Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:34 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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 VariantAnnotation package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VariantAnnotation.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 2115/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
VariantAnnotation 1.45.0 (landing page) Bioconductor Package Maintainer
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: VariantAnnotation |
Version: 1.45.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:VariantAnnotation.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings VariantAnnotation_1.45.0.tar.gz |
StartedAt: 2023-02-07 18:39:37 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 18:51:31 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 713.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: VariantAnnotation.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:VariantAnnotation.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings VariantAnnotation_1.45.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/VariantAnnotation.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-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 ‘VariantAnnotation/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘VariantAnnotation’ version ‘1.45.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'MatrixGenerics', 'GenomeInfoDb', 'GenomicRanges', 'SummarizedExperiment', 'Rsamtools' 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 ‘VariantAnnotation’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ * checking installed package size ... NOTE installed size is 6.9Mb sub-directories of 1Mb or more: R 2.1Mb extdata 1.2Mb libs 3.1Mb * 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 Unexported objects imported by ':::' calls: ‘BiocGenerics:::replaceSlots’ ‘BiocGenerics:::testPackage’ ‘Rsamtools:::.RsamtoolsFile’ ‘Rsamtools:::.RsamtoolsFileList’ ‘Rsamtools:::.io_check_exists’ ‘S4Vectors:::expandByColumnSet’ ‘S4Vectors:::labeledLine’ ‘S4Vectors:::recycleVector’ ‘S4Vectors:::selectSome’ ‘SummarizedExperiment:::.SummarizedExperiment.charbound’ ‘SummarizedExperiment:::.cbind.DataFrame’ ‘rtracklayer:::checkArgFormat’ 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 ... NOTE VRangesForMatching: no visible binding for global variable ‘REF’ VRangesForMatching: no visible binding for global variable ‘ALT’ Undefined global functions or variables: ALT REF * checking Rd files ... WARNING checkRd: (5) PROVEANDb-class.Rd:24-27: \item in \describe must have non-empty label checkRd: (5) PROVEANDb-class.Rd:28-32: \item in \describe must have non-empty label checkRd: (5) PROVEANDb-class.Rd:33-37: \item in \describe must have non-empty label checkRd: (5) PROVEANDb-class.Rd:38-42: \item in \describe must have non-empty label checkRd: (5) PROVEANDb-class.Rd:43-49: \item in \describe must have non-empty label checkRd: (5) PolyPhenDb-class.Rd:25-28: \item in \describe must have non-empty label checkRd: (5) PolyPhenDb-class.Rd:29-33: \item in \describe must have non-empty label checkRd: (5) PolyPhenDb-class.Rd:34-38: \item in \describe must have non-empty label checkRd: (5) PolyPhenDb-class.Rd:39-45: \item in \describe must have non-empty label checkRd: (5) PolyPhenDb-class.Rd:46-52: \item in \describe must have non-empty label checkRd: (5) SIFTDb-class.Rd:24-27: \item in \describe must have non-empty label checkRd: (5) SIFTDb-class.Rd:28-32: \item in \describe must have non-empty label checkRd: (5) SIFTDb-class.Rd:33-37: \item in \describe must have non-empty label checkRd: (5) SIFTDb-class.Rd:38-44: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:106-108: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:109-120: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:128-169: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:170-176: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:177-182: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:183-187: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:188-196: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:197-203: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:204-210: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:211-215: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:216-220: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:221-225: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:226-239: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:240-245: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:253-257: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:258-265: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:266-283: \item in \describe must have non-empty label checkRd: (5) VCF-class.Rd:290-303: \item in \describe must have non-empty label checkRd: (5) VCFHeader-class.Rd:47-51: \item in \describe must have non-empty label checkRd: (5) VCFHeader-class.Rd:58-61: \item in \describe must have non-empty label checkRd: (5) VCFHeader-class.Rd:62-66: \item in \describe must have non-empty label checkRd: (5) VCFHeader-class.Rd:67-86: \item in \describe must have non-empty label checkRd: (5) VCFHeader-class.Rd:87-94: \item in \describe must have non-empty label checkRd: (5) VCFHeader-class.Rd:95-100: \item in \describe must have non-empty label checkRd: (5) VCFHeader-class.Rd:101-106: \item in \describe must have non-empty label checkRd: (5) VCFHeader-class.Rd:107-111: \item in \describe must have non-empty label checkRd: (5) VCFHeader-class.Rd:112-118: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:146-178: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:179-224: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:232-265: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:266-268: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:269-281: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:290-292: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:293-295: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:296-299: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:300-303: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:304-307: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:308-310: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:311-314: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:315-319: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:320-322: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:323-326: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:327-330: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:336-339: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:340-344: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:345-349: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:355-358: \item in \describe must have non-empty label checkRd: (5) VRanges-class.Rd:359-372: \item in \describe must have non-empty label checkRd: (5) VRangesList-class.Rd:35-38: \item in \describe must have non-empty label checkRd: (5) VRangesList-class.Rd:44-47: \item in \describe must have non-empty label checkRd: (5) VRangesList-class.Rd:48-52: \item in \describe must have non-empty label checkRd: (5) VRangesList-class.Rd:58-62: \item in \describe must have non-empty label checkRd: (5) VariantType-class.Rd:134-138: \item in \describe must have non-empty label checkRd: (5) VariantType-class.Rd:139-143: \item in \describe must have non-empty label checkRd: (5) VariantType-class.Rd:144-149: \item in \describe must have non-empty label checkRd: (5) VariantType-class.Rd:150-154: \item in \describe must have non-empty label checkRd: (5) VariantType-class.Rd:155-159: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:31-34: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:35-37: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:42-43: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:44-45: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:46-47: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:48-49: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:50-51: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:52-54: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:59-60: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:61-62: \item in \describe must have non-empty label checkRd: (5) VcfFile-class.Rd:67-69: \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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... WARNING Note: information on .o files is not available File ‘/home/biocbuild/bbs-3.17-bioc/R/library/VariantAnnotation/libs/VariantAnnotation.so’: Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C) Found ‘abort’, possibly from ‘abort’ (C) Found ‘exit’, possibly from ‘exit’ (C) Found ‘stderr’, possibly from ‘stderr’ (C) Found ‘stdout’, possibly from ‘stdout’ (C) File ‘VariantAnnotation/libs/VariantAnnotation.so’: Found non-API calls to R: ‘R_GetConnection’, ‘R_WriteConnection’ Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘VariantAnnotation-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: snpSummary > ### Title: Counts and distribution statistics for SNPs in a VCF object > ### Aliases: snpSummary snpSummary,CollapsedVCF-method > ### Keywords: manip > > ### ** Examples > > fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation") > vcf <- readVcf(fl, "hg19") Killed * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘VariantAnnotation_unit_tests.R’ ERROR Running the tests in ‘tests/VariantAnnotation_unit_tests.R’ failed. Last 13 lines of output: The following object is masked from 'package:S4Vectors': expand [W::bcf_hdr_check_sanity] GL should be declared as Number=G non-single nucleotide variations are set to NA non-single nucleotide variations are set to NA non-single nucleotide variations are set to NA non-single nucleotide variations are set to NA non-single nucleotide variations are set to NA non-single nucleotide variations are set to NA Loading required package: GenomicFeatures Loading required package: AnnotationDbi Killed * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘VariantAnnotation.Rnw’... failed to complete the test ‘filterVcf.Rnw’... OK ERROR Errors in running code in vignettes: when running code in ‘VariantAnnotation.Rnw’ ... Loading required package: BSgenome Loading required package: rtracklayer > vcf_rsids <- names(rowRanges(vcf)) > chr22snps <- snpsBySeqname(SNPlocs.Hsapiens.dbSNP144.GRCh37, + "22") Killed ... incomplete output. Crash? * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘VariantAnnotation.Rnw’ using Sweave 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: MatrixGenerics Loading required package: matrixStats Attaching package: ‘MatrixGenerics’ The following objects are masked from ‘package:matrixStats’: colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomeInfoDb 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: GenomicRanges Loading required package: SummarizedExperiment 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")'. Attaching package: ‘Biobase’ The following object is masked from ‘package:MatrixGenerics’: rowMedians The following objects are masked from ‘package:matrixStats’: anyMissing, rowMedians Loading required package: Rsamtools Loading required package: Biostrings Loading required package: XVector Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Attaching package: ‘VariantAnnotation’ The following object is masked from ‘package:base’: tabulate Loading required package: BSgenome Loading required package: rtracklayer Killed --- re-building ‘filterVcf.Rnw’ using Sweave 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: MatrixGenerics Loading required package: matrixStats Attaching package: ‘MatrixGenerics’ The following objects are masked from ‘package:matrixStats’: colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomeInfoDb 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: GenomicRanges Loading required package: SummarizedExperiment 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")'. Attaching package: ‘Biobase’ The following object is masked from ‘package:MatrixGenerics’: rowMedians The following objects are masked from ‘package:matrixStats’: anyMissing, rowMedians Loading required package: Rsamtools Loading required package: Biostrings Loading required package: XVector Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Attaching package: ‘VariantAnnotation’ The following object is masked from ‘package:base’: tabulate starting prefilter prefiltering 3791 records prefiltered to /tmp/RtmpRloimf/file2b6484f8085b1 prefilter compressing and indexing ‘/tmp/RtmpRloimf/file2b6484f8085b1’ starting filter filtering 48 records completed filtering Loading required package: BiocFileCache Loading required package: dbplyr Attaching package: ‘AnnotationHub’ The following object is masked from ‘package:Biobase’: cache snapshotDate(): 2022-12-16 loading from cache require(“rtracklayer”) Loading required package: GenomicFeatures Loading required package: AnnotationDbi 'select()' returned 1:1 mapping between keys and columns Killed SUMMARY: processing the following files failed: ‘VariantAnnotation.Rnw’ ‘filterVcf.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 3 ERRORs, 2 WARNINGs, 6 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/VariantAnnotation.Rcheck/00check.log’ for details.
VariantAnnotation.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL VariantAnnotation ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘VariantAnnotation’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c dna_hash.c -o dna_hash.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rle.c -o rle.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c strhash.c -o strhash.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c utilities.c -o utilities.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c vcffile.c -o vcffile.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c vcftype.c -o vcftype.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -c writevcf.c -o writevcf.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o /home/biocbuild/bbs-3.17-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-VariantAnnotation/00new/VariantAnnotation/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘tabulate’ in package ‘VariantAnnotation’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (VariantAnnotation)
VariantAnnotation.Rcheck/tests/VariantAnnotation_unit_tests.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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("VariantAnnotation") || stop("unable to load VariantAnnotation package") Loading required package: VariantAnnotation 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: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomeInfoDb 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: GenomicRanges Loading required package: SummarizedExperiment 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")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: Rsamtools Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Attaching package: 'VariantAnnotation' The following object is masked from 'package:base': tabulate [1] TRUE > VariantAnnotation:::.test() Loading required package: RSQLite [W::tbx_parse1] VCF INFO/END=2827680 is smaller than POS at 1:2827692 This tag will be ignored. Note: only one invalid END tag will be reported. [W::bcf_hdr_register_hrec] The definition of Flag "INFO/TS" is invalid, forcing Number=0 [W::bcf_hdr_register_hrec] The definition of Flag "INFO/TS" is invalid, forcing Number=0 starting prefilter prefiltering 10376 records prefiltered to /tmp/Rtmp8g96Av/file2a0916c10c024 compressing and indexing '/tmp/Rtmp8g96Av/file2a0916c10c024' starting filter filtering 10376 records completed filtering compressing and indexing '/tmp/Rtmp8g96Av/file2a0917ab47a1f' Loading required package: survival Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:VariantAnnotation': expand The following object is masked from 'package:S4Vectors': expand [W::bcf_hdr_check_sanity] GL should be declared as Number=G non-single nucleotide variations are set to NA non-single nucleotide variations are set to NA non-single nucleotide variations are set to NA non-single nucleotide variations are set to NA non-single nucleotide variations are set to NA non-single nucleotide variations are set to NA Loading required package: GenomicFeatures Loading required package: AnnotationDbi Killed
VariantAnnotation.Rcheck/VariantAnnotation-Ex.timings
name | user | system | elapsed | |
GLtoGP | 1.516 | 0.196 | 1.719 | |
PROVEANDb-class | 5.137 | 0.989 | 8.617 | |
PolyPhenDb-class | 2.466 | 0.192 | 4.295 | |
SIFTDb-class | 0 | 0 | 0 | |
ScanVcfParam-class | 1.234 | 0.003 | 1.250 | |
VCF-class | 2.054 | 0.032 | 2.090 | |
VCFHeader-class | 0.109 | 0.000 | 0.110 | |
VRanges-class | 0.615 | 0.000 | 0.615 | |
VRangesList-class | 0.590 | 0.004 | 0.594 | |
VariantType-class | 0.006 | 0.004 | 0.010 | |
VcfFile-class | 0.812 | 0.000 | 0.818 | |
filterVcf-methods | 3.480 | 0.117 | 10.579 | |
genotypeToSnpMatrix-methods | 1.681 | 0.100 | 1.810 | |
getTranscriptSeqs-methods | 0.000 | 0.000 | 0.001 | |
indexVcf-method | 0.007 | 0.003 | 0.011 | |
isSNV-methods | 1.244 | 0.000 | 1.247 | |
locateVariants-methods | 29.325 | 0.367 | 29.946 | |
predictCoding-methods | 24.623 | 0.056 | 24.890 | |
probabilityToSnpMatrix | 0.002 | 0.000 | 0.002 | |
readVcf-methods | 4.894 | 0.012 | 4.956 | |
scanVcf-methods | 0.333 | 0.004 | 0.355 | |
seqinfo-method | 0.096 | 0.000 | 0.097 | |