Datasets:

introvoyz045
/

CoRC

# Apply my patches to the swig_wrapper
# These patches are likely specific for the CoRC packages
# which is why I did not commit them upstream to COPASI

wrapper_path <- file.path("..", "R", "swig_wrapper.R")

wrapper_lines <- readLines(wrapper_path)

# replace all checks for null pointers
# previously this was done by an awkward workaround and string comparison
# now use isnullptr::isnullptr
wrapper_lines <- stringr::str_replace_all(
  wrapper_lines,
  'capture\\.output\\((\\w+?)\\) %in% c\\("<pointer: 0x0>", "<pointer: \\(nil\\)>"\\)',
  'isnullptr(\\1)'
)
wrapper_lines <- stringr::str_replace_all(
  wrapper_lines,
  '!\\(isnullptr\\((\\w+?)\\)\\)',
  '!isnullptr(\\1)'
)

# Make all .Call use the COPASI DLLInfo for addressing
wrapper_lines <- stringr::str_replace_all(
  wrapper_lines,
  "\\.Call\\('(.*?)'(.*), PACKAGE='COPASI'\\);",
  ".Call(COPASI$`\\1`\\2);"
)

# remove R_SWIG_getCallbackFunctionStack which is called out in R CMD check
i_empty_lines <- which(wrapper_lines == "")
i_start <- which(wrapper_lines == "R_SWIG_getCallbackFunctionStack =")
stopifnot(length(i_start) == 1)
i_end <- i_empty_lines[i_empty_lines > i_start][1]
wrapper_lines <- wrapper_lines[-(i_start:i_end)]

# remove R_SWIG_addCallbackFunctionStack which is called out in R CMD check
i_empty_lines <- which(wrapper_lines == "")
i_start <- which(wrapper_lines == "R_SWIG_addCallbackFunctionStack =")
stopifnot(length(i_start) == 1)
i_end <- i_empty_lines[i_empty_lines > i_start][1]
wrapper_lines <- wrapper_lines[-(i_start:i_end)]

# # rename COPASI lib to CoRC
# wrapper_lines <- stringr::str_replace_all(
#   wrapper_lines,
#   "\\.Call\\((.*), PACKAGE='COPASI'\\);",
#   paste0(".Call(\\1, PACKAGE='", pkgname, "');")
# )

# remove swig debug info containing personal folder structure
wrapper_lines <- stringr::str_replace_all(
  wrapper_lines,
  '^##.*R.i$',
  ""
)

# using wb write mode allows to use lf line ending on windows
wrapper_con <- file(wrapper_path, open = "wb")
writeLines(wrapper_lines, wrapper_con)
close(wrapper_con)

rm(wrapper_path, wrapper_con, wrapper_lines)

	# Apply my patches to the swig_wrapper
	# These patches are likely specific for the CoRC packages
	# which is why I did not commit them upstream to COPASI

	wrapper_path <- file.path("..", "R", "swig_wrapper.R")

	wrapper_lines <- readLines(wrapper_path)

	# replace all checks for null pointers
	# previously this was done by an awkward workaround and string comparison
	# now use isnullptr::isnullptr
	wrapper_lines <- stringr::str_replace_all(
	wrapper_lines,
	'capture\\.output\\((\\w+?)\\) %in% c\\("<pointer: 0x0>", "<pointer: \\(nil\\)>"\\)',
	'isnullptr(\\1)'
	)
	wrapper_lines <- stringr::str_replace_all(
	wrapper_lines,
	'!\\(isnullptr\\((\\w+?)\\)\\)',
	'!isnullptr(\\1)'
	)

	# Make all .Call use the COPASI DLLInfo for addressing
	wrapper_lines <- stringr::str_replace_all(
	wrapper_lines,
	"\\.Call\\('(.?)'(.), PACKAGE='COPASI'\\);",
	".Call(COPASI$`\\1`\\2);"
	)

	# remove R_SWIG_getCallbackFunctionStack which is called out in R CMD check
	i_empty_lines <- which(wrapper_lines == "")
	i_start <- which(wrapper_lines == "R_SWIG_getCallbackFunctionStack =")
	stopifnot(length(i_start) == 1)
	i_end <- i_empty_lines[i_empty_lines > i_start][1]
	wrapper_lines <- wrapper_lines[-(i_start:i_end)]

	# remove R_SWIG_addCallbackFunctionStack which is called out in R CMD check
	i_empty_lines <- which(wrapper_lines == "")
	i_start <- which(wrapper_lines == "R_SWIG_addCallbackFunctionStack =")
	stopifnot(length(i_start) == 1)
	i_end <- i_empty_lines[i_empty_lines > i_start][1]
	wrapper_lines <- wrapper_lines[-(i_start:i_end)]

	# # rename COPASI lib to CoRC
	# wrapper_lines <- stringr::str_replace_all(
	# wrapper_lines,
	# "\\.Call\\((.*), PACKAGE='COPASI'\\);",
	# paste0(".Call(\\1, PACKAGE='", pkgname, "');")
	# )

	# remove swig debug info containing personal folder structure
	wrapper_lines <- stringr::str_replace_all(
	wrapper_lines,
	'^##.*R.i$',
	""
	)

	# using wb write mode allows to use lf line ending on windows
	wrapper_con <- file(wrapper_path, open = "wb")
	writeLines(wrapper_lines, wrapper_con)
	close(wrapper_con)

	rm(wrapper_path, wrapper_con, wrapper_lines)