[Bioc-devel] [External] Memory error from sesame build
It seems noteworthy that this is occurring only for the i386 build on windows. i've had no luck reproducing the error with * sessionInfo() R version 4.1.2 RC (2021-10-25 r81110) Platform: i386-w64-mingw32/i386 (32-bit) Running under: Windows 10 x64 (build 19043) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] sesame_1.12.5 sesameData_1.12.0 rmarkdown_2.11 [4] ExperimentHub_2.2.0 AnnotationHub_3.2.0 BiocFileCache_2.2.0 [7] dbplyr_2.1.1 BiocGenerics_0.40.0 loaded via a namespace (and not attached): [1] bitops_1.0-7 matrixStats_0.61.0 [3] bit64_4.0.5 filelock_1.0.2 [5] RColorBrewer_1.1-2 httr_1.4.2 [7] GenomeInfoDb_1.30.0 tools_4.1.2 [9] utf8_1.2.2 R6_2.5.1 [11] KernSmooth_2.23-20 DBI_1.1.1 [13] colorspace_2.0-2 withr_2.4.2 [15] DNAcopy_1.68.0 tidyselect_1.1.1 [17] gridExtra_2.3 preprocessCore_1.56.0 [19] bit_4.0.4 curl_4.3.2 [21] compiler_4.1.2 Biobase_2.54.0 [23] DelayedArray_0.20.0 scales_1.1.1 [25] randomForest_4.6-14 proxy_0.4-26 [27] rappdirs_0.3.3 stringr_1.4.0 [29] digest_0.6.28 XVector_0.34.0 [31] pkgconfig_2.0.3 htmltools_0.5.2 [33] MatrixGenerics_1.6.0 fastmap_1.1.0 [35] rlang_0.4.12 RSQLite_2.2.8 [37] shiny_1.7.1 generics_0.1.1 [39] wheatmap_0.1.0 BiocParallel_1.28.0 [41] dplyr_1.0.7 RCurl_1.98-1.5 [43] magrittr_2.0.1 GenomeInfoDbData_1.2.7 [45] Matrix_1.3-4 Rcpp_1.0.7 [47] munsell_0.5.0 S4Vectors_0.32.0 [49] fansi_0.5.0 lifecycle_1.0.1 [51] stringi_1.7.5 yaml_2.2.1 [53] SummarizedExperiment_1.24.0 zlibbioc_1.40.0 [55] plyr_1.8.6 grid_4.1.2 [57] blob_1.2.2 parallel_4.1.2 [59] promises_1.2.0.1 ggrepel_0.9.1 [61] crayon_1.4.2 lattice_0.20-45 [63] Biostrings_2.62.0 KEGGREST_1.34.0 [65] knitr_1.36 pillar_1.6.4 [67] fgsea_1.20.0 GenomicRanges_1.46.0 [69] reshape2_1.4.4 stats4_4.1.2 [71] fastmatch_1.1-3 glue_1.4.2 [73] BiocVersion_3.14.0 evaluate_0.14 [75] data.table_1.14.2 BiocManager_1.30.16 [77] png_0.1-7 vctrs_0.3.8 [79] httpuv_1.6.3 gtable_0.3.0 [81] purrr_0.3.4 assertthat_0.2.1 [83] cachem_1.0.6 ggplot2_3.3.5 [85] xfun_0.27 mime_0.12 [87] xtable_1.8-4 e1071_1.7-9 [89] later_1.3.0 class_7.3-19 [91] tibble_3.1.5 AnnotationDbi_1.56.2 [93] memoise_2.0.1 IRanges_2.28.0 [95] ellipsis_0.3.2 interactiveDisplayBase_1.32.0 or with sessionInfo() R version 4.1.2 RC (2021-10-25 r81110) Platform: i386-w64-mingw32/i386 (32-bit) Running under: Windows 10 x64 (build 19043) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] sesame_1.12.5 sesameData_1.12.0 rmarkdown_2.11 [4] ExperimentHub_2.2.0 AnnotationHub_3.2.0 BiocFileCache_2.2.0 [7] dbplyr_2.1.1 BiocGenerics_0.40.0 loaded via a namespace (and not attached): [1] bitops_1.0-7 matrixStats_0.61.0 [3] bit64_4.0.5 filelock_1.0.2 [5] RColorBrewer_1.1-2 httr_1.4.2 [7] GenomeInfoDb_1.30.0 tools_4.1.2 [9] utf8_1.2.2 R6_2.5.1 [11] KernSmooth_2.23-20 DBI_1.1.1 [13] colorspace_2.0-2 withr_2.4.2 [15] DNAcopy_1.68.0 tidyselect_1.1.1 [17] gridExtra_2.3 preprocessCore_1.56.0 [19] bit_4.0.4 curl_4.3.2 [21] compiler_4.1.2 Biobase_2.54.0 [23] DelayedArray_0.20.0 scales_1.1.1 [25] randomForest_4.6-14 proxy_0.4-26 [27] rappdirs_0.3.3 stringr_1.4.0 [29] digest_0.6.28 XVector_0.34.0 [31] pkgconfig_2.0.3 htmltools_0.5.2 [33] MatrixGenerics_1.6.0 fastmap_1.1.0 [35] rlang_0.4.12 RSQLite_2.2.8 [37] shiny_1.7.1 generics_0.1.1 [39] wheatmap_0.1.0 BiocParallel_1.28.2 [41] dplyr_1.0.7 RCurl_1.98-1.5 [43] magrittr_2.0.1 GenomeInfoDbData_1.2.7 [45] Matrix_1.3-4 Rcpp_1.0.7 [47] munsell_0.5.0 S4Vectors_0.32.3 [49] fansi_0.5.0 lifecycle_1.0.1 [51] stringi_1.7.5 yaml_2.2.1 [53] SummarizedExperiment_1.24.0 zlibbioc_1.40.0 [55] plyr_1.8.6 grid_4.1.2 [57] blob_1.2.2 parallel_4.1.2 [59] promises_1.2.0.1 ggrepel_0.9.1 [61] crayon_1.4.2 lattice_0.20-45 [63] Biostrings_2.62.0 KEGGREST_1.34.0 [65] knitr_1.36 pillar_1.6.4 [67] fgsea_1.20.0 GenomicRanges_1.46.1 [69] reshape2_1.4.4 stats4_4.1.2 [71] fastmatch_1.1-3 glue_1.5.0 [73] BiocVersion_3.14.0 evaluate_0.14 [75] data.table_1.14.2 BiocManager_1.30.16 [77] png_0.1-7 vctrs_0.3.8 [79] httpuv_1.6.3 gtable_0.3.0 [81] purrr_0.3.4 assertthat_0.2.1 [83] cachem_1.0.6 ggplot2_3.3.5 [85] xfun_0.28 mime_0.12 [87] xtable_1.8-4 e1071_1.7-9 [89] later_1.3.0 class_7.3-19 [91] tibble_3.1.6 AnnotationDbi_1.56.2 [93] memoise_2.0.1 IRanges_2.28.0 [95] ellipsis_0.3.2 interactiveDisplayBase_1.32.0
On Sun, Nov 28, 2021 at 6:55 AM Zhou, Wanding <
Wanding.Zhou at pennmedicine.upenn.edu> wrote:
Thank you Tim. That makes sense. It seems only occurring in Windows. Is there a known lower memory limit or stack usage in Windows? Windows Server 2012 R2 Standard / x64 http://bioconductor.org/checkResults/release/bioc-LATEST/sesame/tokay2-checksrc.html Error: cannot allocate vector of size 6.6 Mb Execution halted Error: 'Calloc' could not allocate memory (27514181 of 1 bytes) Fatal error: error during cleanup Thanks again, Wanding On Nov 27, 2021, at 4:15 PM, Tim Triche, Jr. <tim.triche at gmail.com<mailto: tim.triche at gmail.com>> wrote: Recursion issue. Make sure some constructor isn?t constructing itself into oblivion. This is a nasty one --t On Nov 27, 2021, at 5:48 AM, Zhou, Wanding < Wanding.Zhou at pennmedicine.upenn.edu<mailto: Wanding.Zhou at pennmedicine.upenn.edu>> wrote: ?Hi, Recently we are experience some memory issue on both development and release (mostly Windows) that causes the sesame package build to fail. We are trying to address it but it seems to run fine locally on our side. This is the error on the development branch Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) Error: processing vignette 'sesame.Rmd' failed with diagnostics: C stack usage 7977908 is too close to the limit And this is the error on the release branch data = data.frame(estimate=c(runif(10, 0, 10))) plotLollipop(data) Error in grid.newpage() : 'Calloc' could not allocate memory (27541715 of 1 bytes) Calls: <Anonymous> -> print.ggplot -> grid.newpage Let me know if you are aware of something or have a clue. Any insight will be super helpful! Thanks! Zoom link: https://us02web.zoom.us/j/4248839577 ---- Wanding Zhou, Ph.D. Assistant Professor Office: CTRB 9050 3501 Civic Center Blvd Philadelphia, PA 19104 Lab: https://zhou-lab.github.io/ Phone (o): (215) 590-0473 [[alternative HTML version deleted]]
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