Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:39 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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 |
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 578/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
easyRNASeq 2.35.0 (landing page) Nicolas Delhomme
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: easyRNASeq |
Version: 2.35.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings easyRNASeq_2.35.0.tar.gz |
StartedAt: 2023-02-28 02:21:43 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 02:40:37 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 1134.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: easyRNASeq.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings easyRNASeq_2.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/easyRNASeq.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘easyRNASeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘easyRNASeq’ version ‘2.35.0’ * 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 ... 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 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 ... NOTE .parallelize: no visible global function definition for ‘clusterApply’ Undefined global functions or variables: clusterApply * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed easyRNASeq-simpleRNASeq 86.624 1.549 106.606 easyRNASeq-package 58.626 2.375 78.547 easyRNASeq-synthetic-transcripts 41.475 0.492 45.937 BiocFileCache-methods 10.671 1.016 82.046 easyRNASeq-BamFileList 8.756 0.486 22.592 Rsamtools-methods 7.472 0.555 20.940 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ ERROR Running the tests in ‘tests/runTests.R’ failed. Last 13 lines of output: 3: In FUN(X[[i]], ...) : Bam file: 2baec1607f22_TTGCGA.bam is considered unstranded. 4: In FUN(X[[i]], ...) : Bam file: 2baec1607f22_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. 5: In FUN(X[[i]], ...) : Bam file: 2baec164bab29e_ATGGCT.bam is considered unstranded. 6: In FUN(X[[i]], ...) : Bam file: 2baec164bab29e_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. 7: In FUN(X[[i]], ...) : Bam file: 2baec175d93bd9_ACACTG.bam is considered unstranded. 8: In FUN(X[[i]], ...) : Bam file: 2baec175d93bd9_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'. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘simpleRNASeq.Rmd’ using ‘UTF-8’... OK ‘easyRNASeq.Rnw’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/easyRNASeq.Rcheck/00check.log’ for details.
easyRNASeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL easyRNASeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘easyRNASeq’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘BiocGenerics’ for request: ‘clusterApply’ when loading ‘easyRNASeq’ 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 No methods found in package ‘BiocGenerics’ for request: ‘clusterApply’ when loading ‘easyRNASeq’ ** testing if installed package can be loaded from final location No methods found in package ‘BiocGenerics’ for request: ‘clusterApply’ when loading ‘easyRNASeq’ ** testing if installed package keeps a record of temporary installation path * DONE (easyRNASeq)
easyRNASeq.Rcheck/tests/runTests.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (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) No methods found in package 'BiocGenerics' for request: 'clusterApply' when loading 'easyRNASeq' > tutorialData() [1] "/home/biocbuild/.cache/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 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, 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 Timing stopped at: 0.06 0.004 11.02 Error in h(simpleError(msg, call)) : error in evaluating the argument 'table' in selecting a method for function '%in%': Timeout was reached: [www.ensembl.org:443] Operation timed out after 10000 milliseconds with 0 bytes received RUNIT TEST PROTOCOL -- Tue Feb 28 02:35:10 2023 *********************************************** Number of test functions: 20 Number of errors: 1 Number of failures: 0 1 Test Suite : easyRNASeq RUnit Tests - 20 test functions, 1 error, 0 failures ERROR in test_internal_getAnnotation: Error in h(simpleError(msg, call)) : error in evaluating the argument 'table' in selecting a method for function '%in%': Timeout was reached: [www.ensembl.org:443] Operation timed out after 10000 milliseconds with 0 bytes received Test files with failing tests test_annotations.R test_internal_getAnnotation Error in BiocGenerics:::testPackage("easyRNASeq") : unit tests failed for package easyRNASeq In addition: Warning messages: 1: In FUN(X[[i]], ...) : Bam file: 2baec124f7afe7_ACTAGC.bam is considered unstranded. 2: In FUN(X[[i]], ...) : Bam file: 2baec124f7afe7_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. 3: In FUN(X[[i]], ...) : Bam file: 2baec1607f22_TTGCGA.bam is considered unstranded. 4: In FUN(X[[i]], ...) : Bam file: 2baec1607f22_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. 5: In FUN(X[[i]], ...) : Bam file: 2baec164bab29e_ATGGCT.bam is considered unstranded. 6: In FUN(X[[i]], ...) : Bam file: 2baec164bab29e_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. 7: In FUN(X[[i]], ...) : Bam file: 2baec175d93bd9_ACACTG.bam is considered unstranded. 8: In FUN(X[[i]], ...) : Bam file: 2baec175d93bd9_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'. Execution halted
easyRNASeq.Rcheck/easyRNASeq-Ex.timings
name | user | system | elapsed | |
BiocFileCache-methods | 10.671 | 1.016 | 82.046 | |
GenomicRanges-methods | 0.371 | 0.028 | 0.399 | |
IRanges-methods | 0.001 | 0.000 | 0.000 | |
Rsamtools-methods | 7.472 | 0.555 | 20.940 | |
ShortRead-methods | 0.001 | 0.000 | 0.000 | |
easyRNASeq-AnnotParam-accessors | 0.589 | 0.100 | 1.585 | |
easyRNASeq-AnnotParam-class | 0.001 | 0.000 | 0.001 | |
easyRNASeq-AnnotParam | 0.290 | 0.039 | 0.726 | |
easyRNASeq-BamFileList | 8.756 | 0.486 | 22.592 | |
easyRNASeq-BamParam-accessors | 0.002 | 0.000 | 0.001 | |
easyRNASeq-BamParam-class | 0.001 | 0.000 | 0.001 | |
easyRNASeq-BamParam | 0.003 | 0.000 | 0.003 | |
easyRNASeq-RnaSeqParam-accessors | 0.004 | 0.000 | 0.003 | |
easyRNASeq-RnaSeqParam-class | 0.001 | 0.000 | 0.001 | |
easyRNASeq-RnaSeqParam | 0.004 | 0.000 | 0.004 | |
easyRNASeq-accessors | 0 | 0 | 0 | |
easyRNASeq-annotation-methods | 0 | 0 | 0 | |
easyRNASeq-class | 0.001 | 0.000 | 0.001 | |
easyRNASeq-correction-methods | 0 | 0 | 0 | |
easyRNASeq-coverage-methods | 0.001 | 0.000 | 0.001 | |
easyRNASeq-easyRNASeq | 0.001 | 0.000 | 0.001 | |
easyRNASeq-island-methods | 0 | 0 | 0 | |
easyRNASeq-package | 58.626 | 2.375 | 78.547 | |
easyRNASeq-simpleRNASeq | 86.624 | 1.549 | 106.606 | |
easyRNASeq-summarization-methods | 0.000 | 0.000 | 0.001 | |
easyRNASeq-synthetic-transcripts | 41.475 | 0.492 | 45.937 | |
edgeR-methods | 0 | 0 | 0 | |
genomeIntervals-methods | 1.569 | 0.300 | 4.564 | |
parallel-methods | 0.001 | 0.000 | 0.001 | |