Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-02-28 11:38:58 -0500 (Wed, 28 Feb 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4671 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4411 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4438 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4414 |
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 819/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicFeatures 1.55.3 (landing page) H. Pagès
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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: 1.55.3 |
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_1.55.3.tar.gz |
StartedAt: 2024-02-27 06:22:14 -0500 (Tue, 27 Feb 2024) |
EndedAt: 2024-02-27 06:55:02 -0500 (Tue, 27 Feb 2024) |
EllapsedTime: 1967.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GenomicFeatures.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.55.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GenomicFeatures.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 ‘GenomicFeatures/DESCRIPTION’ ... OK * this is package ‘GenomicFeatures’ version ‘1.55.3’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb', '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 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 ':::' call which should be '::': ‘rtracklayer:::tableNames’ See the note in ?`:::` about the use of this operator. 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’ ‘GenomeInfoDb:::check_tax_id’ ‘GenomeInfoDb:::getSeqlevelsReplacementMode’ ‘GenomeInfoDb:::lookup_organism_by_tax_id’ ‘GenomeInfoDb:::lookup_tax_id_by_organism’ ‘GenomeInfoDb:::make_circ_flags_from_circ_seqs’ ‘GenomeInfoDb:::normarg_new2old’ ‘GenomicRanges:::unsafe.transcriptLocs2refLocs’ ‘GenomicRanges:::unsafe.transcriptWidths’ ‘IRanges:::regroupBySupergroup’ ‘S4Vectors:::V_recycle’ ‘S4Vectors:::anyMissingOrOutside’ ‘S4Vectors:::decodeRle’ ‘S4Vectors:::extract_data_frame_rows’ ‘S4Vectors:::quick_togroup’ ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’ ‘rtracklayer:::resourceDescription’ 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 makeFeatureDbFromUCSC 155.989 5.713 224.712 coverageByTranscript 150.106 6.214 178.392 makeTxDbFromBiomart 100.842 5.824 196.035 coordinate-mapping-methods 99.877 6.014 127.096 exonicParts 79.138 3.352 99.266 extractTranscriptSeqs 27.635 0.665 31.976 makeTxDbFromUCSC 20.074 0.370 52.370 makeTxDbFromGFF 18.063 0.197 21.325 transcriptLocs2refLocs 15.823 1.436 20.101 getPromoterSeq-methods 6.348 2.681 14.095 transcriptLengths 8.153 0.072 9.699 makeTxDbFromGRanges 6.298 0.076 7.394 extendExonsIntoIntrons 5.773 0.435 7.417 transcripts 5.932 0.176 7.290 proteinToGenome 4.355 0.097 5.115 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.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 ‘/Users/biocbuild/bbs-3.19-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/4.4-x86_64/Resources/library’ * installing *source* package ‘GenomicFeatures’ ... ** 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
R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 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("GenomicFeatures") || stop("unable to load GenomicFeatures package") Loading required package: GenomicFeatures 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 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: GenomeInfoDb 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: 'rtracklayer' The following object is masked from 'package:BiocIO': FileForFormat Download and preprocess the 'transcripts' data frame ... OK Download and preprocess the 'chrominfo' data frame ... OK Download and preprocess the 'splicings' data frame ... OK Download and preprocess the 'genes' data frame ... 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 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 Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Error in x$.self$finalize() : attempt to apply non-function In addition: Warning messages: 1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence chrUn_gl000237. 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 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. 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 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. 5: 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. 6: In .get_cds_IDX(mcols0$type, mcols0$phase) : The "phase" metadata column contains non-NA values for features of type exon. This information was ignored. 7: 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. Error in x$.self$finalize() : attempt to apply non-function In addition: Warning message: call dbDisconnect() when finished working with a connection '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: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: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: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 -- Tue Feb 27 06:54:22 2024 *********************************************** Number of test functions: 75 Number of errors: 0 Number of failures: 0 1 Test Suite : GenomicFeatures RUnit Tests - 75 test functions, 0 errors, 0 failures Number of test functions: 75 Number of errors: 0 Number of failures: 0 Warning messages: 1: 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. 2: In (function (seqlevels, genome, new_style) : cannot switch some hg19's seqlevels from UCSC to NCBI style 3: In (function (seqlevels, genome, new_style) : cannot switch some hg19's seqlevels from UCSC to NCBI style > > proc.time() user system elapsed 257.200 5.820 343.996
GenomicFeatures.Rcheck/GenomicFeatures-Ex.timings
name | user | system | elapsed | |
FeatureDb-class | 0.125 | 0.009 | 0.155 | |
TxDb-class | 1.318 | 0.201 | 1.766 | |
as-format-methods | 2.841 | 0.149 | 3.447 | |
coordinate-mapping-methods | 99.877 | 6.014 | 127.096 | |
coverageByTranscript | 150.106 | 6.214 | 178.392 | |
exonicParts | 79.138 | 3.352 | 99.266 | |
extendExonsIntoIntrons | 5.773 | 0.435 | 7.417 | |
extractTranscriptSeqs | 27.635 | 0.665 | 31.976 | |
extractUpstreamSeqs | 3.025 | 0.546 | 4.373 | |
features | 0.125 | 0.007 | 0.141 | |
getPromoterSeq-methods | 6.348 | 2.681 | 14.095 | |
id2name | 0.447 | 0.014 | 0.704 | |
makeFeatureDbFromUCSC | 155.989 | 5.713 | 224.712 | |
makeTxDb | 0.224 | 0.005 | 0.271 | |
makeTxDbFromBiomart | 100.842 | 5.824 | 196.035 | |
makeTxDbFromEnsembl | 0.001 | 0.001 | 0.001 | |
makeTxDbFromGFF | 18.063 | 0.197 | 21.325 | |
makeTxDbFromGRanges | 6.298 | 0.076 | 7.394 | |
makeTxDbFromUCSC | 20.074 | 0.370 | 52.370 | |
makeTxDbPackage | 0.602 | 0.039 | 2.872 | |
mapIdsToRanges | 1.502 | 0.019 | 1.763 | |
mapRangesToIds | 1.607 | 0.018 | 1.873 | |
microRNAs | 0.001 | 0.000 | 0.001 | |
nearest-methods | 1.366 | 0.025 | 1.595 | |
proteinToGenome | 4.355 | 0.097 | 5.115 | |
select-methods | 0.454 | 0.020 | 0.568 | |
transcriptLengths | 8.153 | 0.072 | 9.699 | |
transcriptLocs2refLocs | 15.823 | 1.436 | 20.101 | |
transcripts | 5.932 | 0.176 | 7.290 | |
transcriptsBy | 1.922 | 0.039 | 2.299 | |
transcriptsByOverlaps | 0.431 | 0.010 | 0.491 | |