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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CBN2Path.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CBN2Path_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CBN2Path.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.0.0’
* 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 ... NOTE
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              73.654  0.082  73.737
visualizeProbabilities  31.474  0.104  31.579
pathProbQuartetBCBN     30.596  0.373  30.970
bcbn                    14.502  1.243  15.746
jensenShannonDivergence  8.566  0.484   9.050
Predictability           7.392  0.327   7.720
pathProbQuartetRCBN      7.013  0.268   7.281
pathProbQuartetHCBN      5.341  0.231   5.572
pathProbQuartetCTCBN     4.938  0.209   5.147
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/CBN2Path.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL CBN2Path
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘CBN2Path’ ...
** this is package ‘CBN2Path’ version ‘1.0.0’
** 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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-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 version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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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.   :0.09955   Min.   :0.02806   Min.   :0.0000354   Min.   :0.02271  
 1st Qu.:0.75751   1st Qu.:0.63612   1st Qu.:0.1078100   1st Qu.:0.09385  
 Median :0.86409   Median :0.76618   Median :0.2126272   Median :0.11852  
 Mean   :0.83139   Mean   :0.74503   Mean   :0.2424107   Mean   :0.12215  
 3rd Qu.:0.93676   3rd Qu.:0.88006   3rd Qu.:0.3439002   3rd Qu.:0.14663  
 Max.   :0.99998   Max.   :0.99998   Max.   :0.9706468   Max.   :0.32417  
       V5         
 Min.   :-12.090  
 1st Qu.: -7.343  
 Median : -6.932  
 Mean   : -7.062  
 3rd Qu.: -6.644  
 Max.   : -6.234  
       V1                V2                V3                  V4         
 Min.   :0.09252   Min.   :0.02473   Min.   :2.197e-05   Min.   :0.02305  
 1st Qu.:0.75397   1st Qu.:0.63456   1st Qu.:1.065e-01   1st Qu.:0.09517  
 Median :0.86241   Median :0.77052   Median :2.095e-01   Median :0.11946  
 Mean   :0.82917   Mean   :0.74461   Mean   :2.394e-01   Mean   :0.12322  
 3rd Qu.:0.93649   3rd Qu.:0.87955   3rd Qu.:3.398e-01   3rd Qu.:0.14832  
 Max.   :0.99999   Max.   :0.99997   Max.   :9.875e-01   Max.   :0.34472  
       V5         
 Min.   :-11.783  
 1st Qu.: -7.342  
 Median : -6.937  
 Mean   : -7.065  
 3rd Qu.: -6.648  
 Max.   : -6.232  
       V1                V2                V3                  V4         
 Min.   :0.07529   Min.   :0.02952   Min.   :5.882e-05   Min.   :0.01960  
 1st Qu.:0.75587   1st Qu.:0.63640   1st Qu.:1.056e-01   1st Qu.:0.09409  
 Median :0.86397   Median :0.76690   Median :2.089e-01   Median :0.11913  
 Mean   :0.83147   Mean   :0.74246   Mean   :2.405e-01   Mean   :0.12293  
 3rd Qu.:0.94029   3rd Qu.:0.87425   3rd Qu.:3.419e-01   3rd Qu.:0.14739  
 Max.   :0.99999   Max.   :0.99988   Max.   :9.970e-01   Max.   :0.34826  
       V5         
 Min.   :-11.286  
 1st Qu.: -7.361  
 Median : -6.943  
 Mean   : -7.067  
 3rd Qu.: -6.636  
 Max.   : -6.237  
       V1               V2               V3                  V4         
 Min.   :0.0113   Min.   :0.0644   Min.   :0.0000431   Min.   :0.02101  
 1st Qu.:0.7583   1st Qu.:0.6398   1st Qu.:0.1063282   1st Qu.:0.09159  
 Median :0.8655   Median :0.7706   Median :0.2083502   Median :0.11611  
 Mean   :0.8330   Mean   :0.7469   Mean   :0.2365291   Mean   :0.12064  
 3rd Qu.:0.9389   3rd Qu.:0.8797   3rd Qu.:0.3344923   3rd Qu.:0.14525  
 Max.   :1.0000   Max.   :1.0000   Max.   :0.9923146   Max.   :0.31310  
       V5         
 Min.   :-11.599  
 1st Qu.: -7.345  
 Median : -6.933  
 Mean   : -7.065  
 3rd Qu.: -6.643  
 Max.   : -6.238  
[1] "Criterion: 1.00069728869605"
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 
100.501   0.972 101.462