Error: cannot allocate vector of size

Hi,

we are trying to include flowAI into our pipeline analysing mass cytometry samples. But I get this error:

Quality control for the file: 1 Error: cannot allocate vector of size 4538.4 Gb

I guess it has something to do with memory allocation. But the test file has a size of 1.8 Mbit and the created flowSet 4700 bytes. I tried it also to run directly as .fcs file as suggested in the vignette:

fcsfiles <- dir(".", pattern="*fcs$") resQC <- flow_auto_qc(fcsfiles)

But the error stays the same. I never faced any allocation error in R before I would appreciate any suggestion Best, Sebastian

sessionInfo() R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22621)

Matrix products: default

locale: [1] LC_COLLATE=German_Germany.utf8 LC_CTYPE=German_Germany.utf8 LC_MONETARY=German_Germany.utf8 [4] LC_NUMERIC=C LC_TIME=German_Germany.utf8

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] flowAI_1.26.0 flowCore_2.8.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.9 compiler_4.2.0 pillar_1.8.1 RColorBrewer_1.1-3 cytolib_2.8.0
[6] plyr_1.8.7 tools_4.2.0 digest_0.6.29 lattice_0.20-45 evaluate_0.19
[11] lifecycle_1.0.3 tibble_3.1.8 gtable_0.3.1 pkgconfig_2.0.3 rlang_1.0.6
[16] cli_3.4.1 DBI_1.1.3 rstudioapi_0.14 xfun_0.35 fastmap_1.1.0
[21] stringr_1.5.0 dplyr_1.0.10 knitr_1.41 generics_0.1.3 S4Vectors_0.34.0
[26] vctrs_0.5.1 stats4_4.2.0 grid_4.2.0 tidyselect_1.2.0 glue_1.6.2
[31] Biobase_2.56.0 R6_2.5.1 fansi_1.0.3 rmarkdown_2.18 reshape2_1.4.4
[36] RProtoBufLib_2.8.0 ggplot2_3.4.0 magrittr_2.0.3 htmltools_0.5.4 scales_1.2.1
[41] matrixStats_0.62.0 BiocGenerics_0.42.0 changepoint_2.2.4 assertthat_0.2.1 colorspace_2.0-3
[46] utf8_1.2.2 stringi_1.7.8 RcppParallel_5.1.5 munsell_0.5.0 zoo_1.8-11

Hi, It is possible that the file is too small actually and you have a very small number of events. Is it the smallest file you have?

On Wed, 14 Dec 2022 at 13:25, Stacheltier @.***> wrote:

Hi,

we are trying to include flowAI into our pipeline analysing mass cytometry samples. But I get this error:

Quality control for the file: 1 Error: cannot allocate vector of size 4538.4 Gb

I guess it has something to do with memory allocation. But the test file has a size of 1.8 Mbit and the created flowSet 4700 bytes. I tried it also to run directly as .fcs file as suggested in the vignette:

fcsfiles <- dir(".", pattern="*fcs$") resQC <- flow_auto_qc(fcsfiles)

But the error stays the same. I never faced any allocation error in R before I would appreciate any suggestion Best, Sebastian

sessionInfo() R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22621)

Matrix products: default

locale: [1] LC_COLLATE=German_Germany.utf8 LC_CTYPE=German_Germany.utf8 LC_MONETARY=German_Germany.utf8 [4] LC_NUMERIC=C LC_TIME=German_Germany.utf8

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] flowAI_1.26.0 flowCore_2.8.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.9 compiler_4.2.0 pillar_1.8.1 RColorBrewer_1.1-3 cytolib_2.8.0 [6] plyr_1.8.7 tools_4.2.0 digest_0.6.29 lattice_0.20-45 evaluate_0.19 [11] lifecycle_1.0.3 tibble_3.1.8 gtable_0.3.1 pkgconfig_2.0.3 rlang_1.0.6 [16] cli_3.4.1 DBI_1.1.3 rstudioapi_0.14 xfun_0.35 fastmap_1.1.0 [21] stringr_1.5.0 dplyr_1.0.10 knitr_1.41 generics_0.1.3 S4Vectors_0.34.0 [26] vctrs_0.5.1 stats4_4.2.0 grid_4.2.0 tidyselect_1.2.0 glue_1.6.2 [31] Biobase_2.56.0 R6_2.5.1 fansi_1.0.3 rmarkdown_2.18 reshape2_1.4.4 [36] RProtoBufLib_2.8.0 ggplot2_3.4.0 magrittr_2.0.3 htmltools_0.5.4 scales_1.2.1 [41] matrixStats_0.62.0 BiocGenerics_0.42.0 changepoint_2.2.4 assertthat_0.2.1 colorspace_2.0-3 [46] utf8_1.2.2 stringi_1.7.8 RcppParallel_5.1.5 munsell_0.5.0 zoo_1.8-11

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Hi,

thank You for the quick response! I've tried it also with large files (>1Gb). Initially I thought it is a resource problem. Trying around, the import of FCS files seem to be the source of problem. When using read.flowSet/read.FCS /read.flowFrame to import it looks like that "." is introduced as decimal separator resulting in numbers e.g. 0.623 or 1478.2 in some cases. Could that be problema?

During a test I removed all decimal digits during generation of FCS file. Thus, there are no more decimal separators and numbers like above. Afterwards,flow_auto_qc(flowSet_df)works nicely as expected.

Do You have an idea, why I'm facing this data import problems?

best,

Sebastian

Von: Gianni Monaco @.***> Gesendet: Donnerstag, 15. Dezember 2022 16:38 An: giannimonaco/flowAI Cc: Thieme, Sebastian; Author Betreff: Re: [giannimonaco/flowAI] Error: cannot allocate vector of size (Issue #12)

Hi, It is possible that the file is too small actually and you have a very small number of events. Is it the smallest file you have?

On Wed, 14 Dec 2022 at 13:25, Stacheltier @.***> wrote:

Hi,

we are trying to include flowAI into our pipeline analysing mass cytometry samples. But I get this error:

Quality control for the file: 1 Error: cannot allocate vector of size 4538.4 Gb

I guess it has something to do with memory allocation. But the test file has a size of 1.8 Mbit and the created flowSet 4700 bytes. I tried it also to run directly as .fcs file as suggested in the vignette:

fcsfiles <- dir(".", pattern="*fcs$") resQC <- flow_auto_qc(fcsfiles)

But the error stays the same. I never faced any allocation error in R before I would appreciate any suggestion Best, Sebastian

sessionInfo() R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22621)

Matrix products: default

locale: [1] LC_COLLATE=German_Germany.utf8 LC_CTYPE=German_Germany.utf8 LC_MONETARY=German_Germany.utf8 [4] LC_NUMERIC=C LC_TIME=German_Germany.utf8

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] flowAI_1.26.0 flowCore_2.8.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.9 compiler_4.2.0 pillar_1.8.1 RColorBrewer_1.1-3 cytolib_2.8.0 [6] plyr_1.8.7 tools_4.2.0 digest_0.6.29 lattice_0.20-45 evaluate_0.19 [11] lifecycle_1.0.3 tibble_3.1.8 gtable_0.3.1 pkgconfig_2.0.3 rlang_1.0.6 [16] cli_3.4.1 DBI_1.1.3 rstudioapi_0.14 xfun_0.35 fastmap_1.1.0 [21] stringr_1.5.0 dplyr_1.0.10 knitr_1.41 generics_0.1.3 S4Vectors_0.34.0 [26] vctrs_0.5.1 stats4_4.2.0 grid_4.2.0 tidyselect_1.2.0 glue_1.6.2 [31] Biobase_2.56.0 R6_2.5.1 fansi_1.0.3 rmarkdown_2.18 reshape2_1.4.4 [36] RProtoBufLib_2.8.0 ggplot2_3.4.0 magrittr_2.0.3 htmltools_0.5.4 scales_1.2.1 [41] matrixStats_0.62.0 BiocGenerics_0.42.0 changepoint_2.2.4 assertthat_0.2.1 colorspace_2.0-3 [46] utf8_1.2.2 stringi_1.7.8 RcppParallel_5.1.5 munsell_0.5.0 zoo_1.8-11

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Hi Sebastian,

it could be that the problem is in the import of the FCS file. I can't say for sure why this is happening though. Would it be possible for you to share a small FCS file, so that I could try myself too?

Best wishes, Gianni

On Fri, 16 Dec 2022 at 10:35, Stacheltier @.***> wrote:

Hi,

thank You for the quick response! I've tried it also with large files (>1Gb). Initially I thought it is a resource problem. Trying around, the import of FCS files seem to be the source of problem. When using read.flowSet/read.FCS /read.flowFrame to import it looks like that "." is introduced as decimal separator resulting in numbers e.g. 0.623 or 1478.2 in some cases. Could that be problema?

During a test I removed all decimal digits during generation of FCS file. Thus, there are no more decimal separators and numbers like above. Afterwards,flow_auto_qc(flowSet_df)works nicely as expected.

Do You have an idea, why I'm facing this data import problems?

best,

Sebastian

Von: Gianni Monaco @.***> Gesendet: Donnerstag, 15. Dezember 2022 16:38 An: giannimonaco/flowAI Cc: Thieme, Sebastian; Author Betreff: Re: [giannimonaco/flowAI] Error: cannot allocate vector of size (Issue #12)

Hi, It is possible that the file is too small actually and you have a very small number of events. Is it the smallest file you have?

On Wed, 14 Dec 2022 at 13:25, Stacheltier @.***> wrote:

Hi,

we are trying to include flowAI into our pipeline analysing mass cytometry samples. But I get this error:

Quality control for the file: 1 Error: cannot allocate vector of size 4538.4 Gb

I guess it has something to do with memory allocation. But the test file has a size of 1.8 Mbit and the created flowSet 4700 bytes. I tried it also to run directly as .fcs file as suggested in the vignette:

fcsfiles <- dir(".", pattern="*fcs$") resQC <- flow_auto_qc(fcsfiles)

But the error stays the same. I never faced any allocation error in R before I would appreciate any suggestion Best, Sebastian

sessionInfo() R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22621)

Matrix products: default

locale: [1] LC_COLLATE=German_Germany.utf8 LC_CTYPE=German_Germany.utf8 LC_MONETARY=German_Germany.utf8 [4] LC_NUMERIC=C LC_TIME=German_Germany.utf8

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] flowAI_1.26.0 flowCore_2.8.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.9 compiler_4.2.0 pillar_1.8.1 RColorBrewer_1.1-3 cytolib_2.8.0 [6] plyr_1.8.7 tools_4.2.0 digest_0.6.29 lattice_0.20-45 evaluate_0.19 [11] lifecycle_1.0.3 tibble_3.1.8 gtable_0.3.1 pkgconfig_2.0.3 rlang_1.0.6 [16] cli_3.4.1 DBI_1.1.3 rstudioapi_0.14 xfun_0.35 fastmap_1.1.0 [21] stringr_1.5.0 dplyr_1.0.10 knitr_1.41 generics_0.1.3 S4Vectors_0.34.0 [26] vctrs_0.5.1 stats4_4.2.0 grid_4.2.0 tidyselect_1.2.0 glue_1.6.2 [31] Biobase_2.56.0 R6_2.5.1 fansi_1.0.3 rmarkdown_2.18 reshape2_1.4.4 [36] RProtoBufLib_2.8.0 ggplot2_3.4.0 magrittr_2.0.3 htmltools_0.5.4 scales_1.2.1 [41] matrixStats_0.62.0 BiocGenerics_0.42.0 changepoint_2.2.4 assertthat_0.2.1 colorspace_2.0-3 [46] utf8_1.2.2 stringi_1.7.8 RcppParallel_5.1.5 munsell_0.5.0 zoo_1.8-11

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Dear Gianni,

I guess its really a matter of size. I tested subsamples. The original fcs file containe >900T events each 45 parameters.

I managed to get flowAI working with subset of 50T events. Everything above results in memory allocation error. Thus, it seem to be a matter of my PC.

From statistical point of view: Do You think it is possible to split a sample into subsets of 50T events and run flowAI with subsequent concatenation of results? I would like to avoid to cut down to 50T events since I expect very rare populations below 0.01% of total.

Thank You very much and have a nice X-mas!

Sebastian

Von: Gianni Monaco @.***> Gesendet: Freitag, 16. Dezember 2022 22:49 An: giannimonaco/flowAI Cc: Thieme, Sebastian; Author Betreff: Re: [giannimonaco/flowAI] Error: cannot allocate vector of size (Issue #12)

Hi Sebastian,

Best wishes, Gianni

On Fri, 16 Dec 2022 at 10:35, Stacheltier @.***> wrote:

Hi,

thank You for the quick response! I've tried it also with large files (>1Gb). Initially I thought it is a resource problem. Trying around, the import of FCS files seem to be the source of problem. When using read.flowSet/read.FCS /read.flowFrame to import it looks like that "." is introduced as decimal separator resulting in numbers e.g. 0.623 or 1478.2 in some cases. Could that be problema?

During a test I removed all decimal digits during generation of FCS file. Thus, there are no more decimal separators and numbers like above. Afterwards,flow_auto_qc(flowSet_df)works nicely as expected.

Do You have an idea, why I'm facing this data import problems?

best,

Sebastian

Von: Gianni Monaco @.***> Gesendet: Donnerstag, 15. Dezember 2022 16:38 An: giannimonaco/flowAI Cc: Thieme, Sebastian; Author Betreff: Re: [giannimonaco/flowAI] Error: cannot allocate vector of size (Issue #12)

Hi, It is possible that the file is too small actually and you have a very small number of events. Is it the smallest file you have?

On Wed, 14 Dec 2022 at 13:25, Stacheltier @.***> wrote:

Hi,

we are trying to include flowAI into our pipeline analysing mass cytometry samples. But I get this error:

Quality control for the file: 1 Error: cannot allocate vector of size 4538.4 Gb

I guess it has something to do with memory allocation. But the test file has a size of 1.8 Mbit and the created flowSet 4700 bytes. I tried it also to run directly as .fcs file as suggested in the vignette:

fcsfiles <- dir(".", pattern="*fcs$") resQC <- flow_auto_qc(fcsfiles)

But the error stays the same. I never faced any allocation error in R before I would appreciate any suggestion Best, Sebastian

sessionInfo() R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22621)

Matrix products: default

locale: [1] LC_COLLATE=German_Germany.utf8 LC_CTYPE=German_Germany.utf8 LC_MONETARY=German_Germany.utf8 [4] LC_NUMERIC=C LC_TIME=German_Germany.utf8

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] flowAI_1.26.0 flowCore_2.8.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.9 compiler_4.2.0 pillar_1.8.1 RColorBrewer_1.1-3 cytolib_2.8.0 [6] plyr_1.8.7 tools_4.2.0 digest_0.6.29 lattice_0.20-45 evaluate_0.19 [11] lifecycle_1.0.3 tibble_3.1.8 gtable_0.3.1 pkgconfig_2.0.3 rlang_1.0.6 [16] cli_3.4.1 DBI_1.1.3 rstudioapi_0.14 xfun_0.35 fastmap_1.1.0 [21] stringr_1.5.0 dplyr_1.0.10 knitr_1.41 generics_0.1.3 S4Vectors_0.34.0 [26] vctrs_0.5.1 stats4_4.2.0 grid_4.2.0 tidyselect_1.2.0 glue_1.6.2 [31] Biobase_2.56.0 R6_2.5.1 fansi_1.0.3 rmarkdown_2.18 reshape2_1.4.4 [36] RProtoBufLib_2.8.0 ggplot2_3.4.0 magrittr_2.0.3 htmltools_0.5.4 scales_1.2.1 [41] matrixStats_0.62.0 BiocGenerics_0.42.0 changepoint_2.2.4 assertthat_0.2.1 colorspace_2.0-3 [46] utf8_1.2.2 stringi_1.7.8 RcppParallel_5.1.5 munsell_0.5.0 zoo_1.8-11

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Dear Sebastian,

great to hear that you understood what's the problem!

I think that sub-sampling the samples and concatenating them afterward should be fine. You can make sure you always get very similar plots in the report document. If you don't, you might sub-sampling too much.

Have nice holidays and nice Christmas too! Gianni

On Mon, 19 Dec 2022 at 15:47, Stacheltier @.***> wrote:

Dear Gianni,

I guess its really a matter of size. I tested subsamples. The original fcs file containe >900T events each 45 parameters.

I managed to get flowAI working with subset of 50T events. Everything above results in memory allocation error. Thus, it seem to be a matter of my PC.

From statistical point of view: Do You think it is possible to split a sample into subsets of 50T events and run flowAI with subsequent concatenation of results? I would like to avoid to cut down to 50T events since I expect very rare populations below 0.01% of total.

Thank You very much and have a nice X-mas!

Sebastian

Von: Gianni Monaco @.***> Gesendet: Freitag, 16. Dezember 2022 22:49 An: giannimonaco/flowAI Cc: Thieme, Sebastian; Author Betreff: Re: [giannimonaco/flowAI] Error: cannot allocate vector of size (Issue #12)

Hi Sebastian,

it could be that the problem is in the import of the FCS file. I can't say for sure why this is happening though. Would it be possible for you to share a small FCS file, so that I could try myself too?

Best wishes, Gianni

On Fri, 16 Dec 2022 at 10:35, Stacheltier @.***> wrote:

Hi,

thank You for the quick response! I've tried it also with large files (>1Gb). Initially I thought it is a resource problem. Trying around, the import of FCS files seem to be the source of problem. When using read.flowSet/read.FCS /read.flowFrame to import it looks like that "." is introduced as decimal separator resulting in numbers e.g. 0.623 or 1478.2 in some cases. Could that be problema?

During a test I removed all decimal digits during generation of FCS file. Thus, there are no more decimal separators and numbers like above. Afterwards,flow_auto_qc(flowSet_df)works nicely as expected.

Do You have an idea, why I'm facing this data import problems?

best,

Sebastian

Von: Gianni Monaco @.***> Gesendet: Donnerstag, 15. Dezember 2022 16:38 An: giannimonaco/flowAI Cc: Thieme, Sebastian; Author Betreff: Re: [giannimonaco/flowAI] Error: cannot allocate vector of size (Issue #12)

Hi, It is possible that the file is too small actually and you have a very small number of events. Is it the smallest file you have?

On Wed, 14 Dec 2022 at 13:25, Stacheltier @.***> wrote:

Hi,

we are trying to include flowAI into our pipeline analysing mass cytometry samples. But I get this error:

Quality control for the file: 1 Error: cannot allocate vector of size 4538.4 Gb

I guess it has something to do with memory allocation. But the test file has a size of 1.8 Mbit and the created flowSet 4700 bytes. I tried it also to run directly as .fcs file as suggested in the vignette:

fcsfiles <- dir(".", pattern="*fcs$") resQC <- flow_auto_qc(fcsfiles)

But the error stays the same. I never faced any allocation error in R before I would appreciate any suggestion Best, Sebastian

sessionInfo() R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22621)

Matrix products: default

locale: [1] LC_COLLATE=German_Germany.utf8 LC_CTYPE=German_Germany.utf8 LC_MONETARY=German_Germany.utf8 [4] LC_NUMERIC=C LC_TIME=German_Germany.utf8

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] flowAI_1.26.0 flowCore_2.8.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.9 compiler_4.2.0 pillar_1.8.1 RColorBrewer_1.1-3 cytolib_2.8.0 [6] plyr_1.8.7 tools_4.2.0 digest_0.6.29 lattice_0.20-45 evaluate_0.19 [11] lifecycle_1.0.3 tibble_3.1.8 gtable_0.3.1 pkgconfig_2.0.3 rlang_1.0.6 [16] cli_3.4.1 DBI_1.1.3 rstudioapi_0.14 xfun_0.35 fastmap_1.1.0 [21] stringr_1.5.0 dplyr_1.0.10 knitr_1.41 generics_0.1.3 S4Vectors_0.34.0 [26] vctrs_0.5.1 stats4_4.2.0 grid_4.2.0 tidyselect_1.2.0 glue_1.6.2 [31] Biobase_2.56.0 R6_2.5.1 fansi_1.0.3 rmarkdown_2.18 reshape2_1.4.4 [36] RProtoBufLib_2.8.0 ggplot2_3.4.0 magrittr_2.0.3 htmltools_0.5.4 scales_1.2.1 [41] matrixStats_0.62.0 BiocGenerics_0.42.0 changepoint_2.2.4 assertthat_0.2.1 colorspace_2.0-3 [46] utf8_1.2.2 stringi_1.7.8 RcppParallel_5.1.5 munsell_0.5.0 zoo_1.8-11

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giannimonaco / flowAI

Error: cannot allocate vector of size #12