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 12:04 -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 1031/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
InPAS 2.14.0 (landing page) Jianhong Ou
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | 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 InPAS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/InPAS.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: InPAS |
Version: 2.14.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:InPAS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings InPAS_2.14.0.tar.gz |
StartedAt: 2024-12-20 01:24:47 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 01:35:42 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 654.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: InPAS.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:InPAS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings InPAS_2.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/InPAS.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘InPAS/DESCRIPTION’ ... OK * this is package ‘InPAS’ version ‘2.14.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘InPAS’ 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 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘adjust_distalCPs’ ‘adjust_proximalCPs’ ‘adjust_proximalCPsByNBC’ ‘adjust_proximalCPsByPWM’ ‘calculate_mse’ ‘find_valleyBySpline’ ‘get_PAscore’ ‘get_PAscore2’ ‘remove_convergentUTR3s’ ‘search_distalCPs’ ‘search_proximalCPs’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in Rd file 'get_ssRleCov.Rd': ‘[BSgenome:BSgenomeForge]{BSgenome::forgeBSgenomeDataPkg()}’ Missing link or links in Rd file 'set_globals.Rd': ‘[BSgenome:BSgenomeForge]{BSgenome::forgeBSgenomeDataPkg()}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... NOTE Documented arguments not in \usage in Rd file 'get_UTR3TotalCov.Rd': ‘gcCompensationensation’ 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 LazyData ... 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 get_usage4plot 18.270 0.427 18.685 get_chromosomes 6.441 0.260 6.684 extract_UTR3Anno 6.054 0.178 6.232 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/InPAS.Rcheck/00check.log’ for details.
InPAS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL InPAS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘InPAS’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (InPAS)
InPAS.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: x86_64-pc-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. > pkgs_required <- c( + "BSgenome.Mmusculus.UCSC.mm10", + "TxDb.Mmusculus.UCSC.mm10.knownGene", + "EnsDb.Mmusculus.v79", + "rtracklayer", + "GenomicRanges", + "RUnit", + "limma", "future.apply" + ) > for (pkg in pkgs_required) + { + require(pkg, character.only = TRUE) || stop(pkg, " can't be loaded!") + } Loading required package: BSgenome.Mmusculus.UCSC.mm10 Loading required package: BSgenome 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 Loading required package: S4Vectors Loading required package: stats4 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: GenomeInfoDb Loading required package: GenomicRanges Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: BiocIO Loading required package: rtracklayer Attaching package: 'rtracklayer' The following object is masked from 'package:BiocIO': FileForFormat Loading required package: TxDb.Mmusculus.UCSC.mm10.knownGene Loading required package: GenomicFeatures Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: EnsDb.Mmusculus.v79 Loading required package: ensembldb Loading required package: AnnotationFilter Attaching package: 'ensembldb' The following object is masked from 'package:stats': filter Loading required package: RUnit Loading required package: limma Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA Loading required package: future.apply Loading required package: future Attaching package: 'future' The following object is masked from 'package:AnnotationFilter': value > > BiocGenerics:::testPackage("InPAS") InPAS : Version 2.14.0 For more information see our website : https://bioconductor.org/packages/release/bioc/vignettes/InPAS/inst/doc/InPAS.html If you encounter a bug, please report : https://github.com/jianhong/InPAS/InPAS/issues coverage per sample per chromosome start at Fri Dec 20 01:33:35 2024. coverage per sample per chromosome done at Fri Dec 20 01:33:35 2024. total coverage start at Fri Dec 20 01:33:35 2024. total coverage done at Fri Dec 20 01:33:35 2024. backgroud around 3utr done at Fri Dec 20 01:33:35 2024. utr3 TotalCov done at Fri Dec 20 01:33:35 2024. chromsome chr1 coverage merged. Preparation for CPsite search done at Fri Dec 20 01:33:35 2024. No readable configuration file found Created registry in '/home/biocbuild/bbs-3.20-bioc/tmpdir/RtmppCnRLS/006.CPsites.out_chr1' using cluster functions 'Interactive' Adding 1 jobs ... Submitting 1 jobs in 1 chunks using cluster functions 'Interactive' ... coverage per sample per chromosome start at Fri Dec 20 01:33:42 2024. coverage per sample per chromosome done at Fri Dec 20 01:33:42 2024. total coverage start at Fri Dec 20 01:33:42 2024. total coverage done at Fri Dec 20 01:33:42 2024. backgroud around 3utr done at Fri Dec 20 01:33:42 2024. utr3 TotalCov done at Fri Dec 20 01:33:42 2024. chromsome chr1 coverage merged. Preparation for CPsite search done at Fri Dec 20 01:33:42 2024. No readable configuration file found Created registry in '/home/biocbuild/bbs-3.20-bioc/tmpdir/RtmppCnRLS/006.CPsites.out_chr1' using cluster functions 'Interactive' Adding 1 jobs ... Submitting 1 jobs in 1 chunks using cluster functions 'Interactive' ... Error in get_ssRleCov(bedgraph = filenames[i], tag = tags[i], genome = genome, : seqlevelsStyle of genome is different from bedgraph file. RUNIT TEST PROTOCOL -- Fri Dec 20 01:33:44 2024 *********************************************** Number of test functions: 3 Number of errors: 0 Number of failures: 0 1 Test Suite : InPAS RUnit Tests - 3 test functions, 0 errors, 0 failures Number of test functions: 3 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 27.775 0.838 28.606
InPAS.Rcheck/InPAS-Ex.timings
name | user | system | elapsed | |
addInPASTxDb | 0.197 | 0.002 | 0.199 | |
assemble_allCov | 0.002 | 0.000 | 0.001 | |
extract_UTR3Anno | 6.054 | 0.178 | 6.232 | |
filter_testOut | 0.107 | 0.001 | 0.109 | |
gcComp | 0.001 | 0.000 | 0.001 | |
gcContents | 0 | 0 | 0 | |
getInPASTxDb | 0.101 | 0.003 | 0.104 | |
get_UTR3eSet | 0.007 | 0.000 | 0.007 | |
get_chromosomes | 6.441 | 0.260 | 6.684 | |
get_seqLen | 0.129 | 0.002 | 0.131 | |
get_ssRleCov | 0.001 | 0.000 | 0.001 | |
get_usage4plot | 18.270 | 0.427 | 18.685 | |
parse_TxDb | 2.062 | 0.060 | 2.122 | |
run_coverageQC | 0.003 | 0.000 | 0.003 | |
run_singleGroupAnalysis | 0.009 | 0.000 | 0.010 | |
run_singleSampleAnalysis | 0.003 | 0.000 | 0.003 | |
search_CPs | 0.004 | 0.001 | 0.006 | |
setup_CPsSearch | 0.003 | 0.000 | 0.002 | |
setup_GSEA | 0.023 | 0.000 | 0.023 | |
setup_sqlitedb | 0.000 | 0.000 | 0.001 | |
test_dPDUI | 0.019 | 0.000 | 0.020 | |