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###
### Running command:
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### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL BGmix
###
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘BGmix’ ...
** using staged installation
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gcc option to accept ISO C99... none needed
checking for cos in -lm... yes
Untarring Boost header files...
checking for an ANSI C-conforming const... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I ../boostIncl -I/usr/local/include -fPIC -g -O2 -g -O2 -DUSING_R -c BGmix_main.cpp -o BGmix_main.o
BGmix_main.cpp: In function ‘void BGmix(int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double*, double*, double*, int*, int&, double*, int*, char**, char**, char**, char**, char**)’:
BGmix_main.cpp:145:1: error: reference to ‘beta’ is ambiguous
145 | beta = new double*[ngenes];
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:146:29: error: reference to ‘beta’ is ambiguous
146 | for(int i=0; i<ngenes; ++i) beta[i] = new double[neffects];
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:166:8: error: reference to ‘beta’ is ambiguous
166 | beta[i][0] = xx[1][1]*ybar[i][0] - xx[1][0]*ybar[i][1];
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:167:8: error: reference to ‘beta’ is ambiguous
167 | beta[i][1] = xx[0][0]*ybar[i][1] - xx[0][1]*ybar[i][0];
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:169:11: error: reference to ‘beta’ is ambiguous
169 | else beta[i][j] = beta_init;
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:179:9: error: reference to ‘beta’ is ambiguous
179 | if(beta[i][jstar]<0.01 & beta[i][jstar]>-0.01) zg[i]=1;
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:179:31: error: reference to ‘beta’ is ambiguous
179 | if(beta[i][jstar]<0.01 & beta[i][jstar]>-0.01) zg[i]=1;
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:180:14: error: reference to ‘beta’ is ambiguous
180 | else if(beta[i][jstar]>0) zg[i]=2;
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:507:15: error: reference to ‘beta’ is ambiguous
507 | update_beta0(beta, tau, gamma1, xx, indtau, ybar, ydata, like_choice,
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:512:38: error: reference to ‘beta’ is ambiguous
512 | if(move_choice_cut==1) update_tau(beta, tau, gamma1, xx, indtau, ybar, ss, ydata,
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:522:23: error: reference to ‘beta’ is ambiguous
522 | update_tau_logNorm(beta, tau, gamma1, xx, indtau, ybar, ss, ydata,
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:529:34: error: reference to ‘beta’ is ambiguous
529 | if(like_choice==2) update_gamma(beta, tau, gamma1, xx, indtau, ydata, df,
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:536:25: error: reference to ‘beta’ is ambiguous
536 | eta_up, eta_down, beta, tau, gamma1, xx, indtau, ybar, ydata, like_choice,
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:541:32: error: reference to ‘beta’ is ambiguous
541 | update_z_beta1_joint2(zg, beta, nalloc, n_acc, n_try,
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:547:32: error: reference to ‘beta’ is ambiguous
547 | update_z_beta1_joint3(zg, beta, nalloc, n_acc, n_try, wtc, eta_up, eta_down,
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:551:16: error: reference to ‘beta’ is ambiguous
551 | zg, beta, nalloc, ngenes, nconds, jstar, rand);
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:553:30: error: reference to ‘beta’ is ambiguous
553 | lam1, lam2, nlam, zg, beta, nalloc, ngenes, jstar, rand);
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:556:32: error: reference to ‘beta’ is ambiguous
556 | update_z_beta1_joint4(zg, beta, nalloc, n_acc, n_try, wtc, tau_eps, eta_up, eta_down,
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:560:16: error: reference to ‘beta’ is ambiguous
560 | zg, beta, nalloc, ngenes, nconds, jstar, rand);
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:562:30: error: reference to ‘beta’ is ambiguous
562 | lam1, lam2, nlam, zg, beta, nalloc, ngenes, jstar, rand);
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:583:15: error: reference to ‘beta’ is ambiguous
583 | update_beta0(beta, tau, gamma1, xx, indtau, ybar, ydata, like_choice,
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:588:38: error: reference to ‘beta’ is ambiguous
588 | if(move_choice_cut==1) update_tau(beta, tau, gamma1, xx, indtau, ybar, ss, ydata,
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:597:23: error: reference to ‘beta’ is ambiguous
597 | update_tau_logNorm(beta, tau, gamma1, xx, indtau, ybar, ss, ydata,
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:605:34: error: reference to ‘beta’ is ambiguous
605 | if(like_choice==2) update_gamma(beta, tau, gamma1, xx, indtau, ydata, df,
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:611:25: error: reference to ‘beta’ is ambiguous
611 | eta_up, eta_down, beta, tau, gamma1, xx, indtau, ybar, ydata, like_choice,
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:616:32: error: reference to ‘beta’ is ambiguous
616 | update_z_beta1_joint2(zg, beta, nalloc, n_acc, n_try,
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:622:32: error: reference to ‘beta’ is ambiguous
622 | update_z_beta1_joint3(zg, beta, nalloc, n_acc, n_try, wtc, eta_up, eta_down,
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:626:16: error: reference to ‘beta’ is ambiguous
626 | zg, beta, nalloc, ngenes, nconds, jstar, rand);
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:628:30: error: reference to ‘beta’ is ambiguous
628 | lam1, lam2, nlam, zg, beta, nalloc, ngenes, jstar, rand);
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:631:32: error: reference to ‘beta’ is ambiguous
631 | update_z_beta1_joint4(zg, beta, nalloc, n_acc, n_try, wtc, tau_eps, eta_up, eta_down,
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:635:16: error: reference to ‘beta’ is ambiguous
635 | zg, beta, nalloc, ngenes, nconds, jstar, rand);
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:637:30: error: reference to ‘beta’ is ambiguous
637 | lam1, lam2, nlam, zg, beta, nalloc, ngenes, jstar, rand);
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:647:43: error: reference to ‘beta’ is ambiguous
647 | ybar, ss, tau, gamma1, aa, bb, zg, beta, xx, indtau, wtc, tau_eps, eta_up, eta_down,
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:653:54: error: reference to ‘beta’ is ambiguous
653 | ybar, ss, tau, gamma1, df, aa, bb, zg, beta, xx, indtau, wtc, tau_eps, eta_up, eta_down,
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:656:40: error: reference to ‘beta’ is ambiguous
656 | deviance_calc(deviance1, deviance2, beta, tau, gamma1, xx, indtau, ybar, ss, ydata,
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:670:23: error: reference to ‘beta’ is ambiguous
670 | mean_beta[i][j] += beta[i][j];
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:705:22: error: reference to ‘beta’ is ambiguous
705 | beta_file << beta[i][j] << " ";
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp: In function ‘void freeBGmixMemory(int&, int&)’:
BGmix_main.cpp:967:41: error: reference to ‘beta’ is ambiguous
967 | for(int i=0; i<ngenes; ++i) delete [] beta[i];
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
BGmix_main.cpp:968:13: error: reference to ‘beta’ is ambiguous
968 | delete [] beta;
| ^~~~
In file included from /usr/include/c++/10.3.1/cmath:1927,
from /usr/include/c++/10.3.1/valarray:37,
from rand.hh:24,
from updates_BGmix.h:1,
from BGmix_main.cpp:25:
/usr/include/c++/10.3.1/bits/specfun.h:343:5: note: candidates are: ‘template<class _Tpa, class _Tpb> typename __gnu_cxx::__promote_2<_Tp, _Up>::__type std::beta(_Tpa, _Tpb)’
343 | beta(_Tpa __a, _Tpb __b)
| ^~~~
BGmix_main.cpp:76:40: note: ‘double** beta’
76 | static double **ybar, **ss, **ydata, **beta, **tau, **gamma1,
| ^~~~
make: *** [Makevars:9: BGmix_main.o] Error 1
ERROR: compilation failed for package ‘BGmix’
* removing ‘/home/biocbuild/R/R-4.3.0/site-library/BGmix’