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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 version 4.6.0 alpha (2026-03-30 r89742)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-03 01:46:07 UTC
* 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 13.3.0-6ubuntu2~24.04.1) 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              73.985  0.105  74.107
visualizeProbabilities  32.901  0.155  33.061
pathProbQuartetBCBN     30.564  0.718  31.283
bcbn                    15.060  9.726  24.789
jensenShannonDivergence  8.442  0.777   9.223
Predictability           7.633  0.567   8.204
pathProbQuartetRCBN      6.915  0.690   7.606
pathProbQuartetHCBN      5.389  0.590   5.979
pathProbQuartetCTCBN     5.102  0.561   5.663
* 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 13.3.0-6ubuntu2~24.04.1) 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/usr/local/lib -o CBN2Path.so bcbn.o ctcbn.o init.o queue.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm
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 version 4.6.0 alpha (2026-03-30 r89742)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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.   :0.001669   Min.   :0.0002604   Min.   :0.0008343   Min.   :0.02592  
 1st Qu.:0.558249   1st Qu.:0.3823447   1st Qu.:0.3668514   1st Qu.:0.12781  
 Median :0.727623   Median :0.5528186   Median :0.5440090   Median :0.15716  
 Mean   :0.699558   Mean   :0.5532902   Mean   :0.5449961   Mean   :0.16189  
 3rd Qu.:0.873012   3rd Qu.:0.7319520   3rd Qu.:0.7337388   3rd Qu.:0.19425  
 Max.   :0.999973   Max.   :0.9999704   Max.   :0.9999989   Max.   :0.37256  
       V5         
 Min.   :-16.426  
 1st Qu.:-10.289  
 Median : -9.918  
 Mean   :-10.016  
 3rd Qu.: -9.627  
 Max.   : -9.103  
       V1                 V2                  V3                  V4         
 Min.   :0.008095   Min.   :0.0002293   Min.   :0.0001473   Min.   :0.03159  
 1st Qu.:0.562343   1st Qu.:0.3802426   1st Qu.:0.3638874   1st Qu.:0.12728  
 Median :0.730276   Median :0.5520231   Median :0.5457703   Median :0.15883  
 Mean   :0.699552   Mean   :0.5499028   Mean   :0.5472379   Mean   :0.16310  
 3rd Qu.:0.871091   3rd Qu.:0.7260095   3rd Qu.:0.7393932   3rd Qu.:0.19403  
 Max.   :0.999986   Max.   :0.9999230   Max.   :0.9999908   Max.   :0.43817  
       V5         
 Min.   :-14.478  
 1st Qu.:-10.294  
 Median : -9.920  
 Mean   :-10.022  
 3rd Qu.: -9.634  
 Max.   : -9.106  
       V1                 V2                  V3                  V4         
 Min.   :0.002551   Min.   :0.0007197   Min.   :0.0001207   Min.   :0.02076  
 1st Qu.:0.560446   1st Qu.:0.3769686   1st Qu.:0.3708259   1st Qu.:0.12609  
 Median :0.726915   Median :0.5487181   Median :0.5500902   Median :0.15984  
 Mean   :0.697051   Mean   :0.5481080   Mean   :0.5478768   Mean   :0.16217  
 3rd Qu.:0.865447   3rd Qu.:0.7250815   3rd Qu.:0.7330259   3rd Qu.:0.19268  
 Max.   :0.999996   Max.   :0.9999994   Max.   :0.9999740   Max.   :0.38421  
       V5         
 Min.   :-14.359  
 1st Qu.:-10.299  
 Median : -9.930  
 Mean   :-10.029  
 3rd Qu.: -9.638  
 Max.   : -9.099  
       V1                 V2                  V3                  V4         
 Min.   :0.001137   Min.   :9.771e-05   Min.   :6.640e-06   Min.   :0.02914  
 1st Qu.:0.562214   1st Qu.:3.795e-01   1st Qu.:3.647e-01   1st Qu.:0.12568  
 Median :0.729371   Median :5.555e-01   Median :5.497e-01   Median :0.15884  
 Mean   :0.700806   Mean   :5.520e-01   Mean   :5.483e-01   Mean   :0.16240  
 3rd Qu.:0.871102   3rd Qu.:7.291e-01   3rd Qu.:7.403e-01   3rd Qu.:0.19506  
 Max.   :0.999929   Max.   :1.000e+00   Max.   :1.000e+00   Max.   :0.39494  
       V5         
 Min.   :-15.818  
 1st Qu.:-10.303  
 Median : -9.932  
 Mean   :-10.028  
 3rd Qu.: -9.636  
 Max.   : -9.117  
[1] "Criterion: 1.00141680557227"
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 
102.552   1.214 104.361