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Error in FUN(X[[i]], ...) : 'export_.....fcs' is not a valid file in flow_auto_qc()? #15

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denvercal1234GitHub opened this issue Jan 26, 2023 · 1 comment
Open

Error in FUN(X[[i]], ...) : 'export_.....fcs' is not a valid file in flow_auto_qc()? #15

denvercal1234GitHub opened this issue Jan 26, 2023 · 1 comment

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@denvercal1234GitHub
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Hi there,

Thanks for the tool.

I ran flow_auto_qc() on untransformed FCS files (directly exported from FlowJo), but encountered the error below. Would you mind helping me troubleshoot?

Thank you.

export_F37_Live_flowAIresQC <- flow_auto_qc(F37_LiveSinglets_FCS)

Error in FUN(X[[i]], ...) :
'export_F37_Live.fcs' is not a valid file

> session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.2 (2022-10-31)
 os       macOS Ventura 13.1
 system   aarch64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/London
 date     2023-01-26
 rstudio  2022.12.0+353 Elsbeth Geranium (desktop)
 pandoc   2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version    date (UTC) lib source
 abind                  1.4-5      2016-07-21 [2] CRAN (R 4.2.0)
 askpass                1.1        2019-01-13 [2] CRAN (R 4.2.0)
 assertthat             0.2.1      2019-03-21 [1] CRAN (R 4.2.0)
 aws.s3                 0.3.21     2020-04-07 [2] CRAN (R 4.2.0)
 aws.signature          0.6.0      2020-06-01 [2] CRAN (R 4.2.0)
 backports              1.4.1      2021-12-13 [2] CRAN (R 4.2.0)
 base64enc              0.1-3      2015-07-28 [2] CRAN (R 4.2.0)
 beachmat               2.12.0     2022-04-26 [1] Bioconductor
 beeswarm               0.4.0      2021-06-01 [1] CRAN (R 4.2.0)
 Biobase              * 2.58.0     2022-11-07 [1] Bioconductor
 BiocGenerics         * 0.44.0     2022-11-07 [1] Bioconductor
 BiocManager            1.30.19    2022-10-25 [2] CRAN (R 4.2.0)
 BiocNeighbors          1.14.0     2022-04-26 [1] Bioconductor
 BiocParallel           1.30.4     2022-10-11 [1] Bioconductor
 BiocSingular           1.12.0     2022-04-26 [1] Bioconductor
 bitops                 1.0-7      2021-04-24 [2] CRAN (R 4.2.0)
 broom                  1.0.3      2023-01-25 [2] CRAN (R 4.2.0)
 bslib                  0.4.2      2022-12-16 [2] CRAN (R 4.2.0)
 cachem                 1.0.6      2021-08-19 [2] CRAN (R 4.2.0)
 callr                  3.7.3      2022-11-02 [2] CRAN (R 4.2.1)
 car                    3.1-1      2022-10-19 [2] CRAN (R 4.2.0)
 carData                3.0-5      2022-01-06 [2] CRAN (R 4.2.0)
 caret                * 6.0-93     2022-08-09 [2] CRAN (R 4.2.0)
 CATALYST             * 1.20.1     2022-05-22 [1] Bioconductor
 changepoint            2.2.4      2022-11-03 [1] CRAN (R 4.2.0)
 circlize               0.4.15     2022-05-10 [1] CRAN (R 4.2.0)
 class                * 7.3-21     2023-01-23 [2] CRAN (R 4.2.0)
 cli                    3.6.0      2023-01-09 [2] CRAN (R 4.2.0)
 clue                   0.3-63     2022-11-19 [2] CRAN (R 4.2.0)
 cluster                2.1.4      2022-08-22 [2] CRAN (R 4.2.2)
 codetools              0.2-18     2020-11-04 [2] CRAN (R 4.2.2)
 colorRamps           * 2.3.1      2022-05-02 [2] CRAN (R 4.2.0)
 colorspace             2.1-0      2023-01-23 [2] CRAN (R 4.2.0)
 ComplexHeatmap         2.14.0     2022-11-07 [1] Bioconductor
 ConsensusClusterPlus   1.60.0     2022-04-26 [2] Bioconductor
 corpcor                1.6.10     2021-09-16 [2] CRAN (R 4.2.0)
 cowplot                1.1.1      2020-12-30 [2] CRAN (R 4.2.0)
 crayon                 1.5.2      2022-09-29 [2] CRAN (R 4.2.0)
 curl                   5.0.0      2023-01-12 [2] CRAN (R 4.2.0)
 cytolib                2.8.0      2022-04-26 [2] Bioconductor
 CytoML                 2.8.1      2022-08-23 [2] Bioconductor
 CytoNorm             * 0.0.10     2023-01-18 [1] Github (saeyslab/CytoNorm@166f9ff)
 data.table           * 1.14.6     2022-11-16 [2] CRAN (R 4.2.0)
 DBI                    1.1.3      2022-06-18 [2] CRAN (R 4.2.0)
 DelayedArray           0.24.0     2022-11-07 [1] Bioconductor
 DelayedMatrixStats     1.18.2     2022-10-13 [1] Bioconductor
 deldir                 1.0-6      2021-10-23 [2] CRAN (R 4.2.0)
 DEoptimR               1.0-11     2022-04-03 [2] CRAN (R 4.2.0)
 deSolve                1.34       2022-10-22 [2] CRAN (R 4.2.0)
 devtools             * 2.4.5      2022-10-11 [2] CRAN (R 4.2.1)
 digest                 0.6.31     2022-12-11 [2] CRAN (R 4.2.0)
 doParallel             1.0.17     2022-02-07 [2] CRAN (R 4.2.0)
 dplyr                * 1.0.10     2022-09-01 [1] CRAN (R 4.2.0)
 drc                    3.0-1      2016-08-30 [1] CRAN (R 4.2.0)
 ellipsis               0.3.2      2021-04-29 [2] CRAN (R 4.2.0)
 evaluate               0.20       2023-01-17 [2] CRAN (R 4.2.0)
 fansi                  1.0.4      2023-01-22 [2] CRAN (R 4.2.0)
 farver                 2.1.1      2022-07-06 [2] CRAN (R 4.2.0)
 fastmap                1.1.0      2021-01-25 [2] CRAN (R 4.2.0)
 fda                    6.0.5      2022-07-04 [2] CRAN (R 4.2.0)
 fds                    1.8        2018-10-31 [2] CRAN (R 4.2.0)
 flowAI               * 1.26.0     2022-04-26 [1] Bioconductor
 flowCore             * 2.8.0      2022-04-26 [2] Bioconductor
 FlowSOM              * 2.4.0      2022-04-26 [2] Bioconductor
 flowStats            * 4.8.2      2022-07-12 [2] Bioconductor
 flowViz              * 1.60.2     2022-07-03 [2] Bioconductor
 flowVS               * 1.28.0     2022-04-26 [1] Bioconductor
 flowWorkspace          4.8.0      2022-04-26 [2] Bioconductor
 foreach                1.5.2      2022-02-02 [2] CRAN (R 4.2.0)
 fs                     1.6.0      2023-01-23 [2] CRAN (R 4.2.0)
 future                 1.30.0     2022-12-16 [2] CRAN (R 4.2.0)
 future.apply           1.10.0     2022-11-05 [2] CRAN (R 4.2.1)
 generics               0.1.3      2022-07-05 [2] CRAN (R 4.2.0)
 GenomeInfoDb         * 1.34.6     2023-01-04 [1] Bioconductor
 GenomeInfoDbData       1.2.9      2023-01-16 [1] Bioconductor
 GenomicRanges        * 1.50.2     2022-12-18 [1] Bioconductor
 GetoptLong             1.0.5      2020-12-15 [1] CRAN (R 4.2.0)
 ggbeeswarm             0.7.1      2022-12-16 [1] CRAN (R 4.2.0)
 ggcyto                 1.24.1     2022-07-03 [2] Bioconductor
 ggforce                0.4.1      2022-10-04 [2] CRAN (R 4.2.0)
 ggnewscale             0.4.8      2022-10-06 [2] CRAN (R 4.2.0)
 ggplot2              * 3.4.0      2022-11-04 [1] CRAN (R 4.2.1)
 ggpointdensity       * 0.1.0      2019-08-28 [2] CRAN (R 4.2.0)
 ggpubr               * 0.5.0      2022-11-16 [2] CRAN (R 4.2.2)
 ggrepel                0.9.2      2022-11-06 [2] CRAN (R 4.2.1)
 ggridges               0.5.4      2022-09-26 [2] CRAN (R 4.2.0)
 ggsignif               0.6.4      2022-10-13 [2] CRAN (R 4.2.0)
 ggthemes             * 4.2.4      2021-01-20 [2] CRAN (R 4.2.0)
 GlobalOptions          0.1.2      2020-06-10 [1] CRAN (R 4.2.0)
 globals                0.16.2     2022-11-21 [2] CRAN (R 4.2.2)
 glue                   1.6.2      2022-02-24 [2] CRAN (R 4.2.0)
 gower                  1.0.1      2022-12-22 [2] CRAN (R 4.2.0)
 graph                  1.74.0     2022-04-26 [2] Bioconductor
 gridExtra            * 2.3        2017-09-09 [2] CRAN (R 4.2.0)
 gtable                 0.3.1      2022-09-01 [2] CRAN (R 4.2.0)
 gtools                 3.9.4      2022-11-27 [2] CRAN (R 4.2.2)
 hardhat                1.2.0      2022-06-30 [2] CRAN (R 4.2.0)
 hdrcde                 3.4        2021-01-18 [2] CRAN (R 4.2.0)
 hexbin                 1.28.2     2021-01-08 [2] CRAN (R 4.2.0)
 highr                  0.10       2022-12-22 [2] CRAN (R 4.2.0)
 htmltools              0.5.4      2022-12-07 [2] CRAN (R 4.2.0)
 htmlwidgets            1.6.1      2023-01-07 [2] CRAN (R 4.2.0)
 httpuv                 1.6.8      2023-01-12 [2] CRAN (R 4.2.0)
 httr                   1.4.4      2022-08-17 [2] CRAN (R 4.2.0)
 IDPmisc                1.1.20     2020-01-21 [2] CRAN (R 4.2.0)
 igraph               * 1.3.5      2022-09-22 [2] CRAN (R 4.2.0)
 interp                 1.1-3      2022-07-13 [2] CRAN (R 4.2.0)
 ipred                  0.9-13     2022-06-02 [2] CRAN (R 4.2.0)
 IRanges              * 2.32.0     2022-11-07 [1] Bioconductor
 irlba                  2.3.5.1    2022-10-03 [2] CRAN (R 4.2.0)
 iterators              1.0.14     2022-02-05 [2] CRAN (R 4.2.0)
 jpeg                   0.1-10     2022-11-29 [2] CRAN (R 4.2.0)
 jquerylib              0.1.4      2021-04-26 [2] CRAN (R 4.2.0)
 jsonlite               1.8.4      2022-12-06 [2] CRAN (R 4.2.0)
 KernSmooth             2.23-20    2021-05-03 [2] CRAN (R 4.2.2)
 knitr                * 1.42       2023-01-25 [1] CRAN (R 4.2.2)
 ks                     1.14.0     2022-11-24 [2] CRAN (R 4.2.2)
 labeling               0.4.2      2020-10-20 [2] CRAN (R 4.2.0)
 later                  1.3.0      2021-08-18 [2] CRAN (R 4.2.0)
 lattice              * 0.20-45    2021-09-22 [2] CRAN (R 4.2.2)
 latticeExtra           0.6-30     2022-07-04 [2] CRAN (R 4.2.0)
 lava                   1.7.1      2023-01-06 [2] CRAN (R 4.2.0)
 lifecycle              1.0.3.9000 2022-10-17 [2] Github (r-lib/lifecycle@80a1e52)
 listenv                0.9.0      2022-12-16 [2] CRAN (R 4.2.0)
 lubridate              1.9.1      2023-01-24 [2] CRAN (R 4.2.0)
 magrittr               2.0.3      2022-03-30 [2] CRAN (R 4.2.0)
 MASS                   7.3-58.2   2023-01-23 [1] CRAN (R 4.2.0)
 Matrix               * 1.5-3      2022-11-11 [1] CRAN (R 4.2.1)
 MatrixGenerics       * 1.10.0     2022-11-07 [1] Bioconductor
 matrixStats          * 0.63.0     2022-11-18 [2] CRAN (R 4.2.0)
 mclust                 6.0.0      2022-10-31 [2] CRAN (R 4.2.0)
 memoise                2.0.1      2021-11-26 [2] CRAN (R 4.2.0)
 mime                   0.12       2021-09-28 [2] CRAN (R 4.2.0)
 miniUI                 0.1.1.1    2018-05-18 [2] CRAN (R 4.2.0)
 mnormt                 2.1.1      2022-09-26 [2] CRAN (R 4.2.0)
 ModelMetrics           1.2.2.2    2020-03-17 [2] CRAN (R 4.2.0)
 multcomp               1.4-20     2022-08-07 [1] CRAN (R 4.2.0)
 munsell                0.5.0      2018-06-12 [2] CRAN (R 4.2.0)
 mvtnorm                1.1-3      2021-10-08 [2] CRAN (R 4.2.0)
 ncdfFlow               2.42.1     2022-07-03 [2] Bioconductor
 nlme                   3.1-161    2022-12-15 [2] CRAN (R 4.2.0)
 nnet                   7.3-18     2022-09-28 [2] CRAN (R 4.2.2)
 nnls                   1.4        2012-03-19 [1] CRAN (R 4.2.0)
 openssl                2.0.5      2022-12-06 [2] CRAN (R 4.2.0)
 parallelly             1.34.0     2023-01-13 [2] CRAN (R 4.2.0)
 pcaPP                  2.0-3      2022-10-24 [2] CRAN (R 4.2.1)
 PeacoQC              * 1.6.0      2022-04-26 [1] Bioconductor
 pheatmap             * 1.0.12     2019-01-04 [2] CRAN (R 4.2.0)
 pillar                 1.8.1      2022-08-19 [2] CRAN (R 4.2.0)
 pkgbuild               1.4.0      2022-11-27 [2] CRAN (R 4.2.2)
 pkgconfig              2.0.3      2019-09-22 [2] CRAN (R 4.2.0)
 pkgload                1.3.2      2022-11-16 [2] CRAN (R 4.2.0)
 plotrix                3.8-2      2021-09-08 [1] CRAN (R 4.2.0)
 plyr                 * 1.8.8      2022-11-11 [2] CRAN (R 4.2.1)
 png                    0.1-8      2022-11-29 [2] CRAN (R 4.2.0)
 polyclip               1.10-4     2022-10-20 [2] CRAN (R 4.2.0)
 pracma                 2.4.2      2022-09-22 [2] CRAN (R 4.2.0)
 prettyunits            1.1.1      2020-01-24 [2] CRAN (R 4.2.0)
 pROC                   1.18.0     2021-09-03 [2] CRAN (R 4.2.0)
 processx               3.8.0      2022-10-26 [2] CRAN (R 4.2.0)
 prodlim                2019.11.13 2019-11-17 [2] CRAN (R 4.2.0)
 profvis                0.3.7      2020-11-02 [2] CRAN (R 4.2.0)
 promises               1.2.0.1    2021-02-11 [2] CRAN (R 4.2.0)
 ps                     1.7.2      2022-10-26 [2] CRAN (R 4.2.0)
 purrr                  1.0.1      2023-01-10 [2] CRAN (R 4.2.0)
 R6                     2.5.1      2021-08-19 [2] CRAN (R 4.2.0)
 rainbow                3.7        2022-10-09 [2] CRAN (R 4.2.0)
 RBGL                   1.72.0     2022-04-26 [2] Bioconductor
 RColorBrewer         * 1.1-3      2022-04-03 [2] CRAN (R 4.2.0)
 Rcpp                   1.0.10     2023-01-22 [2] CRAN (R 4.2.0)
 RcppParallel           5.1.6      2023-01-09 [2] CRAN (R 4.2.0)
 RCurl                  1.98-1.9   2022-10-03 [2] CRAN (R 4.2.0)
 recipes                1.0.4      2023-01-11 [2] CRAN (R 4.2.0)
 remotes                2.4.2      2021-11-30 [2] CRAN (R 4.2.0)
 reshape2               1.4.4      2020-04-09 [2] CRAN (R 4.2.0)
 reticulate           * 1.27       2023-01-07 [2] CRAN (R 4.2.0)
 Rgraphviz              2.40.0     2022-04-26 [2] Bioconductor
 rJava                  1.0-6      2021-12-10 [1] CRAN (R 4.2.0)
 rjson                  0.2.21     2022-01-09 [1] CRAN (R 4.2.0)
 rlang                  1.0.6      2022-09-24 [2] CRAN (R 4.2.0)
 rmarkdown              2.20       2023-01-19 [2] CRAN (R 4.2.0)
 robustbase             0.95-0     2022-04-02 [2] CRAN (R 4.2.0)
 rpart                  4.1.19     2022-10-21 [2] CRAN (R 4.2.2)
 RProtoBufLib           2.8.0      2022-04-26 [2] Bioconductor
 rrcov                  1.7-2      2022-10-24 [2] CRAN (R 4.2.1)
 RSpectra               0.16-1     2022-04-24 [2] CRAN (R 4.2.0)
 rstatix                0.7.1      2022-11-09 [2] CRAN (R 4.2.1)
 rstudioapi           * 0.14       2022-08-22 [2] CRAN (R 4.2.0)
 rsvd                   1.0.5      2021-04-16 [2] CRAN (R 4.2.0)
 Rtsne                * 0.16       2022-04-17 [2] CRAN (R 4.2.0)
 S4Vectors            * 0.36.1     2022-12-07 [1] Bioconductor
 sandwich               3.0-2      2022-06-15 [1] CRAN (R 4.2.0)
 sass                   0.4.5      2023-01-24 [2] CRAN (R 4.2.0)
 ScaledMatrix           1.4.1      2022-09-11 [1] Bioconductor
 scales               * 1.2.1      2022-08-20 [2] CRAN (R 4.2.0)
 scater                 1.24.0     2022-04-26 [1] Bioconductor
 scattermore            0.8        2022-02-14 [2] CRAN (R 4.2.0)
 scuttle                1.6.3      2022-08-23 [1] Bioconductor
 sessioninfo            1.2.2      2021-12-06 [2] CRAN (R 4.2.0)
 shape                  1.4.6      2021-05-19 [1] CRAN (R 4.2.0)
 shiny                  1.7.4      2022-12-15 [2] CRAN (R 4.2.0)
 SingleCellExperiment * 1.20.0     2022-11-07 [1] Bioconductor
 sparseMatrixStats      1.8.0      2022-04-26 [1] Bioconductor
 Spectre              * 1.0.0      2022-10-19 [2] Github (immunedynamics/spectre@3d0c002)
 stringi                1.7.12     2023-01-11 [2] CRAN (R 4.2.0)
 stringr                1.5.0      2022-12-02 [2] CRAN (R 4.2.0)
 SummarizedExperiment * 1.28.0     2022-11-07 [1] Bioconductor
 survival               3.5-0      2023-01-09 [2] CRAN (R 4.2.0)
 TH.data                1.1-1      2022-04-26 [1] CRAN (R 4.2.0)
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 tidyr                * 1.3.0      2023-01-24 [2] CRAN (R 4.2.0)
 tidyselect             1.2.0      2022-10-10 [2] CRAN (R 4.2.1)
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 timeDate               4022.108   2023-01-07 [2] CRAN (R 4.2.0)
 tweenr                 2.0.2      2022-09-06 [2] CRAN (R 4.2.0)
 umap                 * 0.2.9.0    2022-08-25 [2] CRAN (R 4.2.0)
 urlchecker             1.0.1      2021-11-30 [2] CRAN (R 4.2.0)
 usethis              * 2.1.6      2022-05-25 [2] CRAN (R 4.2.0)
 utf8                   1.2.2      2021-07-24 [2] CRAN (R 4.2.0)
 uwot                 * 0.1.14     2022-08-22 [1] CRAN (R 4.2.0)
 vctrs                  0.5.2      2023-01-23 [1] CRAN (R 4.2.0)
 vipor                  0.4.5      2017-03-22 [1] CRAN (R 4.2.0)
 viridis                0.6.2      2021-10-13 [2] CRAN (R 4.2.0)
 viridisLite            0.4.1      2022-08-22 [2] CRAN (R 4.2.0)
 withr                  2.5.0      2022-03-03 [2] CRAN (R 4.2.0)
 xfun                   0.36       2022-12-21 [2] CRAN (R 4.2.0)
 xlsx                 * 0.6.5      2020-11-10 [1] CRAN (R 4.2.0)
 xlsxjars               0.6.1      2014-08-22 [1] CRAN (R 4.2.0)
 XML                    3.99-0.13  2022-12-04 [2] CRAN (R 4.2.0)
 xml2                   1.3.3      2021-11-30 [2] CRAN (R 4.2.0)
 xtable                 1.8-4      2019-04-21 [2] CRAN (R 4.2.0)
 XVector                0.38.0     2022-11-07 [1] Bioconductor
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 zlibbioc               1.44.0     2022-11-07 [1] Bioconductor
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 [1] /Users/clusteredatom/Library/R/arm64/4.2/library
 [2] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
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