[Bioc-devel] gds nodes dimensions are inconsistent

[Liu, Qian]

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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