* installing *source* package ‘RZooRoH’ ...
** this is package ‘RZooRoH’ version ‘0.3.2.1’
** package ‘RZooRoH’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RZooRoH_init.c -o RZooRoH_init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c random_number_wrapper.c -o random_number_wrapper.o
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -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]
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -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]
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -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]
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -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]
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -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]
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -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]
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -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]
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -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]
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -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]
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -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 -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
ld: warning: could not create compact unwind for _zooem_: does not use standard frame
ld: warning: could not create compact unwind for _zoofb_: does not use standard frame
ld: warning: could not create compact unwind for _zoosim_: does not use standard frame
ld: warning: could not create compact unwind for _zoolayerem_: does not use standard frame
ld: warning: could not create compact unwind for _zoolayerfb_: does not use standard frame
ld: warning: could not create compact unwind for _zoolayerviterbi_: does not use standard frame
ld: warning: could not create compact unwind for _zoolayerlik_: does not use standard frame
ld: warning: could not create compact unwind for _zoolik_: does not use standard frame
ld: warning: could not create compact unwind for _zooviterbi_: does not use standard frame
ld: warning: could not create compact unwind for _allocate_tramp_ctrl: does not use standard frame
ld: warning: could not create compact unwind for ___gcc_nested_func_ptr_created: does not use standard frame
ld: warning: could not create compact unwind for ___gcc_nested_func_ptr_deleted: does not use standard frame
ld: warning: could not create compact unwind for ___emutls_get_address: does not use standard frame
installing to /Volumes/Builds/packages/big-sur-arm64/results/4.5/RZooRoH.Rcheck/00LOCK-RZooRoH/00new/RZooRoH/libs
** generating debug symbols (dSYM)
** 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)