Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:57 -0400 (Fri, 15 Oct 2021).
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1995/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
VariantAnnotation 1.38.0 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: VariantAnnotation |
Version: 1.38.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:VariantAnnotation.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings VariantAnnotation_1.38.0.tar.gz |
StartedAt: 2021-10-15 01:05:03 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 01:15:46 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 643.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: VariantAnnotation.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:VariantAnnotation.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings VariantAnnotation_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/VariantAnnotation.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘VariantAnnotation/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘VariantAnnotation’ version ‘1.38.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘VariantAnnotation’ 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 Unexported objects imported by ':::' calls: ‘Rsamtools:::.RsamtoolsFile’ ‘Rsamtools:::.RsamtoolsFileList’ ‘Rsamtools:::.io_check_exists’ ‘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 ... 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 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 ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/VariantAnnotation/libs/VariantAnnotation.so’: Found ‘___assert_rtn’, possibly from ‘assert’ (C) Found ‘___stderrp’, possibly from ‘stderr’ (C) Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_abort’, possibly from ‘abort’ (C) Found ‘_exit’, possibly from ‘exit’ (C) Found ‘_printf’, possibly from ‘printf’ (C) Found ‘_putchar’, possibly from ‘putchar’ (C) Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C) Found ‘_srand48’, possibly from ‘srand48’ (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. 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed locateVariants-methods 32.310 0.744 33.092 predictCoding-methods 25.659 0.657 26.349 summarizeVariants-methods 10.900 0.199 11.124 PROVEANDb-class 5.449 2.520 12.611 readVcf-methods 5.618 0.106 5.728 filterVcf-methods 3.714 0.167 6.336 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘VariantAnnotation_unit_tests.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: 6 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/VariantAnnotation.Rcheck/00check.log’ for details.
VariantAnnotation.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL VariantAnnotation ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘VariantAnnotation’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c dna_hash.c -o dna_hash.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rle.c -o rle.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c strhash.c -o strhash.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c utilities.c -o utilities.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c vcffile.c -o vcffile.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c vcftype.c -o vcftype.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c writevcf.c -o writevcf.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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 Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, 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 starting prefilter prefiltering 10376 records prefiltered to /tmp/Rtmpu9ECQm/file28602b691f67 compressing and indexing '/tmp/Rtmpu9ECQm/file28602b691f67' starting filter filtering 10376 records completed filtering compressing and indexing '/tmp/Rtmpu9ECQm/file286028cb975' 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 'select()' returned 1:1 mapping between keys and columns Loading required package: BSgenome Loading required package: rtracklayer 'select()' returned many:1 mapping between keys and columns [W::bcf_hdr_check_sanity] PL should be declared as Number=G RUNIT TEST PROTOCOL -- Fri Oct 15 01:15:29 2021 *********************************************** Number of test functions: 99 Number of errors: 0 Number of failures: 0 1 Test Suite : VariantAnnotation RUnit Tests - 99 test functions, 0 errors, 0 failures Number of test functions: 99 Number of errors: 0 Number of failures: 0 Warning messages: 1: info fields with no header: noMatch 2: In .bcfHeaderAsSimpleList(header) : duplicate keys in header will be forced to unique rownames 3: In DataFrame(..., check.names = FALSE) : NAs introduced by coercion 4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 7 out-of-bound ranges located on sequence 70477. 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 6 out-of-bound ranges located on sequence 70477. 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. > > proc.time() user system elapsed 187.407 3.575 191.883
VariantAnnotation.Rcheck/VariantAnnotation-Ex.timings
name | user | system | elapsed | |
GLtoGP | 2.717 | 0.195 | 2.920 | |
PROVEANDb-class | 5.449 | 2.520 | 12.611 | |
PolyPhenDb-class | 1.224 | 0.195 | 1.741 | |
SIFTDb-class | 0.001 | 0.001 | 0.001 | |
ScanVcfParam-class | 1.870 | 0.022 | 1.896 | |
VCF-class | 2.980 | 0.170 | 3.158 | |
VCFHeader-class | 0.149 | 0.001 | 0.150 | |
VRanges-class | 0.893 | 0.006 | 0.901 | |
VRangesList-class | 0.729 | 0.004 | 0.734 | |
VariantType-class | 0.008 | 0.001 | 0.009 | |
VcfFile-class | 1.158 | 0.015 | 1.175 | |
filterVcf-methods | 3.714 | 0.167 | 6.336 | |
genotypeToSnpMatrix-methods | 2.167 | 0.045 | 2.216 | |
getTranscriptSeqs-methods | 0.001 | 0.000 | 0.000 | |
indexVcf-method | 0.010 | 0.002 | 0.011 | |
isSNV-methods | 1.736 | 0.014 | 1.750 | |
locateVariants-methods | 32.310 | 0.744 | 33.092 | |
predictCoding-methods | 25.659 | 0.657 | 26.349 | |
probabilityToSnpMatrix | 0.001 | 0.000 | 0.002 | |
readVcf-methods | 5.618 | 0.106 | 5.728 | |
scanVcf-methods | 0.386 | 0.010 | 0.396 | |
seqinfo-method | 0.094 | 0.000 | 0.095 | |
snpSummary | 0.660 | 0.008 | 0.668 | |
summarizeVariants-methods | 10.900 | 0.199 | 11.124 | |
writeVcf-methods | 3.147 | 0.052 | 3.202 | |