Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 413/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
coMET 1.38.0 (landing page) Tiphaine Martin
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the coMET package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/coMET.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. |
Package: coMET |
Version: 1.38.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:coMET.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings coMET_1.38.0.tar.gz |
StartedAt: 2024-12-20 15:20:01 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 15:29:48 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 586.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: coMET.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:coMET.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings coMET_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/coMET.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘coMET/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘coMET’ version ‘1.38.0’ * 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 ‘coMET’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET' See ‘/Users/biocbuild/bbs-3.20-bioc/meat/coMET.Rcheck/00install.out’ for details. * checking installed package size ... NOTE installed size is 18.9Mb sub-directories of 1Mb or more: data 7.6Mb extdata 10.7Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... 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 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 draw.plot.annotation : <anonymous>: no visible global function definition for 'ggplotGrob' draw.plot.annotation: no visible global function definition for 'viewTracks' draw.plot.annotation: no visible global function definition for 'trackList' eQTL: no visible binding for global variable 'chromosome_stop' eQTL: no visible binding for global variable 'chromosome_start' eQTL: no visible binding for global variable 'chromosome_name' eQTL_GTEx: no visible binding for global variable 'snp_pos' eQTL_GTEx: no visible binding for global variable 'snp_chrom' eQTL_GTEx: no visible binding for global variable 'gene_start' eQTL_GTEx: no visible binding for global variable 'gene_stop' eQTL_GTEx: no visible binding for global variable 'gene_chr' geneExpression_GTEx: no visible global function definition for 'as' metQTL: no visible binding for global variable 'chromosome_stop' metQTL: no visible binding for global variable 'chromosome_start' metQTL: no visible binding for global variable 'chromosome_name' pizza: no visible global function definition for 'par' pizza: no visible global function definition for 'plot.new' pizza: no visible global function definition for 'plot.window' pizza: no visible global function definition for 'polygon' pizza: no visible global function definition for 'lines' pizza: no visible global function definition for 'text' psiQTL_GTEx: no visible binding for global variable 'pos_snp' psiQTL_GTEx: no visible binding for global variable 'chr_snp' psiQTL_GTEx: no visible binding for global variable 'pos_middle_exon' psiQTL_GTEx: no visible binding for global variable 'chr_exon' Undefined global functions or variables: as chr_exon chr_snp chromosome_name chromosome_start chromosome_stop gene_chr gene_start gene_stop ggplotGrob lines par plot.new plot.window polygon pos_middle_exon pos_snp snp_chrom snp_pos text trackList viewTracks Consider adding importFrom("graphics", "lines", "par", "plot.new", "plot.window", "polygon", "text") importFrom("methods", "as") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) ChIPTF_ENCODE.Rd:36: Escaped LaTeX specials: \# * 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 ... NOTE Objects in \usage without \alias in Rd file 'check.configVar.cometlist.Rd': ‘check.configVar.cometlist’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed comet.web 9.958 0.240 16.754 coMET-package 7.678 0.172 13.366 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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 WARNING, 5 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/coMET.Rcheck/00check.log’ for details.
coMET.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL coMET ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘coMET’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET' ** testing if installed package can be loaded from final location Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET' ** testing if installed package keeps a record of temporary installation path * DONE (coMET)
coMET.Rcheck/tests/runTests.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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. > require("coMET") || stop("unable to load Package:coMET") Loading required package: coMET Loading required package: grid Loading required package: biomaRt Loading required package: Gviz Loading required package: S4Vectors 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, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min 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 Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: psych Attaching package: 'psych' The following object is masked from 'package:GenomicRanges': distance The following objects are masked from 'package:IRanges': distance, reflect [1] TRUE Warning message: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET' > BiocGenerics:::testPackage("coMET") RUNIT TEST PROTOCOL -- Fri Dec 20 15:29:33 2024 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : coMET RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 20.080 0.750 20.927
coMET.Rcheck/coMET-Ex.timings
name | user | system | elapsed | |
COSMIC_UCSC | 2.555 | 0.070 | 2.633 | |
ChIPTF_ENCODE | 0.840 | 0.018 | 0.861 | |
ClinVarCnv_UCSC | 0.450 | 0.012 | 0.462 | |
ClinVarMain_UCSC | 0.452 | 0.005 | 0.460 | |
CoreillCNV_UCSC | 0.465 | 0.006 | 0.472 | |
DNAse_UCSC | 0.000 | 0.000 | 0.001 | |
DNaseI_FANTOM | 0.777 | 0.011 | 0.790 | |
DNaseI_RoadMap | 0.257 | 0.006 | 0.265 | |
GAD_UCSC | 0.508 | 0.006 | 0.515 | |
GWAScatalog_UCSC | 0.373 | 0.005 | 0.378 | |
GeneReviews_UCSC | 0.527 | 0.007 | 0.536 | |
HiCdata2matrix | 0.035 | 0.006 | 0.041 | |
HistoneAll_UCSC | 4.637 | 0.023 | 4.674 | |
HistoneOne_UCSC | 0.414 | 0.006 | 0.423 | |
ISCA_UCSC | 0.489 | 0.006 | 0.496 | |
TFBS_FANTOM | 0.485 | 0.005 | 0.492 | |
bindingMotifsBiomart_ENSEMBL | 0.155 | 0.011 | 0.168 | |
chrUCSC2ENSEMBL | 0 | 0 | 0 | |
chromHMM_RoadMap | 0.726 | 0.014 | 0.743 | |
chromatinHMMAll_UCSC | 4.771 | 0.026 | 4.816 | |
chromatinHMMOne_UCSC | 0.504 | 0.009 | 0.513 | |
coMET-package | 7.678 | 0.172 | 13.366 | |
col2HSV | 0.001 | 0.000 | 0.001 | |
comet | 3.236 | 0.052 | 3.301 | |
comet.list | 0.698 | 0.010 | 0.713 | |
comet.web | 9.958 | 0.240 | 16.754 | |
complementary | 0.025 | 0.002 | 0.028 | |
cpgIslands_UCSC | 0.155 | 0.005 | 0.159 | |
dgfootprints_RoadMap | 0.757 | 0.012 | 0.771 | |
eQTL | 1.571 | 0.018 | 1.594 | |
eQTL_GTEx | 1.344 | 0.013 | 1.358 | |
gcContent_UCSC | 1.847 | 0.011 | 1.861 | |
genesName_ENSEMBL | 0.004 | 0.003 | 0.008 | |
genes_ENSEMBL | 0.926 | 0.008 | 0.939 | |
imprintedGenes_GTEx | 4.028 | 0.050 | 4.100 | |
interestGenes_ENSEMBL | 0.768 | 0.008 | 0.783 | |
interestTranscript_ENSEMBL | 0.871 | 0.008 | 0.880 | |
knownGenes_UCSC | 1.000 | 0.007 | 1.013 | |
metQTL | 1.342 | 0.016 | 1.364 | |
miRNATargetRegionsBiomart_ENSEMBL | 0.054 | 0.004 | 0.058 | |
otherRegulatoryRegionsBiomart_ENSEMBL | 0.107 | 0.010 | 0.117 | |
pizza | 0.006 | 0.002 | 0.009 | |
psiQTL_GTEx | 1.259 | 0.014 | 1.280 | |
refGenes_UCSC | 0.943 | 0.009 | 0.956 | |
regulationBiomart_ENSEMBL | 0.397 | 0.005 | 0.403 | |
regulatoryEvidenceBiomart_ENSEMBL | 0.157 | 0.011 | 0.169 | |
regulatoryFeaturesBiomart_ENSEMBL | 0.152 | 0.012 | 0.166 | |
regulatorySegmentsBiomart_ENSEMBL | 0.147 | 0.011 | 0.158 | |
repeatMasker_UCSC | 0.603 | 0.005 | 0.610 | |
segmentalDups_UCSC | 0.448 | 0.005 | 0.454 | |
setColors | 0.001 | 0.001 | 0.000 | |
snpBiomart_ENSEMBL | 0.503 | 0.006 | 0.511 | |
snpLocations_UCSC | 1.203 | 0.009 | 1.217 | |
structureBiomart_ENSEMBL | 0.468 | 0.005 | 0.476 | |
transcript_ENSEMBL | 1.410 | 0.010 | 1.425 | |
xenorefGenes_UCSC | 0.717 | 0.007 | 0.726 | |