o prune.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c rshared.c -o rshared.o
C:/Rtools/mingw_32/bin/gfortran -O3 -mtune=generic -c segmentp.f -o segmentp.o
C:/Rtools/mingw_32/bin/gfortran -O3 -mtune=generic -c smoothCNA.f -o smoothCNA.o
C:/Rtools/mingw_32/bin/gfortran -O3 -mtune=generic -c tailprobs.f -o tailprobs.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o DNAcopy.dll tmp.def cbsWtstats.o cbststats.o changepoints-wtd.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o prune.o rshared.o segmentp.o smoothCNA.o tailprobs.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/DNAcopy.buildbin-libdir/DNAcopy/libs/i386
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DNAcopy'
finding HTML links ... done
CNA html
DNAcopy-internal html
DNAcopy html
coriell html
cytoBand html
exon.segment html
getbdry html
glFrequency html
plot.DNAcopy html
plotSample html
segment html
segments.p html
segments.summary html
smooth.CNA html
subset.CNA html
subset.DNAcopy html
zoomIntoRegion html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'DNAcopy' ...
** libs
C:/Rtools/mingw_64/bin/gfortran -O2 -mtune=generic -c cbsWtstats.f -o cbsWtstats.o
C:/Rtools/mingw_64/bin/gfortran -O2 -mtune=generic -c cbststats.f -o cbststats.o
C:/Rtools/mingw_64/bin/gfortran -O2 -mtune=generic -c changepoints-wtd.f -o changepoints-wtd.o
C:/Rtools/mingw_64/bin/gfortran -O2 -mtune=generic -c changepoints.f -o changepoints.o
C:/Rtools/mingw_64/bin/gfortran -O2 -mtune=generic -c esegment.f -o esegment.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c flchoose.c -o flchoose.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c fphyper.c -o fphyper.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c fpnorm.c -o fpnorm.o
C:/Rtools/mingw_64/bin/gfortran -O2 -mtune=generic -c getbdry.f -o getbdry.o
C:/Rtools/mingw_64/bin/gfortran -O2 -mtune=generic -c prune.f -o prune.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c rshared.c -o rshared.o
C:/Rtools/mingw_64/bin/gfortran -O2 -mtune=generic -c segmentp.f -o segmentp.o
C:/Rtools/mingw_64/bin/gfortran -O2 -mtune=generic -c smoothCNA.f -o smoothCNA.o
C:/Rtools/mingw_64/bin/gfortran -O2 -mtune=generic -c tailprobs.f -o tailprobs.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o DNAcopy.dll tmp.def cbsWtstats.o cbststats.o changepoints-wtd.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o prune.o rshared.o segmentp.o smoothCNA.o tailprobs.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/DNAcopy.buildbin-libdir/DNAcopy/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DNAcopy' as DNAcopy_1.54.0.zip
* DONE (DNAcopy)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'DNAcopy' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
DNAcopy.Rcheck/tests_i386/redundancy,20090610,segment.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> ######################################################################
> # Type: Redundancy test
> # Created by: Henrik Bengtsson <hb@stat.berkeley.edu>
> # Created on: 2009-06-10
> ######################################################################
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Startup
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> library("DNAcopy")
>
> # Record current random seed
> sample(1) # Assert that a random seed exists
[1] 1
> oldSeed <- .Random.seed
> # Alway use the same random seed
> set.seed(0xbeef)
>
> # Tolerance (maybe decrease?)
> tol <- .Machine$double.eps^0.5
>
> print(sessionInfo())
R version 3.5.1 Patched (2018-07-24 r75005)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows Server 2012 R2 x64 (build 9600)
Matrix products: default
locale:
[1] LC_COLLATE=C
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DNAcopy_1.54.0
loaded via a namespace (and not attached):
[1] compiler_3.5.1
>
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Simulating copy-number data
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Number of loci
> J <- 1000
>
> x <- sort(runif(J, min=0, max=1000))
> w <- runif(J)
> mu <- double(J)
> jj <- (200 <= x & x < 300)
> mu[jj] <- mu[jj] + 1
> jj <- (650 <= x & x < 800)
> mu[jj] <- mu[jj] - 1
> w[jj] <- 0.001
> eps <- rnorm(J, sd=1/2)
> y <- mu + eps
>
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Setting up a raw CNA object
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> cnR <- CNA(
+ genomdat = y,
+ chrom = rep(1, times=J),
+ maploc = x,
+ data.type = "logratio",
+ sampleid = "SampleA"
+ )
> print(cnR)
Number of Samples 1
Number of Probes 1000
Data Type logratio
>
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Test: Non-weighted segmentation
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> t <- system.time({
+ fitR <- segment(cnR, verbose=1)
+ })
Analyzing: SampleA
> cat("Processing time:\n")
Processing time:
> print(t)
user system elapsed
0.08 0.00 0.08
> print(fitR)
Call:
segment(x = cnR, verbose = 1)
ID chrom loc.start loc.end num.mark seg.mean
1 SampleA 1 1.368577 199.0840 209 0.0256
2 SampleA 1 201.604291 301.0669 105 1.0099
3 SampleA 1 303.775112 647.4270 337 -0.0084
4 SampleA 1 650.741212 798.9718 138 -0.9792
5 SampleA 1 800.302447 999.3290 211 -0.0289
>
> # Expected results
> # These were obtained by dput(fitR$output) using DNAcopy v1.19.0
> truth <- structure(list(ID = c("SampleA", "SampleA", "SampleA", "SampleA",
+ "SampleA"), chrom = c(1, 1, 1, 1, 1), loc.start = c(1.36857712641358,
+ 201.604291098192, 303.775111911818, 650.741211604327, 800.302447052673
+ ), loc.end = c(199.083976913244, 301.066882908344, 647.42697100155,
+ 798.971758922562, 999.329038895667), num.mark = c(209, 105, 337,
+ 138, 211), seg.mean = c(0.0256, 1.0099, -0.0084, -0.9792, -0.0289
+ )), .Names = c("ID", "chrom", "loc.start", "loc.end", "num.mark",
+ "seg.mean"), row.names = c(NA, -5L), class = "data.frame")
>
> stopifnot(all.equal(fitR$output, truth, tolerance=tol))
>
>
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Test: Weighted segmentation
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> t <- system.time({
+ fitR <- segment(cnR, weights=w, verbose=1)
+ })
Analyzing: SampleA
> cat("Processing time:\n")
Processing time:
> print(t)
user system elapsed
0.06 0.00 0.06
> print(fitR)
Call:
segment(x = cnR, weights = w, verbose = 1)
ID chrom loc.start loc.end num.mark seg.mean
1 SampleA 1 1.368577 199.0840 209 0.0259
2 SampleA 1 201.604291 301.0669 105 1.0004
3 SampleA 1 303.775112 999.3290 686 -0.0233
>
> # Expected results
> # These were obtained by dput(fitR$output) using DNAcopy v1.19.0
> truth <- structure(list(ID = c("SampleA", "SampleA", "SampleA"), chrom = c(1,
+ 1, 1), loc.start = c(1.36857712641358, 201.604291098192, 303.775111911818
+ ), loc.end = c(199.083976913244, 301.066882908344, 999.329038895667
+ ), num.mark = c(209, 105, 686), seg.mean = c(0.0259, 1.0004,
+ -0.0233)), .Names = c("ID", "chrom", "loc.start", "loc.end",
+ "num.mark", "seg.mean"), row.names = c(NA, -3L), class = "data.frame")
>
> stopifnot(all.equal(fitR$output, truth, tolerance=tol))
>
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Cleanup
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Reset to previous random seed
> .Random.seed <- oldSeed
>
> print(sessionInfo())
R version 3.5.1 Patched (2018-07-24 r75005)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows Server 2012 R2 x64 (build 9600)
Matrix products: default
locale:
[1] LC_COLLATE=C
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DNAcopy_1.54.0
loaded via a namespace (and not attached):
[1] compiler_3.5.1
>
>
> ######################################################################
> # HISTORY
> # 2009-06-10
> # o ROBUSTNESS: Added this test to assert that DNAcopy v1.19.2 and
> # newer will numerically give the same results as DNAcopy v1.19.0.
> # This test is ran each time with R CMD check.
> # o Created.
> ######################################################################
>
> proc.time()
user system elapsed
0.48 0.04 0.51
|
DNAcopy.Rcheck/tests_x64/redundancy,20090610,segment.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> ######################################################################
> # Type: Redundancy test
> # Created by: Henrik Bengtsson <hb@stat.berkeley.edu>
> # Created on: 2009-06-10
> ######################################################################
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Startup
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> library("DNAcopy")
>
> # Record current random seed
> sample(1) # Assert that a random seed exists
[1] 1
> oldSeed <- .Random.seed
> # Alway use the same random seed
> set.seed(0xbeef)
>
> # Tolerance (maybe decrease?)
> tol <- .Machine$double.eps^0.5
>
> print(sessionInfo())
R version 3.5.1 Patched (2018-07-24 r75005)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2012 R2 x64 (build 9600)
Matrix products: default
locale:
[1] LC_COLLATE=C
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DNAcopy_1.54.0
loaded via a namespace (and not attached):
[1] compiler_3.5.1
>
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Simulating copy-number data
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Number of loci
> J <- 1000
>
> x <- sort(runif(J, min=0, max=1000))
> w <- runif(J)
> mu <- double(J)
> jj <- (200 <= x & x < 300)
> mu[jj] <- mu[jj] + 1
> jj <- (650 <= x & x < 800)
> mu[jj] <- mu[jj] - 1
> w[jj] <- 0.001
> eps <- rnorm(J, sd=1/2)
> y <- mu + eps
>
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Setting up a raw CNA object
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> cnR <- CNA(
+ genomdat = y,
+ chrom = rep(1, times=J),
+ maploc = x,
+ data.type = "logratio",
+ sampleid = "SampleA"
+ )
> print(cnR)
Number of Samples 1
Number of Probes 1000
Data Type logratio
>
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Test: Non-weighted segmentation
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> t <- system.time({
+ fitR <- segment(cnR, verbose=1)
+ })
Analyzing: SampleA
> cat("Processing time:\n")
Processing time:
> print(t)
user system elapsed
0.08 0.00 0.08
> print(fitR)
Call:
segment(x = cnR, verbose = 1)
ID chrom loc.start loc.end num.mark seg.mean
1 SampleA 1 1.368577 199.0840 209 0.0256
2 SampleA 1 201.604291 301.0669 105 1.0099
3 SampleA 1 303.775112 647.4270 337 -0.0084
4 SampleA 1 650.741212 798.9718 138 -0.9792
5 SampleA 1 800.302447 999.3290 211 -0.0289
>
> # Expected results
> # These were obtained by dput(fitR$output) using DNAcopy v1.19.0
> truth <- structure(list(ID = c("SampleA", "SampleA", "SampleA", "SampleA",
+ "SampleA"), chrom = c(1, 1, 1, 1, 1), loc.start = c(1.36857712641358,
+ 201.604291098192, 303.775111911818, 650.741211604327, 800.302447052673
+ ), loc.end = c(199.083976913244, 301.066882908344, 647.42697100155,
+ 798.971758922562, 999.329038895667), num.mark = c(209, 105, 337,
+ 138, 211), seg.mean = c(0.0256, 1.0099, -0.0084, -0.9792, -0.0289
+ )), .Names = c("ID", "chrom", "loc.start", "loc.end", "num.mark",
+ "seg.mean"), row.names = c(NA, -5L), class = "data.frame")
>
> stopifnot(all.equal(fitR$output, truth, tolerance=tol))
>
>
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Test: Weighted segmentation
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> t <- system.time({
+ fitR <- segment(cnR, weights=w, verbose=1)
+ })
Analyzing: SampleA
> cat("Processing time:\n")
Processing time:
> print(t)
user system elapsed
0.04 0.00 0.05
> print(fitR)
Call:
segment(x = cnR, weights = w, verbose = 1)
ID chrom loc.start loc.end num.mark seg.mean
1 SampleA 1 1.368577 199.0840 209 0.0259
2 SampleA 1 201.604291 301.0669 105 1.0004
3 SampleA 1 303.775112 999.3290 686 -0.0233
>
> # Expected results
> # These were obtained by dput(fitR$output) using DNAcopy v1.19.0
> truth <- structure(list(ID = c("SampleA", "SampleA", "SampleA"), chrom = c(1,
+ 1, 1), loc.start = c(1.36857712641358, 201.604291098192, 303.775111911818
+ ), loc.end = c(199.083976913244, 301.066882908344, 999.329038895667
+ ), num.mark = c(209, 105, 686), seg.mean = c(0.0259, 1.0004,
+ -0.0233)), .Names = c("ID", "chrom", "loc.start", "loc.end",
+ "num.mark", "seg.mean"), row.names = c(NA, -3L), class = "data.frame")
>
> stopifnot(all.equal(fitR$output, truth, tolerance=tol))
>
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Cleanup
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Reset to previous random seed
> .Random.seed <- oldSeed
>
> print(sessionInfo())
R version 3.5.1 Patched (2018-07-24 r75005)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2012 R2 x64 (build 9600)
Matrix products: default
locale:
[1] LC_COLLATE=C
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DNAcopy_1.54.0
loaded via a namespace (and not attached):
[1] compiler_3.5.1
>
>
> ######################################################################
> # HISTORY
> # 2009-06-10
> # o ROBUSTNESS: Added this test to assert that DNAcopy v1.19.2 and
> # newer will numerically give the same results as DNAcopy v1.19.0.
> # This test is ran each time with R CMD check.
> # o Created.
> ######################################################################
>
> proc.time()
user system elapsed
0.46 0.03 0.48
|
|
DNAcopy.Rcheck/examples_i386/DNAcopy-Ex.timings
|
DNAcopy.Rcheck/examples_x64/DNAcopy-Ex.timings
|