This page was generated on 2019-04-09 12:23:29 -0400 (Tue, 09 Apr 2019).
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:podkat.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings podkat_1.15.1.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/podkat.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'podkat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'podkat' version '1.15.1'
* 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 whether package 'podkat' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/AssocTestResultRanges-class.Rd:40: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/AssocTestResultRanges-class.Rd:40: file link 'elementMetadata' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/AssocTestResultRanges-class.Rd:106: file link 'print' in package 'podkat' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/GenotypeMatrix-class.Rd:56: file link 'rownames' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/assocTest-methods.Rd:41: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/assocTest-methods.Rd:103: file link 'makePSOCKcluster' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/assocTest-methods.Rd:246: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/assocTest-methods.Rd:253: file link 'makePSOCKcluster' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/filterResult-methods.Rd:62: file link 'p.adjust' in package 'podkat' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/genotypeMatrix-methods.Rd:33: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/genotypeMatrix-methods.Rd:149: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/genotypeMatrix-methods.Rd:150: file link 'SnpSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/genotypeMatrix-methods.Rd:152: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/partitionRegions-methods.Rd:20: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/partitionRegions-methods.Rd:55: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/qqplot-methods.Rd:76: file link 'qqplot' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/unmasked-datasets.Rd:30: file link 'pseudoautosomal.hg18' in package 'GWASTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/unmasked-datasets.Rd:31: file link 'pseudoautosomal.hg19' in package 'GWASTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/unmasked-datasets.Rd:32: file link 'pseudoautosomal.hg38' in package 'GWASTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/unmaskedRegions.Rd:6: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/unmaskedRegions.Rd:13: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/unmaskedRegions.Rd:19: file link 'pseudoautosomal.hg18' in package 'GWASTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/unmaskedRegions.Rd:20: file link 'pseudoautosomal.hg19' in package 'GWASTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/unmaskedRegions.Rd:21: file link 'pseudoautosomal.hg38' in package 'GWASTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/unmaskedRegions.Rd:29: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/unmaskedRegions.Rd:34: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/unmaskedRegions.Rd:47: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/unmaskedRegions.Rd:51: file link 'pseudoautosomal.hg18' in package 'GWASTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/unmaskedRegions.Rd:52: file link 'pseudoautosomal.hg19' in package 'GWASTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/unmaskedRegions.Rd:53: file link 'pseudoautosomal.hg38' in package 'GWASTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/weights-methods.Rd:20: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/weights-methods.Rd:65: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp0KEWJD/R.INSTALL22f4169127c6/podkat/man/weights-methods.Rd:92: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/podkat.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
assocTest.TabixFile: no visible global function definition for 'path'
readGenotypeMatrix.TabixFile: no visible global function definition for
'path'
readSampleNamesFromVcfHeader: no visible global function definition for
'path'
readVariantInfo.TabixFile: no visible global function definition for
'path'
weights.AssocTestResultRanges.TabixFile: no visible global function
definition for 'path'
assocTest,TabixFile-NullModel: no visible global function definition
for 'path'
readGenotypeMatrix,TabixFile-GRanges: no visible global function
definition for 'path'
readVariantInfo,TabixFile-GRanges: no visible global function
definition for 'path'
Undefined global functions or variables:
path
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/podkat/libs/i386/podkat.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'putchar', possibly from 'putchar' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/podkat/libs/x64/podkat.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'putchar', possibly from 'putchar' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
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.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'podkat-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GenotypeMatrix-class
> ### Title: Class 'GenotypeMatrix'
> ### Aliases: GenotypeMatrix-class class:GenotypeMatrix GenotypeMatrix
> ### [,GenotypeMatrix,index,missing,missing-method
> ### [,GenotypeMatrix,missing,index,missing-method
> ### [,GenotypeMatrix,index,index,missing-method
> ### variantInfo,GenotypeMatrix-method MAF,GenotypeMatrix-method
> ### show,GenotypeMatrix-method
> ### Keywords: classes
>
> ### ** Examples
>
> ## create a toy example
> A <- matrix(rbinom(50, 2, prob=0.2), 5, 10)
> sA <- as(A, "dgCMatrix")
> pos <- sort(sample(1:10000, ncol(A)))
> seqname <- "chr1"
>
> ## variant with 'GRanges' object
> gr <- GRanges(seqnames=seqname, ranges=IRanges(start=pos, width=1))
> gtm <- genotypeMatrix(A, gr)
> gtm
Genotype matrix:
Number of samples: 5
Number of variants: 10
Mean MAF: 0.23
Median MAF: 0.25
Minimum MAF: 0.1
Maximum MAF: 0.4
> as.matrix(gtm)
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 1 0 0 1 0 0 1 1 1
[2,] 0 1 0 1 0 0 0 1 1 0
[3,] 0 1 1 2 1 0 0 0 1 0
[4,] 1 0 0 0 0 1 0 1 0 1
[5,] 0 0 1 1 0 0 1 0 0 1
> variantInfo(gtm)
VariantInfo object with 10 ranges and 1 metadata column:
seqnames ranges strand | MAF
<Rle> <IRanges> <Rle> | <numeric>
[1] chr1 526 * | 0.1
[2] chr1 1069 * | 0.3
[3] chr1 1222 * | 0.2
[4] chr1 2858 * | 0.4
[5] chr1 4344 * | 0.2
[6] chr1 4633 * | 0.1
[7] chr1 5400 * | 0.1
[8] chr1 6519 * | 0.3
[9] chr1 7289 * | 0.3
[10] chr1 9888 * | 0.3
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
> MAF(gtm)
[1] 0.1 0.3 0.2 0.4 0.2 0.1 0.1 0.3 0.3 0.3
>
> ## variant with 'pos' and 'seqnames' object
> genotypeMatrix(sA, pos, seqname)
Genotype matrix:
Number of samples: 5
Number of variants: 10
Mean MAF: 0.23
Median MAF: 0.25
Minimum MAF: 0.1
Maximum MAF: 0.4
>
> ## variant with 'seqname:pos' strings passed through 'pos' argument
> spos <- paste(seqname, pos, sep=":")
> spos
[1] "chr1:526" "chr1:1069" "chr1:1222" "chr1:2858" "chr1:4344" "chr1:4633"
[7] "chr1:5400" "chr1:6519" "chr1:7289" "chr1:9888"
> genotypeMatrix(sA, spos)
Genotype matrix:
Number of samples: 5
Number of variants: 10
Mean MAF: 0.23
Median MAF: 0.25
Minimum MAF: 0.1
Maximum MAF: 0.4
>
> ## read data from VCF file using 'readVcf()' from the 'VariantAnnotation'
> ## package
> if (require(VariantAnnotation))
+ {
+ vcfFile <- system.file("examples/example1.vcf.gz", package="podkat")
+ sp <- ScanVcfParam(info=NA, genome="GT", fixed=c("ALT", "FILTER"))
+ vcf <- readVcf(vcfFile, genome="hgA", param=sp)
+ rowRanges(vcf)
+
+ ## call constructor for 'VCF' object
+ gtm <- genotypeMatrix(vcf)
+ gtm
+ variantInfo(gtm)
+
+ ## alternatively, extract information from 'VCF' object and use
+ ## variant with character matrix and 'GRanges' positions
+ ## note that, in 'VCF' objects, rows correspond to variants and
+ ## columns correspond to samples, therefore, we have to transpose the
+ ## genotype
+ gt <- t(geno(vcf)$GT)
+ gt[1:5, 1:5]
+ gr <- rowRanges(vcf)
+ gtm <- genotypeMatrix(gt, gr)
+ as.matrix(gtm[1:20, 1:5, recomputeMAF=TRUE])
+ }
Loading required package: VariantAnnotation
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 object is masked from 'package:Biostrings':
type
The following objects are masked from 'package:base':
aperm, apply, rowsum
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
Error in validObject(.Object) :
invalid class "VCFHeader" object: 'geno(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
Calls: readVcf ... VCFHeader -> new -> initialize -> initialize -> validObject
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'podkat-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GenotypeMatrix-class
> ### Title: Class 'GenotypeMatrix'
> ### Aliases: GenotypeMatrix-class class:GenotypeMatrix GenotypeMatrix
> ### [,GenotypeMatrix,index,missing,missing-method
> ### [,GenotypeMatrix,missing,index,missing-method
> ### [,GenotypeMatrix,index,index,missing-method
> ### variantInfo,GenotypeMatrix-method MAF,GenotypeMatrix-method
> ### show,GenotypeMatrix-method
> ### Keywords: classes
>
> ### ** Examples
>
> ## create a toy example
> A <- matrix(rbinom(50, 2, prob=0.2), 5, 10)
> sA <- as(A, "dgCMatrix")
> pos <- sort(sample(1:10000, ncol(A)))
> seqname <- "chr1"
>
> ## variant with 'GRanges' object
> gr <- GRanges(seqnames=seqname, ranges=IRanges(start=pos, width=1))
> gtm <- genotypeMatrix(A, gr)
> gtm
Genotype matrix:
Number of samples: 5
Number of variants: 10
Mean MAF: 0.23
Median MAF: 0.25
Minimum MAF: 0.1
Maximum MAF: 0.4
> as.matrix(gtm)
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0 1 0 0 1 0 0 1 1 1
[2,] 0 1 0 1 0 0 0 1 1 0
[3,] 0 1 1 2 1 0 0 0 1 0
[4,] 1 0 0 0 0 1 0 1 0 1
[5,] 0 0 1 1 0 0 1 0 0 1
> variantInfo(gtm)
VariantInfo object with 10 ranges and 1 metadata column:
seqnames ranges strand | MAF
<Rle> <IRanges> <Rle> | <numeric>
[1] chr1 526 * | 0.1
[2] chr1 1069 * | 0.3
[3] chr1 1222 * | 0.2
[4] chr1 2858 * | 0.4
[5] chr1 4344 * | 0.2
[6] chr1 4633 * | 0.1
[7] chr1 5400 * | 0.1
[8] chr1 6519 * | 0.3
[9] chr1 7289 * | 0.3
[10] chr1 9888 * | 0.3
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
> MAF(gtm)
[1] 0.1 0.3 0.2 0.4 0.2 0.1 0.1 0.3 0.3 0.3
>
> ## variant with 'pos' and 'seqnames' object
> genotypeMatrix(sA, pos, seqname)
Genotype matrix:
Number of samples: 5
Number of variants: 10
Mean MAF: 0.23
Median MAF: 0.25
Minimum MAF: 0.1
Maximum MAF: 0.4
>
> ## variant with 'seqname:pos' strings passed through 'pos' argument
> spos <- paste(seqname, pos, sep=":")
> spos
[1] "chr1:526" "chr1:1069" "chr1:1222" "chr1:2858" "chr1:4344" "chr1:4633"
[7] "chr1:5400" "chr1:6519" "chr1:7289" "chr1:9888"
> genotypeMatrix(sA, spos)
Genotype matrix:
Number of samples: 5
Number of variants: 10
Mean MAF: 0.23
Median MAF: 0.25
Minimum MAF: 0.1
Maximum MAF: 0.4
>
> ## read data from VCF file using 'readVcf()' from the 'VariantAnnotation'
> ## package
> if (require(VariantAnnotation))
+ {
+ vcfFile <- system.file("examples/example1.vcf.gz", package="podkat")
+ sp <- ScanVcfParam(info=NA, genome="GT", fixed=c("ALT", "FILTER"))
+ vcf <- readVcf(vcfFile, genome="hgA", param=sp)
+ rowRanges(vcf)
+
+ ## call constructor for 'VCF' object
+ gtm <- genotypeMatrix(vcf)
+ gtm
+ variantInfo(gtm)
+
+ ## alternatively, extract information from 'VCF' object and use
+ ## variant with character matrix and 'GRanges' positions
+ ## note that, in 'VCF' objects, rows correspond to variants and
+ ## columns correspond to samples, therefore, we have to transpose the
+ ## genotype
+ gt <- t(geno(vcf)$GT)
+ gt[1:5, 1:5]
+ gr <- rowRanges(vcf)
+ gtm <- genotypeMatrix(gt, gr)
+ as.matrix(gtm[1:20, 1:5, recomputeMAF=TRUE])
+ }
Loading required package: VariantAnnotation
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 object is masked from 'package:Biostrings':
type
The following objects are masked from 'package:base':
aperm, apply, rowsum
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
Error in validObject(.Object) :
invalid class "VCFHeader" object: 'geno(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
Calls: readVcf ... VCFHeader -> new -> initialize -> initialize -> validObject
Execution halted
* 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: 2 ERRORs, 1 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/podkat.Rcheck/00check.log'
for details.