Venkatraman E. Seshan
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/DNAcopy |
| git_branch: devel |
| git_last_commit: 16d9fe4 |
| git_last_commit_date: 2023-10-24 09:33:33 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:36:24 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 | ||||
| Package 593/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DNAcopy 1.77.0 (landing page) Venkatraman E. Seshan
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the DNAcopy package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: DNAcopy |
| Version: 1.77.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:DNAcopy.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings DNAcopy_1.77.0.tar.gz |
| StartedAt: 2024-03-27 22:05:06 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 22:05:31 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 25.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DNAcopy.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:DNAcopy.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings DNAcopy_1.77.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/DNAcopy.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘DNAcopy/DESCRIPTION’ ... OK
* this is package ‘DNAcopy’ version ‘1.77.0’
* 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
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* used Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 is not available
* checking usage of KIND in Fortran files ... 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.19-bioc/meat/DNAcopy.Rcheck/00check.log’
for details.
DNAcopy.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL DNAcopy
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘DNAcopy’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gfortran -fpic -g -O2 -Wall -c cbsWtstats.f -o cbsWtstats.o
cbsWtstats.f:283:72:
283 | iseg(2) = tmaxj
| ^
Warning: ‘tmaxj’ may be used uninitialized in this function [-Wmaybe-uninitialized]
cbsWtstats.f:282:72:
282 | iseg(1) = tmaxi
| ^
Warning: ‘tmaxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran -fpic -g -O2 -Wall -c cbststats.f -o cbststats.o
cbststats.f:258:72:
258 | tmaxj = sxmxi + i2j
| ^
Warning: ‘sxmxi’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran -fpic -g -O2 -Wall -c changepoints-wtd.f -o changepoints-wtd.o
gfortran -fpic -g -O2 -Wall -c changepoints.f -o changepoints.o
gfortran -fpic -g -O2 -Wall -c esegment.f -o esegment.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c flchoose.c -o flchoose.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fphyper.c -o fphyper.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fpnorm.c -o fpnorm.o
gfortran -fpic -g -O2 -Wall -c getbdry.f -o getbdry.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gfortran -fpic -g -O2 -Wall -c prune.f -o prune.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rshared.c -o rshared.o
gfortran -fpic -g -O2 -Wall -c segmentp.f -o segmentp.o
gfortran -fpic -g -O2 -Wall -c smoothCNA.f -o smoothCNA.o
gfortran -fpic -g -O2 -Wall -c tailprobs.f -o tailprobs.o
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/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 init.o prune.o rshared.o segmentp.o smoothCNA.o tailprobs.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-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)
DNAcopy.Rcheck/tests/redundancy,20090610,segment.Rout
R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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) (2024-03-18 r86148)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS
Matrix products: default
BLAS: /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB LC_COLLATE=C
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: America/New_York
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DNAcopy_1.77.0
loaded via a namespace (and not attached):
[1] compiler_4.4.0
>
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 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
0.036 0.000 0.037
> 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$output, truth, tolerance=tol))
>
>
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Test: Weighted segmentation
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> t <- system.time({
+ fitR <- segment(cnR, weights=w, verbose=1)
+ })
Analyzing: SampleA
> cat("Processing time:\n")
Processing time:
> print(t)
user system elapsed
0.022 0.001 0.022
> print(fitR)
Call:
segment(x = cnR, weights = w, verbose = 1)
ID chrom loc.start loc.end num.mark seg.mean
1 SampleA 1 1.368577 199.0840 209 0.0259
2 SampleA 1 201.604291 301.0669 105 1.0004
3 SampleA 1 303.775112 999.3290 686 -0.0233
>
> # Expected results
> # These were obtained by dput(fitR$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) (2024-03-18 r86148)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS
Matrix products: default
BLAS: /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB LC_COLLATE=C
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: America/New_York
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DNAcopy_1.77.0
loaded via a namespace (and not attached):
[1] compiler_4.4.0
>
>
> ######################################################################
> # 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
0.332 0.057 0.377
DNAcopy.Rcheck/DNAcopy-Ex.timings
| name | user | system | elapsed | |
| CNA | 0.017 | 0.004 | 0.022 | |
| exon.segment | 0.09 | 0.00 | 0.09 | |
| plot.DNAcopy | 0.493 | 0.023 | 0.517 | |
| plotSample | 0.384 | 0.000 | 0.384 | |
| segment | 0.831 | 0.011 | 0.842 | |
| segments.p | 0.062 | 0.004 | 0.066 | |
| segments.summary | 0.045 | 0.016 | 0.060 | |
| smooth.CNA | 0.008 | 0.000 | 0.008 | |
| subset.CNA | 0.005 | 0.000 | 0.006 | |
| zoomIntoRegion | 0.372 | 0.004 | 0.376 | |