Last updated on 2024-11-03 11:49:13 CET.
Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
---|---|---|---|---|---|---|
r-devel-linux-x86_64-debian-clang | 1.24 | 10.27 | 122.92 | 133.19 | OK | |
r-devel-linux-x86_64-debian-gcc | 1.24 | 1.05 | 3.29 | 4.34 | ERROR | |
r-devel-linux-x86_64-fedora-clang | 1.24 | 214.11 | OK | |||
r-devel-linux-x86_64-fedora-gcc | 1.24 | 247.32 | OK | |||
r-devel-windows-x86_64 | 1.24 | 16.00 | 383.00 | 399.00 | OK | |
r-patched-linux-x86_64 | 1.24 | 16.18 | 115.13 | 131.31 | OK | |
r-release-linux-x86_64 | 1.24 | 7.40 | 129.23 | 136.63 | ERROR | |
r-release-macos-arm64 | 1.24 | 104.00 | OK | |||
r-release-macos-x86_64 | 1.24 | 219.00 | OK | |||
r-release-windows-x86_64 | 1.24 | 16.00 | 272.00 | 288.00 | OK | |
r-oldrel-macos-arm64 | 1.24 | 106.00 | OK | |||
r-oldrel-macos-x86_64 | 1.24 | 194.00 | OK | |||
r-oldrel-windows-x86_64 | 1.24 | 18.00 | 313.00 | 331.00 | OK |
Version: 1.24
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.24
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'AER', 'car', 'desplot', 'effects', 'gge', 'gstat', 'HH',
'latticeExtra', 'lme4', 'MCMCglmm', 'pbkrtest', 'qicharts',
'reshape2', 'SpATS'
Flavor: r-release-linux-x86_64
Version: 1.24
Check: examples
Result: ERROR
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
Flavor: r-release-linux-x86_64