Closed denvercal1234GitHub closed 1 year ago
Hi there,
Thanks for the tool.
When I imported the channel values csv, I encountered the warning above.
Would you mind letting me know whether we can safely ignore this warning
Spectre::read.files(file.loc = "/Users/stillhere/..._FlowJoBiExED_ChannelValues", file.type = ".csv", do.embed.file.names = TRUE)
> session_info() ─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.2.3 (2023-03-15) os macOS Ventura 13.3.1 system aarch64, darwin20 ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz Europe/London date 2023-04-26 rstudio 2023.03.0+386 Cherry Blossom (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 [1] CRAN (R 4.2.0) askpass 1.1 2019-01-13 [1] CRAN (R 4.2.0) backports 1.4.1 2021-12-13 [1] CRAN (R 4.2.0) beachmat 2.14.2 2023-04-09 [1] Bioconductor beeswarm 0.4.0 2021-06-01 [1] CRAN (R 4.2.0) BH * 1.81.0-1 2023-01-22 [1] CRAN (R 4.2.0) Biobase * 2.58.0 2022-11-07 [1] Bioconductor BiocGenerics * 0.44.0 2022-11-07 [1] Bioconductor BiocNeighbors 1.16.0 2022-11-07 [1] Bioconductor BiocParallel 1.32.6 2023-03-19 [1] Bioconductor BiocSingular 1.14.0 2022-11-07 [1] Bioconductor bitops 1.0-7 2021-04-24 [1] CRAN (R 4.2.0) broom 1.0.4 2023-03-11 [1] CRAN (R 4.2.0) cachem 1.0.7 2023-02-24 [1] CRAN (R 4.2.0) callr 3.7.3 2022-11-02 [1] CRAN (R 4.2.0) car 3.1-2 2023-03-30 [1] CRAN (R 4.2.0) carData 3.0-5 2022-01-06 [1] CRAN (R 4.2.0) caret * 6.0-94 2023-03-21 [1] CRAN (R 4.2.0) CATALYST * 1.22.0 2022-11-07 [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 [1] CRAN (R 4.2.3) cli 3.6.1 2023-03-23 [1] CRAN (R 4.2.0) clue 0.3-64 2023-01-31 [1] CRAN (R 4.2.0) cluster * 2.1.4 2022-08-22 [1] CRAN (R 4.2.3) codetools 0.2-19 2023-02-01 [1] CRAN (R 4.2.3) colorRamps * 2.3.1 2022-05-02 [1] CRAN (R 4.2.0) colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.2.0) ComplexHeatmap 2.14.0 2022-11-07 [1] Bioconductor ConsensusClusterPlus 1.62.0 2022-11-07 [1] Bioconductor corpcor 1.6.10 2021-09-16 [1] CRAN (R 4.2.0) cowplot 1.1.1 2020-12-30 [1] CRAN (R 4.2.0) crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.0) cytolib 2.10.1 2023-01-23 [1] Bioconductor CytoNorm * 0.0.15 2023-04-25 [1] Github (saeyslab/CytoNorm@78c6675) data.table * 1.14.8 2023-02-17 [1] CRAN (R 4.2.0) DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.0) DelayedArray 0.24.0 2022-11-07 [1] Bioconductor DelayedMatrixStats 1.20.0 2022-12-04 [1] Bioconductor deldir 1.0-6 2021-10-23 [1] CRAN (R 4.2.0) DEoptimR 1.0-12 2023-04-08 [1] CRAN (R 4.2.0) deSolve 1.35 2023-03-12 [1] CRAN (R 4.2.0) devtools * 2.4.5 2022-10-11 [1] CRAN (R 4.2.0) digest 0.6.31 2022-12-11 [1] CRAN (R 4.2.0) doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.2.0) dplyr * 1.1.2 2023-04-20 [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 [1] CRAN (R 4.2.0) evaluate 0.20 2023-01-17 [1] CRAN (R 4.2.0) factoextra * 1.0.7 2020-04-01 [1] CRAN (R 4.2.0) fansi 1.0.4 2023-01-22 [1] CRAN (R 4.2.0) farver 2.1.1 2022-07-06 [1] CRAN (R 4.2.0) fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.2.0) fda 6.0.5 2022-07-04 [1] CRAN (R 4.2.0) fds 1.8 2018-10-31 [1] CRAN (R 4.2.0) flowAI * 1.28.0 2022-11-07 [1] Bioconductor flowAssist * 0.0.0.9000 2023-04-25 [1] Github (ssmpsn2/flowAssist@3910e63) flowClust * 3.36.1 2023-03-26 [1] Bioconductor flowCore * 2.10.0 2022-11-07 [1] Bioconductor FlowSOM * 2.6.0 2022-11-07 [1] Bioconductor flowStats * 4.10.0 2022-11-07 [1] Bioconductor flowTrans * 1.50.0 2022-11-07 [1] Bioconductor flowViz * 1.62.0 2022-11-07 [1] Bioconductor flowVS * 1.30.0 2022-11-07 [1] Bioconductor flowWorkspace * 4.10.1 2023-01-01 [1] Bioconductor foreach 1.5.2 2022-02-02 [1] CRAN (R 4.2.0) fs 1.6.2 2023-04-25 [1] CRAN (R 4.2.0) future 1.32.0 2023-03-07 [1] CRAN (R 4.2.0) future.apply 1.10.0 2022-11-05 [1] CRAN (R 4.2.0) generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0) GenomeInfoDb * 1.34.9 2023-02-05 [1] Bioconductor GenomeInfoDbData 1.2.9 2023-04-24 [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 * 1.26.4 2022-12-14 [1] Bioconductor ggforce 0.4.1 2022-10-04 [1] CRAN (R 4.2.0) ggnewscale 0.4.8 2022-10-06 [1] CRAN (R 4.2.0) ggplot2 * 3.4.2 2023-04-03 [1] CRAN (R 4.2.0) ggpointdensity * 0.1.0 2019-08-28 [1] CRAN (R 4.2.0) ggpubr * 0.6.0 2023-02-10 [1] CRAN (R 4.2.0) ggrepel 0.9.3 2023-02-03 [1] CRAN (R 4.2.0) ggridges 0.5.4 2022-09-26 [1] CRAN (R 4.2.0) ggsignif 0.6.4 2022-10-13 [1] CRAN (R 4.2.0) ggthemes * 4.2.4 2021-01-20 [1] 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 [1] CRAN (R 4.2.0) glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0) gower 1.0.1 2022-12-22 [1] CRAN (R 4.2.0) graph 1.76.0 2022-11-07 [1] Bioconductor gridExtra * 2.3 2017-09-09 [1] CRAN (R 4.2.0) gtable 0.3.3 2023-03-21 [1] CRAN (R 4.2.0) gtools 3.9.4 2022-11-27 [1] CRAN (R 4.2.0) hardhat 1.3.0 2023-03-30 [1] CRAN (R 4.2.0) hdrcde 3.4 2021-01-18 [1] CRAN (R 4.2.0) hexbin 1.28.3 2023-03-21 [1] CRAN (R 4.2.0) htmltools 0.5.5 2023-03-23 [1] CRAN (R 4.2.0) htmlwidgets 1.6.2 2023-03-17 [1] CRAN (R 4.2.0) httpuv 1.6.9 2023-02-14 [1] CRAN (R 4.2.0) IDPmisc 1.1.20 2020-01-21 [1] CRAN (R 4.2.0) igraph * 1.4.2 2023-04-07 [1] CRAN (R 4.2.0) interp 1.1-4 2023-03-31 [1] CRAN (R 4.2.0) ipred 0.9-14 2023-03-09 [1] CRAN (R 4.2.0) IRanges * 2.32.0 2022-11-07 [1] Bioconductor irlba 2.3.5.1 2022-10-03 [1] CRAN (R 4.2.0) iterators 1.0.14 2022-02-05 [1] CRAN (R 4.2.0) jpeg 0.1-10 2022-11-29 [1] CRAN (R 4.2.0) jsonlite 1.8.4 2022-12-06 [1] CRAN (R 4.2.0) KernSmooth 2.23-20 2021-05-03 [1] CRAN (R 4.2.3) knitr * 1.42 2023-01-25 [1] CRAN (R 4.2.0) ks 1.14.0 2022-11-24 [1] CRAN (R 4.2.0) later 1.3.0 2021-08-18 [1] CRAN (R 4.2.0) lattice * 0.21-8 2023-04-05 [1] CRAN (R 4.2.0) latticeExtra 0.6-30 2022-07-04 [1] CRAN (R 4.2.0) lava 1.7.2.1 2023-02-27 [1] CRAN (R 4.2.0) lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.0) listenv 0.9.0 2022-12-16 [1] CRAN (R 4.2.0) lubridate 1.9.2 2023-02-10 [1] CRAN (R 4.2.0) magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0) MASS 7.3-59 2023-04-21 [1] CRAN (R 4.2.0) Matrix * 1.5-4 2023-04-04 [1] CRAN (R 4.2.0) MatrixGenerics * 1.10.0 2022-11-07 [1] Bioconductor matrixStats * 0.63.0 2022-11-18 [1] CRAN (R 4.2.0) mclust 6.0.0 2022-10-31 [1] CRAN (R 4.2.0) memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.0) mime 0.12 2021-09-28 [1] CRAN (R 4.2.0) miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.2.0) mnormt 2.1.1 2022-09-26 [1] CRAN (R 4.2.0) ModelMetrics 1.2.2.2 2020-03-17 [1] CRAN (R 4.2.0) multcomp 1.4-23 2023-03-09 [1] CRAN (R 4.2.0) munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0) mvtnorm 1.1-3 2021-10-08 [1] CRAN (R 4.2.0) NbClust * 3.0.1 2022-05-02 [1] CRAN (R 4.2.0) ncdfFlow * 2.44.0 2022-11-07 [1] Bioconductor nlme 3.1-162 2023-01-31 [1] CRAN (R 4.2.3) nnet 7.3-18 2022-09-28 [1] CRAN (R 4.2.3) nnls 1.4 2012-03-19 [1] CRAN (R 4.2.0) openssl 2.0.6 2023-03-09 [1] CRAN (R 4.2.0) parallelly 1.35.0 2023-03-23 [1] CRAN (R 4.2.0) pcaPP 2.0-3 2022-10-24 [1] CRAN (R 4.2.0) PeacoQC * 1.9.3 2023-04-20 [1] Github (saeyslab/PeacoQC@64c84ad) pheatmap * 1.0.12 2019-01-04 [1] CRAN (R 4.2.0) pillar 1.9.0 2023-03-22 [1] CRAN (R 4.2.0) pkgbuild 1.4.0 2022-11-27 [1] CRAN (R 4.2.0) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0) pkgload 1.3.2 2022-11-16 [1] 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 [1] CRAN (R 4.2.0) png 0.1-8 2022-11-29 [1] CRAN (R 4.2.0) polyclip 1.10-4 2022-10-20 [1] CRAN (R 4.2.0) pracma 2.4.2 2022-09-22 [1] CRAN (R 4.2.0) prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.0) pROC 1.18.0 2021-09-03 [1] CRAN (R 4.2.0) processx 3.8.1 2023-04-18 [1] CRAN (R 4.2.0) prodlim 2023.03.31 2023-04-02 [1] CRAN (R 4.2.0) profvis 0.3.7 2020-11-02 [1] CRAN (R 4.2.0) promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.2.0) ps 1.7.5 2023-04-18 [1] CRAN (R 4.2.0) purrr 1.0.1 2023-01-10 [1] CRAN (R 4.2.0) R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0) rainbow 3.7 2022-10-09 [1] CRAN (R 4.2.0) RColorBrewer * 1.1-3 2022-04-03 [1] CRAN (R 4.2.0) Rcpp 1.0.10 2023-01-22 [1] CRAN (R 4.2.0) RCurl 1.98-1.12 2023-03-27 [1] CRAN (R 4.2.0) recipes 1.0.6 2023-04-25 [1] CRAN (R 4.2.3) remotes 2.4.2 2021-11-30 [1] CRAN (R 4.2.0) reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.2.0) reticulate * 1.28-9000 2023-04-20 [1] Github (rstudio/reticulate@63a5c3e) Rgraphviz 2.42.0 2022-11-07 [1] 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 1.1.0 2023-03-14 [1] CRAN (R 4.2.0) rmarkdown 2.21 2023-03-26 [1] CRAN (R 4.2.0) robustbase 0.95-1 2023-03-29 [1] CRAN (R 4.2.0) rpart 4.1.19 2022-10-21 [1] CRAN (R 4.2.3) RProtoBufLib 2.10.0 2022-11-07 [1] Bioconductor rrcov 1.7-2 2022-10-24 [1] CRAN (R 4.2.0) RSpectra 0.16-1 2022-04-24 [1] CRAN (R 4.2.0) rstatix 0.7.2 2023-02-01 [1] CRAN (R 4.2.0) rstudioapi * 0.14 2022-08-22 [1] CRAN (R 4.2.0) rsvd 1.0.5 2021-04-16 [1] CRAN (R 4.2.0) Rtsne * 0.16 2022-04-17 [1] CRAN (R 4.2.0) S4Vectors * 0.36.2 2023-03-01 [1] Bioconductor sandwich 3.0-2 2022-06-15 [1] CRAN (R 4.2.0) ScaledMatrix 1.6.0 2022-11-07 [1] Bioconductor scales * 1.2.1 2022-08-20 [1] CRAN (R 4.2.0) scater 1.26.1 2022-11-13 [1] Bioconductor scuttle 1.8.4 2023-01-22 [1] Bioconductor sessioninfo 1.2.2 2021-12-06 [1] 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 [1] CRAN (R 4.2.0) SingleCellExperiment * 1.20.1 2023-03-19 [1] Bioconductor sparseMatrixStats 1.10.0 2022-11-07 [1] Bioconductor Spectre * 1.0.0 2023-04-20 [1] Github (immunedynamics/spectre@3d0c002) stringi 1.7.12 2023-01-11 [1] CRAN (R 4.2.0) stringr 1.5.0 2022-12-02 [1] CRAN (R 4.2.0) SummarizedExperiment * 1.28.0 2022-11-07 [1] Bioconductor survival 3.5-5 2023-03-12 [1] CRAN (R 4.2.0) TH.data 1.1-2 2023-04-17 [1] CRAN (R 4.2.0) tibble 3.2.1 2023-03-20 [1] CRAN (R 4.2.0) tidyr * 1.3.0 2023-01-24 [1] CRAN (R 4.2.0) tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0) timechange 0.2.0 2023-01-11 [1] CRAN (R 4.2.0) timeDate 4022.108 2023-01-07 [1] CRAN (R 4.2.0) tweenr 2.0.2 2022-09-06 [1] CRAN (R 4.2.0) umap * 0.2.10.0 2023-02-01 [1] CRAN (R 4.2.0) urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.0) usethis * 2.1.6 2022-05-25 [1] CRAN (R 4.2.0) utf8 1.2.3 2023-01-31 [1] CRAN (R 4.2.0) uwot * 0.1.14 2022-08-22 [1] CRAN (R 4.2.0) vctrs 0.6.2 2023-04-19 [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 [1] CRAN (R 4.2.0) viridisLite 0.4.1 2022-08-22 [1] CRAN (R 4.2.0) withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0) xfun 0.39 2023-04-20 [1] 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 3.99-0.14 2023-03-19 [1] CRAN (R 4.2.0) xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.0) XVector 0.38.0 2022-11-07 [1] Bioconductor zlibbioc 1.44.0 2022-11-07 [1] Bioconductor zoo 1.8-12 2023-04-13 [1] CRAN (R 4.2.0) [1] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
Cannot ignore. Checked the csv revealed problems with exports.
Hi there,
Thanks for the tool.
When I imported the channel values csv, I encountered the warning above.
Would you mind letting me know whether we can safely ignore this warning