Multiple platform build/check report for BioC 3.6 - CHECK report for DNAcopy on tokay1

Package: DNAcopy

Version: 1.52.0

Command: rm -rf DNAcopy.buildbin-libdir DNAcopy.Rcheck && mkdir DNAcopy.buildbin-libdir DNAcopy.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DNAcopy.buildbin-libdir DNAcopy_1.52.0.tar.gz >DNAcopy.Rcheck\00install.out 2>&1 && cp DNAcopy.Rcheck\00install.out DNAcopy-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DNAcopy.buildbin-libdir --install="check:DNAcopy-install.out" --force-multiarch --no-vignettes --timings DNAcopy_1.52.0.tar.gz

StartedAt: 2018-04-11 23:34:44 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:35:32 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 47.9 seconds

RetCode: 0

Status: OK

CheckDir: DNAcopy.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DNAcopy.buildbin-libdir DNAcopy.Rcheck && mkdir DNAcopy.buildbin-libdir DNAcopy.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DNAcopy.buildbin-libdir DNAcopy_1.52.0.tar.gz >DNAcopy.Rcheck\00install.out 2>&1 && cp DNAcopy.Rcheck\00install.out DNAcopy-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DNAcopy.buildbin-libdir --install="check:DNAcopy-install.out" --force-multiarch --no-vignettes --timings DNAcopy_1.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/DNAcopy.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.52.0'
* 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-3.6-bioc/meat/DNAcopy.buildbin-libdir/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 installed files from 'inst/doc' ... OK
* 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-3.6-bioc/meat/DNAcopy.Rcheck/00check.log'
for details.


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˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/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/g++ -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:/local323/lib/i386 -LC:/local323/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/DNAcopy.buildbin-libdir/DNAcopy/libs/i386
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing 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˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/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/g++ -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:/local323/lib/x64 -LC:/local323/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/DNAcopy.buildbin-libdir/DNAcopy/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DNAcopy' as DNAcopy_1.52.0.zip
* DONE (DNAcopy)
In R CMD INSTALL
In R CMD INSTALL


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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 3.4.4 (2018-03-15)
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_1.52.0

loaded via a namespace (and not attached):
[1] compiler_3.4.4
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 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 
   0.22    0.00    0.22 
> 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 3.4.4 (2018-03-15)
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_1.52.0

loaded via a namespace (and not attached):
[1] compiler_3.4.4
> 
> 
> ######################################################################
> # 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 
   0.51    0.03    0.53


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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 3.4.4 (2018-03-15)
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_1.52.0

loaded via a namespace (and not attached):
[1] compiler_3.4.4
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 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 
   0.07    0.00    0.06 
> 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 
   0.25    0.00    0.25 
> 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 3.4.4 (2018-03-15)
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_1.52.0

loaded via a namespace (and not attached):
[1] compiler_3.4.4
> 
> 
> ######################################################################
> # 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 
   0.56    0.03    0.59

name	user	system	elapsed
CNA	0.06	0.00	0.06
exon.segment	0.22	0.01	0.23
plot.DNAcopy	1.32	0.02	1.34
plotSample	0.96	0.01	0.97
segment	1.76	0.00	1.77
segments.p	0.13	0.00	0.12
segments.summary	0.09	0.00	0.09
smooth.CNA	0.05	0.00	0.05
subset.CNA	0	0	0
zoomIntoRegion	0.76	0.02	0.78

name	user	system	elapsed
CNA	0.06	0.00	0.06
exon.segment	0.19	0.01	0.20
plot.DNAcopy	1.12	0.03	1.16
plotSample	0.75	0.00	0.75
segment	1.16	0.01	1.17
segments.p	0.06	0.00	0.06
segments.summary	0.06	0.00	0.06
smooth.CNA	0.02	0.00	0.02
subset.CNA	0	0	0
zoomIntoRegion	0.59	0.03	0.62

CHECK report for DNAcopy on tokay1

Summary

Command output

Installation output

Tests output

Example timings