[Bioc-devel] GenomicFeatures::makeTxDbFromGFF leads to a S4Vectors error
Leonardo Collado Torres
lcollado at jhu.edu
Mon Jan 30 19:10:20 CET 2017
Awesome, thanks Hervé!
On Mon, Jan 30, 2017 at 12:22 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
> Hi Leonardo,
>
> You need the latest version of rtracklayer: 1.35.3. Unfortunately this
> version didn't propagate because of an issue that is not related to
> this:
>
>
> https://bioconductor.org/checkResults/3.5/bioc-LATEST/rtracklayer/malbec2-checksrc.html
>
> In the mean time you can fetch and install rtracklayer 1.35.3 directly
> from svn.
>
> Cheers,
> H.
>
>
> On 01/30/2017 07:53 AM, Leonardo Collado Torres wrote:
>>
>> Hi,
>>
>> I think that a recent change in S4Vectors broke
>> GenomicFeatures::makeTxDbFromGFF(). I ran this code about a week ago
>> without problems, but it's failing now.
>>
>> Best,
>> Leo
>>
>> ## Unevaluated code
>> library('GenomicFeatures')
>> library('devtools')
>>
>> txdb <-
>> makeTxDbFromGFF('ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz',
>> format = 'gff3', organism = 'Homo sapiens')
>>
>> options(width = 120)
>> session_info()
>>
>>
>> ## Evaluated code in R 3.4.0
>>
>>> library('GenomicFeatures')
>>> library('devtools')
>>>
>>> txdb <-
>>> makeTxDbFromGFF('ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz',
>>
>> + format = 'gff3', organism = 'Homo sapiens')
>> Import genomic features from the file as a GRanges object ... trying
>> URL
>> 'ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz'
>> ftp data connection made, file length 46738343 bytes
>> ==================================================
>> downloaded 44.6 MB
>>
>> Error in readGFF(filepath, version = version, columns = columns, tags =
>> tags, :
>> function '_append_string_to_CharAEAE' not provided by package
>> 'S4Vectors'
>>>
>>>
>>> options(width = 120)
>>> session_info()
>>
>> Session info
>> -----------------------------------------------------------------------------------------------------------
>> setting value
>> version R Under development (unstable) (2016-10-26 r71594)
>> system x86_64, darwin13.4.0
>> ui AQUA
>> language (EN)
>> collate en_US.UTF-8
>> tz America/New_York
>> date 2017-01-30
>>
>> Packages
>> ---------------------------------------------------------------------------------------------------------------
>> package * version date source
>> AnnotationDbi * 1.37.1 2017-01-13 Bioconductor
>> Biobase * 2.35.0 2016-10-23 Bioconductor
>> BiocGenerics * 0.21.3 2017-01-12 Bioconductor
>> BiocParallel 1.9.5 2017-01-24 Bioconductor
>> biomaRt 2.31.4 2017-01-13 Bioconductor
>> Biostrings 2.43.3 2017-01-24 Bioconductor
>> bitops 1.0-6 2013-08-17 CRAN (R 3.4.0)
>> DBI 0.5-1 2016-09-10 CRAN (R 3.4.0)
>> devtools * 1.12.0 2016-12-05 CRAN (R 3.4.0)
>> digest 0.6.11 2017-01-03 CRAN (R 3.4.0)
>> GenomeInfoDb * 1.11.6 2016-11-17 Bioconductor
>> GenomicAlignments 1.11.8 2017-01-24 Bioconductor
>> GenomicFeatures * 1.27.6 2016-12-17 Bioconductor
>> GenomicRanges * 1.27.21 2017-01-20 Bioconductor
>> IRanges * 2.9.16 2017-01-28 cran (@2.9.16)
>> lattice 0.20-34 2016-09-06 CRAN (R 3.4.0)
>> Matrix 1.2-8 2017-01-20 CRAN (R 3.4.0)
>> memoise 1.0.0 2016-01-29 CRAN (R 3.4.0)
>> Rcpp 0.12.9 2017-01-14 CRAN (R 3.4.0)
>> RCurl 1.95-4.8 2016-03-01 CRAN (R 3.4.0)
>> Rsamtools 1.27.12 2017-01-24 Bioconductor
>> RSQLite 1.1-2 2017-01-08 CRAN (R 3.4.0)
>> rtracklayer 1.35.1 2016-10-29 Bioconductor
>> S4Vectors * 0.13.11 2017-01-28 cran (@0.13.11)
>> SummarizedExperiment 1.5.3 2016-11-11 Bioconductor
>> withr 1.0.2 2016-06-20 CRAN (R 3.4.0)
>> XML 3.98-1.5 2016-11-10 CRAN (R 3.4.0)
>> XVector 0.15.1 2017-01-24 Bioconductor
>> zlibbioc 1.21.0 2016-10-23 Bioconductor
>>>
>>>
>>
>>
>> ## Evaluate code in 3.3.2
>>
>>> library('GenomicFeatures')
>>> library('devtools')
>>>
>>> txdb <-
>>> makeTxDbFromGFF('ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz',
>>
>> + format = 'gff3', organism = 'Homo sapiens')
>> Import genomic features from the file as a GRanges object ... trying
>> URL
>> 'ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gff3.gz'
>> ftp data connection made, file length 46738343 bytes
>> ==================================================
>> downloaded 44.6 MB
>>
>> OK
>> Prepare the 'metadata' data frame ... OK
>> Make the TxDb object ... OK
>> Warning messages:
>> 1: RSQLite::dbGetPreparedQuery() is deprecated, please switch to
>> DBI::dbGetQuery(params = bind.data).
>> 2: Named parameters not used in query: internal_chrom_id, chrom,
>> length, is_circular
>> 3: Named parameters not used in query: internal_id, name, type, chrom,
>> strand, start, end
>> 4: Named parameters not used in query: internal_id, name, chrom,
>> strand, start, end
>> 5: Named parameters not used in query: internal_id, name, chrom,
>> strand, start, end
>> 6: Named parameters not used in query: internal_tx_id, exon_rank,
>> internal_exon_id, internal_cds_id
>> 7: Named parameters not used in query: gene_id, internal_tx_id
>>>
>>>
>>> options(width = 120)
>>> session_info()
>>
>> Session info
>> -----------------------------------------------------------------------------------------------------------
>> setting value
>> version R version 3.3.2 RC (2016-10-26 r71594)
>> system x86_64, darwin13.4.0
>> ui X11
>> language (EN)
>> collate en_US.UTF-8
>> tz America/New_York
>> date 2017-01-30
>>
>> Packages
>> ---------------------------------------------------------------------------------------------------------------
>> package * version date source
>> AnnotationDbi * 1.36.1 2017-01-13 Bioconductor
>> Biobase * 2.34.0 2016-10-18 Bioconductor
>> BiocGenerics * 0.20.0 2016-10-18 Bioconductor
>> BiocParallel 1.8.1 2016-10-30 Bioconductor
>> biomaRt 2.30.0 2016-10-18 Bioconductor
>> Biostrings 2.42.1 2016-12-01 Bioconductor
>> bitops 1.0-6 2013-08-17 cran (@1.0-6)
>> colorout * 1.1-2 2016-10-19 Github
>> (jalvesaq/colorout at 6d84420)
>> DBI 0.5-1 2016-09-10 cran (@0.5-1)
>> devtools * 1.12.0 2016-06-24 CRAN (R 3.3.0)
>> digest 0.6.12 2017-01-27 CRAN (R 3.3.2)
>> GenomeInfoDb * 1.10.2 2016-12-29 Bioconductor
>> GenomicAlignments 1.10.0 2016-10-18 Bioconductor
>> GenomicFeatures * 1.26.2 2016-12-17 Bioconductor
>> GenomicRanges * 1.26.2 2017-01-02 Bioconductor
>> IRanges * 2.8.1 2016-11-08 Bioconductor
>> lattice 0.20-34 2016-09-06 CRAN (R 3.3.2)
>> Matrix 1.2-8 2017-01-20 CRAN (R 3.3.2)
>> memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
>> Rcpp 0.12.9 2017-01-14 CRAN (R 3.3.2)
>> RCurl 1.95-4.8 2016-03-01 cran (@1.95-4.)
>> Rsamtools 1.26.1 2016-10-22 Bioconductor
>> RSQLite 1.1-2 2017-01-08 CRAN (R 3.3.2)
>> rtracklayer 1.34.1 2016-11-02 Bioconductor
>> S4Vectors * 0.12.1 2016-12-01 Bioconductor
>> SummarizedExperiment 1.4.0 2016-10-18 Bioconductor
>> withr 1.0.2 2016-06-20 CRAN (R 3.3.0)
>> XML 3.98-1.5 2016-11-10 CRAN (R 3.3.2)
>> XVector 0.14.0 2016-10-18 Bioconductor
>> zlibbioc 1.20.0 2016-10-18 Bioconductor
>>>
>>>
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
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