* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘RZooRoH’ ...
** package ‘RZooRoH’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-13) 13.2.0’
using Fortran compiler: ‘GNU Fortran (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/Rtmp4zt2Ux/R.INSTALL2e04af12010504/RZooRoH/src'
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c RZooRoH_init.c -o RZooRoH_init.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c random_number_wrapper.c -o random_number_wrapper.o
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c zooEM.f90 -o zooEM.o
zooEM.f90:12:22:
12 | real(dp) ::sumF(2),F,a,r,gr,loglik,loglik0
| 1
Warning: Unused variable ‘a’ declared at (1) [-Wunused-variable]
zooEM.f90:12:20:
12 | real(dp) ::sumF(2),F,a,r,gr,loglik,loglik0
| 1
Warning: Unused variable ‘f’ declared at (1) [-Wunused-variable]
zooEM.f90:12:27:
12 | real(dp) ::sumF(2),F,a,r,gr,loglik,loglik0
| 1
Warning: Unused variable ‘gr’ declared at (1) [-Wunused-variable]
zooEM.f90:5:51:
5 | integer ::i,j,l,k,nclust,nchr,npos,chr,fpos,lpos,hs,hs2
| 1
Warning: Unused variable ‘hs’ declared at (1) [-Wunused-variable]
zooEM.f90:5:55:
5 | integer ::i,j,l,k,nclust,nchr,npos,chr,fpos,lpos,hs,hs2
| 1
Warning: Unused variable ‘hs2’ declared at (1) [-Wunused-variable]
zooEM.f90:5:15:
5 | integer ::i,j,l,k,nclust,nchr,npos,chr,fpos,lpos,hs,hs2
| 1
Warning: Unused variable ‘l’ declared at (1) [-Wunused-variable]
zooEM.f90:12:24:
12 | real(dp) ::sumF(2),F,a,r,gr,loglik,loglik0
| 1
Warning: Unused variable ‘r’ declared at (1) [-Wunused-variable]
zooEM.f90:12:18:
12 | real(dp) ::sumF(2),F,a,r,gr,loglik,loglik0
| 1
Warning: Unused variable ‘sumf’ declared at (1) [-Wunused-variable]
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c zooFB.f90 -o zooFB.o
zooFB.f90:10:20:
10 | real(dp) ::sumF(2),F,a,r,gr,loglik
| 1
Warning: Unused variable ‘f’ declared at (1) [-Wunused-variable]
zooFB.f90:10:27:
10 | real(dp) ::sumF(2),F,a,r,gr,loglik
| 1
Warning: Unused variable ‘gr’ declared at (1) [-Wunused-variable]
zooFB.f90:4:15:
4 | integer ::i,j,l,k,nclust,nchr,npos,chr,fpos,lpos,hs,hs2
| 1
Warning: Unused variable ‘l’ declared at (1) [-Wunused-variable]
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c zooSIM.f90 -o zooSIM.o
zooSIM.f90:46:39:
46 | genome((current_pos+1):next_pos)=(level+1)
| 1
Warning: Possible change of value in conversion from INTEGER(4) to INTEGER(1) at (1) [-Wconversion]
zooSIM.f90:47:30:
47 | genome((current_pos+1))=-(level+1)
| 1
Warning: Possible change of value in conversion from INTEGER(4) to INTEGER(1) at (1) [-Wconversion]
zooSIM.f90:36:12:
36 | do level=1,nlayer
| 1
Warning: Possible change of value in conversion from INTEGER(4) to INTEGER(1) at (1) [-Wconversion]
zooSIM.f90:5:23:
5 | integer ::i,j,k,l,io,bp,nchr,nlayer,nind,npos,n,chr,state,id,nrec,chrom,chromold
| 1
Warning: Unused variable ‘bp’ declared at (1) [-Wunused-variable]
zooSIM.f90:5:80:
5 | integer ::i,j,k,l,io,bp,nchr,nlayer,nind,npos,n,chr,state,id,nrec,chrom,chromold
| 1
Warning: Unused variable ‘chromold’ declared at (1) [-Wunused-variable]
zooSIM.f90:9:31:
9 | integer(k1) ::genome(300000000),level
| 1
Warning: Array ‘genome’ at (1) is larger than limit set by ‘-fmax-stack-var-size=’, moved from stack to static storage. This makes the procedure unsafe when called recursively, or concurrently from multiple threads. Consider increasing the ‘-fmax-stack-var-size=’ limit (or use ‘-frecursive’, which implies unlimited ‘-fmax-stack-var-size’) - or change the code to use an ALLOCATABLE array. If the variable is never accessed concurrently, this warning can be ignored, and the variable could also be declared with the SAVE attribute. [-Wsurprising]
zooSIM.f90:1:66:
1 | subroutine zoosim(nlayer,nchr,npos,freq,posi,chr_bounds,as,Fs,gerr,nsim,genosim,Frealized,classes)
| 1
Warning: Unused dummy argument ‘gerr’ at (1) [-Wunused-dummy-argument]
zooSIM.f90:5:20:
5 | integer ::i,j,k,l,io,bp,nchr,nlayer,nind,npos,n,chr,state,id,nrec,chrom,chromold
| 1
Warning: Unused variable ‘io’ declared at (1) [-Wunused-variable]
zooSIM.f90:5:13:
5 | integer ::i,j,k,l,io,bp,nchr,nlayer,nind,npos,n,chr,state,id,nrec,chrom,chromold
| 1
Warning: Unused variable ‘j’ declared at (1) [-Wunused-variable]
zooSIM.f90:5:17:
5 | integer ::i,j,k,l,io,bp,nchr,nlayer,nind,npos,n,chr,state,id,nrec,chrom,chromold
| 1
Warning: Unused variable ‘l’ declared at (1) [-Wunused-variable]
zooSIM.f90:5:47:
5 | integer ::i,j,k,l,io,bp,nchr,nlayer,nind,npos,n,chr,state,id,nrec,chrom,chromold
| 1
Warning: Unused variable ‘n’ declared at (1) [-Wunused-variable]
zooSIM.f90:5:40:
5 | integer ::i,j,k,l,io,bp,nchr,nlayer,nind,npos,n,chr,state,id,nrec,chrom,chromold
| 1
Warning: Unused variable ‘nind’ declared at (1) [-Wunused-variable]
zooSIM.f90:6:20:
6 | integer ::nsim,nsnps,chr_bounds(nchr,2)
| 1
Warning: Unused variable ‘nsnps’ declared at (1) [-Wunused-variable]
zooSIM.f90:11:34:
11 | real(dp) ::a,F,xran,Ft,Glen,startp,Lsim,val,gerr,expornd
| 1
Warning: Unused variable ‘startp’ declared at (1) [-Wunused-variable]
zooSIM.f90:11:43:
11 | real(dp) ::a,F,xran,Ft,Glen,startp,Lsim,val,gerr,expornd
| 1
Warning: Unused variable ‘val’ declared at (1) [-Wunused-variable]
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c zooViterbi.f90 -o zooViterbi.o
zooViterbi.f90:8:22:
8 | real(dp) ::sumF(2),F,a,r,gr,loglik,pmax,val(nclust),mind
| 1
Warning: Unused variable ‘a’ declared at (1) [-Wunused-variable]
zooViterbi.f90:8:20:
8 | real(dp) ::sumF(2),F,a,r,gr,loglik,pmax,val(nclust),mind
| 1
Warning: Unused variable ‘f’ declared at (1) [-Wunused-variable]
zooViterbi.f90:8:27:
8 | real(dp) ::sumF(2),F,a,r,gr,loglik,pmax,val(nclust),mind
| 1
Warning: Unused variable ‘gr’ declared at (1) [-Wunused-variable]
zooViterbi.f90:4:51:
4 | integer ::i,j,l,k,nclust,nchr,npos,chr,fpos,lpos,hs,hs2,pos(1),phi(nclust,npos)
| 1
Warning: Unused variable ‘hs’ declared at (1) [-Wunused-variable]
zooViterbi.f90:4:55:
4 | integer ::i,j,l,k,nclust,nchr,npos,chr,fpos,lpos,hs,hs2,pos(1),phi(nclust,npos)
| 1
Warning: Unused variable ‘hs2’ declared at (1) [-Wunused-variable]
zooViterbi.f90:4:15:
4 | integer ::i,j,l,k,nclust,nchr,npos,chr,fpos,lpos,hs,hs2,pos(1),phi(nclust,npos)
| 1
Warning: Unused variable ‘l’ declared at (1) [-Wunused-variable]
zooViterbi.f90:8:34:
8 | real(dp) ::sumF(2),F,a,r,gr,loglik,pmax,val(nclust),mind
| 1
Warning: Unused variable ‘loglik’ declared at (1) [-Wunused-variable]
zooViterbi.f90:8:56:
8 | real(dp) ::sumF(2),F,a,r,gr,loglik,pmax,val(nclust),mind
| 1
Warning: Unused variable ‘mind’ declared at (1) [-Wunused-variable]
zooViterbi.f90:8:24:
8 | real(dp) ::sumF(2),F,a,r,gr,loglik,pmax,val(nclust),mind
| 1
Warning: Unused variable ‘r’ declared at (1) [-Wunused-variable]
zooViterbi.f90:8:18:
8 | real(dp) ::sumF(2),F,a,r,gr,loglik,pmax,val(nclust),mind
| 1
Warning: Unused variable ‘sumf’ declared at (1) [-Wunused-variable]
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c zoolayerEM.f90 -o zoolayerEM.o
zoolayerEM.f90:12:22:
12 | real(dp) ::sumF(2),F,a,r,gr,loglik,loglik0,d
| 1
Warning: Unused variable ‘a’ declared at (1) [-Wunused-variable]
zoolayerEM.f90:12:20:
12 | real(dp) ::sumF(2),F,a,r,gr,loglik,loglik0,d
| 1
Warning: Unused variable ‘f’ declared at (1) [-Wunused-variable]
zoolayerEM.f90:15:39:
15 | real(dp) ::global(nclust),fromi(nclust),ini(nclust),mux(nclust),EL(nclust)
| 1
Warning: Unused variable ‘fromi’ declared at (1) [-Wunused-variable]
zoolayerEM.f90:14:24:
14 | real(dp) ::lseg,fromitoj,minrate,maxrate,convf,convthr
| 1
Warning: Unused variable ‘fromitoj’ declared at (1) [-Wunused-variable]
zoolayerEM.f90:12:27:
12 | real(dp) ::sumF(2),F,a,r,gr,loglik,loglik0,d
| 1
Warning: Unused variable ‘gr’ declared at (1) [-Wunused-variable]
zoolayerEM.f90:5:51:
5 | integer ::i,j,l,k,nclust,nchr,npos,chr,fpos,lpos,hs,hs2
| 1
Warning: Unused variable ‘hs’ declared at (1) [-Wunused-variable]
zoolayerEM.f90:5:55:
5 | integer ::i,j,l,k,nclust,nchr,npos,chr,fpos,lpos,hs,hs2
| 1
Warning: Unused variable ‘hs2’ declared at (1) [-Wunused-variable]
zoolayerEM.f90:15:51:
15 | real(dp) ::global(nclust),fromi(nclust),ini(nclust),mux(nclust),EL(nclust)
| 1
Warning: Unused variable ‘ini’ declared at (1) [-Wunused-variable]
zoolayerEM.f90:6:58:
6 | integer ::isF(nclust),chr_limits(nchr,2),IT(nclust,nclust),posi(npos)
| 1
Warning: Unused variable ‘it’ declared at (1) [-Wunused-variable]
zoolayerEM.f90:14:15:
14 | real(dp) ::lseg,fromitoj,minrate,maxrate,convf,convthr
| 1
Warning: Unused variable ‘lseg’ declared at (1) [-Wunused-variable]
zoolayerEM.f90:2:40:
2 | onerate,niter,minrate,maxrate,convthr,iter)
| 1
Warning: Unused dummy argument ‘maxrate’ at (1) [-Wunused-dummy-argument]
zoolayerEM.f90:2:32:
2 | onerate,niter,minrate,maxrate,convthr,iter)
| 1
Warning: Unused dummy argument ‘minrate’ at (1) [-Wunused-dummy-argument]
zoolayerEM.f90:15:63:
15 | real(dp) ::global(nclust),fromi(nclust),ini(nclust),mux(nclust),EL(nclust)
| 1
Warning: Unused variable ‘mux’ declared at (1) [-Wunused-variable]
zoolayerEM.f90:2:18:
2 | onerate,niter,minrate,maxrate,convthr,iter)
| 1
Warning: Unused dummy argument ‘onerate’ at (1) [-Wunused-dummy-argument]
zoolayerEM.f90:12:24:
12 | real(dp) ::sumF(2),F,a,r,gr,loglik,loglik0,d
| 1
Warning: Unused variable ‘r’ declared at (1) [-Wunused-variable]
zoolayerEM.f90:12:18:
12 | real(dp) ::sumF(2),F,a,r,gr,loglik,loglik0,d
| 1
Warning: Unused variable ‘sumf’ declared at (1) [-Wunused-variable]
zoolayerEM.f90:10:82:
10 | real(dp) ::alpha(nclust,npos),scaling(npos),trans(nclust,nclust),T2(nclust,nclust),pinit(nclust)
| 1
Warning: Unused variable ‘t2’ declared at (1) [-Wunused-variable]
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c zoolayerFB.f90 -o zoolayerFB.o
zoolayerFB.f90:10:22:
10 | real(dp) ::sumF(2),F,a,r,gr,loglik,d
| 1
Warning: Unused variable ‘a’ declared at (1) [-Wunused-variable]
zoolayerFB.f90:10:20:
10 | real(dp) ::sumF(2),F,a,r,gr,loglik,d
| 1
Warning: Unused variable ‘f’ declared at (1) [-Wunused-variable]
zoolayerFB.f90:10:27:
10 | real(dp) ::sumF(2),F,a,r,gr,loglik,d
| 1
Warning: Unused variable ‘gr’ declared at (1) [-Wunused-variable]
zoolayerFB.f90:4:51:
4 | integer ::i,j,l,k,nclust,nchr,npos,chr,fpos,lpos,hs,hs2
| 1
Warning: Unused variable ‘hs’ declared at (1) [-Wunused-variable]
zoolayerFB.f90:4:55:
4 | integer ::i,j,l,k,nclust,nchr,npos,chr,fpos,lpos,hs,hs2
| 1
Warning: Unused variable ‘hs2’ declared at (1) [-Wunused-variable]
zoolayerFB.f90:5:58:
5 | integer ::isF(nclust),chr_limits(nchr,2),IT(nclust,nclust),posi(npos)
| 1
Warning: Unused variable ‘it’ declared at (1) [-Wunused-variable]
zoolayerFB.f90:10:24:
10 | real(dp) ::sumF(2),F,a,r,gr,loglik,d
| 1
Warning: Unused variable ‘r’ declared at (1) [-Wunused-variable]
zoolayerFB.f90:10:18:
10 | real(dp) ::sumF(2),F,a,r,gr,loglik,d
| 1
Warning: Unused variable ‘sumf’ declared at (1) [-Wunused-variable]
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c zoolayerViterbi.f90 -o zoolayerViterbi.o
zoolayerViterbi.f90:8:22:
8 | real(dp) ::sumF(2),F,a,r,gr,loglik,pmax,val(nclust),mind,d
| 1
Warning: Unused variable ‘a’ declared at (1) [-Wunused-variable]
zoolayerViterbi.f90:8:20:
8 | real(dp) ::sumF(2),F,a,r,gr,loglik,pmax,val(nclust),mind,d
| 1
Warning: Unused variable ‘f’ declared at (1) [-Wunused-variable]
zoolayerViterbi.f90:8:27:
8 | real(dp) ::sumF(2),F,a,r,gr,loglik,pmax,val(nclust),mind,d
| 1
Warning: Unused variable ‘gr’ declared at (1) [-Wunused-variable]
zoolayerViterbi.f90:4:51:
4 | integer ::i,j,l,k,nclust,nchr,npos,chr,fpos,lpos,hs,hs2,pos(1),phi(nclust,npos)
| 1
Warning: Unused variable ‘hs’ declared at (1) [-Wunused-variable]
zoolayerViterbi.f90:4:55:
4 | integer ::i,j,l,k,nclust,nchr,npos,chr,fpos,lpos,hs,hs2,pos(1),phi(nclust,npos)
| 1
Warning: Unused variable ‘hs2’ declared at (1) [-Wunused-variable]
zoolayerViterbi.f90:5:58:
5 | integer ::isF(nclust),chr_limits(nchr,2),IT(nclust,nclust),posi(npos),states(npos)
| 1
Warning: Unused variable ‘it’ declared at (1) [-Wunused-variable]
zoolayerViterbi.f90:8:34:
8 | real(dp) ::sumF(2),F,a,r,gr,loglik,pmax,val(nclust),mind,d
| 1
Warning: Unused variable ‘loglik’ declared at (1) [-Wunused-variable]
zoolayerViterbi.f90:8:56:
8 | real(dp) ::sumF(2),F,a,r,gr,loglik,pmax,val(nclust),mind,d
| 1
Warning: Unused variable ‘mind’ declared at (1) [-Wunused-variable]
zoolayerViterbi.f90:8:24:
8 | real(dp) ::sumF(2),F,a,r,gr,loglik,pmax,val(nclust),mind,d
| 1
Warning: Unused variable ‘r’ declared at (1) [-Wunused-variable]
zoolayerViterbi.f90:8:18:
8 | real(dp) ::sumF(2),F,a,r,gr,loglik,pmax,val(nclust),mind,d
| 1
Warning: Unused variable ‘sumf’ declared at (1) [-Wunused-variable]
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c zoolayerlik.f90 -o zoolayerlik.o
zoolayerlik.f90:8:22:
8 | real(dp) ::sumF(2),F,a,r,gr,loglik,d
| 1
Warning: Unused variable ‘a’ declared at (1) [-Wunused-variable]
zoolayerlik.f90:8:20:
8 | real(dp) ::sumF(2),F,a,r,gr,loglik,d
| 1
Warning: Unused variable ‘f’ declared at (1) [-Wunused-variable]
zoolayerlik.f90:8:27:
8 | real(dp) ::sumF(2),F,a,r,gr,loglik,d
| 1
Warning: Unused variable ‘gr’ declared at (1) [-Wunused-variable]
zoolayerlik.f90:4:51:
4 | integer ::i,j,l,k,nclust,nchr,npos,chr,fpos,lpos,hs,hs2
| 1
Warning: Unused variable ‘hs’ declared at (1) [-Wunused-variable]
zoolayerlik.f90:4:55:
4 | integer ::i,j,l,k,nclust,nchr,npos,chr,fpos,lpos,hs,hs2
| 1
Warning: Unused variable ‘hs2’ declared at (1) [-Wunused-variable]
zoolayerlik.f90:8:24:
8 | real(dp) ::sumF(2),F,a,r,gr,loglik,d
| 1
Warning: Unused variable ‘r’ declared at (1) [-Wunused-variable]
zoolayerlik.f90:8:18:
8 | real(dp) ::sumF(2),F,a,r,gr,loglik,d
| 1
Warning: Unused variable ‘sumf’ declared at (1) [-Wunused-variable]
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c zoolik.f90 -o zoolik.o
zoolik.f90:9:20:
9 | real(dp) ::sumF(2),F,a,r,gr,loglik
| 1
Warning: Unused variable ‘f’ declared at (1) [-Wunused-variable]
zoolik.f90:9:27:
9 | real(dp) ::sumF(2),F,a,r,gr,loglik
| 1
Warning: Unused variable ‘gr’ declared at (1) [-Wunused-variable]
zoolik.f90:4:15:
4 | integer ::i,j,l,k,nclust,nchr,npos,chr,fpos,lpos,hs,hs2
| 1
Warning: Unused variable ‘l’ declared at (1) [-Wunused-variable]
gcc-13 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o RZooRoH.so RZooRoH_init.o random_number_wrapper.o zooEM.o zooFB.o zooSIM.o zooViterbi.o zoolayerEM.o zoolayerFB.o zoolayerViterbi.o zoolayerlik.o zoolik.o -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmp4zt2Ux/R.INSTALL2e04af12010504/RZooRoH/src'
make[1]: Entering directory '/tmp/Rtmp4zt2Ux/R.INSTALL2e04af12010504/RZooRoH/src'
make[1]: Leaving directory '/tmp/Rtmp4zt2Ux/R.INSTALL2e04af12010504/RZooRoH/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-RZooRoH/00new/RZooRoH/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘RZooRoH’
finding HTML links ... done
BBB_NMP_GP_subset html
BBB_NMP_ad_subset html
BBB_NMP_pl_subset html
BBB_PE_gt_subset html
BBB_samples html
RZooRoH-package html
cumhbd html
genoex html
genosim html
probhbd html
rara_mix10r html
realized html
rohbd html
soay_mix10r html
typs html
typsfrq html
wilt_mix10r html
zoodata html
zoodoris html
zoomodel html
zooplot_hbdseg html
zooplot_individuals html
zooplot_partitioning html
zooplot_prophbd html
zoorun html
zoosimd html
** building package indices
** installing vignettes
** 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 (RZooRoH)