Running examples in ‘agridat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: carmer.density
> ### Title: Nonlinear maize yield-density model
> ### Aliases: carmer.density
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> library(agridat)
> data(carmer.density)
> dat <- carmer.density
> dat$gen <- factor(dat$gen, levels=c('Hy2x0h7','WF9xC103','R61x187-2',
+                              'WF9x38-11','WF9xB14','C103xB14',
+                              '0h43xB37','WF9xH60'))
> 
> # Separate analysis for each hybrid
> # Model: y = x * a * k^x.  Table 1 of Carmer and Jackobs.
> out <- data.frame(a=rep(NA,8), k=NA)
> preds <- NULL
> rownames(out) <- levels(dat$gen)
> newdat <- data.frame(pop=seq(2,8,by=.1))
> for(i in levels(dat$gen)){
+   print(i)
+   dati <- subset(dat, gen==i)
+   mi <- nls(yield ~ pop * a * k^pop, data=dati, start=list(a=10,k=1))
+   out[i, ] <- mi$m$getPars()
+   # Predicted values
+   pi <- cbind(gen=i, newdat, pred= predict(mi, newdat=newdat))
+   preds <- rbind(preds, pi)
+ }
[1] "Hy2x0h7"
[1] "WF9xC103"
[1] "R61x187-2"
[1] "WF9x38-11"
[1] "WF9xB14"
[1] "C103xB14"
[1] "0h43xB37"
[1] "WF9xH60"
> # Optimum plant density is -1/log(k)
> out$pop.opt <- -1/log(out$k)
> round(out, 3)
              a     k pop.opt
Hy2x0h7   0.782 0.865   6.875
WF9xC103  1.039 0.825   5.192
R61x187-2 0.998 0.798   4.441
WF9x38-11 1.042 0.825   5.203
WF9xB14   1.067 0.806   4.647
C103xB14  0.813 0.860   6.653
0h43xB37  0.673 0.862   6.740
WF9xH60   0.858 0.854   6.358
> ##               a     k pop.opt
> ## Hy2x0h7   0.782 0.865   6.875
> ## WF9xC103  1.039 0.825   5.192
> ## R61x187-2 0.998 0.798   4.441
> ## WF9x38-11 1.042 0.825   5.203
> ## WF9xB14   1.067 0.806   4.647
> ## C103xB14  0.813 0.860   6.653
> ## 0h43xB37  0.673 0.862   6.740
> ## WF9xH60   0.858 0.854   6.358
> 
> 
> # Fit an overall fixed-effect with random deviations for each hybrid.
> libs(nlme)
> m1 <- nlme(yield ~ pop * a * k^pop,
+            fixed = a + k ~ 1,
+            random = a + k ~ 1|gen,
+            data=dat, start=c(a=10,k=1))
> # summary(m1) # Random effect for 'a' probably not needed
> 
> 
> libs(latticeExtra)
Installing package into ‘/home/hornik/tmp/scratch/RtmpZOvTMW/RLIBS_32932c451d9b0e’
(as ‘lib’ is unspecified)
also installing the dependencies ‘Rcpp’, ‘deldir’, ‘RcppEigen’, ‘png’, ‘jpeg’, ‘interp’

* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-6) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpomQneI/R.INSTALL3322a74762c2bd/Rcpp/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I../inst/include/  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c api.cpp -o api.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I../inst/include/  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c attributes.cpp -o attributes.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I../inst/include/  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c barrier.cpp -o barrier.o
In file included from barrier.cpp:31:
barrier.cpp: In function ‘SEXPREC** get_vector_ptr(SEXP)’:
../inst/include/Rcpp/r/compat.h:34:26: error: ‘VECTOR_PTR_RO’ was not declared in this scope; did you mean ‘VECTOR_PTR’?
   34 | # define RCPP_VECTOR_PTR VECTOR_PTR_RO
      |                          ^~~~~~~~~~~~~
barrier.cpp:74:30: note: in expansion of macro ‘RCPP_VECTOR_PTR’
   74 |     return const_cast<SEXP*>(RCPP_VECTOR_PTR(x));                                                       // #nocov end
      |                              ^~~~~~~~~~~~~~~
make[1]: *** [/home/hornik/tmp/R.check/r-release-gcc/Work/build/etc/Makeconf:202: barrier.o] Error 1
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpomQneI/R.INSTALL3322a74762c2bd/Rcpp/src'
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/home/hornik/tmp/scratch/RtmpZOvTMW/RLIBS_32932c451d9b0e/Rcpp’
Warning in install.packages(p) :
  installation of package ‘Rcpp’ had non-zero exit status
* installing *source* package ‘deldir’ ...
** package ‘deldir’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-6) 14.2.0’
using Fortran compiler: ‘GNU Fortran (Debian 14.2.0-6) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpRxkQBQ/R.INSTALL33658055dd253c/deldir/src'
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  acchk.f90 -o acchk.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  addpt.f90 -o addpt.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  adjchk.f90 -o adjchk.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  binsrt.f90 -o binsrt.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  circen.f90 -o circen.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  cross.f90 -o cross.o
cross.f90:101:23:

  101 | cprd = (a*d - b*c)/smin
      |                       ^
Warning: ‘smin’ may be used uninitialized [-Wmaybe-uninitialized]
cross.f90:23:8:

   23 |     smin = -one
      |        ^
note: ‘smin’ was declared here
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  delet.f90 -o delet.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  delet1.f90 -o delet1.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  delout.f90 -o delout.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  delseg.f90 -o delseg.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  dirout.f90 -o dirout.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  dirseg.f90 -o dirseg.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  dldins.f90 -o dldins.o
gcc-14 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c init.c -o init.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  initad.f90 -o initad.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  insrt.f90 -o insrt.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  insrt1.f90 -o insrt1.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  intri.f90 -o intri.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  locn.f90 -o locn.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  master.f90 -o master.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  mnnd.f90 -o mnnd.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  pred.f90 -o pred.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  qtest.f90 -o qtest.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  qtest1.f90 -o qtest1.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  stoke.f90 -o stoke.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  succ.f90 -o succ.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  swap.f90 -o swap.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  testeq.f90 -o testeq.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  triar.f90 -o triar.o
gfortran-14  -fpic  -g -O2 -Wall -pedantic -mtune=native  -c  trifnd.f90 -o trifnd.o
gcc-14 -shared -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -Wl,-O1 -o deldir.so acchk.o addpt.o adjchk.o binsrt.o circen.o cross.o delet.o delet1.o delout.o delseg.o dirout.o dirseg.o dldins.o init.o initad.o insrt.o insrt1.o intri.o locn.o master.o mnnd.o pred.o qtest.o qtest1.o stoke.o succ.o swap.o testeq.o triar.o trifnd.o -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpRxkQBQ/R.INSTALL33658055dd253c/deldir/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpRxkQBQ/R.INSTALL33658055dd253c/deldir/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpRxkQBQ/R.INSTALL33658055dd253c/deldir/src'
installing to /home/hornik/tmp/scratch/RtmpZOvTMW/RLIBS_32932c451d9b0e/00LOCK-deldir/00new/deldir/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (deldir)
* installing *source* package ‘png’ ...
** package ‘png’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-6) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpzzJjHg/R.INSTALL33994d5888a00e/png/src'
gcc-14 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   `libpng-config --cflags` -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c dummy.c -o dummy.o
gcc-14 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   `libpng-config --cflags` -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c read.c -o read.o
gcc-14 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   `libpng-config --cflags` -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c write.c -o write.o
gcc-14 -shared -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -Wl,-O1 -o png.so dummy.o read.o write.o -lpng16 -lz -lm -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpzzJjHg/R.INSTALL33994d5888a00e/png/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpzzJjHg/R.INSTALL33994d5888a00e/png/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpzzJjHg/R.INSTALL33994d5888a00e/png/src'
installing to /home/hornik/tmp/scratch/RtmpZOvTMW/RLIBS_32932c451d9b0e/00LOCK-png/00new/png/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (png)
* installing *source* package ‘jpeg’ ...
** package ‘jpeg’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-6) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpGpenia/R.INSTALL33a9e47d5b5306/jpeg/src'
gcc-14 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c read.c -o read.o
gcc-14 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c reg.c -o reg.o
gcc-14 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c write.c -o write.o
gcc-14 -shared -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -Wl,-O1 -o jpeg.so read.o reg.o write.o -ljpeg -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpGpenia/R.INSTALL33a9e47d5b5306/jpeg/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpGpenia/R.INSTALL33a9e47d5b5306/jpeg/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpGpenia/R.INSTALL33a9e47d5b5306/jpeg/src'
installing to /home/hornik/tmp/scratch/RtmpZOvTMW/RLIBS_32932c451d9b0e/00LOCK-jpeg/00new/jpeg/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (jpeg)
ERROR: dependency ‘Rcpp’ is not available for package ‘RcppEigen’
* removing ‘/home/hornik/tmp/scratch/RtmpZOvTMW/RLIBS_32932c451d9b0e/RcppEigen’
Warning in install.packages(p) :
  installation of package ‘RcppEigen’ had non-zero exit status
ERROR: dependencies ‘Rcpp’, ‘RcppEigen’ are not available for package ‘interp’
* removing ‘/home/hornik/tmp/scratch/RtmpZOvTMW/RLIBS_32932c451d9b0e/interp’
Warning in install.packages(p) :
  installation of package ‘interp’ had non-zero exit status
ERROR: dependency ‘interp’ is not available for package ‘latticeExtra’
* removing ‘/home/hornik/tmp/scratch/RtmpZOvTMW/RLIBS_32932c451d9b0e/latticeExtra’
Warning in install.packages(p) :
  installation of package ‘latticeExtra’ had non-zero exit status
Error in library(p, character.only = TRUE) : 
  there is no package called ‘latticeExtra’
Calls: libs -> library
Execution halted