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
>
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