Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:40 -0400 (Wed, 21 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" | 4414 |
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 | ERROR | skipped | skipped | |||||||||
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. |
Package: coMET |
Version: 1.37.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:coMET.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings coMET_1.37.0.tar.gz |
StartedAt: 2024-08-20 23:37:21 -0400 (Tue, 20 Aug 2024) |
EndedAt: 2024-08-20 23:46:57 -0400 (Tue, 20 Aug 2024) |
EllapsedTime: 575.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: coMET.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:coMET.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings coMET_1.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/coMET.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * 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 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 'F:/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 10.6Mb * 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 ... ERROR Running examples in 'coMET-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: imprintedGenes_GTEx > ### Title: Creates a imprinted genes track from GTEx > ### Aliases: imprintedGenes_GTEx > ### Keywords: hplot > > ### ** Examples > > library("Gviz") > gen<-"hg19" > chr<- "chr6" > start <- 144251437 > end <- 144330541 > > if(interactive()){ + allIGtrack <- imprintedGenes_GTEx(gen,chr,start, end, + tissues="all", classification="imprinted",showId=TRUE) + allimprintedIGtrack <- imprintedGenes_GTEx(gen,chr,start, end, + tissues="all", classification="imprinted",showId=TRUE) + StomachIGtrack <-imprintedGenes_GTEx(gen,chr,start, end, + tissues="Stomach", classification="all",showId=TRUE) + PancreasIGtrack <- imprintedGenes_GTEx(gen,chr,start, end, + tissues="Pancreas", classification="all",showId=TRUE) + PancreasimprintedIGtrack <- imprintedGenes_GTEx(gen,chr,start, end, + tissues="Pancreas", classification="biallelic",showId=TRUE) + + imprintinglist <- list(allIGtrack,allimprintedIGtrack, + StomachIGtrack,PancreasIGtrack,PancreasimprintedIGtrack) + + plotTracks(imprintinglist, from = start, to = end, + fontfamily="sans",fontfamily.title="sans") + + } else { + + data(allIGtrack) + data(allimprintedIGtrack) + data(StomachIGtrack) + data(PancreasIGtrack) + data(PancreasimprintedIGtrack) + + imprintinglist <- list(allIGtrack,allimprintedIGtrack, + StomachIGtrack,PancreasIGtrack,PancreasimprintedIGtrack) + + plotTracks(imprintinglist, from = start, to = end, + fontfamily="sans",fontfamily.title="sans") + } Error in do.call(c, obj@http_config) : no slot of name "http_config" for this object of class "Mart" Calls: plotTracks ... list2 -> martHTTPConfig -> martHTTPConfig -> do.call Execution halted * 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 ERROR, 1 WARNING, 5 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/coMET.Rcheck/00check.log' for details.
coMET.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL coMET ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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 20 23:46:42 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 17.48 1.31 19.00
coMET.Rcheck/coMET-Ex.timings
name | user | system | elapsed | |
COSMIC_UCSC | 2.53 | 0.11 | 2.64 | |
ChIPTF_ENCODE | 1.18 | 0.02 | 1.18 | |
ClinVarCnv_UCSC | 0.53 | 0.03 | 0.56 | |
ClinVarMain_UCSC | 0.44 | 0.02 | 0.45 | |
CoreillCNV_UCSC | 0.56 | 0.03 | 0.60 | |
DNAse_UCSC | 0 | 0 | 0 | |
DNaseI_FANTOM | 0.99 | 0.03 | 1.01 | |
DNaseI_RoadMap | 0.33 | 0.00 | 0.33 | |
GAD_UCSC | 0.65 | 0.00 | 0.66 | |
GWAScatalog_UCSC | 0.56 | 0.00 | 0.56 | |
GeneReviews_UCSC | 0.79 | 0.04 | 0.83 | |
HiCdata2matrix | 0.06 | 0.00 | 0.06 | |
HistoneAll_UCSC | 7.06 | 0.10 | 7.16 | |
HistoneOne_UCSC | 0.56 | 0.00 | 0.56 | |
ISCA_UCSC | 0.63 | 0.00 | 0.64 | |
TFBS_FANTOM | 0.65 | 0.01 | 0.67 | |
bindingMotifsBiomart_ENSEMBL | 0.24 | 0.04 | 0.27 | |
chrUCSC2ENSEMBL | 0 | 0 | 0 | |
chromHMM_RoadMap | 0.97 | 0.03 | 1.00 | |
chromatinHMMAll_UCSC | 5.51 | 0.04 | 5.56 | |
chromatinHMMOne_UCSC | 0.64 | 0.02 | 0.66 | |
coMET-package | 7.98 | 0.33 | 12.71 | |
col2HSV | 0 | 0 | 0 | |
comet | 3.58 | 0.12 | 3.70 | |
comet.list | 1.08 | 0.05 | 1.12 | |
comet.web | 8.14 | 0.48 | 17.52 | |
complementary | 0.03 | 0.00 | 0.03 | |
cpgIslands_UCSC | 0.14 | 0.00 | 0.14 | |
dgfootprints_RoadMap | 1.21 | 0.00 | 1.20 | |
eQTL | 1.75 | 0.08 | 1.83 | |
eQTL_GTEx | 1.81 | 0.03 | 1.85 | |
gcContent_UCSC | 1.53 | 0.03 | 1.56 | |
genesName_ENSEMBL | 0 | 0 | 0 | |
genes_ENSEMBL | 0.92 | 0.02 | 0.94 | |