Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:31 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 772/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicFeatures 1.51.4 (landing page) H. Pagès
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ||||||||
Package: GenomicFeatures |
Version: 1.51.4 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicFeatures.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GenomicFeatures_1.51.4.tar.gz |
StartedAt: 2022-12-29 00:04:13 -0500 (Thu, 29 Dec 2022) |
EndedAt: 2022-12-29 00:18:11 -0500 (Thu, 29 Dec 2022) |
EllapsedTime: 837.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GenomicFeatures.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicFeatures.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GenomicFeatures_1.51.4.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/GenomicFeatures.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * 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 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed makeFeatureDbFromUCSC 75.32 3.25 105.38 coverageByTranscript 59.42 1.83 61.27 makeTxDbFromBiomart 52.11 2.24 181.34 coordinate-mapping-methods 44.05 2.37 53.50 exonicParts 33.37 1.41 35.66 extractTranscriptSeqs 12.00 0.59 12.68 transcriptLocs2refLocs 7.02 1.14 8.25 makeTxDbFromUCSC 7.75 0.19 27.34 makeTxDbFromGFF 6.84 0.03 6.89 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'run_unitTests.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... 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, 2 NOTEs See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/GenomicFeatures.Rcheck/00check.log' for details.
GenomicFeatures.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL GenomicFeatures ### ############################################################################## ############################################################################## * installing to library 'F:/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
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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 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 '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 RUNIT TEST PROTOCOL -- Thu Dec 29 00:17:56 2022 *********************************************** Number of test functions: 73 Number of errors: 0 Number of failures: 0 1 Test Suite : GenomicFeatures RUnit Tests - 73 test functions, 0 errors, 0 failures Number of test functions: 73 Number of errors: 0 Number of failures: 0 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 exon. This information was ignored. 6: 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. 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. 8: In (function (seqlevels, genome, new_style) : cannot switch some of hg19's seqlevels from UCSC to NCBI style 9: In (function (seqlevels, genome, new_style) : cannot switch some of hg19's seqlevels from UCSC to NCBI style > > proc.time() user system elapsed 91.10 2.65 127.29
GenomicFeatures.Rcheck/GenomicFeatures-Ex.timings
name | user | system | elapsed | |
FeatureDb-class | 0.00 | 0.03 | 0.03 | |
TxDb-class | 0.50 | 0.05 | 0.55 | |
as-format-methods | 1.67 | 0.05 | 1.73 | |
coordinate-mapping-methods | 44.05 | 2.37 | 53.50 | |
coverageByTranscript | 59.42 | 1.83 | 61.27 | |
exonicParts | 33.37 | 1.41 | 35.66 | |
extendExonsIntoIntrons | 2.21 | 0.22 | 2.69 | |
extractTranscriptSeqs | 12.00 | 0.59 | 12.68 | |
extractUpstreamSeqs | 2.11 | 0.25 | 2.73 | |
features | 0.05 | 0.00 | 0.05 | |
getPromoterSeq-methods | 0.65 | 0.05 | 0.70 | |
id2name | 0.16 | 0.00 | 0.18 | |
makeFeatureDbFromUCSC | 75.32 | 3.25 | 105.38 | |
makeTxDb | 0.35 | 0.01 | 0.36 | |
makeTxDbFromBiomart | 52.11 | 2.24 | 181.34 | |
makeTxDbFromEnsembl | 0 | 0 | 0 | |
makeTxDbFromGFF | 6.84 | 0.03 | 6.89 | |
makeTxDbFromGRanges | 2.34 | 0.06 | 2.41 | |
makeTxDbFromUCSC | 7.75 | 0.19 | 27.34 | |
makeTxDbPackage | 0.25 | 0.03 | 2.12 | |
mapIdsToRanges | 0.57 | 0.00 | 0.57 | |
mapRangesToIds | 0.53 | 0.02 | 0.54 | |
microRNAs | 0 | 0 | 0 | |
nearest-methods | 0.78 | 0.06 | 0.85 | |
proteinToGenome | 1.28 | 0.03 | 1.31 | |
select-methods | 0.14 | 0.01 | 0.16 | |
transcriptLengths | 3.17 | 0.02 | 3.18 | |
transcriptLocs2refLocs | 7.02 | 1.14 | 8.25 | |
transcripts | 2.43 | 0.05 | 2.47 | |
transcriptsBy | 0.92 | 0.04 | 0.97 | |
transcriptsByOverlaps | 0.15 | 0.00 | 0.15 | |