gatingset_to_flowjo docker image can't find path #164
Description
Describe the bug
With gatingset_to_flowjo(), docker file can not rename a temp file to the requested file on Windows.
The likely reason (or my guess) is that the path name for both the temp file and the file specified in the R command shows up using Windows backslashes rather than the universal forward slashes or escaped double back slashes that might allow the (linux-based??) docker image to find the file.
The temp file mentioned in the warning does exist, can be found using Windows file explorer, and looks like at least some semblance of the expected .xml.
Note: I expect that the printed message, "INFO: Could not find files for the given pattern(s)." is associated with missing schema files as reported in issue #162 although I can't be sure.
To Reproduce
The instruction that produced this error is as follows:
> gatingset_to_flowjo(gsSamp, "./WM278_PhysSumit2025_FJ_Rev1.wsp")
INFO: Could not find files for the given pattern(s).
Using docker image public.ecr.aws/x4k5d9i7/cytoverse/gs-to-wsp:latest to write FlowJo workspace...
[1] FALSE
Warning message:
In file.rename(tmpfile, outFile) :
cannot rename file 'C:\Users\rbaer\AppData\Local\Temp\RtmpKemyiS\filee44c2b1b3eee' to 'C:\Users\rbaer\Desktop\PhysSummit\ 2025\Integrated_WM278-Bait_M0-M1-M2/WM278_PhysSumit2025_FJ_Rev1.wsp', reason 'The system cannot find the path specified'
Expected behavior
It will produce a usable flowjo workspace file in the current directory and named, "WM278_PhysSumit2025_FJ_Rev1.wsp"
Docker Version
Docker was installed from the windows store
C:\Users\rbaer>docker version
Client:
Version: 28.1.1
API version: 1.49
Go version: go1.23.8
Git commit: 4eba377
Built: Fri Apr 18 09:53:24 2025
OS/Arch: windows/amd64
Context: desktop-linux
Server: Docker Desktop 4.41.2 (191736)
Engine:
Version: 28.1.1
API version: 1.49 (minimum version 1.24)
Go version: go1.23.8
Git commit: 01f442b
Built: Fri Apr 18 09:52:57 2025
OS/Arch: linux/amd64
Experimental: false
containerd:
Version: 1.7.27
GitCommit: 05044ec0a9a75232cad458027ca83437aae3f4da
runc:
Version: 1.2.5
GitCommit: v1.2.5-0-g59923ef
docker-init:
Version: 0.19.0
SessionInfo:
> sessionInfo()
R version 4.5.0 (2025-04-11 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 27863)
Matrix products: default
LAPACK version 3.12.1
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] shiny_1.10.0 ggsignif_0.6.4 ggpubr_0.6.0 patchwork_1.3.0
[5] lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
[9] purrr_1.0.4 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[13] tidyverse_2.0.0 CytoML_2.20.0 ggcyto_1.36.0 ncdfFlow_2.54.0
[17] BH_1.87.0-1 ggplot2_3.5.2 cytoverse_0.0.0.9000 CytoExploreR_1.1.0
[21] openCyto_2.20.0 flowWorkspace_4.20.0 flowCore_2.20.0
loaded via a namespace (and not attached):
[1] RBGL_1.84.0 gridExtra_2.3 rlang_1.1.6 magrittr_2.0.3
[5] matrixStats_1.5.0 compiler_4.5.0 png_0.1-8 vctrs_0.6.5
[9] reshape2_1.4.4 pkgconfig_2.0.3 crayon_1.5.3 fastmap_1.2.0
[13] backports_1.5.0 promises_1.3.2 rmarkdown_2.29 tzdb_0.5.0
[17] graph_1.86.0 xfun_0.52 cachem_1.1.0 jsonlite_2.0.0
[21] later_1.4.2 broom_1.0.8 parallel_4.5.0 R6_2.6.1
[25] bslib_0.9.0 stringi_1.8.7 RColorBrewer_1.1-3 reticulate_1.42.0
[29] car_3.1-3 jquerylib_0.1.4 Rcpp_1.0.14 knitr_1.50
[33] zoo_1.8-14 httpuv_1.6.16 Matrix_1.7-3 timechange_0.3.0
[37] tidyselect_1.2.1 abind_1.4-8 rstudioapi_0.17.1 yaml_2.3.10
[41] lattice_0.22-7 plyr_1.8.9 Biobase_2.68.0 withr_3.0.2
[45] askpass_1.2.1 evaluate_1.0.3 Rtsne_0.17 EmbedSOM_2.2
[49] pillar_1.10.2 carData_3.0-5 flowAI_1.38.0 stats4_4.5.0
[53] generics_0.1.4 S4Vectors_0.46.0 hms_1.1.3 scales_1.4.0
[57] xtable_1.8-4 glue_1.8.0 changepoint_2.3 tools_4.5.0
[61] hexbin_1.28.5 robustbase_0.99-4-1 data.table_1.17.2 RSpectra_0.16-2
[65] fs_1.6.6 visNetwork_2.1.2 XML_3.99-0.18 grid_4.5.0
[69] flowClust_3.46.0 RProtoBufLib_2.20.0 umap_0.2.10.0 colorspace_2.1-1
[73] Formula_1.2-5 cli_3.6.5 rsvd_1.0.5 rhandsontable_0.3.8
[77] cytolib_2.20.0 Rgraphviz_2.52.0 gtable_0.3.6 DEoptimR_1.1-3-1
[81] rstatix_0.7.2 sass_0.4.10 digest_0.6.37 BiocGenerics_0.54.0
[85] htmlwidgets_1.6.4 farver_2.1.2 memoise_2.0.1 htmltools_0.5.8.1
[89] lifecycle_1.0.4 mime_0.13 openssl_2.3.2 MASS_7.3-65
Additional context
Add any other context about the problem here.