Error testing with example data #11
Description
Hi, I get the following error trying the code on GitHub: Can you please help with this?
> library(linseed)
lo <- LinseedObject$new("GSE19830", samples=10:42, topGenes=10000)
Found 1 file(s)
GSE19830_series_matrix.txt.gz
Error in normalize.quantiles(expressionData) :
ERROR; return code from pthread_create() is 22
> session
sessionInfo sessioninfo::
> sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 11 (bullseye)
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.13.so
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] linseed_0.99.2 Biobase_2.58.0 BiocGenerics_0.44.0
loaded via a namespace (and not attached):
[1] fs_1.6.1 usethis_2.1.6 devtools_2.4.5
[4] doParallel_1.0.17 RColorBrewer_1.1-3 progress_1.2.2
[7] rprojroot_2.0.3 tools_4.2.3 profvis_0.3.7
[10] utf8_1.2.3 R6_2.5.1 colorspace_2.1-0
[13] urlchecker_1.0.1 withr_2.5.0 tidyselect_1.2.0
[16] prettyunits_1.1.1 processx_3.8.0 curl_5.0.0
[19] compiler_4.2.3 preprocessCore_1.60.2 cli_3.6.1
[22] xml2_1.3.3 desc_1.4.2 scales_1.2.1
[25] readr_2.1.4 callr_3.7.3 NMF_0.28
[28] stringr_1.5.0 digest_0.6.31 R.utils_2.12.3
[31] GEOquery_2.66.0 pkgconfig_2.0.3 htmltools_0.5.5
[34] sessioninfo_1.2.2 fastmap_1.1.1 limma_3.54.2
[37] htmlwidgets_1.6.2 rlang_1.1.0 shiny_1.7.4
[40] generics_0.1.3 combinat_0.0-8 R.oo_1.26.0
[43] dplyr_1.1.1 magrittr_2.0.3 Matrix_1.5-4
[46] Rcpp_1.0.10 munsell_0.5.0 fansi_1.0.4
[49] lifecycle_1.0.3 R.methodsS3_1.8.2 stringi_1.7.12
[52] pkgbuild_1.4.0 Rtsne_0.16 plyr_1.8.8
[55] grid_4.2.3 parallel_4.2.3 promises_1.2.0.1
[58] crayon_1.5.2 miniUI_0.1.1.1 lattice_0.21-8
[61] hms_1.1.3 ps_1.7.4 pillar_1.9.0
[64] rngtools_1.5.2 corpcor_1.6.10 reshape2_1.4.4
[67] codetools_0.2-19 pkgload_1.3.2 glue_1.6.2
[70] data.table_1.14.8 remotes_2.4.2 BiocManager_1.30.20
[73] vctrs_0.6.1 tzdb_0.3.0 httpuv_1.6.9
[76] foreach_1.5.2 gtable_0.3.3 purrr_1.0.1
[79] tidyr_1.3.0 cachem_1.0.7 ggplot2_3.4.2
[82] gridBase_0.4-7 mime_0.12 xtable_1.8-4
[85] later_1.3.0 tibble_3.2.1 iterators_1.0.14
[88] registry_0.5-1 memoise_2.0.1 cluster_2.1.4
[91] ellipsis_0.3.2