New issue occuring with the re-running of previous gating templates and generating new gates

[Andyroo1966]

Describe the bug
When trying to create a gate using cyto_gate_draw after successfully defining the population the percentage is displayed and the console outputs"
"Select at least 3 points to construct a polygon gate around the CD8 population.

Adding newly constructed gate(s) to zombies.csv .
...
Error in nrow(fr) <= minEvents :
comparison (<=) is not possible for language types"

I am running a newly compiled CytoExploreR from installed using remotes::install_github("DillonHammill/CytoExploreR") using R version 4.4.1

The bug occurs with a R 4.4.1 install on both aarch64-apple-darwin23.4.0 and aarch64 fedora.

I can successfully gate populations from this dataset using opencyto.

To Reproduce
Steps to reproduce the behavior:

1. Generate a gating set
2. cyto_gate_draw(gs,channels = c("CD4","CD8"),parent="live",alias="test",gatingTemplate = "zombies.csv",popup=FALSE)
   Interaction with plot screen to define gate. Complete the process.
   Console output as above. No gating information written to nominated gating template file. The defined gate not added to the current gating set.

Expected behavior
The new defined gate added to the gating template.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: mac silicon running either Mac OS Sonoma or under VMware, Fedora 41

Additional context
This same error is occuring when a previously generated gating template is rerun. It errors when the cyto_draw_gate entries begin in the gating template.

R script:
library(openCyto)
library(ggcyto)
library(CytoExploreR)
#setwd("~/"). Adjust to file location as necessary
read<-list.files(pattern="ID_001_D0_Native_Heart.fcs")
t1<-read.flowSet(read)
t1_comp<-compensate(t1, t1[[1]]@description$SPILL)
EM<-list.files(pattern="Experiment-M")
dt<-read.csv(EM,header = TRUE)
BiocGenerics::colnames(t1_comp)<-as.character(dt$Marker)
trans<-transform(t1_comp,transformList(cyto_fluor_channels(t1_comp),arcsinhTransform(transformationId="fluorTransform",a=0,b=(1/150),c=0)))
gs<-GatingSet(trans)
gtFile<-"zombies.csv"
gating_T<-gatingTemplate(gtFile, autostart = 1L)
gating(gating_T, gs)

zombies.csv
ID_001_D0_Native_Heart.fcs.zip
Experiment-Markers.csv

[Andyroo1966]

I have just run through this gating action on the attached files but in an R install running on Ubuntu 21 X86 architecture and it works fine... Looks like it is an aarch64 issue.

[DillonHammill]

@Andyroo1966 I am aware of this issue and I will push a fix tomorrow for you.

[Andyroo1966]

Awesome Sent from Outlook for Android<https://aka.ms/AAb9ysg>

…

________________________________ From: Dillon Hammill ***@***.***> Sent: Tuesday, July 23, 2024 4:47:38 PM To: DillonHammill/CytoExploreR ***@***.***> Cc: Andyroo1966 ***@***.***>; Mention ***@***.***> Subject: Re: [DillonHammill/CytoExploreR] New issue occuring with the re-running of previous gating templates and generating new gates (Issue #210) @Andyroo1966<https://github.com/Andyroo1966> I am aware of this issue and I will push a fix tomorrow for you. — Reply to this email directly, view it on GitHub<#210 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIEA6TOGKAIC6SIOA2KVXTDZNYKCVAVCNFSM6AAAAABLJWFCGCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENBUGYYTQOBRGY>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[Andyroo1966]

Hi Dillon, I didn't miss the push, did I?

regards

[Andyroo1966]

On 12 Sept 2024, I have updated flowCore and flowWorkspace using BiocManager on mac silicon (Mac OS 14.6.1).
flowCore would not build without editting the cytolib file: transformation.hpp. The build had errored because it could not find within this file:
struct ciLessBoost : std::__binary_function<std::string, std::string, bool>
rather the file contains
struct ciLessBoost : std::binary_function<std::string, std::string, bool>

I added the __ and saved this change to transformation.hpp. Now flowCore successfully installed, followed by a successful store of flowWorkspace.
I then forced a reinstall of CytoExploreR.

The issues that were defined here are now resolved.

regards