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epiverse-trace / episoap

[Not published - under active development] A Store of Outbreak Analytics Pipelines Provided as Rmarkdown Report Templates
https://epiverse-trace.github.io/episoap/
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Error when knitting template- renv? #99

Closed CarmenTamayo closed 8 months ago

CarmenTamayo commented 10 months ago

Hello, I've been getting a very lengthy error message whenever I try to knit either of the templates (both in the main and severity branches), the file knits until it reaches 5% (5% [lockfile]), then the error message appears. I think the error has to do with {renv}, I've experienced similar errors before with this package.

This is the full error message:

../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Fx, *Fz ;
                           ^
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
    Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                         ^
In file included from ../Core/cholmod_transpose.c:125:
../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Fx, *Fz ;
                 ^
../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Fx, *Fz ;
                           ^
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
    Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                         ^
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
    Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                              ^
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
    Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                    ^
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
    Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                       ^
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
    Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                    ^
../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Fx, *Fz ;
                 ^
../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Fx, *Fz ;
                           ^
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
    Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                         ^
In file included from ../Core/cholmod_transpose.c:128:
../Core/t_cholmod_transpose.c:42:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Fx, *Fz ;
                 ^
../Core/t_cholmod_transpose.c:42:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Fx, *Fz ;
                           ^
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
    Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                         ^
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
    Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                              ^
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
    Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                    ^
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
    Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                       ^
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
    Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                    ^
../Core/t_cholmod_transpose.c:139:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Fx, *Fz ;
                 ^
../Core/t_cholmod_transpose.c:139:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Fx, *Fz ;
                           ^
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
    Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                         ^
In file included from ../Core/cholmod_transpose.c:130:
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
    Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                         ^
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
    Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                              ^
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
    Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                    ^
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
    Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                       ^
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
    Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                    ^
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
    Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                         ^
In file included from ../Core/cholmod_transpose.c:133:
../Core/t_cholmod_transpose.c:43:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
    Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                         ^
../Core/t_cholmod_transpose.c:43:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
    Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                              ^
../Core/t_cholmod_transpose.c:44:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
    Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                    ^
../Core/t_cholmod_transpose.c:44:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
    Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                       ^
../Core/t_cholmod_transpose.c:44:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
    Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                    ^
../Core/t_cholmod_transpose.c:140:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
    Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                         ^
56 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Core/cholmod_triplet.c -o cholmod_l_triplet.o
In file included from ../Core/cholmod_triplet.c:105:
../Core/t_cholmod_triplet.c:28:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
    double *Rx, *Rz, *Tx, *Tz ;
            ^
../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
    double *Rx, *Rz, *Tx, *Tz ;
                 ^
../Core/t_cholmod_triplet.c:28:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
    double *Rx, *Rz, *Tx, *Tz ;
                      ^
../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
    double *Rx, *Rz, *Tx, *Tz ;
                           ^
In file included from ../Core/cholmod_triplet.c:107:
../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
    double *Rx, *Rz, *Tx, *Tz ;
                 ^
../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
    double *Rx, *Rz, *Tx, *Tz ;
                           ^
In file included from ../Core/cholmod_triplet.c:109:
../Core/t_cholmod_triplet.c:28:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
    double *Rx, *Rz, *Tx, *Tz ;
                 ^
../Core/t_cholmod_triplet.c:28:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
    double *Rx, *Rz, *Tx, *Tz ;
                           ^
../Core/cholmod_triplet.c:341:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
    Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
                   ^
../Core/cholmod_triplet.c:342:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
    Int i, j, p, k, stype, nrow, ncol, nz, ok ;
                                           ^
10 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Core/cholmod_version.c -o cholmod_l_version.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Check/cholmod_check.c -o cholmod_l_check.o
../Check/cholmod_check.c:204:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable]
    Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
                                                            ^
../Check/cholmod_check.c:950:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
    Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
                                    ^
../Check/cholmod_check.c:1494:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
    Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor,
                                     ^
../Check/cholmod_check.c:1495:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
        count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
               ^
../Check/cholmod_check.c:1497:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
        ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
        ^
5 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Check/cholmod_read.c -o cholmod_l_read.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Check/cholmod_write.c -o cholmod_l_write.o
../Check/cholmod_write.c:366:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable]
    Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
                                ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o
../Cholesky/cholmod_analyze.c:416:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
    Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                  ^
../Cholesky/cholmod_analyze.c:416:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
    Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                            ^
../Cholesky/cholmod_analyze.c:419:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
    Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
                                                                    ^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o
../Cholesky/cholmod_factorize.c:111:37: warning: variable 'n' set but not used [-Wunused-but-set-variable]
    Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
                                    ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o
In file included from ../Cholesky/cholmod_rowfac.c:161:
../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                 ^
../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                           ^
../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                     ^
../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                               ^
../Cholesky/t_cholmod_rowfac.c:50:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
        use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                                    ^
In file included from ../Cholesky/cholmod_rowfac.c:163:
../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                 ^
../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                           ^
../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                     ^
../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                               ^
../Cholesky/t_cholmod_rowfac.c:50:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
        use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                                    ^
In file included from ../Cholesky/cholmod_rowfac.c:165:
../Cholesky/t_cholmod_rowfac.c:50:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
        use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                                    ^
In file included from ../Cholesky/cholmod_rowfac.c:169:
../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                 ^
../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                           ^
../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                     ^
../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                               ^
../Cholesky/t_cholmod_rowfac.c:50:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
        use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                                    ^
In file included from ../Cholesky/cholmod_rowfac.c:171:
../Cholesky/t_cholmod_rowfac.c:46:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                 ^
../Cholesky/t_cholmod_rowfac.c:46:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                           ^
../Cholesky/t_cholmod_rowfac.c:46:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                     ^
../Cholesky/t_cholmod_rowfac.c:46:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                               ^
../Cholesky/t_cholmod_rowfac.c:50:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
        use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                                    ^
In file included from ../Cholesky/cholmod_rowfac.c:173:
../Cholesky/t_cholmod_rowfac.c:50:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
        use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                                    ^
22 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o
In file included from ../Cholesky/cholmod_solve.c:63:
../Cholesky/t_cholmod_solve.c:61:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
    double *Lx, *Yx, *Yz ;
                      ^
In file included from ../Cholesky/cholmod_solve.c:66:
../Cholesky/t_cholmod_solve.c:61:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
    double *Lx, *Yx, *Yz ;
                      ^
../Cholesky/cholmod_solve.c:334:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
    Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
            ^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o
In file included from ../MatrixOps/cholmod_sdmult.c:44:
../MatrixOps/t_cholmod_sdmult.c:49:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                 ^
../MatrixOps/t_cholmod_sdmult.c:49:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                           ^
../MatrixOps/t_cholmod_sdmult.c:49:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                     ^
../MatrixOps/t_cholmod_sdmult.c:49:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                              ^
../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
    Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                ^
In file included from ../MatrixOps/cholmod_sdmult.c:46:
../MatrixOps/t_cholmod_sdmult.c:49:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                 ^
../MatrixOps/t_cholmod_sdmult.c:49:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                           ^
../MatrixOps/t_cholmod_sdmult.c:49:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                     ^
../MatrixOps/t_cholmod_sdmult.c:49:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
    double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                              ^
../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
    Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                ^
In file included from ../MatrixOps/cholmod_sdmult.c:48:
../MatrixOps/t_cholmod_sdmult.c:52:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
    Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                ^
11 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Modify/cholmod_updown.c -o cholmod_l_updown.o
../Modify/cholmod_updown.c:433:33: warning: variable 'ps1' set but not used [-Wunused-but-set-variable]
        *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
                                       ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o
In file included from ../Supernodal/cholmod_super_numeric.c:82:
../Supernodal/t_cholmod_super_numeric.c:108:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
    double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                           ^
../Supernodal/t_cholmod_super_numeric.c:108:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
    double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                ^
../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable]
        *Previous;
         ^
../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable]
        pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1,
        ^
../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable]
        tail, nscol_new = 0;
        ^
In file included from ../Supernodal/cholmod_super_numeric.c:84:
../Supernodal/t_cholmod_super_numeric.c:108:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
    double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                           ^
../Supernodal/t_cholmod_super_numeric.c:108:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
    double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                ^
../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable]
        *Previous;
         ^
../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable]
        pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1,
        ^
../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable]
        tail, nscol_new = 0;
        ^
In file included from ../Supernodal/cholmod_super_numeric.c:86:
../Supernodal/t_cholmod_super_numeric.c:111:10: warning: variable 'Previous' set but not used [-Wunused-but-set-variable]
        *Previous;
         ^
../Supernodal/t_cholmod_super_numeric.c:113:9: warning: unused variable 'pj' [-Wunused-variable]
        pj, d, kd1, kd2, info, ndcol, ndrow, pdi, pdx, pdend, pdi1, pdi2, pdx1,
        ^
../Supernodal/t_cholmod_super_numeric.c:116:9: warning: unused variable 'tail' [-Wunused-variable]
        tail, nscol_new = 0;
        ^
13 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o
In file included from ../Supernodal/cholmod_super_solve.c:26:
../Supernodal/t_cholmod_super_solve.c:30:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
        nsrow2, n, ps2, j, i, d, nrhs ;
                ^
../Supernodal/t_cholmod_super_solve.c:238:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
        nsrow2, n, ps2, j, i, d, nrhs ;
                ^
In file included from ../Supernodal/cholmod_super_solve.c:28:
../Supernodal/t_cholmod_super_solve.c:30:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
        nsrow2, n, ps2, j, i, d, nrhs ;
                ^
../Supernodal/t_cholmod_super_solve.c:238:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
        nsrow2, n, ps2, j, i, d, nrhs ;
                ^
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DDLONG -c  ../Supernodal/cholmod_super_symbolic.c -o cholmod_l_super_symbolic.o
../Supernodal/cholmod_super_symbolic.c:562:7: warning: variable 'totsize' set but not used [-Wunused-but-set-variable]
                Int totsize ;
                    ^
../Supernodal/cholmod_super_symbolic.c:181:17: warning: unused variable 'env_use_gpu' [-Wunused-variable]
    const char* env_use_gpu;
                ^
../Supernodal/cholmod_super_symbolic.c:182:17: warning: unused variable 'env_max_bytes' [-Wunused-variable]
    const char* env_max_bytes;
                ^
../Supernodal/cholmod_super_symbolic.c:183:12: warning: unused variable 'max_bytes' [-Wunused-variable]
    size_t max_bytes;
           ^
../Supernodal/cholmod_super_symbolic.c:184:17: warning: unused variable 'env_max_fraction' [-Wunused-variable]
    const char* env_max_fraction;
                ^
../Supernodal/cholmod_super_symbolic.c:185:12: warning: unused variable 'max_fraction' [-Wunused-variable]
    double max_fraction;
           ^
6 warnings generated.
ar -rucs ../../CHOLMOD.a cholmod_aat.o cholmod_add.o cholmod_band.o cholmod_change_factor.o cholmod_common.o cholmod_complex.o cholmod_copy.o cholmod_dense.o cholmod_error.o cholmod_factor.o cholmod_memory.o cholmod_sparse.o cholmod_transpose.o cholmod_triplet.o cholmod_version.o cholmod_check.o cholmod_read.o cholmod_write.o cholmod_amd.o cholmod_analyze.o cholmod_colamd.o cholmod_etree.o cholmod_factorize.o cholmod_postorder.o cholmod_rcond.o cholmod_resymbol.o cholmod_rowcolcounts.o cholmod_rowfac.o cholmod_solve.o cholmod_spsolve.o cholmod_drop.o cholmod_horzcat.o cholmod_norm.o cholmod_scale.o cholmod_sdmult.o cholmod_ssmult.o cholmod_submatrix.o cholmod_vertcat.o cholmod_symmetry.o cholmod_rowadd.o cholmod_rowdel.o cholmod_updown.o cholmod_super_numeric.o cholmod_super_solve.o cholmod_super_symbolic.o  cholmod_l_aat.o cholmod_l_add.o cholmod_l_band.o cholmod_l_change_factor.o cholmod_l_common.o cholmod_l_complex.o cholmod_l_copy.o cholmod_l_dense.o cholmod_l_error.o cholmod_l_factor.o cholmod_l_memory.o cholmod_l_sparse.o cholmod_l_transpose.o cholmod_l_triplet.o cholmod_l_version.o cholmod_l_check.o cholmod_l_read.o cholmod_l_write.o cholmod_l_amd.o cholmod_l_analyze.o cholmod_l_colamd.o cholmod_l_etree.o cholmod_l_factorize.o cholmod_l_postorder.o cholmod_l_rcond.o cholmod_l_resymbol.o cholmod_l_rowcolcounts.o cholmod_l_rowfac.o cholmod_l_solve.o cholmod_l_spsolve.o cholmod_l_drop.o cholmod_l_horzcat.o cholmod_l_norm.o cholmod_l_scale.o cholmod_l_sdmult.o cholmod_l_ssmult.o cholmod_l_submatrix.o cholmod_l_vertcat.o cholmod_l_symmetry.o cholmod_l_rowadd.o cholmod_l_rowdel.o cholmod_l_updown.o cholmod_l_super_numeric.o cholmod_l_super_solve.o cholmod_l_super_symbolic.o 
( cd Source ; make -f "/Library/Frameworks/R.framework/Resources/etc/Makeconf" -f Makefile lib )
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c colamd.c -o colamd.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDLONG -c colamd.c -o colamd_l.o
ar -rucs ../../COLAMD.a colamd.o colamd_l.o
( cd Source ; make -f "/Library/Frameworks/R.framework/Resources/etc/Makeconf" -f Makefile lib )
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDINT -c amd_1.c -o amd_i_1.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDLONG -c amd_1.c -o amd_l_1.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDINT -c amd_2.c -o amd_i_2.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDLONG -c amd_2.c -o amd_l_2.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDINT -c amd_order.c -o amd_i_order.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDLONG -c amd_order.c -o amd_l_order.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDINT -c amd_control.c -o amd_i_control.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDLONG -c amd_control.c -o amd_l_control.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDINT -c amd_info.c -o amd_i_info.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDLONG -c amd_info.c -o amd_l_info.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../Include -I../../SuiteSparse_config  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o
ar -rucs ../../AMD.a amd_i_aat.o amd_l_aat.o amd_i_1.o amd_l_1.o amd_i_2.o amd_l_2.o amd_i_postorder.o amd_l_postorder.o amd_i_post_tree.o amd_l_post_tree.o amd_i_defaults.o amd_l_defaults.o amd_i_order.o amd_l_order.o amd_i_control.o amd_l_control.o amd_i_info.o amd_l_info.o amd_i_valid.o amd_l_valid.o amd_i_preprocess.o amd_l_preprocess.o amd_i_dump.o amd_l_dump.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DNTIMER  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c SuiteSparse_config.c -o SuiteSparse_config.o
ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
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 Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o packedMatrix.o unpackedMatrix.o sparse.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -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: -single_module is obsolete
ld: warning: -multiply_defined is obsolete
ld: warning: search path '/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0' not found
ld: warning: search path '/opt/gfortran/lib' not found
ld: library 'gfortran' not found
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [Matrix.so] Error 1
ERROR: compilation failed for package ‘Matrix’
* removing ‘/private/var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T/Rtmpvhn4LR/renv-use-libpath-752e191a6ad9/.renv/1/Matrix’
install of package 'Matrix' failed [error code 1]
Backtrace:
  1. renv::use(...)
  2. (function() {...
  3. renv::install(packages = remotes, library = library, prompt = FALSE)
  4. renv:::renv_install_impl(records)
  5. renv:::renv_install_staged(records)
     ...
  8. renv:::renv_install_package(record)
 10. renv:::renv_install_package_impl(record)
 11. renv:::r_cmd_install(package, path)
 12. renv:::r_exec_error(package, output, "install", status)
 13. renv:::abort(all)

Execution halted
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/MASS: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/.renv-sandbox: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/cluster: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/parallel: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/tools: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/methods: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/boot: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/datasets: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/nnet: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/tcltk: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/utils: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/stats4: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/rpart: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/lattice: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/nlme: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/splines: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/grDevices: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/class: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/mgcv: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/codetools: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/spatial: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/graphics: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/foreign: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/compiler: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/Matrix: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/KernSmooth: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/base: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/stats: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/survival: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox/grid: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR/renv-sandbox: Permission denied
rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmpvhn4LR: Permission denied
Bisaloo commented 10 months ago

I think the important line is:

ld: library 'gfortran' not found

Could you try one of the solution here please? https://fortran-lang.org/en/learn/os_setup/install_gfortran/#macos

Please reach out to me on slack or to any mac user close to you if the instructions on this page do not speak to you.

CarmenTamayo commented 10 months ago

Hi Hugo, thanks for your response, I followed the instructions to install gfortran, (from here https://github.com/fxcoudert/gfortran-for-macOS/releases), I restarted the session after but I'm still getting the error... maybe I've missed something

Bisaloo commented 10 months ago

We had a look at this today. #102 is not solving this issue as for some reason, the Matrix package is recompiled even for recent versions.

Digging a little bit more, we identified that the issue is that, even though it's installed, the gfortran compiler location is not detected properly and R is looking for it in the wrong place.

CarmenTamayo commented 10 months ago

For now I'm rendering the templates by disabling renv until a solution is found

Bisaloo commented 10 months ago

Could you try to see if this solves your issue: https://github.com/coatless-mac/macrtools?

CarmenTamayo commented 10 months ago

I followed the steps and installed macrtools, then restarted R and made sure I was using the latest version of {episoap}, then attempted to knit the transmissibility report, then it was stuck rendering on 5% [lockfile] for at least 30 mins, and then I received the following error message:

Quitting from lines 48-172 [lockfile] (Untitled.Rmd) Error: ! Error installing package 'sodium':

Execution halted rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/MASS: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/.renv-sandbox: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/cluster: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/parallel: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/tools: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/methods: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/boot: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/datasets: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/nnet: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/tcltk: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/utils: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/stats4: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/rpart: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/lattice: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/nlme: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/splines: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/grDevices: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/class: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/mgcv: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/codetools: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/spatial: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/graphics: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/foreign: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/compiler: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/Matrix: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/KernSmooth: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/base: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/stats: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/survival: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox/grid: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj/renv-sandbox: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//RtmpKXpLYj: Permission denied

Bisaloo commented 10 months ago

Hah, this is great news! We're making progress!

You're now missing another system dependency: libsodium. You can follow the instructions in the error message (brew install libsodium) to install it.

CarmenTamayo commented 10 months ago

Hah, this is great news! We're making progress!

You're now missing another system dependency: libsodium. You can follow the instructions in the error message (brew install libsodium) to install it.

Okay I did this and it seems to work now! I tried several times and I was getting an error at some points but it seems to not be happening anymore... Thank you!!! Hopefully things are okay now moving forward

CarmenTamayo commented 10 months ago

Just in case it's useful, I'm still getting this message even if the report is rendered:

[WARNING] Citeproc: citation Wallinga2007-hw not found

Output created: Untitled.html rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/MASS: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/.renv-sandbox: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/cluster: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/parallel: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/tools: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/methods: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/boot: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/datasets: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/nnet: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/tcltk: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/utils: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/stats4: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/rpart: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/lattice: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/nlme: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/splines: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/grDevices: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/class: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/mgcv: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/codetools: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/spatial: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/graphics: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/foreign: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/compiler: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/Matrix: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/KernSmooth: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/base: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/stats: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/survival: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox/grid: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL/renv-sandbox: Permission denied rm: /var/folders/m1/v1v927494mz7zfjcm_26598m0000gn/T//Rtmp8UKdTL: Permission denied

Bisaloo commented 8 months ago

Closing as solved. More details are available in a recent blog post: https://github.com/epiverse-trace/epiverse-trace.github.io/pull/154.