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CHECK report for DNAcopy on celaya2

This page was generated on 2019-04-09 12:48:51 -0400 (Tue, 09 Apr 2019).

Package 446/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DNAcopy 1.57.0
Venkatraman E. Seshan
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/DNAcopy
Branch: master
Last Commit: 8fd6a64
Last Changed Date: 2018-10-30 11:54:26 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: DNAcopy
Version: 1.57.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DNAcopy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DNAcopy_1.57.0.tar.gz
StartedAt: 2019-04-09 01:29:17 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:30:07 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 50.0 seconds
RetCode: 0
Status:  OK 
CheckDir: DNAcopy.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DNAcopy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DNAcopy_1.57.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DNAcopy.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DNAcopy/DESCRIPTION’ ... OK
* this is package ‘DNAcopy’ version ‘1.57.0’
* 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 for sufficient/correct file permissions ... 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
* 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/DNAcopy.Rcheck/00check.log’
for details.

Installation output

DNAcopy.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DNAcopy
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘DNAcopy’ ...
** using staged installation
** libs
gfortran  -fPIC  -Wall -g -O2  -c cbsWtstats.f -o cbsWtstats.o
cbsWtstats.f:283:0:

       iseg(2) = tmaxj
 
Warning: ‘tmaxj’ may be used uninitialized in this function [-Wmaybe-uninitialized]
cbsWtstats.f:282:0:

       iseg(1) = tmaxi
 
Warning: ‘tmaxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran  -fPIC  -Wall -g -O2  -c cbststats.f -o cbststats.o
cbststats.f:258:0:

                      tmaxj = sxmxi + i2j
 
Warning: ‘sxmxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran  -fPIC  -Wall -g -O2  -c changepoints-wtd.f -o changepoints-wtd.o
gfortran  -fPIC  -Wall -g -O2  -c changepoints.f -o changepoints.o
gfortran  -fPIC  -Wall -g -O2  -c esegment.f -o esegment.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c flchoose.c -o flchoose.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c fphyper.c -o fphyper.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c fpnorm.c -o fpnorm.o
gfortran  -fPIC  -Wall -g -O2  -c getbdry.f -o getbdry.o
gfortran  -fPIC  -Wall -g -O2  -c prune.f -o prune.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c rshared.c -o rshared.o
gfortran  -fPIC  -Wall -g -O2  -c segmentp.f -o segmentp.o
gfortran  -fPIC  -Wall -g -O2  -c smoothCNA.f -o smoothCNA.o
gfortran  -fPIC  -Wall -g -O2  -c tailprobs.f -o tailprobs.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o DNAcopy.so 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 -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-DNAcopy/00new/DNAcopy/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DNAcopy)

Tests output

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


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 Under development (unstable) (2019-03-18 r76245)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] DNAcopy_1.57.0

loaded via a namespace (and not attached):
[1] compiler_3.6.0
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 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 
  0.049   0.004   0.165 
> 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 
  0.030   0.002   0.055 
> 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 Under development (unstable) (2019-03-18 r76245)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] DNAcopy_1.57.0

loaded via a namespace (and not attached):
[1] compiler_3.6.0
> 
> 
> ######################################################################
> # 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 
  0.616   0.184   1.126

Example timings

DNAcopy.Rcheck/DNAcopy-Ex.timings

nameusersystemelapsed
CNA0.0300.0050.034
exon.segment0.0950.0020.096
plot.DNAcopy1.0920.0392.072
plotSample0.8940.0161.458
segment1.8210.0302.563
segments.p0.1070.0040.112
segments.summary0.0640.0050.069
smooth.CNA0.0110.0050.016
subset.CNA0.0080.0030.011
zoomIntoRegion0.6820.0170.700