Valerie Obenchain
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/VariantAnnotation |
| Branch: RELEASE_3_9 |
| Last Commit: fb1ab00 |
| Last Changed Date: 2019-05-19 09:52:56 -0400 (Sun, 19 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:00:10 -0400 (Wed, 16 Oct 2019).
| Package 1706/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| VariantAnnotation 1.30.1 Valerie Obenchain
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: VariantAnnotation |
| Version: 1.30.1 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:VariantAnnotation.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings VariantAnnotation_1.30.1.tar.gz |
| StartedAt: 2019-10-16 05:40:00 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:48:01 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 480.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: VariantAnnotation.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:VariantAnnotation.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings VariantAnnotation_1.30.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/VariantAnnotation.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.30.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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
* checking installed package size ... NOTE
installed size is 5.9Mb
sub-directories of 1Mb or more:
R 1.8Mb
extdata 1.2Mb
libs 2.4Mb
* 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
'library' or 'require' call to ‘snpStats’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
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’
probabilityToSnpMatrix: no visible global function definition for
‘post2g’
Undefined global functions or variables:
ALT REF post2g
* 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.9-bioc/R/library/VariantAnnotation/libs/VariantAnnotation.so’:
Found ‘__assert_fail’, possibly from ‘assert’ (C)
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘putchar’, possibly from ‘putchar’ (C)
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Found ‘srand48’, possibly from ‘srand48’ (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. 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
predictCoding-methods 29.689 0.095 29.864
locateVariants-methods 29.166 0.313 29.485
summarizeVariants-methods 9.340 0.007 9.361
PROVEANDb-class 5.123 0.610 8.733
PolyPhenDb-class 1.245 0.071 6.241
* 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: 4 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/VariantAnnotation.Rcheck/00check.log’
for details.
VariantAnnotation.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL VariantAnnotation
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘VariantAnnotation’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c rle.c -o rle.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c strhash.c -o strhash.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c utilities.c -o utilities.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c vcffile.c -o vcffile.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c vcftype.c -o vcftype.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.9-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-3.9-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-3.9-bioc/R/library/Rhtslib/usrlib/libhts.a -lz -lm -lbz2 -llzma -lpthread -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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("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, which.max, which.min
Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
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/RtmpKkehb7/file6417cc66e21
compressing and indexing '/tmp/RtmpKkehb7/file6417cc66e21'
starting filter
filtering 10376 records
completed filtering
compressing and indexing '/tmp/RtmpKkehb7/file64177986592c'
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 -- Wed Oct 16 05:47:55 2019
***********************************************
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
119.173 1.371 122.201
VariantAnnotation.Rcheck/VariantAnnotation-Ex.timings
| name | user | system | elapsed | |
| GLtoGP | 1.590 | 0.232 | 1.835 | |
| PROVEANDb-class | 5.123 | 0.610 | 8.733 | |
| PolyPhenDb-class | 1.245 | 0.071 | 6.241 | |
| SIFTDb-class | 0.000 | 0.001 | 0.002 | |
| ScanVcfParam-class | 1.025 | 0.006 | 1.036 | |
| VCF-class | 1.445 | 0.035 | 1.479 | |
| VCFHeader-class | 0.311 | 0.004 | 0.316 | |
| VRanges-class | 0.401 | 0.000 | 0.402 | |
| VRangesList-class | 0.388 | 0.000 | 0.388 | |
| VariantType-class | 0.007 | 0.000 | 0.006 | |
| VcfFile-class | 1.573 | 0.007 | 1.597 | |
| filterVcf-methods | 1.862 | 0.040 | 1.902 | |
| genotypeToSnpMatrix-methods | 1.089 | 0.080 | 1.168 | |
| getTranscriptSeqs-methods | 0 | 0 | 0 | |
| indexVcf-method | 0.009 | 0.000 | 0.018 | |
| isSNV-methods | 0.731 | 0.000 | 0.730 | |
| locateVariants-methods | 29.166 | 0.313 | 29.485 | |
| predictCoding-methods | 29.689 | 0.095 | 29.864 | |
| probabilityToSnpMatrix | 0.059 | 0.000 | 0.060 | |
| readVcf-methods | 4.486 | 0.004 | 4.491 | |
| scanVcf-methods | 0.415 | 0.000 | 0.415 | |
| seqinfo-method | 0.086 | 0.000 | 0.085 | |
| snpSummary | 0.373 | 0.000 | 0.374 | |
| summarizeVariants-methods | 9.340 | 0.007 | 9.361 | |
| writeVcf-methods | 2.254 | 0.004 | 2.258 | |