Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-18 12:04 -0400 (Sat, 18 Oct 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" | 4887 |
lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
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 841/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicFeatures 1.61.6 (landing page) H. Pagès
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the GenomicFeatures package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicFeatures.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: GenomicFeatures |
Version: 1.61.6 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicFeatures_1.61.6.tar.gz |
StartedAt: 2025-10-17 22:26:39 -0400 (Fri, 17 Oct 2025) |
EndedAt: 2025-10-17 22:42:35 -0400 (Fri, 17 Oct 2025) |
EllapsedTime: 955.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GenomicFeatures.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicFeatures_1.61.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/GenomicFeatures.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK * this is package ‘GenomicFeatures’ version ‘1.61.6’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'IRanges', 'Seqinfo', 'GenomicRanges', 'AnnotationDbi' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘GenomicFeatures’ 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 dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘AnnotationDbi:::.getMetaValue’ ‘AnnotationDbi:::.valid.colnames’ ‘AnnotationDbi:::.valid.metadata.table’ ‘AnnotationDbi:::.valid.table.colnames’ ‘AnnotationDbi:::dbEasyQuery’ ‘AnnotationDbi:::dbQuery’ ‘AnnotationDbi:::smartKeys’ ‘BiocGenerics:::testPackage’ ‘GenomicRanges:::unsafe.transcriptLocs2refLocs’ ‘GenomicRanges:::unsafe.transcriptWidths’ ‘IRanges:::regroupBySupergroup’ ‘S4Vectors:::V_recycle’ ‘S4Vectors:::decodeRle’ ‘S4Vectors:::extract_data_frame_rows’ ‘Seqinfo:::getSeqlevelsReplacementMode’ ‘Seqinfo:::normarg_new2old’ See the note in ?`:::` about the use of this operator. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed exonicParts 119.130 16.516 179.065 coverageByTranscript 78.427 6.982 96.160 coordinate-mapping-methods 70.164 6.987 115.511 extractTranscriptSeqs 14.479 1.069 18.436 getPromoterSeq-methods 5.713 6.092 34.577 transcriptLocs2refLocs 9.019 1.970 14.960 transcriptLengths 4.658 0.142 5.108 extendExonsIntoIntrons 3.377 1.007 9.010 extractUpstreamSeqs 1.937 0.867 6.830 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.R’ ERROR Running the tests in ‘tests/run_unitTests.R’ failed. Last 13 lines of output: Error in BiocGenerics:::testPackage("GenomicFeatures") : unit tests failed for package GenomicFeatures Calls: <Anonymous> -> <Anonymous> In addition: Warning messages: 1: In .makeTxDb_normarg_chrominfo(chrominfo) : genome version information is not available for this TxDb object 2: In (function (seqlevels, genome, new_style) : cannot switch some hg19's seqlevels from UCSC to NCBI style 3: In .makeTxDb_normarg_chrominfo(chrominfo) : genome version information is not available for this TxDb object 4: In (function (seqlevels, genome, new_style) : cannot switch some hg19's seqlevels from UCSC to NCBI style Execution halted * 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 ERROR, 1 NOTE See ‘/Users/biocbuild/bbs-3.22-bioc/meat/GenomicFeatures.Rcheck/00check.log’ for details.
GenomicFeatures.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenomicFeatures ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘GenomicFeatures’ ... ** this is package ‘GenomicFeatures’ version ‘1.61.6’ ** 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 (GenomicFeatures)
GenomicFeatures.Rcheck/tests/run_unitTests.Rout.fail
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 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("GenomicFeatures") || stop("unable to load GenomicFeatures package") Loading required package: GenomicFeatures 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 Loading required package: S4Vectors Loading required package: stats4 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: Seqinfo Loading required package: GenomicRanges 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 > GenomicFeatures:::.test() Loading required package: BSgenome Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: BiocIO Loading required package: rtracklayer Attaching package: 'txdbmaker' The following objects are masked from 'package:GenomicFeatures': UCSCFeatureDbTableSchema, browseUCSCtrack, getChromInfoFromBiomart, makeFDbPackageFromUCSC, makeFeatureDbFromUCSC, makePackageName, makeTxDb, makeTxDbFromBiomart, makeTxDbFromEnsembl, makeTxDbFromGFF, makeTxDbFromGRanges, makeTxDbFromUCSC, makeTxDbPackage, makeTxDbPackageFromBiomart, makeTxDbPackageFromUCSC, supportedMiRBaseBuildValues, supportedUCSCFeatureDbTables, supportedUCSCFeatureDbTracks, supportedUCSCtables Timing stopped at: 0.011 0 0.01 Error in checkIdentical(res, exp) : FALSE In addition: Warning messages: 1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequences a, b, and c. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. 2: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence c. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. 3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence c. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. 4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 4 out-of-bound ranges located on sequences 1, 2, 3, and 4. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. 5: In .get_cds_IDX(mcols0$type, mcols0$phase) : The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored. 6: In .makeTxDb_normarg_chrominfo(chrominfo) : genome version information is not available for this TxDb object Timing stopped at: 1.308 0.65 2.117 Error in checkTrue("uc001aaa.3" %in% k1) : Test not TRUE Timing stopped at: 0.018 0 0.019 Error in checkTrue(length(res) == 21, length(unique(unlist(res2)))) : Test not TRUE 22 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK RUNIT TEST PROTOCOL -- Fri Oct 17 22:42:20 2025 *********************************************** Number of test functions: 67 Number of errors: 0 Number of failures: 3 1 Test Suite : GenomicFeatures RUnit Tests - 67 test functions, 0 errors, 3 failures FAILURE in test_getTableColMapping: Error in checkIdentical(res, exp) : FALSE FAILURE in test_keys_advancedArgs: Error in checkTrue("uc001aaa.3" %in% k1) : Test not TRUE FAILURE in test_makeColAbbreviations: Error in checkTrue(length(res) == 21, length(unique(unlist(res2)))) : Test not TRUE 22 Test files with failing tests test_select-methods.R test_getTableColMapping test_keys_advancedArgs test_makeColAbbreviations Error in BiocGenerics:::testPackage("GenomicFeatures") : unit tests failed for package GenomicFeatures Calls: <Anonymous> -> <Anonymous> In addition: Warning messages: 1: In .makeTxDb_normarg_chrominfo(chrominfo) : genome version information is not available for this TxDb object 2: In (function (seqlevels, genome, new_style) : cannot switch some hg19's seqlevels from UCSC to NCBI style 3: In .makeTxDb_normarg_chrominfo(chrominfo) : genome version information is not available for this TxDb object 4: In (function (seqlevels, genome, new_style) : cannot switch some hg19's seqlevels from UCSC to NCBI style Execution halted
GenomicFeatures.Rcheck/GenomicFeatures-Ex.timings
name | user | system | elapsed | |
FeatureDb-class | 0.841 | 0.015 | 0.866 | |
TxDb-class | 1.593 | 0.195 | 1.841 | |
as-format-methods | 1.354 | 0.034 | 1.599 | |
coordinate-mapping-methods | 70.164 | 6.987 | 115.511 | |
coverageByTranscript | 78.427 | 6.982 | 96.160 | |
exonicParts | 119.130 | 16.516 | 179.065 | |
extendExonsIntoIntrons | 3.377 | 1.007 | 9.010 | |
extractTranscriptSeqs | 14.479 | 1.069 | 18.436 | |
extractUpstreamSeqs | 1.937 | 0.867 | 6.830 | |
features | 0.065 | 0.005 | 0.072 | |
getPromoterSeq-methods | 5.713 | 6.092 | 34.577 | |
id2name | 0.226 | 0.015 | 0.307 | |
mapIdsToRanges | 0.807 | 0.057 | 1.114 | |
mapRangesToIds | 0.976 | 0.040 | 1.068 | |
nearest-methods | 0.724 | 0.035 | 0.842 | |
proteinToGenome | 2.026 | 0.153 | 2.377 | |
select-methods | 0.219 | 0.012 | 0.288 | |
transcriptLengths | 4.658 | 0.142 | 5.108 | |
transcriptLocs2refLocs | 9.019 | 1.970 | 14.960 | |
transcripts | 3.272 | 0.274 | 3.604 | |
transcriptsBy | 1.257 | 0.032 | 1.318 | |
transcriptsByOverlaps | 0.233 | 0.006 | 0.242 | |