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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:CBN2Path.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings CBN2Path_1.1.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/CBN2Path.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘CBN2Path/DESCRIPTION’ ... OK
* this is package ‘CBN2Path’ version ‘1.1.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CBN2Path’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
  CITATION.cff
Most likely ‘inst/CITATION’ should be used instead.
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bcbn: no visible global function definition for ‘SnowParam’
bcbn: no visible binding for global variable ‘datasets’
ctcbn: no visible global function definition for ‘SnowParam’
generateGeomNodePoint: no visible binding for global variable ‘nodes’
generateGeomNodeText: no visible binding for global variable ‘nodes’
generateGgText: no visible binding for global variable ‘x’
generateGgText: no visible binding for global variable ‘y’
generateGgText: no visible binding for global variable ‘label’
generateMatrixGenotypes : f1 : <anonymous>: no visible global function
  definition for ‘combn’
hcbn: no visible global function definition for ‘SnowParam’
variableCapSize: no visible binding for global variable ‘edges’
variableCapSize: no visible binding for global variable ‘x’
variableCapSize: no visible binding for global variable ‘y’
visualizeCBNModel: no visible binding for global variable ‘name’
visualizeFitnessLandscape: no visible binding for global variable ‘x’
visualizeFitnessLandscape: no visible binding for global variable ‘y’
visualizeFitnessLandscape: no visible binding for global variable
  ‘name’
visualizeProbabilities: no visible binding for global variable ‘name’
Undefined global functions or variables:
  SnowParam combn datasets edges label name nodes x y
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
hcbnSingle              75.103  0.075  75.722
visualizeProbabilities  32.344  0.138  32.484
pathProbQuartetBCBN     31.069  0.693  31.763
bcbn                    15.086  9.552  24.641
jensenShannonDivergence  8.487  0.799   9.286
Predictability           7.620  0.367   7.988
pathProbQuartetRCBN      6.914  0.708   7.623
pathProbQuartetHCBN      5.328  0.624   5.952
pathProbQuartetCTCBN     5.020  0.585   5.605
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/CBN2Path.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL CBN2Path
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘CBN2Path’ ...
** this is package ‘CBN2Path’ version ‘1.1.4’
** using staged installation
checking for gcc... gcc -std=gnu2x
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc -std=gnu2x accepts -g... yes
checking for gcc -std=gnu2x option to enable C11 features... none needed
checking for gsl-config... /usr/bin/gsl-config
checking if GSL version >= 2.5... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/include -I.  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c bcbn.c -o bcbn.o
bcbn.c: In function ‘bcbn_write_poset’:
bcbn.c:228:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  228 |     for (j=0; j<n; j++)
      |     ^~~
bcbn.c:232:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  232 |       fprintf(output, "0 0\n");
      |       ^~~~~~~
bcbn.c: In function ‘bcbn_is_equal_int_matrix’:
bcbn.c:332:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  332 |     for (j=0; j<n; j++)
      |     ^~~
bcbn.c:336:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  336 |       return 1;
      |       ^~~~~~
bcbn.c: In function ‘bcbn_free_lattice_children’:
bcbn.c:433:7: warning: unused variable ‘i’ [-Wunused-variable]
  433 |   int i;
      |       ^
bcbn.c: In function ‘bcbn_print_genotype’:
bcbn.c:641:7: warning: unused variable ‘i’ [-Wunused-variable]
  641 |   int i;
      |       ^
bcbn.c: In function ‘bcbn_bfs_order_ideals’:
bcbn.c:691:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  691 |         for (j=0; j<lin_ext_size; j++)
      |         ^~~
bcbn.c:697:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  697 |           if (! is_in)  // add to linear extension:
      |           ^~
bcbn.c: In function ‘bcbn_hamming_distance’:
bcbn.c:794:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  794 |   for(i=0; i<n; i++)
      |   ^~~
bcbn.c:801:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  801 |     free(g);
      |     ^~~~
bcbn.c: In function ‘compute_all_cbn_prob’:
bcbn.c:1056:13: warning: unused variable ‘k’ [-Wunused-variable]
 1056 |   int i,j,c,k;
      |             ^
bcbn.c:1056:9: warning: unused variable ‘j’ [-Wunused-variable]
 1056 |   int i,j,c,k;
      |         ^
bcbn.c: In function ‘bcbn_reduce_to_cover_relations’:
bcbn.c:1212:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1212 |     for (j=0; j<n; j++)
      |     ^~~
bcbn.c:1219:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1219 |       while (empty(&q) == FALSE)
      |       ^~~~~
bcbn.c: In function ‘compute_likelihood’:
bcbn.c:1281:15: warning: unused variable ‘likelihood’ [-Wunused-variable]
 1281 |   long double likelihood, likelihood_d;
      |               ^~~~~~~~~~
bcbn.c: In function ‘relocate_theta_i’:
bcbn.c:1367:25: warning: variable ‘x’ set but not used [-Wunused-but-set-variable]
 1367 |   double alpha,beta,var,x;
      |                         ^
bcbn.c:1367:21: warning: unused variable ‘var’ [-Wunused-variable]
 1367 |   double alpha,beta,var,x;
      |                     ^~~
bcbn.c: In function ‘compute_theta_transition_prob’:
bcbn.c:1380:25: warning: variable ‘x’ set but not used [-Wunused-but-set-variable]
 1380 |   double alpha,beta,var,x;
      |                         ^
bcbn.c:1380:21: warning: unused variable ‘var’ [-Wunused-variable]
 1380 |   double alpha,beta,var,x;
      |                     ^~~
bcbn.c: In function ‘propose_new_cover_relation’:
bcbn.c:1449:11: warning: unused variable ‘k’ [-Wunused-variable]
 1449 |   int i,j,k,N_compatible,N_all_comp;
      |           ^
bcbn.c: In function ‘get_tp_for_new_cover_move’:
bcbn.c:1550:35: warning: unused variable ‘k’ [-Wunused-variable]
 1550 |   int i,j,N_all_comp,N_compatible,k;
      |                                   ^
bcbn.c:1550:22: warning: unused variable ‘N_compatible’ [-Wunused-variable]
 1550 |   int i,j,N_all_comp,N_compatible,k;
      |                      ^~~~~~~~~~~~
bcbn.c:1550:11: warning: variable ‘N_all_comp’ set but not used [-Wunused-but-set-variable]
 1550 |   int i,j,N_all_comp,N_compatible,k;
      |           ^~~~~~~~~~
bcbn.c: In function ‘relocate_epsilon’:
bcbn.c:1675:25: warning: unused variable ‘x’ [-Wunused-variable]
 1675 |   double alpha,beta,var,x;
      |                         ^
bcbn.c:1675:21: warning: unused variable ‘var’ [-Wunused-variable]
 1675 |   double alpha,beta,var,x;
      |                     ^~~
bcbn.c:1675:16: warning: unused variable ‘beta’ [-Wunused-variable]
 1675 |   double alpha,beta,var,x;
      |                ^~~~
bcbn.c:1675:10: warning: unused variable ‘alpha’ [-Wunused-variable]
 1675 |   double alpha,beta,var,x;
      |          ^~~~~
bcbn.c: In function ‘propose_new_bcbn_transitive_closure_relation’:
bcbn.c:1755:11: warning: unused variable ‘k’ [-Wunused-variable]
 1755 |   int i,j,k,N_compatible,N_all_comp;
      |           ^
bcbn.c: In function ‘propose_delete_bcbn_transitive_closure_relation’:
bcbn.c:1878:26: warning: variable ‘N_all_comp’ set but not used [-Wunused-but-set-variable]
 1878 |   int i,j,k,N_compatible,N_all_comp;
      |                          ^~~~~~~~~~
bcbn.c:1878:13: warning: unused variable ‘N_compatible’ [-Wunused-variable]
 1878 |   int i,j,k,N_compatible,N_all_comp;
      |             ^~~~~~~~~~~~
bcbn.c:1878:11: warning: unused variable ‘k’ [-Wunused-variable]
 1878 |   int i,j,k,N_compatible,N_all_comp;
      |           ^
bcbn.c: In function ‘get_tp_for_delete_bcbn_transitive_closure_relation_move’:
bcbn.c:1957:7: warning: unused variable ‘c’ [-Wunused-variable]
 1957 |   int c = 0;
      |       ^
bcbn.c:1946:26: warning: variable ‘N_all_comp’ set but not used [-Wunused-but-set-variable]
 1946 |   int i,j,k,N_compatible,N_all_comp;
      |                          ^~~~~~~~~~
bcbn.c:1946:13: warning: unused variable ‘N_compatible’ [-Wunused-variable]
 1946 |   int i,j,k,N_compatible,N_all_comp;
      |             ^~~~~~~~~~~~
bcbn.c:1946:11: warning: unused variable ‘k’ [-Wunused-variable]
 1946 |   int i,j,k,N_compatible,N_all_comp;
      |           ^
bcbn.c: In function ‘get_tp_for_new_bcbn_transitive_closure_relation_move’:
bcbn.c:2008:7: warning: unused variable ‘c’ [-Wunused-variable]
 2008 |   int c = 0;
      |       ^
bcbn.c:1997:26: warning: variable ‘N_all_comp’ set but not used [-Wunused-but-set-variable]
 1997 |   int i,j,k,N_compatible,N_all_comp;
      |                          ^~~~~~~~~~
bcbn.c:1997:13: warning: unused variable ‘N_compatible’ [-Wunused-variable]
 1997 |   int i,j,k,N_compatible,N_all_comp;
      |             ^~~~~~~~~~~~
bcbn.c:1997:11: warning: unused variable ‘k’ [-Wunused-variable]
 1997 |   int i,j,k,N_compatible,N_all_comp;
      |           ^
bcbn.c: In function ‘start_Exp_theta_MH’:
bcbn.c:2362:7: warning: unused variable ‘accepted’ [-Wunused-variable]
 2362 |   int accepted = 0;
      |       ^~~~~~~~
bcbn.c:2358:9: warning: unused variable ‘j’ [-Wunused-variable]
 2358 |   int i,j,k = 0;
      |         ^
bcbn.c:2358:7: warning: unused variable ‘i’ [-Wunused-variable]
 2358 |   int i,j,k = 0;
      |       ^
bcbn.c: In function ‘run_MH_sampler’:
bcbn.c:2620:22: warning: unused variable ‘MH_ratio’ [-Wunused-variable]
 2620 |   long double alpha, MH_ratio;
      |                      ^~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/include -I.  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ctcbn.c -o ctcbn.o
In file included from ctcbn.c:3:
ct-cbn.h: In function ‘print_int_array’:
ct-cbn.h:184:7: warning: unused variable ‘j’ [-Wunused-variable]
  184 |   int j;
      |       ^
ct-cbn.h: In function ‘write_poset’:
ct-cbn.h:274:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  274 |     for (j=1; j<=n; j++)
      |     ^~~
ct-cbn.h:278:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  278 |       fprintf(output, "0\n");
      |       ^~~~~~~
ct-cbn.h: In function ‘print_genotype’:
ct-cbn.h:803:7: warning: unused variable ‘i’ [-Wunused-variable]
  803 |   int i;
      |       ^
ct-cbn.h: In function ‘bfs_order_ideals’:
ct-cbn.h:853:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  853 |         for (j=0; j<lin_ext_size; j++)
      |         ^~~
ct-cbn.h:859:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  859 |           if (! is_in)  // add to linear extension:
      |           ^~
ct-cbn.h: In function ‘hamming_distance’:
ct-cbn.h:956:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  956 |   for(i=0; i<n; i++)
      |   ^~~
ct-cbn.h:963:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  963 |     free(g);
      |     ^~~~
ct-cbn.h: In function ‘is_after’:
ct-cbn.h:1198:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1198 |     for ( a=0; a<=M->n; a++ )
      |     ^~~
ct-cbn.h:1201:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1201 |       return 1;
      |       ^~~~~~
ct-cbn.h: In function ‘is_strict_after’:
ct-cbn.h:1211:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1211 |     for ( a=0; a<=M->n; a++ )
      |     ^~~
ct-cbn.h:1214:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1214 |       return 1;
      |       ^~~~~~
ct-cbn.h: In function ‘compute_all_exp’:
ct-cbn.h:1283: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
 1283 | #pragma omp parallel for private(i,c,k,j,g, all_pred_in_k, pred,l)
      | 
ct-cbn.h:1318:11: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1318 |           for (l = 0; l < m; l++)
      |           ^~~
ct-cbn.h:1346:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1346 |             Exp[pos][i] = censexp[pos][i][m-1];
      |             ^~~
ct-cbn.h: In function ‘EM_epsilon’:
ct-cbn.h:1440:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1440 |       for(i = 1; i < m; i++)
      |       ^~~
ct-cbn.h:1447:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1447 |         loglik_new += log (prob_tmp) * D[k].count;
      |         ^~~~~~~~~~
ct-cbn.h: In function ‘compute_loglik’:
ct-cbn.h:1471:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1471 |     for(i = 1; i < m; i++)
      |     ^~~
ct-cbn.h:1477:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1477 |       loglik[k] = log (prob_tmp) ;
      |       ^~~~~~
ct-cbn.h: In function ‘MLE’:
ct-cbn.h:1833:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1833 |     for (k=0; k<N_u; k++)
      |     ^~~
ct-cbn.h:1839:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1839 |       lambda[i] = (double) N / sum;
      |       ^~~~~~
ct-cbn.h: In function ‘EM’:
ct-cbn.h:1920:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 1920 |     for (k=0; k<N_u; k++)
      |     ^~~
ct-cbn.h:1939:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 1939 |       if (verbose)
      |       ^~
ct-cbn.h: In function ‘violation_map’:
ct-cbn.h:2488:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 2488 |   for (i=1; i<=n; i++)
      |   ^~~
ct-cbn.h:2502:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 2502 |     qsort(V, idx, sizeof(int *), compare_violation_pairs);  // small violators first
      |     ^~~~~
ct-cbn.h: In function ‘reduce_to_cover_relations’:
ct-cbn.h:2524:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 2524 |     for (j=1; j<=n; j++)
      |     ^~~
ct-cbn.h:2531:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 2531 |       while (empty(&q) == FALSE)
      |       ^~~~~
ct-cbn.h: In function ‘try_edge’:
ct-cbn.h:2741:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 2741 |     for(j=0;j<n*n;j++)
      |     ^~~
ct-cbn.h:2744:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 2744 |       R4[i] = c;
      |       ^~
ct-cbn.h:2784:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 2784 |             for(i=1;i<n+1;i++)
      |             ^~~
ct-cbn.h:2790:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 2790 |               if(c == 1)
      |               ^~
ct-cbn.h:2943:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 2943 |             for(i=1;i<n+1;i++)
      |             ^~~
ct-cbn.h:2949:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 2949 |               if(c == 1)
      |               ^~
ct-cbn.h:2721:17: warning: variable ‘alpha_new’ set but not used [-Wunused-but-set-variable]
 2721 |   double alpha, alpha_new;
      |                 ^~~~~~~~~
ct-cbn.h: In function ‘local_search’:
ct-cbn.h:3134:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 3134 |     for(j=1;j<=M->n;j++)
      |     ^~~
ct-cbn.h:3161:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 3161 |       print_double_matrix(loglik_next, M->n, M->n);
      |       ^~~~~~~~~~~~~~~~~~~
ct-cbn.h: In function ‘is_equal_int_matrix’:
ct-cbn.h:3196:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 3196 |     for (j=0; j<n; j++)
      |     ^~~
ct-cbn.h:3200:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
 3200 |       return 1;
      |       ^~~~~~
ct-cbn.h: In function ‘ML_path’:
ct-cbn.h:3305:7: warning: variable ‘mut_next’ set but not used [-Wunused-but-set-variable]
 3305 |   int mut_next, index_next;
      |       ^~~~~~~~
ctcbn.c: In function ‘ctcbn_’:
ctcbn.c:88:7: warning: unused variable ‘c’ [-Wunused-variable]
   88 |   int c = 0;
      |       ^
ctcbn.c:84:7: warning: unused variable ‘GPS’ [-Wunused-variable]
   84 |   int GPS = 0;
      |       ^~~
ctcbn.c:79:7: warning: unused variable ‘verbose’ [-Wunused-variable]
   79 |   int verbose = 0;
      |       ^~~~~~~
ctcbn.c: In function ‘hcbn_’:
ctcbn.c:319:7: warning: unused variable ‘c’ [-Wunused-variable]
  319 |   int c = 0;
      |       ^
ctcbn.c:314:7: warning: variable ‘N_iter’ set but not used [-Wunused-but-set-variable]
  314 |   int N_iter = 0;
      |       ^~~~~~
ctcbn.c:313:10: warning: unused variable ‘T’ [-Wunused-variable]
  313 |   double T = REAL(temp)[0];
      |          ^
ctcbn.c:308:7: warning: unused variable ‘t_flag’ [-Wunused-variable]
  308 |   int t_flag = 1;
      |       ^~~~~~
ctcbn.c:306:7: warning: unused variable ‘l_flag’ [-Wunused-variable]
  306 |   int l_flag = 0;
      |       ^~~~~~
ctcbn.c:305:7: warning: unused variable ‘gps_flag’ [-Wunused-variable]
  305 |   int gps_flag = 0;
      |       ^~~~~~~~
ctcbn.c:304:7: warning: variable ‘e_flag’ set but not used [-Wunused-but-set-variable]
  304 |   int e_flag = 0;
      |       ^~~~~~
ctcbn.c:303:7: warning: unused variable ‘f_flag’ [-Wunused-variable]
  303 |   int f_flag = 0;
      |       ^~~~~~
ctcbn.c:302:7: warning: unused variable ‘error_flag’ [-Wunused-variable]
  302 |   int error_flag = 0;
      |       ^~~~~~~~~~
ctcbn.c:468:10: warning: ‘rOutput’ may be used uninitialized [-Wmaybe-uninitialized]
  468 |   return char_to_sexp(rOutput);
      |          ^~~~~~~~~~~~~~~~~~~~~
ctcbn.c:320:9: note: ‘rOutput’ was declared here
  320 |   char* rOutput;
      |         ^~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/include -I.  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c init.c -o init.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/include -I.  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c queue.c -o queue.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o CBN2Path.so bcbn.o ctcbn.o init.o queue.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-CBN2Path/00new/CBN2Path/libs
** R
** 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 (CBN2Path)

R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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Type 'license()' or 'licence()' for distribution details.

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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(CBN2Path)
> 
> test_check("CBN2Path")
chain: 1
0
chain: 2
0
chain: 3
0
chain: 4
0
       V1                 V2                  V3                  V4         
 Min.   :0.003746   Min.   :8.709e-05   Min.   :0.0001679   Min.   :0.01433  
 1st Qu.:0.632615   1st Qu.:2.140e-01   1st Qu.:0.4297040   1st Qu.:0.09782  
 Median :0.773027   Median :3.970e-01   Median :0.5742621   Median :0.12688  
 Mean   :0.745951   Mean   :4.259e-01   Mean   :0.5741430   Mean   :0.13071  
 3rd Qu.:0.885558   3rd Qu.:6.197e-01   3rd Qu.:0.7222342   3rd Qu.:0.15936  
 Max.   :0.999931   Max.   :1.000e+00   Max.   :0.9999269   Max.   :0.33909  
       V5         
 Min.   :-14.408  
 1st Qu.: -8.775  
 Median : -8.382  
 Mean   : -8.502  
 3rd Qu.: -8.090  
 Max.   : -7.664  
       V1                V2                  V3                  V4         
 Min.   :0.04197   Min.   :6.689e-05   Min.   :0.0003083   Min.   :0.02052  
 1st Qu.:0.63655   1st Qu.:2.147e-01   1st Qu.:0.4299622   1st Qu.:0.09864  
 Median :0.77558   Median :4.027e-01   Median :0.5740555   Median :0.12708  
 Mean   :0.74923   Mean   :4.303e-01   Mean   :0.5717067   Mean   :0.13169  
 3rd Qu.:0.89117   3rd Qu.:6.234e-01   3rd Qu.:0.7177801   3rd Qu.:0.16065  
 Max.   :0.99998   Max.   :9.998e-01   Max.   :0.9999824   Max.   :0.39231  
       V5         
 Min.   :-15.224  
 1st Qu.: -8.770  
 Median : -8.378  
 Mean   : -8.499  
 3rd Qu.: -8.088  
 Max.   : -7.662  
       V1                V2                  V3                 V4         
 Min.   :0.01478   Min.   :0.0001166   Min.   :0.004316   Min.   :0.02010  
 1st Qu.:0.63026   1st Qu.:0.2157473   1st Qu.:0.430060   1st Qu.:0.09915  
 Median :0.77227   Median :0.3971418   Median :0.574555   Median :0.12622  
 Mean   :0.74564   Mean   :0.4285128   Mean   :0.571871   Mean   :0.13077  
 3rd Qu.:0.88742   3rd Qu.:0.6242420   3rd Qu.:0.716676   3rd Qu.:0.15853  
 Max.   :0.99997   Max.   :0.9998752   Max.   :0.999724   Max.   :0.35772  
       V5         
 Min.   :-12.662  
 1st Qu.: -8.770  
 Median : -8.376  
 Mean   : -8.499  
 3rd Qu.: -8.090  
 Max.   : -7.664  
       V1                V2                  V3                 V4         
 Min.   :0.02178   Min.   :1.312e-05   Min.   :0.005038   Min.   :0.01325  
 1st Qu.:0.63062   1st Qu.:2.139e-01   1st Qu.:0.431375   1st Qu.:0.09901  
 Median :0.77182   Median :3.983e-01   Median :0.574120   Median :0.12504  
 Mean   :0.74387   Mean   :4.293e-01   Mean   :0.572673   Mean   :0.13059  
 3rd Qu.:0.88816   3rd Qu.:6.272e-01   3rd Qu.:0.718528   3rd Qu.:0.15850  
 Max.   :1.00000   Max.   :9.999e-01   Max.   :0.999975   Max.   :0.36714  
       V5         
 Min.   :-12.495  
 1st Qu.: -8.764  
 Median : -8.379  
 Mean   : -8.495  
 3rd Qu.: -8.094  
 Max.   : -7.661  
[1] "Criterion: 1.00076105272267"
Potential scale reduction factors:

     Point est. Upper C.I.
[1,]          1          1
[2,]          1          1
[3,]          1          1
[4,]          1          1
[5,]          1          1

Multivariate psrf

1
[1] "##########################################"
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 9 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
 99.396   1.023 100.421