Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-11-02 11:40:36 -0400 (Thu, 02 Nov 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
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 544/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
derfinder 1.36.0 (landing page) Leonardo Collado-Torres
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the derfinder package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/derfinder.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: derfinder |
Version: 1.36.0 |
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:derfinder.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings derfinder_1.36.0.tar.gz |
StartedAt: 2023-11-02 09:56:14 -0000 (Thu, 02 Nov 2023) |
EndedAt: 2023-11-02 10:04:46 -0000 (Thu, 02 Nov 2023) |
EllapsedTime: 511.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: derfinder.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:derfinder.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings derfinder_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/derfinder.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘derfinder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘derfinder’ version ‘1.36.0’ * package encoding: UTF-8 * 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 ‘derfinder’ 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 ... WARNING A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... WARNING * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘GenomeInfoDb:::.guessSpeciesStyle’ ‘GenomeInfoDb:::.supportedSeqnameMappings’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.smootherFstats’ * 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘derfinder-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: railMatrix > ### Title: Identify regions data by a coverage filter and get a count > ### matrix from BigWig files > ### Aliases: railMatrix > > ### ** Examples > > > ## BigWig files are not supported in Windows > if (.Platform$OS.type != "windows") { + ## Get data + library("derfinderData") + + ## Identify sample files + sampleFiles <- rawFiles(system.file("extdata", "AMY", + package = + "derfinderData" + ), samplepatt = "bw", fileterm = NULL) + names(sampleFiles) <- gsub(".bw", "", names(sampleFiles)) + + ## Create the mean bigwig file. This file is normally created by Rail + ## but in this example we'll create it manually. + library("GenomicRanges") + fullCov <- fullCoverage(files = sampleFiles, chrs = "chr21") + meanCov <- Reduce("+", fullCov$chr21) / ncol(fullCov$chr21) + createBw(list("chr21" = DataFrame("meanChr21" = meanCov)), + keepGR = + FALSE + ) + + summaryFile <- "meanChr21.bw" + + ## Get the regions + regionMat <- railMatrix( + chrs = "chr21", summaryFiles = summaryFile, + sampleFiles = sampleFiles, L = 76, cutoff = 5.1, + maxClusterGap = 3000L + ) + + ## Explore results + names(regionMat$chr21) + regionMat$chr21$regions + dim(regionMat$chr21$coverageMatrix) + } Loading required package: stats4 Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: IRanges * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test-all.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 933085 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 ERROR Running the tests in ‘tests/test-all.R’ failed. Complete output: > ## Disable the tests if the system variable 'R_DISABLE_TESTS' is set to TRUE > > flag <- as.logical(Sys.getenv("R_DISABLE_TESTS")) > if (is.na(flag) | flag == FALSE) { + library("testthat") + test_check("derfinder") + } Loading required package: derfinder * 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 ERRORs, 2 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs-3.18-bioc/meat/derfinder.Rcheck/00check.log’ for details.
derfinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL derfinder ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘derfinder’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (derfinder)
derfinder.Rcheck/tests/test-all.Rout.fail
R version 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (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. > ## Disable the tests if the system variable 'R_DISABLE_TESTS' is set to TRUE > > flag <- as.logical(Sys.getenv("R_DISABLE_TESTS")) > if (is.na(flag) | flag == FALSE) { + library("testthat") + test_check("derfinder") + } Loading required package: derfinder
derfinder.Rcheck/derfinder-Ex.timings
name | user | system | elapsed | |
analyzeChr | 1.567 | 0.128 | 1.713 | |
annotateRegions | 0.499 | 0.032 | 0.534 | |
calculatePvalues | 1.306 | 0.060 | 1.369 | |
calculateStats | 0.639 | 0.068 | 0.708 | |
coerceGR | 0.108 | 0.009 | 0.117 | |
collapseFullCoverage | 0.007 | 0.001 | 0.008 | |
coverageToExon | 6.802 | 0.764 | 7.583 | |
createBw | 0.248 | 0.000 | 0.256 | |
createBwSample | 0.092 | 0.000 | 0.092 | |
define_cluster | 0.008 | 0.000 | 0.009 | |
derfinder-deprecated | 0.000 | 0.003 | 0.003 | |
extendedMapSeqlevels | 0.100 | 0.005 | 0.116 | |
filterData | 0.186 | 0.004 | 0.190 | |
findRegions | 0.743 | 0.025 | 0.788 | |
fullCoverage | 0.358 | 0.011 | 0.388 | |
getRegionCoverage | 0.443 | 0.062 | 2.206 | |
getTotalMapped | 0.013 | 0.000 | 0.014 | |
loadCoverage | 0.195 | 0.028 | 0.224 | |
makeGenomicState | 5.578 | 0.335 | 5.951 | |
makeModels | 0.020 | 0.004 | 0.026 | |
mergeResults | 0.578 | 0.020 | 0.622 | |
preprocessCoverage | 0.522 | 0.027 | 0.554 | |