Dear Dr. Zheng & SeqArray maintainer,
I have a Bioconductor package called "GDSArray" that interfaces GDS file nodes
as DelayedArray instances. In this new Bioc devel version of 3.11, this package
failed all platforms. The debugging shows inconsistent dimensions calculated
from different SeqArray / gdsfmt functions. Following is some reproducible code
showing that the "annotation/info/AA" node has different dimension from "AC"
and the overall "num.variant" calculated from "SeqSummary". It works fine in
the Bioc 3.10 (dimension of AA is 1348).Thanks!
Best,
Qian
```{r}
library(SeqArray)
file <- seqExampleFileName("gds")
f <- seqOpen(file)
objdesp.gdsn(index.gdsn(f, "annotation/info/AA"))$dim
## [1] 1328
objdesp.gdsn(index.gdsn(f, "annotation/info/AC"))$dim
## [1] 1348
seqSummary(f, verbose=FALSE)$num.variant
## [1] 1348
seqClose(f)
!> sessionInfo()
R Under development (unstable) (2020-01-07 r77631)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS
Matrix products: default
BLAS: /home/qian/miniconda3/envs/r-devel/lib/R/lib/libRblas.so
LAPACK: /home/qian/miniconda3/envs/r-devel/lib/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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] SeqArray_1.27.8 gdsfmt_1.23.5
loaded via a namespace (and not attached):
[1] IRanges_2.21.2 Biostrings_2.55.4 crayon_1.3.4
[4] bitops_1.0-6 GenomeInfoDb_1.23.1 stats4_4.0.0
[7] zlibbioc_1.33.1 XVector_0.27.0 S4Vectors_0.25.11
[10] tools_4.0.0 RCurl_1.95-4.12 parallel_4.0.0
[13] compiler_4.0.0 BiocGenerics_0.33.0 GenomicRanges_1.39.1
[16] GenomeInfoDbData_1.2.2
```
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