[Bioc-devel] Request un-deprecation of bioconductor package TnT

Hi, The package TnT (https://bioconductor.org/checkResults/release/bioc-LATEST/TnT/ ) was deprecated due to check error. I have made fixes to the issue on both devel and 3.19 branch, and I would like to request un-deprecation of t

[Bioc-devel] "index" option of filterVcf in VariantAnnotation package

Dear all, The `index` option of filterVcf function in VariantAnnotation package currently does not seem to work. The following is a minimal reproducible example:   R> vcf <- VcfFile(system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation"))   R> filterVcf(vcf, destination = tempfile(),

Re: [Bioc-devel] as.data.frame for GRanges when one meta column is a data frame

etadata column is a data.frame. In particular, this > exception > would lead to inconsistent behavior if the data.frame column is > replaced > with a DataFrame. > > For the record, here is the commit that refactored as.data.frame() > to un-nest everything: > > > h

[Bioc-devel] as.data.frame for GRanges when one meta column is a data frame

Dear all, It seems that the devel branch of Bioconductor has made changes/improvements on the behavior of as.data.frame. In the case that input is a GRanges with a meta column of data frame, as.data.frame in devel will flatten the nested data frame. I made an example below: library(GenomicRanges

Re: [Bioc-devel] [Fwd: Problem showing a GRanges with a meta data column of data frame]

IRanges 2.15.11). > > The updated packages will become available via biocLite() in the > next 24h (if everything goes as expected). > > Best, > H. > > On 05/14/2018 07:38 PM, Jialin Ma wrote: > > Sorry, forgot to attach the session info: > > > > sessionInfo() &

[Bioc-devel] [Fwd: Problem showing a GRanges with a meta data column of data frame]

magrittr_1.5 loaded via a namespace (and not attached): [1] zlibbioc_1.26.0compiler_3.5.0 XVector_0.20.0 [4] tools_3.5.0GenomeInfoDbData_1.1.0 RCurl_1.95- 4.10 [7] yaml_2.1.19bitops_1.0-6 Forwarded Message From: Jialin Ma

[Bioc-devel] Problem showing a GRanges with a meta data column of data frame

Hi all, I recently upgraded R to 3.5 and use the new release of Bioconductor. The new version of S4Vectors seems to have problem showing a GRanges with a meta-data column of a data frame. One simplified example is: gr <- GRanges('chr2', IRanges(1, 11)) gr$df <- data.frame(a = 32) rep(gr, 11) ##

Re: [Bioc-devel] Printing DataFrame with nested data.frame/DataFrame/DataFrameList

). Both should become available > via biocLite() in about 24 hours. > > Let us know if you still see "show" problems after you update. > > Thanks, > H. > > On 09/28/2017 01:19 AM, Jialin Ma wrote: > > Dear all, > > > > I have a packag

[Bioc-devel] Printing DataFrame with nested data.frame/DataFrame/DataFrameList

Dear all, I have a package in reviewing at https://github.com/Bioconductor/Contributions/issues/487, in which I would like to use a GRanges with nested data.frame or DataFrameList to represent the track data internally. However, the default show method does not seem to work well with such structu