Awesome, thanks Hervé! On Mon, Jan 30, 2017 at 12:22 PM, Hervé Pagès <hpa...@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@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@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: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319
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