Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:45 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 616/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
easyRNASeq 2.43.0 (landing page) Nicolas Delhomme
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the easyRNASeq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/easyRNASeq.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: easyRNASeq |
Version: 2.43.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings easyRNASeq_2.43.0.tar.gz |
StartedAt: 2024-12-22 19:09:47 -0500 (Sun, 22 Dec 2024) |
EndedAt: 2024-12-22 19:13:53 -0500 (Sun, 22 Dec 2024) |
EllapsedTime: 245.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: easyRNASeq.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings easyRNASeq_2.43.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/easyRNASeq.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * 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 ‘easyRNASeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘easyRNASeq’ version ‘2.43.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Files named as vignettes but with no recognized vignette engine: ‘inst/doc/01-Introduction.Rmd’ ‘inst/doc/02-AnnotParam.Rmd’ ‘inst/doc/03-SyntheticTranscripts.Rmd’ ‘inst/doc/04-BamParam.Rmd’ ‘inst/doc/05-RnaSeqParam.Rmd’ ‘inst/doc/06-simpleRNASeq.Rmd’ ‘inst/doc/07-cleanUp.Rmd’ ‘inst/doc/08-Session-Info.Rmd’ ‘inst/doc/09-Acknowledgments.Rmd’ ‘inst/doc/10-Foonotes.Rmd’ ‘inst/doc/11-Images.Rmd’ ‘inst/doc/12-Appendix.Rmd’ (Is a VignetteBuilder field missing?) * 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 ‘easyRNASeq’ 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 whether startup messages can be suppressed ... 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 ... OK * checking Rd files ... NOTE checkRd: (-1) easyRNASeq-AnnotParam.Rd:40-43: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyRNASeq-AnnotParam.Rd:44-51: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyRNASeq-RnaSeqParam-class.Rd:14: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyRNASeq-RnaSeqParam-class.Rd:15: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyRNASeq-annotation-methods.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyRNASeq-annotation-methods.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyRNASeq-correction-methods.Rd:48-50: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyRNASeq-correction-methods.Rd:51-54: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyRNASeq-datasets.Rd:11-21: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyRNASeq-internal-AnnotParam-methods.Rd:25: Lost braces 25 | These are \code{\linkS4class{AnnotParam}}{AnnotParam} class internal methods: | ^ checkRd: (-1) easyRNASeq-package.Rd:109-112: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyRNASeq-package.Rd:113-121: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: BiocFileCache-methods.Rd: BiocFileCache-class GenomicRanges-methods.Rd: GRangesList-class, GAlignments-class, DataFrame-class IRanges-methods.Rd: IRangesList-class Rsamtools-methods.Rd: BamFile-class ShortRead-methods.Rd: AlignedRead-class, SRFilter-class basename-methods.Rd: BamFile-class easyRNASeq-annotation-internal-methods.Rd: Genome_intervals_stranded-class easyRNASeq-class.Rd: GRangesList-class, RleList-class easyRNASeq-coverage-methods.Rd: Rle-class easyRNASeq-easyRNASeq.Rd: GRangesList-class easyRNASeq-simpleRNASeq.Rd: BamFile-class edgeR-methods.Rd: DGEList-class file.exists-methods.Rd: BamFile-class genomeIntervals-methods.Rd: Genome_intervals-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Documented arguments not in \usage in Rd file 'easyRNASeq-annotation-internal-methods.Rd': ‘annotation.type’ ‘fields’ ‘filename’ ‘format’ ‘gAnnot’ ‘nbCore’ Objects in \usage without \alias in Rd file 'easyRNASeq-coverage-methods.Rd': ‘\S4method{fetchCoverage}{RNAseq}’ Documented arguments not in \usage in Rd file 'easyRNASeq-internal-AnnotParam-methods.Rd': ‘...’ Documented arguments not in \usage in Rd file 'easyRNASeq-internal-methods.Rd': ‘arg’ ‘chr.names’ ‘fun’ ‘organism’ ‘type’ ‘value’ ‘x’ ‘...’ Documented arguments not in \usage in Rd file 'easyRNASeq-summarization-internal-methods.Rd': ‘chr.map’ ‘chr.sel’ ‘cList’ ‘count’ ‘filename’ ‘filter’ ‘format’ ‘gapped’ ‘min.cov’ ‘min.length’ ‘max.gap’ ‘plot’ ‘rnaSeq’ ‘summarization’ ‘silent’ ‘subType’ ‘type’ ‘validity.check’ ‘values’ ‘...’ 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 line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... 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 easyRNASeq-simpleRNASeq 37.640 0.531 38.558 easyRNASeq-package 24.487 0.437 25.328 easyRNASeq-synthetic-transcripts 19.311 0.298 19.964 BiocFileCache-methods 3.164 0.406 14.906 * 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, 2 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/easyRNASeq.Rcheck/00check.log’ for details.
easyRNASeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL easyRNASeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘easyRNASeq’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘basename’ from package ‘base’ in package ‘easyRNASeq’ Creating a generic function for ‘file.exists’ from package ‘base’ in package ‘easyRNASeq’ ** 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 (easyRNASeq)
easyRNASeq.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 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. > # get the example data > library(easyRNASeq) > tutorialData() [1] "/Users/biocbuild/Library/Caches/easyRNASeq" > > # set the env.var > #TUTORIAL.DATA <- get("TUTORIAL.DATA",envir=as.environment("package:easyRNASeq")) > > # run the tests > BiocGenerics:::testPackage("easyRNASeq") Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following object is masked from 'package:easyRNASeq': basename 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors 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 No validation performed at that stage Validated a datasource of type biomaRt No validation performed at that stage Validated a datasource of type rda Read 1000 records Validated a datasource of type gtf Read 999 records Validated a datasource of type gff3 RUNIT TEST PROTOCOL -- Sun Dec 22 19:13:48 2024 *********************************************** Number of test functions: 20 Number of errors: 0 Number of failures: 0 1 Test Suite : easyRNASeq RUnit Tests - 20 test functions, 0 errors, 0 failures Number of test functions: 20 Number of errors: 0 Number of failures: 0 Warning messages: 1: In FUN(X[[i]], ...) : Bam file: 178b815783bc9_TTGCGA.bam is considered unstranded. 2: In FUN(X[[i]], ...) : Bam file: 178b815783bc9_TTGCGA.bam Strandedness could not be determined using 19659 regions spanning 1381886 bp on either strand at a 90% cutoff; 73.37 percent appear to be stranded. 3: In FUN(X[[i]], ...) : Bam file: 178b85f760f3b_ATGGCT.bam is considered unstranded. 4: In FUN(X[[i]], ...) : Bam file: 178b85f760f3b_ATGGCT.bam Strandedness could not be determined using 18462 regions spanning 1280337 bp on either strand at a 90% cutoff; 74.26 percent appear to be stranded. 5: In FUN(X[[i]], ...) : Bam file: 178b8633c44db_ACTAGC.bam is considered unstranded. 6: In FUN(X[[i]], ...) : Bam file: 178b8633c44db_ACTAGC.bam Strandedness could not be determined using 14772 regions spanning 1023473 bp on either strand at a 90% cutoff; 76.6 percent appear to be stranded. 7: In FUN(X[[i]], ...) : Bam file: 178b86ed40b9c_ACACTG.bam is considered unstranded. 8: In FUN(X[[i]], ...) : Bam file: 178b86ed40b9c_ACACTG.bam Strandedness could not be determined using 18615 regions spanning 1300192 bp on either strand at a 90% cutoff; 73.67 percent appear to be stranded. 9: In simpleRNASeq(bamFiles = bamFiles, param = param, verbose = FALSE) : As of version 2.15.5, easyRNASeq assumes that, if the data is strand specific, the sequencing was done using a protocol such as the Illumina TruSeq, where the reverse strand is quantified - i.e. the strandProtocol argument of the BamParam class defaults to 'reverse'. > > # cleanup > # removebfc(easyRNASeq:::.get_cache(),ask=FALSE) > > proc.time() user system elapsed 26.529 0.742 33.805
easyRNASeq.Rcheck/easyRNASeq-Ex.timings
name | user | system | elapsed | |
BiocFileCache-methods | 3.164 | 0.406 | 14.906 | |
GenomicRanges-methods | 0.099 | 0.009 | 0.110 | |
IRanges-methods | 0 | 0 | 0 | |
Rsamtools-methods | 0.804 | 0.088 | 1.220 | |
ShortRead-methods | 0.000 | 0.001 | 0.000 | |
easyRNASeq-AnnotParam-accessors | 0.053 | 0.004 | 0.079 | |
easyRNASeq-AnnotParam-class | 0.001 | 0.000 | 0.000 | |
easyRNASeq-AnnotParam | 0.050 | 0.005 | 0.078 | |
easyRNASeq-BamFileList | 1.118 | 0.106 | 1.667 | |
easyRNASeq-BamParam-accessors | 0.000 | 0.000 | 0.001 | |
easyRNASeq-BamParam-class | 0 | 0 | 0 | |
easyRNASeq-BamParam | 0.001 | 0.000 | 0.000 | |
easyRNASeq-RnaSeqParam-accessors | 0.001 | 0.000 | 0.001 | |
easyRNASeq-RnaSeqParam-class | 0 | 0 | 0 | |
easyRNASeq-RnaSeqParam | 0.001 | 0.000 | 0.001 | |
easyRNASeq-accessors | 0 | 0 | 0 | |
easyRNASeq-annotation-methods | 0.000 | 0.000 | 0.001 | |
easyRNASeq-class | 0 | 0 | 0 | |
easyRNASeq-correction-methods | 0 | 0 | 0 | |
easyRNASeq-coverage-methods | 0 | 0 | 0 | |
easyRNASeq-easyRNASeq | 0 | 0 | 0 | |
easyRNASeq-island-methods | 0 | 0 | 0 | |
easyRNASeq-package | 24.487 | 0.437 | 25.328 | |
easyRNASeq-simpleRNASeq | 37.640 | 0.531 | 38.558 | |
easyRNASeq-summarization-methods | 0 | 0 | 0 | |
easyRNASeq-synthetic-transcripts | 19.311 | 0.298 | 19.964 | |
edgeR-methods | 0 | 0 | 0 | |
genomeIntervals-methods | 0.512 | 0.274 | 1.110 | |
parallel-methods | 0.001 | 0.000 | 0.000 | |