CRAN Package Check Results for Package agridat

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

Check Details

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