[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) ## No error

rep(gr, 12) ## Error when printing
# GRanges object with 12 ranges and 1 metadata column:
# Error in .Call2("vector_OR_factor_extract_ranges", x, start, width,
PACKAGE = "S4Vectors") : 
#   'end' must be <= 'length(x)'

Any help would be appreciated!

Best regards,
Jialin

Sorry, forgot to attach the session info:

sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE Tumbleweed

Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices
utils     datasets
[8] methods   base

other attached packages:
[1] GenomicRanges_1.32.2 GenomeInfoDb_1.16.0  IRanges_2.14.8
[4] S4Vectors_0.18.1     BiocGenerics_0.26.0  magrittr_1.5

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


-------- Forwarded Message --------
From: Jialin Ma <marlin- at gmx.cn>
To: bioc-devel <bioc-devel at r-project.org>
Subject: Problem showing a GRanges with a meta data column of data
frame
Date: Tue, 15 May 2018 10:17:35 +0800
Mailer: Evolution 3.24.4

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) ## No error

rep(gr, 12) ## Error when printing
# GRanges object with 12 ranges and 1 metadata column:
# Error in .Call2("vector_OR_factor_extract_ranges", x, start, width,
PACKAGE = "S4Vectors") :
#   'end' must be <= 'length(x)'

Any help would be appreciated!

Best regards,
Jialin

Hi Jialin,

Thanks for the report. This should be fixed in BioC 3.7 (S4Vectors
0.18.2 and IRanges 2.14.10) and BioC devel (S4Vectors 0.19.3 and
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()
R version 3.5.0 (2018-04-23)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE Tumbleweed

Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices
utils     datasets
[8] methods   base

other attached packages:
[1] GenomicRanges_1.32.2 GenomeInfoDb_1.16.0  IRanges_2.14.8
[4] S4Vectors_0.18.1     BiocGenerics_0.26.0  magrittr_1.5

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


-------- Forwarded Message --------
From: Jialin Ma <marlin- at gmx.cn>
To: bioc-devel <bioc-devel at r-project.org>
Subject: Problem showing a GRanges with a meta data column of data
frame
Date: Tue, 15 May 2018 10:17:35 +0800
Mailer: Evolution 3.24.4

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) ## No error

rep(gr, 12) ## Error when printing
# GRanges object with 12 ranges and 1 metadata column:
# Error in .Call2("vector_OR_factor_extract_ranges", x, start,
width,
PACKAGE = "S4Vectors") :
#   'end' must be <= 'length(x)'

Any help would be appreciated!

Best regards,
Jialin