some tests of https://github.com/tudelft3d/prepair for Win64

prepair_tests.R

library(sf)
library(tidyverse)

setwd('C:/data/prepair_test')

# a file with known problems, also at https://github.com/obrl-soil/bits-n-pieces/tree/master/r2p
tester <- read_sf('C:/data/r2p/cat_v_pretty.gpkg')

# I used the QGIS topology checker tool to find invalid geometries. Row 130 is no good:
plot(st_geometry(tester[130, ]))

# test if prepair can fix it
bad_130 <- st_as_text(st_geometry(tester[130, ]))
fixed_130 <- system2('prepair.exe', args = c('--wkt', paste0('"', bad_130, '"')), stdout = TRUE)

# cool! re-sf the output:
fixed_130 <- st_as_sf(data.frame('ID' = 130, 'geometry' = fixed_130), wkt = 'geometry',
                      agr = 'constant', crs = st_crs(tester)$proj4string)

plot(st_geometry(fixed_130)) # looks the same, good good

# If I replace the geometry for that row, the resulting file should have one less invalid geometry
tester_fixed <- tester
st_geometry(tester_fixed[130, ]) <- st_geometry(fixed_130[1, ])

identical(st_geometry(tester[130, ]), 
          st_geometry(tester_fixed[130, ])) # FALSE, mission accomplished

tester_fixed <- st_cast(tester_fixed, 'MULTIPOLYGON') # since the replacement polygon is this type
st_write(tester_fixed, 'C:/data/prepair_test/tester_fixed_130.gpkg', delete_dsn = TRUE) 
# spoiler: it does! now for the other problem polygons...

# I need a function to fix all the problem geometries in the above file:
fixer_upper <- function(bad_sfobj = NULL) {
  message(paste0(Sys.time(), ': prepair iteration in progress...'))
  g       <- st_geometry(bad_sfobj)
          
  new_g   <- lapply(seq_along(g), function(gx) {
    
    gxt <- st_as_text(g[gx])
    
    # hahaha this is so terrible but some wkts are too big to paste into cmd:
    fixed <- if(nchar(gxt) > 7500) {
      write(gxt, file = 'C:/DATA/prepair_test/prepair_temp.txt')
      f <- system2('prepair.exe', 
                    args = c('-f', 'C:/DATA/prepair_test/prepair_temp.txt'),
                    stdout = TRUE)
      do.call('paste0', as.list(f))
    } else {
      system2('prepair.exe', args = c('--wkt', paste0('"', gxt, '"')), stdout = TRUE)
    }
            
    gx_fix <- st_as_sf(data.frame('ID' = gx, 'geometry' = fixed), wkt = 'geometry',
                       agr = 'constant', crs = st_crs(bad_sfobj)$proj4string)
    
    # for testing - 5-10 geoms/sec, probs 90% of time is wasted on write/read above
    print(paste0(gx, ' complete'))
    gx_fix
  })
  
  message(paste0(Sys.time(), ': assembling repaired geometries...'))
  new_g <- do.call('rbind', new_g) # secondary bottleneck, ~1 minute for 3600 rows
  st_geometry(bad_sfobj) <- st_geometry(new_g)
  message(paste0(Sys.time(), ': ...repair complete'))
  bad_sfobj <- st_cast(bad_sfobj, 'MULTIPOLYGON')
}

fixed_up <- fixer_upper(tester)

st_write(fixed_up, 'C:/data/prepair_test/fixed_up.shp', delete_dsn = TRUE)

# the output passes the QGIS topo check for invalid geometries \o/

I tried your file that failed: it's fine here. Under macOS.

It's either something with the precision libraries and Windows; or the fact that your WKT conversion is not giving your enough precision. I suggest you try to read a SHP directly and output a SHP too, instead of converting to text.

In any ways, the fixed one is there:
https://www.dropbox.com/sh/gun9s55ptx3rudk/AADHbAbQbgbNrkZvgB2zfm_ea?dl=0

I think it may be a Windows issue then @hugoledoux, on the command line prepair.exe --ogr bad_poly_37.shp still causes a crash.

Edit: Whoops, turns out I'd grabbed the old build by mistake. The new build works perfectly, although I did have to copy over libmpfr-4.dll and libgmp-10.dll from the older version first.