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This page was generated on 2021-10-15 15:06:34 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the easyRNASeq package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 546/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
easyRNASeq 2.28.0 (landing page) Nicolas Delhomme
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: easyRNASeq |
Version: 2.28.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings easyRNASeq_2.28.0.tar.gz |
StartedAt: 2021-10-14 18:38:40 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 18:53:30 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 890.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: easyRNASeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings easyRNASeq_2.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/easyRNASeq.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘easyRNASeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘easyRNASeq’ version ‘2.28.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 R 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 ... NOTE Namespace in Imports field not imported from: ‘locfit’ All declared Imports should be used. * 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 ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * 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 148.711 2.549 158.261 easyRNASeq-package 96.267 2.125 102.519 easyRNASeq-synthetic-transcripts 67.355 1.094 69.141 BiocFileCache-methods 29.254 1.111 42.928 easyRNASeq-BamFileList 21.304 0.570 26.261 Rsamtools-methods 16.302 0.491 21.157 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/easyRNASeq.Rcheck/00check.log’ for details.
easyRNASeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL easyRNASeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) 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: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, 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, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' 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 -- Thu Oct 14 18:53:19 2021 *********************************************** 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: 15186343c1e42_ATGGCT.bam is considered unstranded. 2: In FUN(X[[i]], ...) : Bam file: 15186343c1e42_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. 3: In FUN(X[[i]], ...) : Bam file: 1518638eb9f3a_ACACTG.bam is considered unstranded. 4: In FUN(X[[i]], ...) : Bam file: 1518638eb9f3a_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. 5: In FUN(X[[i]], ...) : Bam file: 1518639dcc1a5_ACTAGC.bam is considered unstranded. 6: In FUN(X[[i]], ...) : Bam file: 1518639dcc1a5_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: 151863d7e607a_TTGCGA.bam is considered unstranded. 8: In FUN(X[[i]], ...) : Bam file: 151863d7e607a_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. 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 129.366 3.044 152.226
easyRNASeq.Rcheck/easyRNASeq-Ex.timings
name | user | system | elapsed | |
BiocFileCache-methods | 29.254 | 1.111 | 42.928 | |
GenomicRanges-methods | 0.598 | 0.022 | 0.620 | |
IRanges-methods | 0.001 | 0.000 | 0.000 | |
Rsamtools-methods | 16.302 | 0.491 | 21.157 | |
ShortRead-methods | 0.001 | 0.001 | 0.002 | |
easyRNASeq-AnnotParam-accessors | 1.075 | 0.056 | 1.380 | |
easyRNASeq-AnnotParam-class | 0.001 | 0.001 | 0.002 | |
easyRNASeq-AnnotParam | 1.119 | 0.030 | 1.377 | |
easyRNASeq-BamFileList | 21.304 | 0.570 | 26.261 | |
easyRNASeq-BamParam-accessors | 0.001 | 0.000 | 0.002 | |
easyRNASeq-BamParam-class | 0.000 | 0.001 | 0.001 | |
easyRNASeq-BamParam | 0.002 | 0.001 | 0.003 | |
easyRNASeq-RnaSeqParam-accessors | 0.002 | 0.000 | 0.003 | |
easyRNASeq-RnaSeqParam-class | 0.001 | 0.001 | 0.001 | |
easyRNASeq-RnaSeqParam | 0.006 | 0.002 | 0.007 | |
easyRNASeq-accessors | 0.000 | 0.001 | 0.001 | |
easyRNASeq-annotation-methods | 0.001 | 0.001 | 0.001 | |
easyRNASeq-class | 0.001 | 0.001 | 0.001 | |
easyRNASeq-correction-methods | 0.001 | 0.001 | 0.001 | |
easyRNASeq-coverage-methods | 0.001 | 0.001 | 0.001 | |
easyRNASeq-easyRNASeq | 0.000 | 0.000 | 0.001 | |
easyRNASeq-island-methods | 0.000 | 0.000 | 0.001 | |
easyRNASeq-package | 96.267 | 2.125 | 102.519 | |
easyRNASeq-simpleRNASeq | 148.711 | 2.549 | 158.261 | |
easyRNASeq-summarization-methods | 0.000 | 0.001 | 0.001 | |
easyRNASeq-synthetic-transcripts | 67.355 | 1.094 | 69.141 | |
edgeR-methods | 0 | 0 | 0 | |
genomeIntervals-methods | 2.861 | 1.489 | 4.885 | |
parallel-methods | 0.000 | 0.000 | 0.001 | |