Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-27 12:07 -0400 (Sat, 27 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4832 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4620 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4565 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
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 1798/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RNAmodR 1.23.2 (landing page) Felix G.M. Ernst
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the RNAmodR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RNAmodR.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: RNAmodR |
Version: 1.23.2 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:RNAmodR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RNAmodR_1.23.2.tar.gz |
StartedAt: 2025-09-26 11:23:21 -0000 (Fri, 26 Sep 2025) |
EndedAt: 2025-09-26 11:37:38 -0000 (Fri, 26 Sep 2025) |
EllapsedTime: 856.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RNAmodR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:RNAmodR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RNAmodR_1.23.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/RNAmodR.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RNAmodR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RNAmodR’ version ‘1.23.2’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘RNAmodR’ 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 dependencies in R code ... NOTE Unexported objects imported by ':::' calls: 'BiocGenerics:::replaceSlots' 'Biostrings:::XString' 'IRanges:::.valid.CompressedList' 'IRanges:::coerceToCompressedList' 'S4Vectors:::.valid.DataFrame' 'S4Vectors:::labeledLine' 'S4Vectors:::make_zero_col_DataFrame' 'S4Vectors:::prepare_objects_to_bind' See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: '.get_inosine_score' * 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 ... NOTE Documented arguments not in \usage in Rd file 'RNAmodR-internals.Rd': ‘object’ ‘range’ ‘data’ ‘modType’ ‘scoreFun’ ‘source’ ‘type’ ‘j’ ‘value’ 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed stats 61.698 5.886 85.147 CoverageSequenceData-class 11.375 1.007 23.461 ModInosine 11.518 0.847 20.903 EndSequenceData-class 9.026 0.843 18.417 PileupSequenceData-class 7.719 0.589 16.224 ProtectedEndSequenceData-class 7.579 0.604 15.635 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 2 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/RNAmodR.Rcheck/00check.log’ for details.
RNAmodR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL RNAmodR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘RNAmodR’ ... ** this is package ‘RNAmodR’ version ‘1.23.2’ ** using staged installation ** R ** data ** 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 (RNAmodR)
RNAmodR.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > library(testthat) > library(RNAmodR) Loading required package: S4Vectors 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 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 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: GenomicRanges Loading required package: Seqinfo Loading required package: Modstrings Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Attaching package: 'RNAmodR' The following object is masked from 'package:testthat': compare > > test_check("RNAmodR") [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/10e9037590832a_2547' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/10e9037590832a_2547' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/10e9037590832a_2547' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/10e9037590832a_2547' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/10e9037590832a_2547' [E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/10e9037590832a_2547' [ FAIL 0 | WARN 2 | SKIP 9 | PASS 192 ] ══ Skipped tests (9) ═══════════════════════════════════════════════════════════ • On Bioconductor (9): 'test-0SequenceData.R:53:3', 'test-0SequenceDataFrame.R:23:3', 'test-1SequenceDataSet.R:57:3', 'test-2Modifier.R:85:3', 'test-3normalization.R:3:3', 'test-3subset.R:4:3', 'test-3zcomparison.R:4:3', 'test-4roc.R:3:3', 'test-8visualization.R:158:3' [ FAIL 0 | WARN 2 | SKIP 9 | PASS 192 ] > > proc.time() user system elapsed 61.933 1.572 81.538
RNAmodR.Rcheck/RNAmodR-Ex.timings
name | user | system | elapsed | |
CoverageSequenceData-class | 11.375 | 1.007 | 23.461 | |
EndSequenceData-class | 9.026 | 0.843 | 18.417 | |
ModInosine-functions | 0.820 | 0.032 | 0.854 | |
ModInosine | 11.518 | 0.847 | 20.903 | |
Modifier-functions | 0.271 | 0.024 | 0.301 | |
NormEndSequenceData-class | 0 | 0 | 0 | |
PileupSequenceData-class | 7.719 | 0.589 | 16.224 | |
ProtectedEndSequenceData-class | 7.579 | 0.604 | 15.635 | |
RNAmodR-development | 0.092 | 0.004 | 0.101 | |
SequenceData-functions | 0.082 | 0.000 | 0.083 | |
SequenceDataFrame-class | 0.053 | 0.000 | 0.053 | |
SequenceDataList-class | 0.141 | 0.000 | 0.143 | |
SequenceDataSet-class | 0.090 | 0.000 | 0.092 | |
SequenceModDNAStringSetTrack-class | 1.464 | 0.093 | 1.665 | |
SequenceModRNAStringSetTrack-class | 0.033 | 0.000 | 0.034 | |
aggregate | 0.663 | 0.000 | 0.669 | |
compareByCoord | 3.114 | 0.012 | 3.432 | |
modify | 0.720 | 0.008 | 1.140 | |
plotData | 2.331 | 0.098 | 2.509 | |
plotROC | 1.986 | 0.082 | 2.185 | |
settings | 0.104 | 0.000 | 0.105 | |
stats | 61.698 | 5.886 | 85.147 | |
subsetByCoord | 0.808 | 0.012 | 1.006 | |