Many warnings of singular system in R 4.2, mixsqp_0.3-47

[mwslawinska]

Hi, I'm getting the same issue as reported in https://github.com/stephens999/ashr/issues/131#issue-1225218103. I updated mixsqp, but the issue persists. Thanks for help!

sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default BLAS: /opt/share/software/packages/R-4.2.0-debian-9/lib/R/lib/libRblas.so LAPACK: /opt/share/software/packages/R-4.2.0-debian-9/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] grid stats4 stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] mixsqp_0.3-47 ashr_2.2-54 [3] unikn_0.5.0 dendextend_1.16.0 [5] cluster_2.1.3 digest_0.6.29 [7] circlize_0.4.15 ComplexHeatmap_2.12.1 [9] ggrepel_0.9.1 RColorBrewer_1.1-3 [11] tibble_3.1.8 apeglm_1.18.0 [13] ggplot2_3.3.6 dplyr_1.0.9 [15] DESeq2_1.36.0 SummarizedExperiment_1.26.1 [17] MatrixGenerics_1.8.1 matrixStats_0.62.0 [19] GenomicFeatures_1.48.3 AnnotationDbi_1.58.0 [21] Biobase_2.56.0 GenomicRanges_1.48.0 [23] GenomeInfoDb_1.32.3 IRanges_2.30.1 [25] S4Vectors_0.34.0 BiocGenerics_0.42.0 [27] tximport_1.24.0 readr_2.1.2 [29] tximportData_1.24.0

loaded via a namespace (and not attached): [1] colorspace_2.0-3 rjson_0.2.21 ellipsis_0.3.2 [4] XVector_0.36.0 GlobalOptions_0.1.2 clue_0.3-61 [7] bit64_4.0.5 fansi_1.0.3 mvtnorm_1.1-3 [10] xml2_1.3.3 codetools_0.2-18 splines_4.2.0 [13] doParallel_1.0.17 cachem_1.0.6 geneplotter_1.74.0 [16] Rsamtools_2.12.0 annotate_1.74.0 dbplyr_2.2.1 [19] png_0.1-7 compiler_4.2.0 httr_1.4.4 [22] assertthat_0.2.1 Matrix_1.4-1 fastmap_1.1.0 [25] cli_3.3.0 prettyunits_1.1.1 tools_4.2.0 [28] coda_0.19-4 gtable_0.3.0 glue_1.6.2 [31] GenomeInfoDbData_1.2.8 rappdirs_0.3.3 Rcpp_1.0.9 [34] bbmle_1.0.25 vctrs_0.4.1 Biostrings_2.64.1 [37] rtracklayer_1.56.1 iterators_1.0.14 stringr_1.4.1 [40] irlba_2.3.5 lifecycle_1.0.1 restfulr_0.0.15 [43] XML_3.99-0.10 zlibbioc_1.42.0 MASS_7.3-56 [46] scales_1.2.1 hms_1.1.2 parallel_4.2.0 [49] yaml_2.3.5 curl_4.3.2 memoise_2.0.1 [52] gridExtra_2.3 emdbook_1.3.12 biomaRt_2.52.0 [55] bdsmatrix_1.3-6 SQUAREM_2021.1 stringi_1.7.8 [58] RSQLite_2.2.16 genefilter_1.78.0 BiocIO_1.6.0 [61] foreach_1.5.2 filelock_1.0.2 BiocParallel_1.30.3 [64] truncnorm_1.0-8 shape_1.4.6 rlang_1.0.4 [67] pkgconfig_2.0.3 bitops_1.0-7 invgamma_1.1 [70] lattice_0.20-45 purrr_0.3.4 GenomicAlignments_1.32.1 [73] bit_4.0.4 tidyselect_1.1.2 plyr_1.8.7 [76] magrittr_2.0.3 R6_2.5.1 generics_0.1.3 [79] DelayedArray_0.22.0 DBI_1.1.3 pillar_1.8.1 [82] withr_2.5.0 survival_3.3-1 KEGGREST_1.36.3 [85] RCurl_1.98-1.8 crayon_1.5.1 utf8_1.2.2 [88] BiocFileCache_2.4.0 tzdb_0.3.0 viridis_0.6.2 [91] GetoptLong_1.0.5 progress_1.2.2 locfit_1.5-9.6 [94] blob_1.2.3 xtable_1.8-4 numDeriv_2016.8-1.1 [97] munsell_0.5.0 viridisLite_0.4.1

[pcarbo]

@mwslawinska Could you please share some code we can use to reproduce the problem?

[mwslawinska]

@pcarbo, sure, e.g. the code in https://github.com/stephens999/ashr/issues/131#issue-1225218103 gives me this issue:

beta = c(rep(0,100),rnorm(100))
sebetahat = abs(rnorm(200,0,1))
betahat = rnorm(200,beta,sebetahat)
beta.ash = ash(betahat, sebetahat)

[pcarbo]

Which version of RcppArmadillo do you have?

[mwslawinska]

I updated it to RcppArmadillo_0.11.2.4.0 and I don't get the warnings anymore, thanks a lot!

[pcarbo]

Great! Thanks for letting us know.