[Bioc-devel] as(vcf, "VRanges") is broken in devel, possibly caused by S4Vectors:::recycleVector()

[Robert Castelo]

hi,

got it, the current version on svn of VariantAnnotation (1.21.19) is 
ahead of what's available via biocLite(). i've checked out 
VariantAnnotation 1.21.19, installed it and the bug has dissapeared. 
problem solved.

thanks!

robert.

On 04/19/2017 05:39 PM, Michael Lawrence wrote:
> Not reproducing for me. This is with S4Vectors, VariantAnnotation,
> etc, from svn.
>
> R Under development (unstable) (2016-12-13 r71785)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Arch Linux
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats4    parallel  stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>  [1] VariantAnnotation_1.21.19  Rsamtools_1.27.16
>  [3] Biostrings_2.43.5          XVector_0.15.2
>  [5] SummarizedExperiment_1.5.9 DelayedArray_0.1.11
>  [7] matrixStats_0.51.0         Biobase_2.34.0
>  [9] GenomicRanges_1.27.22      GenomeInfoDb_1.11.9
> [11] IRanges_2.9.19             S4Vectors_0.13.15
> [13] BiocGenerics_0.21.3
>
> loaded via a namespace (and not attached):
>  [1] Rcpp_0.12.8              AnnotationDbi_1.36.0     GenomicAlignments_1.10.0
>  [4] zlibbioc_1.20.0          BiocParallel_1.8.1       BSgenome_1.42.0
>  [7] lattice_0.20-34          tools_3.4.0              grid_3.4.0
> [10] DBI_0.5-1                digest_0.6.10            Matrix_1.2-7.1
> [13] GenomeInfoDbData_0.99.0  rtracklayer_1.35.9       bitops_1.0-6
> [16] biomaRt_2.30.0           RCurl_1.95-4.8           memoise_1.0.0
> [19] RSQLite_1.1-1            compiler_3.4.0           BiocInstaller_1.25.3
> [22] GenomicFeatures_1.27.14  XML_3.98-1.5
>
>
>
> On Wed, Apr 19, 2017 at 7:06 AM, Robert Castelo <robert.castelo at upf.edu> wrote:
>> hi,
>>
>> it seems that recent changes to S4Vectors are breaking the coercion from the
>> '*VCF' class to the 'VRanges' class. the traceback points to the private
>> function 'recycleVector() from the 'S4Vectors' package, please find below
>> the minimal example that reproduces the problem with the session
>> information.
>>
>> cheers,
>>
>> robert.
>>
>> library(VariantAnnotation)
>> example(VRanges)
>> as(vcf, "VRanges")
>> Error in ans[] <- x : replacement has length zero
>> traceback()
>> 4: S4Vectors:::recycleVector(ref, maxLen)
>> 3: VRanges(seqnames, ranges, ref, alt, totalDepth, refDepth, altDepth,
>>        hardFilters = FilterRules(), sampleNames = sampleNames,
>> softFilterMatrix = filter,
>>        meta)
>> 2: asMethod(object)
>> 1: as(vcf, "VRanges")
>>
>> sessionInfo()
>> R Under development (unstable) (2017-03-23 r72385)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: CentOS Linux 7 (Core)
>>
>> Matrix products: default
>> BLAS: /opt/R/R-devel/lib64/R/lib/libRblas.so
>> LAPACK: /opt/R/R-devel/lib64/R/lib/libRlapack.so
>>
>> locale:
>>  [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C
>>  [3] LC_TIME=en_US.UTF8        LC_COLLATE=en_US.UTF8
>>  [5] LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8
>>  [7] LC_PAPER=en_US.UTF8       LC_NAME=C
>>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats4    parallel  stats     graphics  grDevices
>> [6] utils     datasets  methods   base
>>
>> other attached packages:
>>  [1] VariantAnnotation_1.21.18  Rsamtools_1.27.16
>>  [3] Biostrings_2.43.8          XVector_0.15.2
>>  [5] SummarizedExperiment_1.5.9 DelayedArray_0.1.11
>>  [7] matrixStats_0.52.2         Biobase_2.35.1
>>  [9] GenomicRanges_1.27.23      GenomeInfoDb_1.11.10
>> [11] IRanges_2.9.19             S4Vectors_0.13.15
>> [13] BiocGenerics_0.21.3        BiocInstaller_1.25.3
>> [15] setwidth_1.0-4             colorout_1.1-2
>>
>> loaded via a namespace (and not attached):
>>  [1] Rcpp_0.12.10              AnnotationDbi_1.37.4
>>  [3] GenomicAlignments_1.11.12 zlibbioc_1.21.0
>>  [5] BiocParallel_1.9.6        BSgenome_1.43.7
>>  [7] lattice_0.20-35           tools_3.4.0
>>  [9] grid_3.4.0                DBI_0.6-1
>> [11] digest_0.6.12             Matrix_1.2-9
>> [13] GenomeInfoDbData_0.99.0   rtracklayer_1.35.12
>> [15] bitops_1.0-6              biomaRt_2.31.10
>> [17] RCurl_1.95-4.8            memoise_1.0.0
>> [19] RSQLite_1.1-2             compiler_3.4.0
>> [21] GenomicFeatures_1.27.14   XML_3.98-1.6
>>
>

-- 
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550