[Bioc-devel] GenomicRanges::cbind() problem
Robert Castelo
robert.castelo at upf.edu
Tue Sep 12 15:48:06 CEST 2017
yep, i've cloned, built and installed the latest S4Vectors and then
qpgraph builds and checks cleanly. thanks!!!!
robert.
On 09/12/2017 03:06 PM, Michael Lawrence wrote:
> I think this was fixed in S4Vectors a couple of days ago but I forgot
> to bump the version (just did). Sorry.
>
> On Tue, Sep 12, 2017 at 12:06 AM, Robert Castelo <robert.castelo at upf.edu> wrote:
>> dear GenomicRanges developers,
>>
>> my package qpgraph is breaking in devel due to the following behavior of
>> GenomicRanges:
>>
>> library(GenomicRanges)
>> gr <- GRanges(seqnames=rep("1", 10), IRanges(1:10, width=1))
>> mcols(gr)
>> DataFrame with 10 rows and 0 columns
>> mcols(gr) <- cbind(mcols(gr), DataFrame(test=rep(1, 10)))
>> gr
>> GRanges object with 10 ranges and 1 metadata column:
>> seqnames ranges strand | dfs
>> <Rle> <IRanges> <Rle> | <numeric>
>> [1] 1 [ 1, 1] * | 1
>> [2] 1 [ 2, 2] * | 1
>> [3] 1 [ 3, 3] * | 1
>> [4] 1 [ 4, 4] * | 1
>> [5] 1 [ 5, 5] * | 1
>> [6] 1 [ 6, 6] * | 1
>> [7] 1 [ 7, 7] * | 1
>> [8] 1 [ 8, 8] * | 1
>> [9] 1 [ 9, 9] * | 1
>> [10] 1 [10, 10] * | 1
>> -------
>> seqinfo: 1 sequence from an unspecified genome; no seqlengths
>>
>> notice that the metadata column i've added should be called 'test' and it is
>> called 'dfs' instead. this does not happen in release:
>>
>> library(GenomicRanges)
>> gr <- GRanges(seqnames=rep("1", 10), IRanges(1:10, width=1))
>> mcols(gr)
>> DataFrame with 10 rows and 0 columns
>> mcols(gr) <- cbind(mcols(gr), DataFrame(test=rep(1, 10)))
>> gr
>> GRanges object with 10 ranges and 1 metadata column:
>> seqnames ranges strand | test
>> <Rle> <IRanges> <Rle> | <numeric>
>> [1] 1 [ 1, 1] * | 1
>> [2] 1 [ 2, 2] * | 1
>> [3] 1 [ 3, 3] * | 1
>> [4] 1 [ 4, 4] * | 1
>> [5] 1 [ 5, 5] * | 1
>> [6] 1 [ 6, 6] * | 1
>> [7] 1 [ 7, 7] * | 1
>> [8] 1 [ 8, 8] * | 1
>> [9] 1 [ 9, 9] * | 1
>> [10] 1 [10, 10] * | 1
>> -------
>> seqinfo: 1 sequence from an unspecified genome; no seqlengths
>>
>> i guess that if doing 'cbind()' with an empty 'DataFrame' is not allowed
>> anymore, the correct behavior should be giving an error but renaming the
>> column seems bogus to me.
>>
>> please find below my session information bits for both, devel and release.
>>
>> cheers,
>>
>> robert.
>>
>> devel sessionInfo():
>>
>> R version 3.4.0 (2017-04-21)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: CentOS Linux 7 (Core)
>>
>> Matrix products: default
>> BLAS: /opt/R/R-3.4.0_BioCdevel/lib64/R/lib/libRblas.so
>> LAPACK: /opt/R/R-3.4.0_BioCdevel/lib64/R/lib/libRlapack.so
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF8 LC_COLLATE=en_US.UTF8
>> [5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8
>> [7] LC_PAPER=en_US.UTF8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] parallel stats4 stats graphics grDevices utils datasets
>> [8] methods base
>>
>> other attached packages:
>> [1] GenomicRanges_1.29.13 GenomeInfoDb_1.13.4 IRanges_2.11.15
>> [4] S4Vectors_0.15.7 BiocGenerics_0.23.1 colorout_1.1-2
>>
>> loaded via a namespace (and not attached):
>> [1] zlibbioc_1.23.0 compiler_3.4.0 tools_3.4.0
>> [4] XVector_0.17.1 GenomeInfoDbData_0.99.1 RCurl_1.95-4.8
>> [7] bitops_1.0-6
>>
>> release sessionInfo():
>>
>> R version 3.4.0 (2017-04-21)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: CentOS Linux 7 (Core)
>>
>> Matrix products: default
>> BLAS: /opt/R/R-3.4.0/lib64/R/lib/libRblas.so
>> LAPACK: /opt/R/R-3.4.0/lib64/R/lib/libRlapack.so
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF8 LC_COLLATE=en_US.UTF8
>> [5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8
>> [7] LC_PAPER=en_US.UTF8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] parallel stats4 stats graphics grDevices utils datasets
>> [8] methods base
>>
>> other attached packages:
>> [1] GenomicRanges_1.28.4 GenomeInfoDb_1.12.2 IRanges_2.10.3
>> [4] S4Vectors_0.14.3 BiocGenerics_0.22.0 colorout_1.1-2
>>
>> loaded via a namespace (and not attached):
>> [1] zlibbioc_1.22.0 compiler_3.4.0 XVector_0.16.0
>> [4] GenomeInfoDbData_0.99.0 RCurl_1.95-4.8 bitops_1.0-6
>>
>> --
>> Robert Castelo, PhD
>> Associate Professor
>> Dept. of Experimental and Health Sciences
>> Universitat Pompeu Fabra (UPF)
>> Barcelona Biomedical Research Park (PRBB)
>> Dr Aiguader 88
>> E-08003 Barcelona, Spain
>> telf: +34.933.160.514
>> fax: +34.933.160.550
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
--
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550
More information about the Bioc-devel
mailing list