fix errors

fix errors brought up by R-CMD check

Author: DivitP

glmmTMB/DESCRIPTION

@@ -55,6 +55,7 @@ License: AGPL-3
 Depends: R (>= 3.6.0)
 Imports:
     methods,
+    RTMB,
     TMB (>= 1.9.0),
     lme4 (>= 1.1-18.9000),
     Matrix,
@@ -109,4 +110,4 @@ LazyData: TRUE
 BugReports: https://github.com/glmmTMB/glmmTMB/issues
 NeedsCompilation: yes
 Encoding: UTF-8
-RoxygenNote: 7.3.3
+Config/roxygen2/version: 8.0.0

glmmTMB/R/family.R

@@ -12,8 +12,17 @@ family_factory <- function(default_link, family, variance) {
 }
 
 ## suppress code warnings for nbinom1/nbinom2; can't use .Theta <- NULL trick here ...
-utils::globalVariables(".Theta")
-utils::globalVariables(".Phi")
+# utils::globalVariables(".Theta")
+# utils::globalVariables(".Phi")
+
+## also suppresses warnings for variables injected into scope by RTMB::getAll()
+## in rtmb_tpl() (see R/rtmb_tpl.R)
+utils::globalVariables(c(
+    ".Theta", ".Phi",
+    "b", "theta", "XS", "Z", "offset", "link",
+    "betazi", "XziS", "offsetzi",
+    "XdistS", "betadisp", "offsetdisp"
+))
 
 ## see whether calling function has been called from glm.fit ...
 in_glm_fit <- function() {

glmmTMB/R/rtmb_tpl.R

@@ -87,7 +87,7 @@ termwise_nll <- function(U, theta, term) {
     n <- term$blockSize
     reps <- term$blockReps
     logsd <- head(theta, n)
-    corr_transf <- tail(theta, -n)
+    corr_transf <- theta[-(seq_len(n))]
     sd <- exp(logsd)
     us <- RTMB::unstructured(n)
     C <- us$corr(corr_transf)