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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