Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:42 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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" | 4415 |
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 87/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
APAlyzer 1.19.0 (landing page) Ruijia Wang
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the APAlyzer package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/APAlyzer.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: APAlyzer |
Version: 1.19.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:APAlyzer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings APAlyzer_1.19.0.tar.gz |
StartedAt: 2024-08-26 18:53:50 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 19:05:05 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 675.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: APAlyzer.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:APAlyzer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings APAlyzer_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/APAlyzer.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘APAlyzer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘APAlyzer’ version ‘1.19.0’ * package encoding: UTF-8 * 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 ... NOTE Found the following hidden files and directories: .BBSoptions .travis.yml 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 ‘APAlyzer’ 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 ... 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 ... WARNING 'library' or 'require' call not declared from: ‘HybridMTest’ 'library' or 'require' call to ‘HybridMTest’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .GTF2LE: no visible binding for global variable ‘group_name’ .GTF2refUTRraw: no visible binding for global variable ‘GENEID’ .annotatePASRegion: no visible global function definition for ‘queryHits’ APABox: no visible binding for global variable ‘APAreg’ APABox: no visible binding for global variable ‘RED’ APAVolcano: no visible binding for global variable ‘APAreg’ APAVolcano: no visible binding for global variable ‘color’ PASEXP_IPA: no visible global function definition for ‘Print’ ThreeMostPairBam: no visible global function definition for ‘Print’ download_testbam: no visible global function definition for ‘download.file’ Undefined global functions or variables: APAreg GENEID Print RED color download.file group_name queryHits Consider adding importFrom("utils", "download.file") to your NAMESPACE file. * checking Rd files ... NOTE prepare_Rd: download_testbam.Rd:7-8: Dropping empty section \arguments * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed download_testbam 9.726 18.749 260.333 PASEXP_3UTR 15.236 5.229 20.826 PASEXP_IPA 14.999 0.733 17.466 GENEXP_CDS 12.374 2.769 14.941 * 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, 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/APAlyzer.Rcheck/00check.log’ for details.
APAlyzer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL APAlyzer ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘APAlyzer’ ... ** using staged installation ** R ** 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 (APAlyzer)
APAlyzer.Rcheck/tests/runTests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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. > require("APAlyzer") || stop("unable to load Package:APAlyzer") Loading required package: APAlyzer [1] TRUE > require("GenomicRanges") || stop("unable to load Package:GenomicRanges") Loading required package: GenomicRanges 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 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 [1] TRUE > require("GenomicFeatures") || stop("unable to load Package:GenomicFeatures") 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")'. [1] TRUE > require("GenomicAlignments") || stop("unable to load Package:GenomicAlignments") Loading required package: GenomicAlignments Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars The following object is masked from 'package:Biobase': rowMedians Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: Rsamtools [1] TRUE > require("DESeq2") || stop("unable to load Package:DESeq2") Loading required package: DESeq2 [1] TRUE > require("SummarizedExperiment") || stop("unable to load Package:SummarizedExperiment") [1] TRUE > require("Rsubread") || stop("unable to load Package:Rsubread") Loading required package: Rsubread [1] TRUE > require("stats") || stop("unable to load Package:stats") [1] TRUE > require("testthat") || stop("unable to load testthat") Loading required package: testthat [1] TRUE > test_check("APAlyzer") [1] "SRR316184, Strand: forward, finished" [1] "SRR316185, Strand: forward, finished" [1] "SRR316186, Strand: forward, finished" [1] "SRR316187, Strand: forward, finished" [1] "SRR316188, Strand: forward, finished" [1] "SRR316189, Strand: forward, finished" ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.19.1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SRR316184.bam || || || || Paired-end : no || || Count read pairs : no || || Annotation : R data.frame || || Dir for temp files : . || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file .Rsubread_UserProvidedAnnotation_pid14949 ... || || Features : 536 || || Meta-features : 536 || || Chromosomes/contigs : 1 || || || || Process BAM file SRR316184.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 422429 || || Successfully assigned alignments : 6262 (1.5%) || || Running time : 0.01 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.19.1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SRR316184.bam || || || || Paired-end : no || || Count read pairs : no || || Annotation : R data.frame || || Dir for temp files : . || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file .Rsubread_UserProvidedAnnotation_pid14949 ... || || Features : 536 || || Meta-features : 536 || || Chromosomes/contigs : 1 || || || || Process BAM file SRR316184.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 422429 || || Successfully assigned alignments : 6258 (1.5%) || || Running time : 0.01 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.19.1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SRR316184.bam || || || || Paired-end : no || || Count read pairs : no || || Annotation : R data.frame || || Dir for temp files : . || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file .Rsubread_UserProvidedAnnotation_pid14949 ... || || Features : 222 || || Meta-features : 222 || || Chromosomes/contigs : 1 || || || || Process BAM file SRR316184.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 422429 || || Successfully assigned alignments : 22878 (5.4%) || || Running time : 0.01 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || \\============================================================================// [1] "SRR316184, Strand: forward, finished" ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.19.1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SRR316185.bam || || || || Paired-end : no || || Count read pairs : no || || Annotation : R data.frame || || Dir for temp files : . || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file .Rsubread_UserProvidedAnnotation_pid14949 ... || || Features : 536 || || Meta-features : 536 || || Chromosomes/contigs : 1 || || || || Process BAM file SRR316185.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 437626 || || Successfully assigned alignments : 5390 (1.2%) || || Running time : 0.01 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.19.1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SRR316185.bam || || || || Paired-end : no || || Count read pairs : no || || Annotation : R data.frame || || Dir for temp files : . || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file .Rsubread_UserProvidedAnnotation_pid14949 ... || || Features : 536 || || Meta-features : 536 || || Chromosomes/contigs : 1 || || || || Process BAM file SRR316185.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 437626 || || Successfully assigned alignments : 5387 (1.2%) || || Running time : 0.01 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.19.1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || SRR316185.bam || || || || Paired-end : no || || Count read pairs : no || || Annotation : R data.frame || || Dir for temp files : . || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file .Rsubread_UserProvidedAnnotation_pid14949 ... || || Features : 222 || || Meta-features : 222 || || Chromosomes/contigs : 1 || || || || Process BAM file SRR316185.bam... || || Strand specific : stranded || || Single-end reads are included. || || Total alignments : 437626 || || Successfully assigned alignments : 23378 (5.3%) || || Running time : 0.01 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || \\============================================================================// [1] "SRR316185, Strand: forward, finished" [1] "Reading and extracting (Strand = forward-reverse): untreated3_chr4.bam" [1] "Exporting: untreated3_chr4.3most.bam" [ FAIL 0 | WARN 1 | SKIP 0 | PASS 8 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 8 ] > > proc.time() user system elapsed 39.782 6.396 53.355
APAlyzer.Rcheck/APAlyzer-Ex.timings
name | user | system | elapsed | |
APABox | 0.520 | 0.035 | 0.566 | |
APAVolcano | 0.497 | 0.028 | 0.530 | |
APAdiff | 1.815 | 0.049 | 1.883 | |
GENEXP_CDS | 12.374 | 2.769 | 14.941 | |
PAS2GEF | 0.017 | 0.102 | 2.533 | |
PASEXP_3UTR | 15.236 | 5.229 | 20.826 | |
PASEXP_IPA | 14.999 | 0.733 | 17.466 | |
REF3UTR | 0.198 | 0.019 | 0.356 | |
REF4PAS | 0.147 | 0.014 | 0.307 | |
REFCDS | 0.624 | 0.047 | 0.679 | |
ThreeMostPairBam | 2.400 | 0.326 | 2.756 | |
download_testbam | 9.726 | 18.749 | 260.333 | |