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.z...@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.tri...@gmail.com<mailto: > tim.tri...@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.z...@pennmedicine.upenn.edu<mailto: > wanding.z...@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]] > > _______________________________________________ > Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
