Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-02-07 11:05:14 -0500 (Tue, 07 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4483 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" | 4249 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4272 |
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 GenomicFeatures package: - Please 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 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 774/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicFeatures 1.51.4 (landing page) H. Pagès
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
Package: GenomicFeatures |
Version: 1.51.4 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GenomicFeatures_1.51.4.tar.gz |
StartedAt: 2023-02-06 20:54:01 -0500 (Mon, 06 Feb 2023) |
EndedAt: 2023-02-06 21:06:47 -0500 (Mon, 06 Feb 2023) |
EllapsedTime: 765.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GenomicFeatures.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GenomicFeatures_1.51.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GenomicFeatures.Rcheck’ * using R Under development (unstable) (2023-01-10 r83596) * using platform: x86_64-pc-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 ‘GenomicFeatures/DESCRIPTION’ ... OK * this is package ‘GenomicFeatures’ version ‘1.51.4’ * 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 ... WARNING checkRd: (5) FeatureDb-class.Rd:31-34: \item in \describe must have non-empty label checkRd: (5) TxDb-class.Rd:30-33: \item in \describe must have non-empty label checkRd: (5) TxDb-class.Rd:34-39: \item in \describe must have non-empty label checkRd: (5) TxDb-class.Rd:40-43: \item in \describe must have non-empty label checkRd: (5) TxDb-class.Rd:44-52: \item in \describe must have non-empty label checkRd: (5) TxDb-class.Rd:53-59: \item in \describe must have non-empty label checkRd: (5) TxDb-class.Rd:60-65: \item in \describe must have non-empty label checkRd: (5) TxDb-class.Rd:66-71: \item in \describe must have non-empty label checkRd: (5) TxDb-class.Rd:72-80: \item in \describe must have non-empty label checkRd: (5) select-methods.Rd:21-25: \item in \describe must have non-empty label checkRd: (5) select-methods.Rd:26-50: \item in \describe must have non-empty label checkRd: (5) select-methods.Rd:51-55: \item in \describe must have non-empty label checkRd: (5) select-methods.Rd:56-62: \item in \describe must have non-empty label * 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 ... ERROR Running examples in ‘GenomicFeatures-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: makeTxDbFromBiomart > ### Title: Make a TxDb object from annotations available on a BioMart > ### database > ### Aliases: makeTxDbFromBiomart getChromInfoFromBiomart > > ### ** Examples > > ## --------------------------------------------------------------------- > ## A. BASIC USAGE > ## --------------------------------------------------------------------- > > ## We can use listDatasets() from the biomaRt package to list the > ## datasets available in the "ENSEMBL_MART_ENSEMBL" BioMart database: > library(biomaRt) > listMarts(host="https://www.ensembl.org") biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 108 2 ENSEMBL_MART_MOUSE Mouse strains 108 3 ENSEMBL_MART_SNP Ensembl Variation 108 4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 108 > mart <- useEnsembl(biomart="ENSEMBL_MART_ENSEMBL", host="https://www.ensembl.org") Error in if (Sys.time() - as.POSIXct(cache_entry$create_time) < 7) { : the condition has length > 1 Calls: useEnsembl -> .listEnsembl Execution halted * 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: the condition has length > 1 Test files with failing tests test_makeTxDbFromBiomart.R test_makeTxDbFromBiomart Error in BiocGenerics:::testPackage("GenomicFeatures") : unit tests failed for package GenomicFeatures Calls: <Anonymous> -> <Anonymous> In addition: Warning message: 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 in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘GenomicFeatures.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/GenomicFeatures.Rcheck/00check.log’ for details.
GenomicFeatures.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GenomicFeatures ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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.fail
R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-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. > 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, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' 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: rtracklayer Timing stopped at: 0.738 0.076 2.808 Error in if (Sys.time() - as.POSIXct(cache_entry$create_time) < 7) { : the condition has length > 1 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. 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 '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 Error in x$.self$finalize() : attempt to apply non-function In addition: Warning messages: 1: 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. 2: 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. 3: 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. 4: In (function (seqlevels, genome, new_style) : cannot switch some hg19's seqlevels from UCSC to NCBI style Error in x$.self$finalize() : attempt to apply non-function In addition: Warning message: call dbDisconnect() when finished working with a connection Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function RUNIT TEST PROTOCOL -- Mon Feb 6 21:05:56 2023 *********************************************** Number of test functions: 73 Number of errors: 1 Number of failures: 0 1 Test Suite : GenomicFeatures RUnit Tests - 73 test functions, 1 error, 0 failures ERROR in test_makeTxDbFromBiomart: Error in if (Sys.time() - as.POSIXct(cache_entry$create_time) < 7) { : the condition has length > 1 Test files with failing tests test_makeTxDbFromBiomart.R test_makeTxDbFromBiomart Error in BiocGenerics:::testPackage("GenomicFeatures") : unit tests failed for package GenomicFeatures Calls: <Anonymous> -> <Anonymous> In addition: Warning message: 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 | 0.052 | 0.000 | 0.052 | |
TxDb-class | 0.587 | 0.071 | 0.659 | |
as-format-methods | 1.977 | 0.057 | 2.034 | |
coordinate-mapping-methods | 49.392 | 3.591 | 53.731 | |
coverageByTranscript | 68.837 | 2.948 | 71.792 | |
exonicParts | 36.222 | 1.552 | 37.776 | |
extendExonsIntoIntrons | 2.597 | 0.116 | 2.733 | |
extractTranscriptSeqs | 11.932 | 0.508 | 12.440 | |
extractUpstreamSeqs | 1.447 | 0.160 | 1.607 | |
features | 0.069 | 0.004 | 0.073 | |
getPromoterSeq-methods | 0.602 | 0.008 | 0.610 | |
id2name | 0.189 | 0.000 | 0.189 | |
makeFeatureDbFromUCSC | 67.557 | 5.626 | 179.085 | |
makeTxDb | 0.098 | 0.004 | 0.103 | |