Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:46 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 410/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
coMET 1.37.0 (landing page) Tiphaine Martin
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: coMET |
Version: 1.37.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:coMET.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings coMET_1.37.0.tar.gz |
StartedAt: 2024-08-27 03:40:00 -0000 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 03:51:00 -0000 (Tue, 27 Aug 2024) |
EllapsedTime: 660.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: coMET.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:coMET.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings coMET_1.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/coMET.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) 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 ‘coMET/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘coMET’ version ‘1.37.0’ * 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/coMET.Rcheck/00install.out’ for details. * checking installed package size ... NOTE installed size is 19.0Mb 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed comet.web 10.863 1.338 37.077 coMET-package 8.896 1.211 29.324 HistoneAll_UCSC 6.465 0.080 6.558 chromatinHMMAll_UCSC 6.253 0.048 6.314 imprintedGenes_GTEx 5.622 0.144 5.778 * 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/coMET.Rcheck/00check.log’ for details.
coMET.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL coMET ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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, 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 -- Tue Aug 27 03:50:55 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 20.826 1.101 21.962
coMET.Rcheck/coMET-Ex.timings
name | user | system | elapsed | |
COSMIC_UCSC | 2.689 | 0.144 | 2.837 | |
ChIPTF_ENCODE | 1.125 | 0.008 | 1.135 | |
ClinVarCnv_UCSC | 0.624 | 0.024 | 0.649 | |
ClinVarMain_UCSC | 0.655 | 0.032 | 0.688 | |
CoreillCNV_UCSC | 0.659 | 0.020 | 0.680 | |
DNAse_UCSC | 0 | 0 | 0 | |
DNaseI_FANTOM | 0.905 | 0.016 | 0.922 | |
DNaseI_RoadMap | 0.264 | 0.012 | 0.276 | |
GAD_UCSC | 0.631 | 0.000 | 0.633 | |
GWAScatalog_UCSC | 0.538 | 0.012 | 0.552 | |
GeneReviews_UCSC | 0.822 | 0.008 | 0.832 | |
HiCdata2matrix | 0.037 | 0.000 | 0.038 | |
HistoneAll_UCSC | 6.465 | 0.080 | 6.558 | |
HistoneOne_UCSC | 0.534 | 0.012 | 0.547 | |
ISCA_UCSC | 0.684 | 0.007 | 0.693 | |
TFBS_FANTOM | 0.636 | 0.000 | 0.637 | |
bindingMotifsBiomart_ENSEMBL | 0.207 | 0.004 | 0.211 | |
chrUCSC2ENSEMBL | 0 | 0 | 0 | |
chromHMM_RoadMap | 0.999 | 0.008 | 1.009 | |
chromatinHMMAll_UCSC | 6.253 | 0.048 | 6.314 | |
chromatinHMMOne_UCSC | 0.647 | 0.032 | 0.681 | |
coMET-package | 8.896 | 1.211 | 29.324 | |
col2HSV | 0.000 | 0.000 | 0.001 | |
comet | 4.224 | 0.208 | 4.444 | |
comet.list | 1.160 | 0.028 | 1.192 | |
comet.web | 10.863 | 1.338 | 37.077 | |
complementary | 0.036 | 0.000 | 0.035 | |
cpgIslands_UCSC | 0.328 | 0.040 | 0.368 | |
dgfootprints_RoadMap | 1.080 | 0.163 | 1.246 | |
eQTL | 2.213 | 0.152 | 2.370 | |
eQTL_GTEx | 2.170 | 0.268 | 2.442 | |
gcContent_UCSC | 1.875 | 0.179 | 2.059 | |
genesName_ENSEMBL | 0.003 | 0.000 | 0.003 | |
genes_ENSEMBL | 1.200 | 0.028 | 1.231 | |
imprintedGenes_GTEx | 5.622 | 0.144 | 5.778 | |
interestGenes_ENSEMBL | 1.137 | 0.008 | 1.148 | |
interestTranscript_ENSEMBL | 1.197 | 0.028 | 1.227 | |
knownGenes_UCSC | 1.373 | 0.036 | 1.412 | |
metQTL | 1.859 | 0.027 | 1.890 | |
miRNATargetRegionsBiomart_ENSEMBL | 0.068 | 0.000 | 0.069 | |
otherRegulatoryRegionsBiomart_ENSEMBL | 0.146 | 0.003 | 0.151 | |
pizza | 0.009 | 0.000 | 0.010 | |
psiQTL_GTEx | 1.721 | 0.019 | 1.744 | |
refGenes_UCSC | 1.360 | 0.047 | 1.410 | |
regulationBiomart_ENSEMBL | 0.497 | 0.008 | 0.505 | |
regulatoryEvidenceBiomart_ENSEMBL | 0.202 | 0.004 | 0.206 | |
regulatoryFeaturesBiomart_ENSEMBL | 0.235 | 0.000 | 0.235 | |
regulatorySegmentsBiomart_ENSEMBL | 0.204 | 0.000 | 0.205 | |
repeatMasker_UCSC | 0.721 | 0.004 | 0.726 | |
segmentalDups_UCSC | 0.628 | 0.012 | 0.640 | |
setColors | 0.001 | 0.000 | 0.001 | |
snpBiomart_ENSEMBL | 0.635 | 0.000 | 0.636 | |
snpLocations_UCSC | 1.654 | 0.020 | 1.676 | |
structureBiomart_ENSEMBL | 0.645 | 0.020 | 0.666 | |
transcript_ENSEMBL | 2.018 | 0.064 | 2.086 | |
xenorefGenes_UCSC | 0.910 | 0.000 | 0.912 | |