[Bioc-devel] [External] Memory error from sesame build
Vincent Carey
@tvjc @end|ng |rom ch@nn|ng@h@rv@rd@edu
Sun Nov 28 13:05:40 CET 2021
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 using 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 using gmail.com<mailto:
> tim.triche using 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 using pennmedicine.upenn.edu<mailto:
> Wanding.Zhou using 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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