Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:28 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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To the developers/maintainers of the segmentSeq package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/segmentSeq.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1817/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
segmentSeq 2.33.0 (landing page) Thomas J. Hardcastle
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: segmentSeq |
Version: 2.33.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings segmentSeq_2.33.0.tar.gz |
StartedAt: 2023-02-07 15:16:06 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 15:28:24 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 738.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: segmentSeq.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings segmentSeq_2.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/segmentSeq.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘segmentSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘segmentSeq’ version ‘2.33.0’ * 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 ‘segmentSeq’ 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 ... NOTE heuristicSeg : <anonymous>: no visible binding for global variable ‘sDP’ Undefined global functions or variables: sDP * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed classifySeg 40.767 0.593 48.096 lociLikelihoods 18.379 0.008 22.090 heuristicSeg 17.841 0.010 19.559 plotGenome 9.792 0.044 10.486 getCounts 6.663 1.847 26.322 processAD 5.327 0.083 6.120 segData-class 5.283 0.012 5.735 segmentSeq-package 5.287 0.003 5.691 normaliseNC 5.023 0.055 5.348 readMeths 4.043 0.040 5.057 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘methylationAnalysis.Rnw’... failed to complete the test ‘segmentSeq.Rnw’... failed to complete the test ERROR Errors in running code in vignettes: when running code in ‘methylationAnalysis.Rnw’ ... > if (nrow(sD) != 249271) stop("sD object is the wrong size (should have 249271 rows). Failure.") > thresh = 0.2 > hS <- heuristicSeg(sD = sD, aD = mD, prop = thresh, + cl = cl, gap = 100, getLikes = FALSE) Number of candidate loci: 249271 Number of candidate nulls: 163635..Killed ... incomplete output. Crash? when running code in ‘segmentSeq.Rnw’ ... > if (nrow(sD) != 1452) stop("sD object is the wrong size (should have 1452 rows). Failure.") > hS <- heuristicSeg(sD = sD, aD = aD, RKPM = 1000, + largeness = 1e+08, getLikes = TRUE, cl = cl) Number of candidate loci: 1452 Evaluating candidate loci...done. >Chr1 Killed ... incomplete output. Crash? * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘methylationAnalysis.Rnw’ using Sweave Loading required package: baySeq Loading required package: GenomicRanges 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 objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: abind Loading required package: parallel Loading required package: ShortRead Loading required package: BiocParallel Loading required package: Biostrings Loading required package: XVector Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Loading required package: Rsamtools Loading required package: GenomicAlignments Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: ‘MatrixGenerics’ The following objects are masked from ‘package:matrixStats’: colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: ‘Biobase’ The following object is masked from ‘package:MatrixGenerics’: rowMedians The following objects are masked from ‘package:matrixStats’: anyMissing, rowMedians Reading files.......done! Finding unique cytosines......done! Processing samples.......done! Chromosome: Chr1 Finding start-stop co-ordinates...done! 249271 candidate loci found. Number of candidate loci: 249271 Number of candidate nulls: 163635......done! Strand * Checking overlaps.....done. Selecting loci...done! Plotting sample: 1 Plotting sample: 2 Plotting sample: 3 Plotting sample: 4 Plotting sample: 1 Plotting sample: 2 Plotting sample: 3 Plotting sample: 4 Finding priors...Killed --- re-building ‘segmentSeq.Rnw’ using Sweave Loading required package: baySeq Loading required package: GenomicRanges 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 objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: abind Loading required package: parallel Loading required package: ShortRead Loading required package: BiocParallel Loading required package: Biostrings Loading required package: XVector Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Loading required package: Rsamtools Loading required package: GenomicAlignments Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: ‘MatrixGenerics’ The following objects are masked from ‘package:matrixStats’: colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: ‘Biobase’ The following object is masked from ‘package:MatrixGenerics’: rowMedians The following objects are masked from ‘package:matrixStats’: anyMissing, rowMedians Reading files........done! Analysing tags...........done! Chromosome: >Chr1 Finding start-stop co-ordinates...done! 1452 candidate loci found. Number of candidate loci: 1452 Evaluating candidate loci...done. >Chr1 Strand * Checking overlaps.....done. Selecting loci...done! Extending loci.....done! Finding priors...done. Getting likelihoods for replicate group AGO4... Length of priorReps:1014 Length of priorSubset:507 Length of subset:507 Length of postRows:507 ...done! Getting likelihoods for replicate group AGO6... Length of priorReps:1014 Length of priorSubset:507 Length of subset:507 Length of postRows:507 ...done! Finding candidate priors...done. Finding priors...done. Segmentation split into 1 parts. Establishing likelihoods of loci; Part 1 of 1 Establishing likelihoods of loci... ...for replicate group AGO4......done. ...for replicate group AGO6......done. Killed SUMMARY: processing the following files failed: ‘methylationAnalysis.Rnw’ ‘segmentSeq.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/segmentSeq.Rcheck/00check.log’ for details.
segmentSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL segmentSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘segmentSeq’ ... ** using staged installation ** R ** data ** 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 (segmentSeq)
segmentSeq.Rcheck/segmentSeq-Ex.timings
name | user | system | elapsed | |
alignmentData-class | 4.228 | 0.004 | 4.419 | |
classifySeg | 40.767 | 0.593 | 48.096 | |
findChunks | 4.287 | 0.004 | 4.888 | |
getCounts | 6.663 | 1.847 | 26.322 | |
getOverlaps | 4.297 | 0.012 | 4.932 | |
heuristicSeg | 17.841 | 0.010 | 19.559 | |
lociLikelihoods | 18.379 | 0.008 | 22.090 | |
normaliseNC | 5.023 | 0.055 | 5.348 | |
plotGenome | 9.792 | 0.044 | 10.486 | |
processAD | 5.327 | 0.083 | 6.120 | |
readMethods | 4.181 | 0.008 | 4.782 | |
readMeths | 4.043 | 0.040 | 5.057 | |
segData-class | 5.283 | 0.012 | 5.735 | |
segmentSeq-package | 5.287 | 0.003 | 5.691 | |
thresholdFinder | 4.055 | 0.080 | 4.624 | |