| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:27 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the DNAcopy package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 549/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DNAcopy 1.73.0 (landing page) Venkatraman E. Seshan
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: DNAcopy |
| Version: 1.73.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DNAcopy.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings DNAcopy_1.73.0.tar.gz |
| StartedAt: 2022-12-28 23:22:48 -0500 (Wed, 28 Dec 2022) |
| EndedAt: 2022-12-28 23:23:22 -0500 (Wed, 28 Dec 2022) |
| EllapsedTime: 33.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DNAcopy.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DNAcopy.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings DNAcopy_1.73.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/DNAcopy.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DNAcopy/DESCRIPTION' ... OK
* this is package 'DNAcopy' version '1.73.0'
* 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
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* 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 ... NOTE
checkRd: (-1) coriell.Rd:13: Escaped LaTeX specials: \_
* 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 x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/DNAcopy/libs/x64/DNAcopy.dll':
Found '_assert', possibly from 'assert' (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 nor [v]sprintf. 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 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: 2 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/DNAcopy.Rcheck/00check.log'
for details.
DNAcopy.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL DNAcopy ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'DNAcopy' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.2.0' using Fortran compiler: 'GNU Fortran (GCC) 12.2.0' gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c cbsWtstats.f -o cbsWtstats.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c cbststats.f -o cbststats.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c changepoints-wtd.f -o changepoints-wtd.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c changepoints.f -o changepoints.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c esegment.f -o esegment.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c flchoose.c -o flchoose.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fphyper.c -o fphyper.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fpnorm.c -o fpnorm.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c getbdry.f -o getbdry.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c prune.f -o prune.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c rshared.c -o rshared.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c segmentp.f -o segmentp.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c smoothCNA.f -o smoothCNA.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c tailprobs.f -o tailprobs.o 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:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -lgfortran -lm -lquadmath -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-DNAcopy/00new/DNAcopy/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DNAcopy)
DNAcopy.Rcheck/tests/redundancy,20090610,segment.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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 Under development (unstable) (2022-12-25 r83502 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server x64 (build 20348)
Matrix products: default
locale:
[1] LC_COLLATE=C
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DNAcopy_1.73.0
loaded via a namespace (and not attached):
[1] compiler_4.3.0
>
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 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
0.06 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$output, truth, tolerance=tol))
>
>
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Test: Weighted segmentation
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> t <- system.time({
+ fitR <- segment(cnR, weights=w, verbose=1)
+ })
Analyzing: SampleA
> cat("Processing time:\n")
Processing time:
> print(t)
user system elapsed
0.05 0.00 0.05
> print(fitR)
Call:
segment(x = cnR, weights = w, verbose = 1)
ID chrom loc.start loc.end num.mark seg.mean
1 SampleA 1 1.368577 199.0840 209 0.0259
2 SampleA 1 201.604291 301.0669 105 1.0004
3 SampleA 1 303.775112 999.3290 686 -0.0233
>
> # Expected results
> # These were obtained by dput(fitR$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 Under development (unstable) (2022-12-25 r83502 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server x64 (build 20348)
Matrix products: default
locale:
[1] LC_COLLATE=C
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DNAcopy_1.73.0
loaded via a namespace (and not attached):
[1] compiler_4.3.0
>
>
> ######################################################################
> # 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
0.31 0.04 0.34
DNAcopy.Rcheck/DNAcopy-Ex.timings
| name | user | system | elapsed | |
| CNA | 0.00 | 0.02 | 0.01 | |
| exon.segment | 0.20 | 0.00 | 0.21 | |
| plot.DNAcopy | 0.58 | 0.00 | 0.58 | |
| plotSample | 0.51 | 0.00 | 0.52 | |
| segment | 1.13 | 0.00 | 1.12 | |
| segments.p | 0.08 | 0.00 | 0.08 | |
| segments.summary | 0.04 | 0.00 | 0.05 | |
| smooth.CNA | 0.02 | 0.00 | 0.01 | |
| subset.CNA | 0 | 0 | 0 | |
| zoomIntoRegion | 0.39 | 0.00 | 0.39 | |