* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘RZooRoH’ ...
** package ‘RZooRoH’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-8) 14.2.0’
using Fortran compiler: ‘GNU Fortran (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/tmp/Rtmp3dHxtk/R.INSTALL1db1e26e04c7f0/RZooRoH/src'
gcc-14 -I"/home/hornik/tmp/R.check/r-devel-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-14 -I"/home/hornik/tmp/R.check/r-devel-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-14 -fpic -g -O2 -Wall -pedantic -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-14 -fpic -g -O2 -Wall -pedantic -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-14 -fpic -g -O2 -Wall -pedantic -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-14 -fpic -g -O2 -Wall -pedantic -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-14 -fpic -g -O2 -Wall -pedantic -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-14 -fpic -g -O2 -Wall -pedantic -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-14 -fpic -g -O2 -Wall -pedantic -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-14 -fpic -g -O2 -Wall -pedantic -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-14 -fpic -g -O2 -Wall -pedantic -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-14 -shared -L/home/hornik/tmp/R.check/r-devel-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-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmp3dHxtk/R.INSTALL1db1e26e04c7f0/RZooRoH/src'
make[1]: Entering directory '/tmp/Rtmp3dHxtk/R.INSTALL1db1e26e04c7f0/RZooRoH/src'
make[1]: Leaving directory '/tmp/Rtmp3dHxtk/R.INSTALL1db1e26e04c7f0/RZooRoH/src'
installing to /home/hornik/tmp/R.check/r-devel-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
** 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)