Error in normalize.quantiles.use.target(matrix(IR1), as.vector(IG0)) : ERROR; return code from pthread_create() is 22
OberhammerF opened this issue · comments
when running the example code to try the preprocessing, i get an error. If anybody knows how to resolve this, I would be very glad!
Many thanks in advance
Code i am using:
sdf = sesameDataGet('EPIC.1.SigDF')
sdf_preped = openSesame(sdf, prep="DB", func=NULL)
Error:
Error in normalize.quantiles.use.target(matrix(IR1), as.vector(IG0)) :
ERROR; return code from pthread_create() is 22
Session Info
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS
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-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] reactable_0.4.4 qs_0.25.5 details_0.3.0 gridExtra_2.3 plotly_4.10.3
[6] eulerr_7.0.0 summarytools_1.0.1 cowplot_1.1.1 RColorBrewer_1.1-3 sesame_1.20.0
[11] sesameData_1.20.0 ExperimentHub_2.10.0 AnnotationHub_3.10.1 BiocFileCache_2.10.2 dbplyr_2.4.0
[16] BiocGenerics_0.48.1 readxl_1.4.3 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.0
[21] dplyr_1.1.3 purrr_1.0.2 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
[26] ggplot2_3.4.4 tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] jsonlite_1.8.7 rstudioapi_0.15.0 shape_1.4.6 magrittr_2.0.3
[5] magick_2.8.1 farver_2.1.1 rmarkdown_2.25 GlobalOptions_0.1.2
[9] zlibbioc_1.48.2 vctrs_0.6.4 memoise_2.0.1 RCurl_1.98-1.12
[13] base64enc_0.1-3 htmltools_0.5.6.1 S4Arrays_1.2.1 curl_5.1.0
[17] cellranger_1.1.0 SparseArray_1.2.4 sass_0.4.7 bslib_0.5.1
[21] desc_1.4.2 htmlwidgets_1.6.2 plyr_1.8.9 cachem_1.0.8
[25] mime_0.12 lifecycle_1.0.3 iterators_1.0.14 pkgconfig_2.0.3
[29] Matrix_1.6-1.1 R6_2.5.1 fastmap_1.1.1 GenomeInfoDbData_1.2.11
[33] MatrixGenerics_1.14.0 shiny_1.7.5.1 clue_0.3-65 digest_0.6.33
[37] colorspace_2.1-0 AnnotationDbi_1.64.1 S4Vectors_0.40.2 rprojroot_2.0.3
[41] crosstalk_1.2.0 GenomicRanges_1.54.1 RSQLite_2.3.2 labeling_0.4.3
[45] filelock_1.0.2 fansi_1.0.5 timechange_0.2.0 httr_1.4.7
[49] abind_1.4-5 compiler_4.3.1 bit64_4.0.5 withr_2.5.1
[53] doParallel_1.0.17 pander_0.6.5 backports_1.4.1 BiocParallel_1.36.0
[57] DBI_1.1.3 MASS_7.3-60 rappdirs_0.3.3 DelayedArray_0.28.0
[61] rjson_0.2.21 tools_4.3.1 interactiveDisplayBase_1.40.0 httpuv_1.6.12
[65] clipr_0.8.0 glue_1.6.2 promises_1.2.1 checkmate_2.3.0
[69] cluster_2.1.4 reshape2_1.4.4 generics_0.1.3 gtable_0.3.4
[73] tzdb_0.4.0 preprocessCore_1.64.0 RApiSerialize_0.1.2 data.table_1.14.8
[77] hms_1.1.3 stringfish_0.15.8 xml2_1.3.5 utf8_1.2.4
[81] XVector_0.42.0 BiocVersion_3.18.1 foreach_1.5.2 pillar_1.9.0
[85] later_1.3.1 circlize_0.4.15 pryr_0.1.6 lattice_0.21-8
[89] bit_4.0.5 tidyselect_1.2.0 ComplexHeatmap_2.18.0 Biostrings_2.70.3
[93] wheatmap_0.2.0 knitr_1.44 IRanges_2.36.0 SummarizedExperiment_1.32.0
[97] stats4_4.3.1 xfun_0.40 Biobase_2.62.0 rapportools_1.1
[101] matrixStats_1.0.0 DT_0.30 stringi_1.7.12 lazyeval_0.2.2
[105] yaml_2.3.7 evaluate_0.22 codetools_0.2-19 tcltk_4.3.1
[109] BiocManager_1.30.22 cli_3.6.1 RcppParallel_5.1.7 xtable_1.8-4
[113] jquerylib_0.1.4 munsell_0.5.0 Rcpp_1.0.11 GenomeInfoDb_1.38.8
[117] png_0.1-8 parallel_4.3.1 ellipsis_0.3.2 blob_1.2.4
[121] bitops_1.0-7 viridisLite_0.4.2 scales_1.2.1 crayon_1.5.2
[125] GetoptLong_1.0.5 rlang_1.1.1 KEGGREST_1.42.0
updating sesame to 1.21.15 did not resolve the problem.
BiocManager::install("preprocessCore", configure.args="--disable-threading") and restarting R studio fixed it!