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) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:22:40 -0400 (Tue, 09 Apr 2019).
| Package 446/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DNAcopy 1.57.0 Venkatraman E. Seshan
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| 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 00:34:01 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 00:34:37 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 36.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DNAcopy.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DNAcopy.Rcheck’ * using R Under development (unstable) (2018-11-27 r75683) * 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.
DNAcopy.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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’ ... ** libs gfortran -fPIC -g -O2 -c cbsWtstats.f -o cbsWtstats.o gfortran -fPIC -g -O2 -c cbststats.f -o cbststats.o gfortran -fPIC -g -O2 -c changepoints-wtd.f -o changepoints-wtd.o gfortran -fPIC -g -O2 -c changepoints.f -o changepoints.o gfortran -fPIC -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 -g -O2 -c getbdry.f -o getbdry.o gfortran -fPIC -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 -g -O2 -c segmentp.f -o segmentp.o gfortran -fPIC -g -O2 -c smoothCNA.f -o smoothCNA.o gfortran -fPIC -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/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 * DONE (DNAcopy)
DNAcopy.Rcheck/tests/redundancy,20090610,segment.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences" Copyright (C) 2018 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 <[email protected]> > # 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) (2018-11-27 r75683) 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 0.039 0.001 0.040 > 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$output, truth, tolerance=tol)) > > > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Test: Weighted segmentation > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > t <- system.time({ + fitR <- segment(cnR, weights=w, verbose=1) + }) Analyzing: SampleA > cat("Processing time:\n") Processing time: > print(t) user system elapsed 0.026 0.001 0.026 > print(fitR) Call: segment(x = cnR, weights = w, verbose = 1) ID chrom loc.start loc.end num.mark seg.mean 1 SampleA 1 1.368577 199.0840 209 0.0259 2 SampleA 1 201.604291 301.0669 105 1.0004 3 SampleA 1 303.775112 999.3290 686 -0.0233 > > # Expected results > # These were obtained by dput(fitR$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) (2018-11-27 r75683) 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 0.417 0.076 0.462
DNAcopy.Rcheck/DNAcopy-Ex.timings
| name | user | system | elapsed | |
| CNA | 0.019 | 0.003 | 0.022 | |
| exon.segment | 0.062 | 0.001 | 0.063 | |
| plot.DNAcopy | 0.961 | 0.017 | 1.000 | |
| plotSample | 0.759 | 0.008 | 0.777 | |
| segment | 1.575 | 0.014 | 1.606 | |
| segments.p | 0.072 | 0.001 | 0.073 | |
| segments.summary | 0.066 | 0.002 | 0.068 | |
| smooth.CNA | 0.008 | 0.002 | 0.010 | |
| subset.CNA | 0.004 | 0.001 | 0.006 | |
| zoomIntoRegion | 0.719 | 0.003 | 0.730 | |