Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:03 -0400 (Fri, 15 Oct 2021).

CHECK results for DNAcopy on tokay2

To the developers/maintainers of the DNAcopy package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DNAcopy.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 523/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DNAcopy 1.66.0  (landing page)
Venkatraman E. Seshan
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/DNAcopy
git_branch: RELEASE_3_13
git_last_commit: d6ba71e
git_last_commit_date: 2021-05-19 11:34:26 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DNAcopy
Version: 1.66.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DNAcopy.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DNAcopy_1.66.0.tar.gz
StartedAt: 2021-10-14 22:27:38 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 22:28:22 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 44.3 seconds
RetCode: 0
Status:   OK  
CheckDir: DNAcopy.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DNAcopy.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DNAcopy_1.66.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/DNAcopy.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.66.0'
* 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 LazyData ... 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-3.13-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)
  Found 'rand', possibly from 'rand' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/DNAcopy/libs/x64/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 'rand', possibly from 'rand' (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-3.13-bioc/meat/DNAcopy.Rcheck/00check.log'
for details.

Installation output

DNAcopy.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/DNAcopy_1.66.0.tar.gz && rm -rf DNAcopy.buildbin-libdir && mkdir DNAcopy.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DNAcopy.buildbin-libdir DNAcopy_1.66.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL DNAcopy_1.66.0.zip && rm DNAcopy_1.66.0.tar.gz DNAcopy_1.66.0.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  111k  100  111k    0     0   367k      0 --:--:-- --:--:-- --:--:--  368k

install for i386

* installing *source* package 'DNAcopy' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c cbsWtstats.f -o cbsWtstats.o
"C:/rtools40/mingw32/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c cbststats.f -o cbststats.o
"C:/rtools40/mingw32/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c changepoints-wtd.f -o changepoints-wtd.o
"C:/rtools40/mingw32/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c changepoints.f -o changepoints.o
"C:/rtools40/mingw32/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c esegment.f -o esegment.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c flchoose.c -o flchoose.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fphyper.c -o fphyper.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fpnorm.c -o fpnorm.o
"C:/rtools40/mingw32/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c getbdry.f -o getbdry.o
"C:/rtools40/mingw32/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c prune.f -o prune.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rshared.c -o rshared.o
"C:/rtools40/mingw32/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c segmentp.f -o segmentp.o
"C:/rtools40/mingw32/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c smoothCNA.f -o smoothCNA.o
"C:/rtools40/mingw32/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c tailprobs.f -o tailprobs.o
C:/rtools40/mingw32/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-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/DNAcopy.buildbin-libdir/00LOCK-DNAcopy/00new/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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'DNAcopy' ...
** libs
"C:/rtools40/mingw64/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c cbsWtstats.f -o cbsWtstats.o
"C:/rtools40/mingw64/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c cbststats.f -o cbststats.o
"C:/rtools40/mingw64/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c changepoints-wtd.f -o changepoints-wtd.o
"C:/rtools40/mingw64/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c changepoints.f -o changepoints.o
"C:/rtools40/mingw64/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c esegment.f -o esegment.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c flchoose.c -o flchoose.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fphyper.c -o fphyper.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fpnorm.c -o fpnorm.o
"C:/rtools40/mingw64/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c getbdry.f -o getbdry.o
"C:/rtools40/mingw64/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c prune.f -o prune.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rshared.c -o rshared.o
"C:/rtools40/mingw64/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c segmentp.f -o segmentp.o
"C:/rtools40/mingw64/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c smoothCNA.f -o smoothCNA.o
"C:/rtools40/mingw64/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign  -c tailprobs.f -o tailprobs.o
C:/rtools40/mingw64/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-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/DNAcopy.buildbin-libdir/DNAcopy/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DNAcopy' as DNAcopy_1.66.0.zip
* DONE (DNAcopy)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'DNAcopy' successfully unpacked and MD5 sums checked

Tests output

DNAcopy.Rcheck/tests_i386/redundancy,20090610,segment.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 4.1.1 (2021-08-10)
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_1.66.0

loaded via a namespace (and not attached):
[1] compiler_4.1.1
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 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 
   0.14    0.00    0.14 
> 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 
   0.08    0.00    0.08 
> 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 4.1.1 (2021-08-10)
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_1.66.0

loaded via a namespace (and not attached):
[1] compiler_4.1.1
> 
> 
> ######################################################################
> # 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 
   0.54    0.10    0.62

DNAcopy.Rcheck/tests_x64/redundancy,20090610,segment.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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> ######################################################################
> # 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 4.1.1 (2021-08-10)
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_1.66.0

loaded via a namespace (and not attached):
[1] compiler_4.1.1
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 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 4.1.1 (2021-08-10)
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_1.66.0

loaded via a namespace (and not attached):
[1] compiler_4.1.1
> 
> 
> ######################################################################
> # 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 
   0.37    0.04    0.40

Example timings

DNAcopy.Rcheck/examples_i386/DNAcopy-Ex.timings

nameusersystemelapsed
CNA0.040.000.03
exon.segment0.310.000.31
plot.DNAcopy0.850.020.86
plotSample0.590.000.60
segment1.220.001.22
segments.p0.080.000.07
segments.summary0.060.000.07
smooth.CNA0.020.000.01
subset.CNA000
zoomIntoRegion0.790.000.80

DNAcopy.Rcheck/examples_x64/DNAcopy-Ex.timings

nameusersystemelapsed
CNA0.020.010.03
exon.segment0.230.000.23
plot.DNAcopy0.680.000.69
plotSample0.440.030.47
segment0.920.040.95
segments.p0.080.000.08
segments.summary0.050.000.04
smooth.CNA000
subset.CNA0.010.000.02
zoomIntoRegion0.750.000.75