| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-13 11:32 -0500 (Fri, 13 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4863 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 292/2352 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CBN2Path 1.1.4 (landing page) William Choi-Kim
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| See other builds for CBN2Path in R Universe. | ||||||||||||||
|
To the developers/maintainers of the CBN2Path package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CBN2Path.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: CBN2Path |
| Version: 1.1.4 |
| 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 |
| StartedAt: 2026-02-12 22:00:48 -0500 (Thu, 12 Feb 2026) |
| EndedAt: 2026-02-12 22:19:40 -0500 (Thu, 12 Feb 2026) |
| EllapsedTime: 1132.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CBN2Path.Rcheck |
| Warnings: 0 |
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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 73.178 0.445 73.637
visualizeProbabilities 33.437 0.175 34.193
pathProbQuartetBCBN 31.402 0.741 32.143
bcbn 15.125 9.390 24.520
jensenShannonDivergence 8.516 0.847 9.364
Predictability 7.678 0.360 8.043
pathProbQuartetRCBN 7.234 0.743 7.977
pathProbQuartetHCBN 5.565 0.617 6.183
pathProbQuartetCTCBN 5.073 0.618 5.692
* 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.
CBN2Path.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL CBN2Path
###
##############################################################################
##############################################################################
* 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)
CBN2Path.Rcheck/tests/testthat.Rout
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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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. :0.1535 Min. :0.0001051 Min. :1.665e-05 Min. :0.0218
1st Qu.:0.8150 1st Qu.:0.2972538 1st Qu.:2.406e-01 1st Qu.:0.1117
Median :0.9015 Median :0.4525152 Median :4.039e-01 Median :0.1399
Mean :0.8692 Mean :0.4710250 Mean :4.342e-01 Mean :0.1442
3rd Qu.:0.9573 3rd Qu.:0.6280371 3rd Qu.:6.078e-01 3rd Qu.:0.1733
Max. :1.0000 Max. :0.9998738 Max. :9.998e-01 Max. :0.3611
V5
Min. :-14.287
1st Qu.: -8.745
Median : -8.338
Mean : -8.445
3rd Qu.: -8.024
Max. : -7.484
V1 V2 V3 V4
Min. :0.1375 Min. :0.0003193 Min. :0.000151 Min. :0.02953
1st Qu.:0.8153 1st Qu.:0.2948332 1st Qu.:0.245528 1st Qu.:0.11256
Median :0.9038 Median :0.4421250 Median :0.411870 Median :0.13994
Mean :0.8706 Mean :0.4648124 Mean :0.440802 Mean :0.14327
3rd Qu.:0.9589 3rd Qu.:0.6198933 3rd Qu.:0.618627 3rd Qu.:0.17077
Max. :1.0000 Max. :0.9999011 Max. :0.999896 Max. :0.33723
V5
Min. :-12.968
1st Qu.: -8.717
Median : -8.314
Mean : -8.428
3rd Qu.: -8.005
Max. : -7.484
V1 V2 V3 V4
Min. :0.01137 Min. :0.0003781 Min. :1.480e-06 Min. :0.02678
1st Qu.:0.81334 1st Qu.:0.2937386 1st Qu.:2.427e-01 1st Qu.:0.11294
Median :0.90239 Median :0.4467087 Median :4.072e-01 Median :0.13978
Mean :0.86996 Mean :0.4661829 Mean :4.408e-01 Mean :0.14331
3rd Qu.:0.95914 3rd Qu.:0.6217611 3rd Qu.:6.229e-01 3rd Qu.:0.17254
Max. :0.99998 Max. :0.9999503 Max. :9.999e-01 Max. :0.36653
V5
Min. :-12.725
1st Qu.: -8.727
Median : -8.312
Mean : -8.429
3rd Qu.: -8.008
Max. : -7.481
V1 V2 V3 V4
Min. :0.1174 Min. :0.0001202 Min. :1.492e-05 Min. :0.02959
1st Qu.:0.8130 1st Qu.:0.2934944 1st Qu.:2.383e-01 1st Qu.:0.11244
Median :0.9045 Median :0.4530175 Median :4.000e-01 Median :0.14000
Mean :0.8684 Mean :0.4714609 Mean :4.317e-01 Mean :0.14254
3rd Qu.:0.9605 3rd Qu.:0.6320090 3rd Qu.:6.032e-01 3rd Qu.:0.16786
Max. :1.0000 Max. :0.9998734 Max. :1.000e+00 Max. :0.35306
V5
Min. :-13.885
1st Qu.: -8.742
Median : -8.317
Mean : -8.437
3rd Qu.: -8.003
Max. : -7.482
[1] "Criterion: 1.00041051240342"
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
98.743 1.139 99.879
CBN2Path.Rcheck/CBN2Path-Ex.timings
| name | user | system | elapsed | |
| Base2IndVec | 0 | 0 | 0 | |
| Base2Indexing | 0.001 | 0.000 | 0.001 | |
| EdgeMarginalized | 0.009 | 0.004 | 0.013 | |
| Predictability | 7.678 | 0.360 | 8.043 | |
| Spock | 0.019 | 0.000 | 0.019 | |
| bcbn | 15.125 | 9.390 | 24.520 | |
| ctcbn | 0.854 | 0.079 | 0.933 | |
| ctcbnSingle | 0.186 | 0.003 | 0.189 | |
| generateData | 0.013 | 0.023 | 0.036 | |
| generateMatrixGenotypes | 0.000 | 0.001 | 0.002 | |
| generateTCGAMatrix | 0.001 | 0.000 | 0.001 | |
| genotypeFeasibility | 0 | 0 | 0 | |
| genotypeMatrixMutator | 0.001 | 0.001 | 0.001 | |
| getExamples | 0.004 | 0.000 | 0.004 | |
| getRawTCGAData | 0.073 | 0.005 | 0.628 | |
| hcbn | 2.160 | 0.238 | 2.398 | |
| hcbnSingle | 73.178 | 0.445 | 73.637 | |
| jensenShannonDivergence | 8.516 | 0.847 | 9.364 | |
| pathEdgeMapper | 0.002 | 0.000 | 0.002 | |
| pathNormalization | 0.010 | 0.002 | 0.011 | |
| pathProbCBN | 0.007 | 0.000 | 0.007 | |
| pathProbQuartetBCBN | 31.402 | 0.741 | 32.143 | |
| pathProbQuartetCTCBN | 5.073 | 0.618 | 5.692 | |
| pathProbQuartetHCBN | 5.565 | 0.617 | 6.183 | |
| pathProbQuartetRCBN | 7.234 | 0.743 | 7.977 | |
| pathProbSSWM | 0.003 | 0.000 | 0.003 | |
| pathwayCompatibilityQuartet | 0.005 | 0.000 | 0.005 | |
| pathwayFeasibility | 0.000 | 0.001 | 0.002 | |
| pathwayGenotypeCompatibility | 0.000 | 0.001 | 0.000 | |
| pathwayWeightingRCBN | 0.011 | 0.001 | 0.011 | |
| permutations | 0 | 0 | 0 | |
| posetWeightingRCBN | 0.012 | 0.001 | 0.012 | |
| readLambda | 0.003 | 0.001 | 0.004 | |
| readPattern | 0.023 | 0.051 | 0.074 | |
| readPoset | 0.004 | 0.001 | 0.005 | |
| readTime | 0.023 | 0.052 | 0.075 | |
| transitiveClosure | 0.001 | 0.001 | 0.002 | |
| visualizeCBNModel | 0.505 | 0.007 | 0.516 | |
| visualizeFitnessLandscape | 0.976 | 0.004 | 1.165 | |
| visualizeProbabilities | 33.437 | 0.175 | 34.193 | |