Finally, ASAN working

.vscode/configurationCache.log

@@ -0,0 +1 @@
+{"buildTargets":["README.md","build","check","clean","debug","docs","inst/NEWS","install","update"],"launchTargets":[],"customConfigurationProvider":{"workspaceBrowse":{"browsePath":[],"compilerArgs":[]},"fileIndex":[]}}

.vscode/dryrun.log

@@ -0,0 +1,5 @@
+make --dry-run --always-make --keep-going --print-directory
+make: Entering directory '/home/george/Documents/development/defm'
+Rscript -e 'devtools::document()'
+make: Leaving directory '/home/george/Documents/development/defm'
+

.vscode/targets.log

@@ -0,0 +1,347 @@
+make all --print-data-base --no-builtin-variables --no-builtin-rules --question
+make: *** No rule to make target 'all'.  Stop.
+
+# GNU Make 4.3
+# Built for x86_64-pc-linux-gnu
+# Copyright (C) 1988-2020 Free Software Foundation, Inc.
+# License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
+# This is free software: you are free to change and redistribute it.
+# There is NO WARRANTY, to the extent permitted by law.
+
+# Make data base, printed on Thu Aug 10 12:09:17 2023
+
+# Variables
+
+# environment
+GDK_BACKEND = x11
+# environment
+LC_ALL = C
+# environment
+GNOME_SHELL_SESSION_MODE = ubuntu
+# environment
+SSH_AGENT_LAUNCHER = gnome-keyring
+# environment
+GJS_DEBUG_OUTPUT = stderr
+# environment
+VSCODE_CRASH_REPORTER_PROCESS_TYPE = extensionHost
+# environment
+VSCODE_CWD = /home/george
+# default
+MAKE_COMMAND := make
+# environment
+QT_ACCESSIBILITY = 1
+# automatic
+@D = $(patsubst %/,%,$(dir $@))
+# environment
+VSCODE_HANDLES_UNCAUGHT_ERRORS = true
+# default
+.VARIABLES := 
+# environment
+PWD = /home/george/Documents/development/defm
+# automatic
+%D = $(patsubst %/,%,$(dir $%))
+# environment
+XDG_DATA_DIRS = /usr/share/ubuntu:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop
+# automatic
+^D = $(patsubst %/,%,$(dir $^))
+# automatic
+%F = $(notdir $%)
+# environment
+VSCODE_CODE_CACHE_PATH = /home/george/.config/Code - Insiders/CachedData/bf9c8105647b1e9d244f0f00155c21298e7554cf
+# environment
+LANG = C
+# environment
+XAUTHORITY = /run/user/1000/.mutter-Xwaylandauth.TAOL91
+# default
+.LOADED := 
+# default
+.INCLUDE_DIRS = /usr/local/include /usr/include /usr/include
+# makefile
+MAKEFLAGS = pqrR
+# makefile
+CURDIR := /home/george/Documents/development/defm
+# environment
+APPLICATION_INSIGHTS_NO_DIAGNOSTIC_CHANNEL = 1
+# environment
+LESSOPEN = | /usr/bin/lesspipe %s
+# automatic
+*D = $(patsubst %/,%,$(dir $*))
+# environment
+MFLAGS = -pqrR
+# environment
+SSH_AUTH_SOCK = /run/user/1000/keyring/ssh
+# default
+.SHELLFLAGS := -c
+# environment
+WAYLAND_DISPLAY = wayland-0
+# environment
+XDG_CONFIG_DIRS = /etc/xdg/xdg-ubuntu:/etc/xdg
+# automatic
++D = $(patsubst %/,%,$(dir $+))
+# environment
+XDG_SESSION_DESKTOP = ubuntu
+# makefile (from 'Makefile', line 1)
+MAKEFILE_LIST := Makefile
+# automatic
+@F = $(notdir $@)
+# environment
+VSCODE_PID = 10072
+# environment
+XDG_SESSION_TYPE = wayland
+# automatic
+?D = $(patsubst %/,%,$(dir $?))
+# environment
+SESSION_MANAGER = local/george-XPS-13-9310:@/tmp/.ICE-unix/4115,unix/george-XPS-13-9310:/tmp/.ICE-unix/4115
+# automatic
+*F = $(notdir $*)
+# environment
+CHROME_DESKTOP = code-insiders-url-handler.desktop
+# environment
+DBUS_SESSION_BUS_ADDRESS = unix:path=/run/user/1000/bus
+# automatic
+<D = $(patsubst %/,%,$(dir $<))
+# environment
+VSCODE_NLS_CONFIG = {"locale":"en-us","osLocale":"en-us","availableLanguages":{},"_languagePackSupport":true}
+# default
+MAKE_HOST := x86_64-pc-linux-gnu
+# environment
+GNOME_DESKTOP_SESSION_ID = this-is-deprecated
+# makefile
+SHELL = /bin/sh
+# default
+MAKECMDGOALS := all
+# environment
+XMODIFIERS = @im=ibus
+# environment
+GJS_DEBUG_TOPICS = JS ERROR;JS LOG
+# environment
+SHLVL = 0
+# environment
+MAKELEVEL := 0
+# environment
+IM_CONFIG_CHECK_ENV = 1
+# default
+MAKE = $(MAKE_COMMAND)
+# environment
+PATH = /home/george/bin:/home/george/.local/bin:/home/george/bin:/home/george/bin:/home/george/.local/bin:/home/george/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin
+# default
+MAKEFILES := 
+# automatic
+^F = $(notdir $^)
+# environment
+INVOCATION_ID = 20a92b9d9eee408497da7b39ad631566
+# environment
+USERNAME = george
+# environment
+GNOME_SETUP_DISPLAY = :1
+# environment
+LESSCLOSE = /usr/bin/lesspipe %s %s
+# automatic
+?F = $(notdir $?)
+# environment
+XDG_CURRENT_DESKTOP = Unity
+# automatic
++F = $(notdir $+)
+# environment
+DESKTOP_SESSION = ubuntu
+# environment
+ORIGINAL_XDG_CURRENT_DESKTOP = ubuntu:GNOME
+# 'override' directive
+GNUMAKEFLAGS := 
+# environment
+LOGNAME = george
+# environment
+GIO_LAUNCHED_DESKTOP_FILE = /usr/share/applications/code-insiders.desktop
+# makefile
+.DEFAULT_GOAL := docs
+# environment
+SYSTEMD_EXEC_PID = 4139
+# environment
+DISPLAY = :0
+# environment
+USER = george
+# environment
+GTK_MODULES = gail:atk-bridge
+# default
+MAKE_VERSION := 4.3
+# environment
+MANAGERPID = 2113
+# environment
+GIO_LAUNCHED_DESKTOP_FILE_PID = 10072
+# environment
+_ = /usr/share/code-insiders/code-insiders
+# environment
+XDG_RUNTIME_DIR = /run/user/1000
+# environment
+JOURNAL_STREAM = 8:35786
+# environment
+XDG_SESSION_CLASS = user
+# environment
+VSCODE_AMD_ENTRYPOINT = vs/workbench/api/node/extensionHostProcess
+# environment
+HOME = /home/george
+# environment
+QT_IM_MODULE = ibus
+# environment
+ELECTRON_RUN_AS_NODE = 1
+# environment
+VSCODE_IPC_HOOK = /run/user/1000/vscode-ffa97c55-1.82-main.sock
+# environment
+IM_CONFIG_PHASE = 1
+# default
+.RECIPEPREFIX := 
+# automatic
+<F = $(notdir $<)
+# default
+SUFFIXES := 
+# default
+.FEATURES := target-specific order-only second-expansion else-if shortest-stem undefine oneshell nocomment grouped-target extra-prereqs archives jobserver output-sync check-symlink load
+# environment
+XDG_MENU_PREFIX = gnome-
+# environment
+GDMSESSION = ubuntu
+# variable set hash-table stats:
+# Load=94/1024=9%, Rehash=0, Collisions=2/124=2%
+
+# Pattern-specific Variable Values
+
+# No pattern-specific variable values.
+
+# Directories
+
+# . (device 64769, inode 2371474): 31 files, no impossibilities.
+
+# 31 files, no impossibilities in 1 directories.
+
+# Implicit Rules
+
+# No implicit rules.
+
+# Files
+
+check: build
+#  Implicit rule search has not been done.
+#  Modification time never checked.
+#  File has not been updated.
+#  recipe to execute (from 'Makefile', line 11):
+	R CMD check --as-cran defm_*.tar.gz
+
+update:
+#  Phony target (prerequisite of .PHONY).
+#  Implicit rule search has not been done.
+#  File does not exist.
+#  File has not been updated.
+#  recipe to execute (from 'Makefile', line 14):
+	rsync -avz ../barry/barry.hpp inst/include/barry.hpp && \
+		rsync -avz ../barry/defm.hpp inst/include/defm.hpp
+
+inst/NEWS: NEWS.md
+#  Implicit rule search has not been done.
+#  Modification time never checked.
+#  File has not been updated.
+#  recipe to execute (from 'Makefile', line 31):
+	Rscript -e "rmarkdown::pandoc_convert('NEWS.md', 'plain', output='inst/NEWS')" && \
+		head -n 80 inst/NEWS
+
+docs:
+#  Implicit rule search has not been done.
+#  Modification time never checked.
+#  File has not been updated.
+#  recipe to execute (from 'Makefile', line 2):
+	Rscript -e 'devtools::document()'
+
+debug:
+#  Implicit rule search has not been done.
+#  Modification time never checked.
+#  File has not been updated.
+#  recipe to execute (from 'Makefile', line 18):
+	$(MAKE) clean && \
+		DEFM_CONFIG="-DBARRY_DEBUG" R CMD INSTALL .
+
+# Not a target:
+Makefile:
+#  Implicit rule search has been done.
+#  Last modified 2023-08-10 09:07:20.519611123
+#  File has been updated.
+#  Successfully updated.
+
+README.md: README.Rmd
+#  Implicit rule search has not been done.
+#  Modification time never checked.
+#  File has not been updated.
+#  recipe to execute (from 'Makefile', line 26):
+	Rscript --vanilla -e 'rmarkdown::render("README.Rmd")'
+
+clean:
+#  Phony target (prerequisite of .PHONY).
+#  Implicit rule search has not been done.
+#  File does not exist.
+#  File has not been updated.
+#  recipe to execute (from 'Makefile', line 22):
+	Rscript --vanilla -e 'devtools::clean_dll()'; \
+		rm -rf *.Rcmdcheck 
+
+# Not a target:
+NEWS.md:
+#  Implicit rule search has not been done.
+#  Modification time never checked.
+#  File has not been updated.
+
+# Not a target:
+.DEFAULT:
+#  Implicit rule search has not been done.
+#  Modification time never checked.
+#  File has not been updated.
+
+# Not a target:
+all:
+#  Command line target.
+#  Implicit rule search has been done.
+#  File does not exist.
+#  File has not been updated.
+
+build:
+#  Phony target (prerequisite of .PHONY).
+#  Implicit rule search has not been done.
+#  File does not exist.
+#  File has not been updated.
+#  recipe to execute (from 'Makefile', line 5):
+
+	R CMD build .
+
+
+install:
+#  Implicit rule search has not been done.
+#  Modification time never checked.
+#  File has not been updated.
+#  recipe to execute (from 'Makefile', line 8):
+	R CMD INSTALL .
+
+# Not a target:
+README.Rmd:
+#  Implicit rule search has not been done.
+#  Modification time never checked.
+#  File has not been updated.
+
+.PHONY: build update clean
+#  Implicit rule search has not been done.
+#  Modification time never checked.
+#  File has not been updated.
+
+# files hash-table stats:
+# Load=16/1024=2%, Rehash=0, Collisions=0/32=0%
+# VPATH Search Paths
+
+# No 'vpath' search paths.
+
+# No general ('VPATH' variable) search path.
+
+# strcache buffers: 1 (0) / strings = 45 / storage = 415 B / avg = 9 B
+# current buf: size = 8162 B / used = 415 B / count = 45 / avg = 9 B
+
+# strcache performance: lookups = 66 / hit rate = 31%
+# hash-table stats:
+# Load=45/8192=1%, Rehash=0, Collisions=0/66=0%
+# Finished Make data base on Thu Aug 10 12:09:17 2023
+
+

NAMESPACE

@@ -3,9 +3,9 @@
 S3method("+",DEFM)
 S3method(as.data.frame,defm_motif_census)
 S3method(names,defm_motif_census)
+S3method(nobs,DEFM)
 S3method(print,DEFM)
 S3method(print,defm_motif_census)
-S3method(stats4::nobs,DEFM)
 export(defm_mle)
 export(get_X_names)
 export(get_Y_names)
@@ -18,7 +18,6 @@ export(motif_census)
 export(ncol_defm_x)
 export(ncol_defm_y)
 export(new_defm)
-export(nobs.DEFM)
 export(nobs_defm)
 export(nrow_defm)
 export(nterms_defm)
@@ -31,6 +30,8 @@ export(term_defm_logit_intercept)
 export(term_defm_ones)
 export(term_defm_transition)
 export(term_defm_transition_formula)
+import(stats4)
 importFrom(Rcpp,sourceCpp)
 importFrom(stats,pnorm)
+importFrom(stats4,nobs)
 useDynLib(defm, .registration = TRUE)

R/RcppExports.R

@@ -39,8 +39,8 @@
 NULL
 
 #' 
-new_defm_cpp <- function(id, Y, X, order = 1L) {
-    .Call(`_defm_new_defm`, id, Y, X, order)
+new_defm_cpp <- function(id, Y, X, order = 1L, copy_data = TRUE) {
+    .Call(`_defm_new_defm`, id, Y, X, order, copy_data)
 }
 
 set_names <- function(m, ynames, xnames) {