[Bioc-devel] GenomicFeatures::makeTxDbFromGFF leads to a S4Vectors error
Hervé Pagès
hpages at fredhutch.org
Mon Jan 30 18:22:32 CET 2017
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
>>
>
> _______________________________________________
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> 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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