* installing *source* package ‘RZooRoH’ ...
** 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) 12.2.0’
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 -single_module -multiply_defined suppress -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-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: could not create compact unwind for _zooem_: registers 74 and 75 not saved contiguously in frame
ld: warning: could not create compact unwind for _zoofb_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _zoosim_: registers 74 and 75 not saved contiguously in frame
ld: warning: could not create compact unwind for _zooviterbi_: register 77 saved somewhere other than in frame
ld: warning: could not create compact unwind for _zoolayerem_: registers 76 and 77 not saved contiguously in frame
ld: warning: could not create compact unwind for _zoolayerfb_: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _zoolayerlik_: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _zoolik_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _zoolayerviterbi_: registers 78 and 79 not saved contiguously in frame
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
installing to /Volumes/Builds/packages/big-sur-arm64/results/4.3/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)