Closed smgogarten closed 4 months ago
SeqVarTools is failing checks because seqMissing(per.variant=FALSE) returns an empty vector:
seqMissing(per.variant=FALSE)
> gds <- seqOpen(seqExampleFileName("gds")) > mr <- seqMissing(gds, per.variant=TRUE) > head(mr) [1] 0.36666667 0.41111111 0.14444444 0.18888889 0.01111111 0.01111111 > mr <- seqMissing(gds, per.variant=FALSE) > mr numeric(0) > sessionInfo() R version 4.3.2 (2023-10-31) Platform: aarch64-unknown-linux-gnu (64-bit) Running under: Ubuntu 22.04.3 LTS Matrix products: default BLAS: /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0 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 time zone: Etc/UTC tzcode source: system (glibc) attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] SeqArray_1.42.3 gdsfmt_1.38.0 loaded via a namespace (and not attached): [1] GenomeInfoDb_1.38.8 zlibbioc_1.48.2 GenomeInfoDbData_1.2.11 [4] parallel_4.3.2 XVector_0.42.0 BiocGenerics_0.48.1 [7] RCurl_1.98-1.14 Biostrings_2.70.3 stats4_4.3.2 [10] bitops_1.0-7 GenomicRanges_1.54.1 IRanges_2.36.0 [13] compiler_4.3.2 tools_4.3.2 S4Vectors_0.40.2 [16] crayon_1.5.2
I have noticed that. A fix SeqArray_v1.42.4 will be committed to BioC tonight.
SeqVarTools is failing checks because
seqMissing(per.variant=FALSE)
returns an empty vector: