* installing *source* package ‘sequoia’ ...
** package ‘sequoia’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
using SDK: ‘MacOSX11.3.sdk’
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c MkRelA.f90 -o MkRelA.o
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c Sequoia.f90 -o Sequoia.o
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c SimGenoErrors.f90 -o SimGenoErrors.o
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c countpairOH.f90 -o countpairOH.o
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c ester.f90 -o ester.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 init.c -o init.o
countpairOH.f90:2:2:
2 | implicit none
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:4:2:
4 | integer, intent(IN) :: ng, nm, np, maxoh
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:5:2:
5 | integer, intent(IN) :: pairids(2*np), genofr(ng*nm)
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:6:2:
6 | integer, intent(INOUT) :: ohrf(np)
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:7:2:
7 | integer :: i,j, l,x, pairs(np, 2), Genos(nm, ng), IsOppHom(-1:2,-1:2)
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:9:2:
9 | pairs(:,1) = pairids(1:np)
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:10:2:
10 | pairs(:,2) = pairids((np+1):(2*np))
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:13:2:
13 | Genos = -1
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:14:2:
14 | j = 0
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:15:2:
15 | do l=1,nm
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:16:2:
16 | do i=1, ng
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:17:2:
17 | j = j+1
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:18:2:
18 | if (GenoFR(j)>=0) then
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:19:2:
19 | Genos(l,i) = GenoFR(j)
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:20:2:
20 | endif
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:21:2:
21 | enddo
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:22:2:
22 | enddo
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:25:2:
25 | IsOppHom = 0
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:30:2:
30 | do x=1, np
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:32:2:
32 | ohrf(x) = calcOH(pairs(x,1), pairs(x,2))
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:33:2:
33 | enddo
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
countpairOH.f90:37:2:
37 | integer function calcOH(i,j) result(OH_ij)
| 1
Warning: Nonconforming tab character at (1) [-Wtabs]
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pretty_R_print.c -o pretty_R_print.o
Sequoia.f90:3913:58:
3913 | double precision :: LLcp(3,2), LLU(4), U, ALR(3,2), ALRtmp, LLtmp, LLtrio(6), &
| 1
Warning: Unused variable ‘alrtmp’ declared at (1) [-Wunused-variable]
Sequoia.f90:16080:47:
16080 | integer :: i, r, AncB(2,mxA), Bi, AncBi(2, mxA), catA, catB, GA(2), catG, &
| 1
Warning: Unused variable ‘ancbi’ 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 sequoia.so MkRelA.o Sequoia.o SimGenoErrors.o countpairOH.o ester.o init.o pretty_R_print.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 _countpairoh_: registers 27 and 28 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
ld: warning: could not create compact unwind for _mkerrors_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _getrel_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _ester_calcll_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _ester_parprob_: register 20 saved somewhere other than in frame
ld: warning: could not create compact unwind for _ester_getoff_: registers 25 and 26 not saved contiguously in frame
ld: warning: could not create compact unwind for _estg_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _ester_getgenerations_: register 24 saved somewhere other than in frame
ld: warning: could not create compact unwind for _estallg_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _ester_calcprobs_: registers 25 and 26 not saved contiguously in frame
ld: warning: could not create compact unwind for _ester_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for ___global_MOD_mk_seq: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for ___ohfun_MOD_calc_qlr_po: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for ___ohfun_MOD_mk_qpo: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for ___ohfun_MOD_init_oh: registers 23 and 24 not saved contiguously in frame
ld: warning: could not create compact unwind for ___sort_module_MOD_sort_sibships: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _erstop_: register 24 saved somewhere other than in frame
ld: warning: could not create compact unwind for ___global_MOD_rprint: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for ___global_MOD_getap: register 26 saved somewhere other than in frame
ld: warning: could not create compact unwind for ___calclik_MOD_fslik: registers 21 and 22 not saved contiguously in frame
ld: warning: could not create compact unwind for _prepagedata_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _allocarrays_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _estbyrange_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _pairqhs_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _pairqfs_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _getancest_: registers 23 and 24 not saved contiguously in frame
ld: warning: could not create compact unwind for _chkancest_: register 24 saved somewhere other than in frame
ld: warning: could not create compact unwind for _getpoconfigs_.part.0.constprop.0: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _isselfed_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _rprint_tbl_update_b_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _checkselfed_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _calcagelr_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _parprob_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for ___calclik_MOD_calclind: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _mergesibs_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _calcp2_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _addfa_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _qfs_: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _qfsgp_: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _qgp_: registers 23 and 24 not saved contiguously in frame
ld: warning: could not create compact unwind for _getfocal_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _getoff_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _oppmerge_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _lla2llr_: register 75 saved somewhere other than in frame
ld: warning: could not create compact unwind for _chkvalidgp_: registers 23 and 24 not saved contiguously in frame
ld: warning: could not create compact unwind for _triofsfa_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _triohsgp_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _trioha_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _trioggp_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _triofa_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _triohs_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _triofs_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _connected_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _clusthsha_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _fshc_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _fsmerge_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _addhaselfed_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _calcalrmerge_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _pairdhc_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _calcalr_addsib_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _pairfsfc_: registers 25 and 26 not saved contiguously in frame
ld: warning: could not create compact unwind for _pairfsselfed_: registers 25 and 26 not saved contiguously in frame
ld: warning: could not create compact unwind for _pairhsgp_: registers 25 and 26 not saved contiguously in frame
ld: warning: could not create compact unwind for _pairfsha_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _pairfax_: registers 25 and 26 not saved contiguously in frame
ld: warning: could not create compact unwind for _pairga_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _findee_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _chkdoquick_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _addggp_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _dummyhfa_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _parenthfs_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _addgau_: register 77 saved somewhere other than in frame
ld: warning: could not create compact unwind for _pairua_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _chktoomanysibs_: register 22 saved somewhere other than in frame
ld: warning: could not create compact unwind for _calccll_: register 75 saved somewhere other than in frame
ld: warning: could not create compact unwind for _chkvalidpar_: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _pairhscc_: registers 25 and 26 not saved contiguously in frame
ld: warning: could not create compact unwind for _pairhspo_: registers 25 and 26 not saved contiguously in frame
ld: warning: could not create compact unwind for _pairpox_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _uclust_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _estagedif_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _upair_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _calcu_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _triogp_: registers 23 and 24 not saved contiguously in frame
ld: warning: could not create compact unwind for _hsmating_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _pairhshai_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _addsibinbr_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _pairfaha_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _updatell_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _calcbysibs_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _calcbydown_: registers 74 and 75 not saved contiguously in frame
ld: warning: could not create compact unwind for _calcbyup_: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _setestby_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _makefs_: registers 21 and 22 not saved contiguously in frame
ld: warning: could not create compact unwind for _readinputped_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _doadd_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _removefs_: registers 21 and 22 not saved contiguously in frame
ld: warning: could not create compact unwind for _removesib_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _setpartmp_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _pairpo_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _addparent_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _chkpo_: registers 23 and 24 not saved contiguously in frame
ld: warning: could not create compact unwind for _addgp_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _pairgp_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _pairggp_: registers 25 and 26 not saved contiguously in frame
ld: warning: could not create compact unwind for _addfs_: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _addsib_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _sibchk_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _dummygp_: registers 76 and 77 not saved contiguously in frame
ld: warning: could not create compact unwind for _checkmerge_: register 75 saved somewhere other than in frame
ld: warning: could not create compact unwind for _setpar_: registers 21 and 22 not saved contiguously in frame
ld: warning: could not create compact unwind for _chkgps_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _newsibship_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _updatemate_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _checkmono_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _domerge_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _checkdropsibship_: register 20 saved somewhere other than in frame
ld: warning: could not create compact unwind for _dofsmerge_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _merging_.part.0: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _gpfilter_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _calc4u_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _calcpx2_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _pairhsha_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _pairhalfsib_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _pairpoha_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _pairfullsib_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _paircc_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _checkadd_: registers 74 and 75 not saved contiguously in frame
ld: warning: could not create compact unwind for _checkpair_: registers 76 and 77 not saved contiguously in frame
ld: warning: could not create compact unwind for _findpairs_: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _checkrel_: register 28 saved somewhere other than in frame
ld: warning: could not create compact unwind for _clustering_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _checkmayberev_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _calccandparll_: registers 74 and 75 not saved contiguously in frame
ld: warning: could not create compact unwind for _calcpogpz_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _checkparentpair_: register 28 saved somewhere other than in frame
ld: warning: could not create compact unwind for _triads_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _selectparent_: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _parentage_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _fsibsgps_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _sibgrandparents_: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _sibparent_: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _qfsmerge_: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _getgenerations_: register 24 saved somewhere other than in frame
ld: warning: could not create compact unwind for ___sort_module_MOD_getrank_i: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _updateallprobs_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _initiate_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _duplicates_: register 73 saved somewhere other than in frame
ld: warning: could not create compact unwind for _findambig_: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _getpairll_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _calcparentllr_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _getpedllr_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _moreparent_: registers 72 and 73 not saved contiguously in frame
ld: warning: could not create compact unwind for _ggpairs_: register 77 saved somewhere other than in frame
ld: warning: could not create compact unwind for _checkpedigree_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _sibships_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _parents_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _makeped_: registers 27 and 28 not saved contiguously in frame
ld: warning: could not create compact unwind for _getbyprobs_: registers 27 and 28 not saved contiguously in frame
installing to /Volumes/Builds/packages/big-sur-arm64/results/4.4/sequoia.Rcheck/00LOCK-sequoia/00new/sequoia/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 (sequoia)