| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:31 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 2133/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| VariantAnnotation 1.44.1 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: VariantAnnotation |
| Version: 1.44.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VariantAnnotation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VariantAnnotation_1.44.1.tar.gz |
| StartedAt: 2023-04-10 23:16:03 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 23:23:23 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 440.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: VariantAnnotation.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VariantAnnotation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VariantAnnotation_1.44.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/VariantAnnotation.Rcheck’
* using R version 4.2.3 (2023-03-15)
* 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 ‘1.44.1’
* 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
* checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
R 3.1Mb
extdata 1.2Mb
* 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 ... 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/4.2/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)
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 19.936 0.884 20.891
predictCoding-methods 16.437 0.721 17.197
PROVEANDb-class 4.661 1.854 9.295
summarizeVariants-methods 5.184 0.138 5.331
filterVcf-methods 2.437 0.157 6.425
* 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-3.16-bioc/meat/VariantAnnotation.Rcheck/00check.log’
for details.
VariantAnnotation.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL VariantAnnotation ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2/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/4.2/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/4.2/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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
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/Rtmp3dFTEe/file936f21f2d4f3
compressing and indexing '/tmp/Rtmp3dFTEe/file936f21f2d4f3'
starting filter
filtering 10376 records
completed filtering
compressing and indexing '/tmp/Rtmp3dFTEe/file936f4d7aaeee'
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 -- Mon Apr 10 23:23:09 2023
***********************************************
Number of test functions: 100
Number of errors: 0
Number of failures: 0
1 Test Suite :
VariantAnnotation RUnit Tests - 100 test functions, 0 errors, 0 failures
Number of test functions: 100
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
102.279 3.262 106.118
VariantAnnotation.Rcheck/VariantAnnotation-Ex.timings
| name | user | system | elapsed | |
| GLtoGP | 1.312 | 0.176 | 1.498 | |
| PROVEANDb-class | 4.661 | 1.854 | 9.295 | |
| PolyPhenDb-class | 2.115 | 0.199 | 2.996 | |
| SIFTDb-class | 0.000 | 0.000 | 0.001 | |
| ScanVcfParam-class | 1.018 | 0.029 | 1.051 | |
| VCF-class | 1.546 | 0.071 | 1.621 | |
| VCFHeader-class | 0.088 | 0.002 | 0.090 | |
| VRanges-class | 0.419 | 0.003 | 0.424 | |
| VRangesList-class | 0.391 | 0.005 | 0.397 | |
| VariantType-class | 0.005 | 0.001 | 0.006 | |
| VcfFile-class | 0.493 | 0.004 | 0.500 | |
| filterVcf-methods | 2.437 | 0.157 | 6.425 | |
| genotypeToSnpMatrix-methods | 1.086 | 0.041 | 1.129 | |
| getTranscriptSeqs-methods | 0 | 0 | 0 | |
| indexVcf-method | 0.006 | 0.002 | 0.009 | |
| isSNV-methods | 0.778 | 0.011 | 0.789 | |
| locateVariants-methods | 19.936 | 0.884 | 20.891 | |
| predictCoding-methods | 16.437 | 0.721 | 17.197 | |
| probabilityToSnpMatrix | 0.001 | 0.001 | 0.002 | |
| readVcf-methods | 3.028 | 0.048 | 3.084 | |
| scanVcf-methods | 0.264 | 0.017 | 0.285 | |
| seqinfo-method | 0.054 | 0.000 | 0.055 | |
| snpSummary | 0.262 | 0.006 | 0.268 | |
| summarizeVariants-methods | 5.184 | 0.138 | 5.331 | |
| writeVcf-methods | 1.470 | 0.032 | 1.502 | |