Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:08 -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 |
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 HiTC package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiTC.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 907/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HiTC 1.43.0 (landing page) Nicolas Servant
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: HiTC |
Version: 1.43.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:HiTC.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings HiTC_1.43.0.tar.gz |
StartedAt: 2023-02-07 04:36:15 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 04:43:58 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 462.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: HiTC.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:HiTC.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings HiTC_1.43.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/HiTC.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 ‘HiTC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘HiTC’ version ‘1.43.0’ * 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 ‘HiTC’ 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: SIGNIFICANT USER-VISIBLE CHANGES Cannot process chunk/lines: BUG FIXES Cannot process chunk/lines: NEW FEATURES * 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 directionalityIndex: no visible global function definition for ‘subjectHits’ directionalityIndex: no visible global function definition for ‘queryHits’ getBlocsIndex: no visible global function definition for ‘Rle’ getExpectedCountsMean: no visible global function definition for ‘Rle’ normLGF: no visible global function definition for ‘glm.nb’ slidingWindow: no visible binding for global variable ‘consV’ splitCombinedContacts : <anonymous>: no visible global function definition for ‘seqlevels<-’ divide,HTCexp-HTCexp: no visible global function definition for ‘queryHits’ divide,HTCexp-HTCexp: no visible global function definition for ‘subjectHits’ isBinned,HTCexp: no visible global function definition for ‘countMatches’ substract,HTCexp-HTCexp: no visible global function definition for ‘queryHits’ substract,HTCexp-HTCexp: no visible global function definition for ‘subjectHits’ Undefined global functions or variables: Rle consV countMatches glm.nb queryHits seqlevels<- subjectHits * checking Rd files ... WARNING checkRd: (5) HTClist-class.Rd:52-54: \item in \describe must have non-empty label * 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 directionalityIndex 18.994 0.407 19.410 CQC 5.317 0.068 5.392 mapC 4.933 0.172 5.105 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘HiC_analysis.Rnw’... failed to complete the test ‘HiTC.Rnw’... OK ERROR Errors in running code in vignettes: when running code in ‘HiC_analysis.Rnw’ ... Total Reads = 21565450 Number of Interactions = 3657661 Median Frequency = 1 Sparsity = 0.1 > head(summary(hic_imr90_40)) as(<dsCMatrix>, "dgTMatrix") is deprecated since Matrix 1.5-0; do as(as(., "generalMatrix"), "TsparseMatrix") instead Killed ... incomplete output. Crash? * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘HiC_analysis.Rnw’ using Sweave Loading required package: HiTC Loading required package: IRanges 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 Loading required package: stats4 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: HiCDataHumanIMR90 as(<dsCMatrix>, "dgTMatrix") is deprecated since Matrix 1.5-0; do as(as(., "generalMatrix"), "TsparseMatrix") instead Killed --- re-building ‘HiTC.Rnw’ using Sweave Loading required package: IRanges 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 Loading required package: stats4 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: Matrix Attaching package: ‘Matrix’ The following object is masked from ‘package:S4Vectors’: expand Reading file ... Convert my5C matrix file in HTCexp object(s) Reading file ... Convert my5C matrix file in HTCexp object(s) Reading file ... Convert my5C matrix file in HTCexp object(s) Reading file ... Convert my5C matrix file in HTCexp object(s) Reading file ... Convert my5C matrix file in HTCexp object(s) Reading file ... Convert my5C matrix file in HTCexp object(s) as(<dsCMatrix>, "dgTMatrix") is deprecated since Matrix 1.5-0; do as(as(., "generalMatrix"), "TsparseMatrix") instead Warning: file stem ‘./HiTC-qcc’ is not portable Get data ... Generate quality control plots ... minrange= 1 - maxrange= 741 Warning: file stem ‘./HiTC-bin5C’ is not portable Bin size 'xgi' =102420 [3x34140] Bin size 'ygi' =102420 [3x34140] minrange= 3 - maxrange= 477.2 Lowess fit ... Standard deviation calculation ... Delta=8876.395 Calculating stdev ... Warning: file stem ‘./HiTC-norm5Cznorm’ is not portable Lowess fit ... Standard deviation calculation ... Delta=8876.395 Calculating stdev ... minrange= 0.027 - maxrange= 2.139 Warning: file stem ‘./HiTC-annot5C’ is not portable Bin size 'xgi' =102087 [3x34029] Bin size 'ygi' =102087 [3x34029] Loading required package: rtracklayer minrange= 0.5 - maxrange= 10 Warning: file stem ‘./HiTC-comp5C’ is not portable Bin size 'xgi' =102087 [3x34029] Bin size 'ygi' =102087 [3x34029] minrange= 0.5 - maxrange= 10 minrange= 0.5 - maxrange= 10 Warning: file stem ‘./HiTC-mapClist’ is not portable Plotting chr12chr12... minrange= 1 - maxrange= 100 Plotting chr12chr13... minrange= 1 - maxrange= 20 Plotting chr12chr14... minrange= 1 - maxrange= 39 Plotting chr13chr13... minrange= 1 - maxrange= 100 Plotting chr13chr14... minrange= 1 - maxrange= 18 Plotting chr14chr14... minrange= 1 - maxrange= 100 Warning: file stem ‘./HiTC-mapChic’ is not portable Plotting chr14chr14... minrange= 1 - maxrange= 100 Warning: file stem ‘./HiTC-mapNormhic’ is not portable Lowess fit ... Plotting chr14chr14... minrange= 0.015 - maxrange= 2.519 Warning: file stem ‘./HiTC-mapCorhic’ is not portable Plotting chr14chr14... minrange= 0 - maxrange= 1 Warning: file stem ‘./HiTC-mapPCAhic’ is not portable Lowess fit ... --- finished re-building ‘HiTC.Rnw’ SUMMARY: processing the following file failed: ‘HiC_analysis.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/HiTC.Rcheck/00check.log’ for details.
HiTC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL HiTC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘HiTC’ ... ** 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 (HiTC)
HiTC.Rcheck/HiTC-Ex.timings
name | user | system | elapsed | |
CQC | 5.317 | 0.068 | 5.392 | |
HTCexp-class | 3.199 | 0.101 | 3.303 | |
HTClist-class | 1.686 | 0.012 | 1.705 | |
Nora_5C | 0.242 | 0.004 | 0.246 | |
binningC | 1.503 | 0.008 | 1.512 | |
directionalityIndex | 18.994 | 0.407 | 19.410 | |
discretize | 0 | 0 | 0 | |
export.my5C | 0 | 0 | 0 | |
exportC | 0 | 0 | 0 | |
extractRegion | 0.405 | 0.000 | 0.405 | |
getAnnotatedRestrictionSites | 0.000 | 0.000 | 0.001 | |
getExpectedCounts | 1.610 | 0.388 | 1.870 | |
getPearsonMap | 0.673 | 0.040 | 0.717 | |
getRestrictionFragmentsPerChromosome | 0 | 0 | 0 | |
import.my5C | 0.118 | 0.020 | 0.137 | |
importC | 0 | 0 | 0 | |
intervalsDist | 1.302 | 0.232 | 1.533 | |
mapC | 4.933 | 0.172 | 5.105 | |
normICE | 0 | 0 | 0 | |
normLGF | 0 | 0 | 0 | |
pca.hic | 0.657 | 0.001 | 0.663 | |
removeIntervals | 0.281 | 0.000 | 0.281 | |
setGenomicFeatures | 0.000 | 0.000 | 0.001 | |
setIntervalScale | 1.076 | 0.000 | 1.076 | |