Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:14:51 -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 ATACCoGAPS package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ATACCoGAPS.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 91/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ATACCoGAPS 1.1.0 (landing page) Rossin Erbe
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: ATACCoGAPS |
Version: 1.1.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ATACCoGAPS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ATACCoGAPS_1.1.0.tar.gz |
StartedAt: 2023-02-06 17:50:11 -0000 (Mon, 06 Feb 2023) |
EndedAt: 2023-02-06 18:14:48 -0000 (Mon, 06 Feb 2023) |
EllapsedTime: 1477.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: ATACCoGAPS.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ATACCoGAPS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings ATACCoGAPS_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ATACCoGAPS.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 ‘ATACCoGAPS/DESCRIPTION’ ... OK * this is package ‘ATACCoGAPS’ version ‘1.1.0’ * 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 ‘ATACCoGAPS’ 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 ... NOTE Package in Depends field not imported from: ‘CoGAPS’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE cgapsPlot: no visible global function definition for ‘rainbow’ cgapsPlot: no visible global function definition for ‘par’ cgapsPlot: no visible global function definition for ‘legend’ findOverlap: no visible global function definition for ‘queryHits’ geneAccessibility: no visible global function definition for ‘subjectHits’ heatmapGeneAccessibility: no visible global function definition for ‘rainbow’ heatmapPatternMarkers: no visible global function definition for ‘rainbow’ heatmapPatternMatrix: no visible global function definition for ‘rainbow’ paths: no visible global function definition for ‘p.adjust’ Undefined global functions or variables: legend p.adjust par queryHits rainbow subjectHits Consider adding importFrom("grDevices", "rainbow") importFrom("graphics", "legend", "par") importFrom("stats", "p.adjust") to your NAMESPACE file. * 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘ATACCoGAPS-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: simpleMotifTFMatch > ### Title: Motif/TF Matching in a Single Function > ### Aliases: simpleMotifTFMatch > > ### ** Examples > > data("schepCogapsResult") > data(schepGranges) > > motifResults = simpleMotifTFMatch(cogapsResult = schepCogapsResult, + generanges = schepGranges, organism = "Homo sapiens", + genome = "hg19", motifsPerRegion = 1) 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 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Killed * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘ATACCoGAPS.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/ATACCoGAPS.Rcheck/00check.log’ for details.
ATACCoGAPS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ATACCoGAPS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘ATACCoGAPS’ ... ** using staged installation ** R ** data ** 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 (ATACCoGAPS)
ATACCoGAPS.Rcheck/ATACCoGAPS-Ex.timings
name | user | system | elapsed | |
RNAseqTFValidation | 0 | 0 | 0 | |
applyGREAT | 173.218 | 1.719 | 312.811 | |
cgapsPlot | 0.338 | 0.008 | 0.357 | |
dataSubsetBySparsity | 0.820 | 0.052 | 0.904 | |
foldAccessibility | 6.805 | 0.255 | 7.318 | |
geneAccessibility | 5.154 | 0.040 | 5.235 | |
genePatternMatch | 39.546 | 0.631 | 40.945 | |
heatmapGeneAccessibility | 5.426 | 0.119 | 5.686 | |
heatmapPatternMarkers | 2.838 | 0.072 | 2.991 | |
heatmapPatternMatrix | 1.007 | 0.028 | 1.055 | |
motifPatternMatch | 63.118 | 2.773 | 68.523 | |
motifSummarization | 0 | 0 | 0 | |
pathwayMatch | 46.029 | 0.172 | 46.228 | |
patternMarkerCellClassifier | 0.197 | 0.008 | 0.205 | |
peaksToGRanges | 0.429 | 0.008 | 0.457 | |