Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 587/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DNAcopy 1.81.0 (landing page) Venkatraman E. Seshan
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: DNAcopy |
Version: 1.81.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:DNAcopy.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DNAcopy_1.81.0.tar.gz |
StartedAt: 2024-12-24 06:15:19 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 06:15:43 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 24.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DNAcopy.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:DNAcopy.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DNAcopy_1.81.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/DNAcopy.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DNAcopy/DESCRIPTION’ ... OK * this is package ‘DNAcopy’ version ‘1.81.0’ * 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ * used Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’ * 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 ...Warning: program compiled against libxml 212 using older 211 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.21-bioc/meat/DNAcopy.Rcheck/00check.log’ for details.
DNAcopy.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL DNAcopy ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘DNAcopy’ ... ** using staged installation ** libs using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ using Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran -fPIC -g -O2 -Wall -Werror=format-security -c cbsWtstats.f -o cbsWtstats.o f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran cbsWtstats.f:282:72: 282 | iseg(1) = tmaxi | ^ Warning: ‘tmaxi’ may be used uninitialized [-Wmaybe-uninitialized] cbsWtstats.f:17:16: 17 | 2 tmaxi, tmaxj, nal0 | ^ note: ‘tmaxi’ was declared here cbsWtstats.f:283:72: 283 | iseg(2) = tmaxj | ^ Warning: ‘tmaxj’ may be used uninitialized [-Wmaybe-uninitialized] cbsWtstats.f:17:23: 17 | 2 tmaxi, tmaxj, nal0 | ^ note: ‘tmaxj’ was declared here /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran -fPIC -g -O2 -Wall -Werror=format-security -c cbststats.f -o cbststats.o f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran cbststats.f:258:72: 258 | tmaxj = sxmxi + i2j | ^ Warning: ‘sxmxi’ may be used uninitialized [-Wmaybe-uninitialized] cbststats.f:11:63: 11 | 1 nb2, bi, bj, ilo, ihi, jlo, jhi, alenmax, i2j, sxmxi, | ^ note: ‘sxmxi’ was declared here /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran -fPIC -g -O2 -Wall -Werror=format-security -c changepoints-wtd.f -o changepoints-wtd.o f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran -fPIC -g -O2 -Wall -Werror=format-security -c changepoints.f -o changepoints.o f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran -fPIC -g -O2 -Wall -Werror=format-security -c esegment.f -o esegment.o f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c flchoose.c -o flchoose.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c fphyper.c -o fphyper.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c fpnorm.c -o fpnorm.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran -fPIC -g -O2 -Wall -Werror=format-security -c getbdry.f -o getbdry.o f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c init.c -o init.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran -fPIC -g -O2 -Wall -Werror=format-security -c prune.f -o prune.o f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c rshared.c -o rshared.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran -fPIC -g -O2 -Wall -Werror=format-security -c segmentp.f -o segmentp.o f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran -fPIC -g -O2 -Wall -Werror=format-security -c smoothCNA.f -o smoothCNA.o f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gfortran -fPIC -g -O2 -Wall -Werror=format-security -c tailprobs.f -o tailprobs.o f951: Warning: ‘-Werror=’ argument ‘-Werror=format-security’ is not valid for Fortran /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -shared -L/home/biocbuild/R/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 -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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) (2024-11-24 r87369) Platform: aarch64-unknown-linux-gnu Running under: openEuler 24.03 (LTS) Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.25.so; LAPACK version 3.11.0 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: UTC tzcode source: system (glibc) attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] DNAcopy_1.81.0 loaded via a namespace (and not attached): [1] compiler_4.5.0 > > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # 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 0.043 0.000 0.042 > 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$output, truth, tolerance=tol)) > > > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Test: Weighted segmentation > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > t <- system.time({ + fitR <- segment(cnR, weights=w, verbose=1) + }) Analyzing: SampleA > cat("Processing time:\n") Processing time: > print(t) user system elapsed 0.027 0.000 0.026 > print(fitR) Call: segment(x = cnR, weights = w, verbose = 1) ID chrom loc.start loc.end num.mark seg.mean 1 SampleA 1 1.368577 199.0840 209 0.0259 2 SampleA 1 201.604291 301.0669 105 1.0004 3 SampleA 1 303.775112 999.3290 686 -0.0233 > > # Expected results > # These were obtained by dput(fitR$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) (2024-11-24 r87369) Platform: aarch64-unknown-linux-gnu Running under: openEuler 24.03 (LTS) Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.25.so; LAPACK version 3.11.0 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: UTC tzcode source: system (glibc) attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] DNAcopy_1.81.0 loaded via a namespace (and not attached): [1] compiler_4.5.0 > > > ###################################################################### > # 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 0.376 0.046 0.530
DNAcopy.Rcheck/DNAcopy-Ex.timings
name | user | system | elapsed | |
CNA | 0.015 | 0.008 | 0.023 | |
exon.segment | 0.096 | 0.000 | 0.097 | |
plot.DNAcopy | 0.662 | 0.012 | 0.675 | |
plotSample | 0.513 | 0.000 | 0.513 | |
segment | 1.102 | 0.043 | 1.148 | |
segments.p | 0.079 | 0.000 | 0.080 | |
segments.summary | 0.061 | 0.008 | 0.069 | |
smooth.CNA | 0.009 | 0.000 | 0.009 | |
subset.CNA | 0.006 | 0.000 | 0.005 | |
zoomIntoRegion | 0.502 | 0.000 | 0.503 | |