Multiple platform build/check report for BioC 3.21 - INSTALL results for XNAString on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4777
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4545
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4528
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4458
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*
INSTALL results for XNAString on nebbiolo1

To the developers/maintainers of the XNAString package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/XNAString.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.
raw results
Summary

Package: XNAString
Version: 1.15.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL XNAString
StartedAt: 2025-03-20 15:48:02 -0400 (Thu, 20 Mar 2025)
EndedAt: 2025-03-20 15:48:07 -0400 (Thu, 20 Mar 2025)
EllapsedTime: 5.1 seconds
RetCode: 1
Status: ERROR
Command output

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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL XNAString
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘XNAString’ ...
** this is package ‘XNAString’ version ‘1.15.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ViennaRNA/utils/cpu.c -o ViennaRNA/utils/cpu.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ViennaRNA/utils/msa_utils.c -o ViennaRNA/utils/msa_utils.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ViennaRNA/utils/structure_tree.c -o ViennaRNA/utils/structure_tree.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ViennaRNA/utils/higher_order_functions.c -o ViennaRNA/utils/higher_order_functions.o
ViennaRNA/utils/higher_order_functions.c: In function ‘zip_add_min_dispatcher’:
ViennaRNA/utils/higher_order_functions.c:116:1: warning: label ‘exec_fun_zip_add_min’ defined but not used [-Wunused-label]
  116 | exec_fun_zip_add_min:
      | ^~~~~~~~~~~~~~~~~~~~
ViennaRNA/utils/higher_order_functions.c:96:16: warning: unused variable ‘features’ [-Wunused-variable]
   96 |   unsigned int features = vrna_cpu_simd_capabilities();
      |                ^~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ViennaRNA/utils/string_utils.c -o ViennaRNA/utils/string_utils.o
ViennaRNA/utils/string_utils.c: In function ‘vrna_strjoin’:
ViennaRNA/utils/string_utils.c:391:36: warning: unused variable ‘num_strings’ [-Wunused-variable]
  391 |   size_t      n, offset, *lengths, num_strings, mem_strings, total_length;
      |                                    ^~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ViennaRNA/utils/structure_utils.c -o ViennaRNA/utils/structure_utils.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ViennaRNA/utils/utils.c -o ViennaRNA/utils/utils.o
ViennaRNA/utils/utils.c:60:15: warning: ‘scale2’ defined but not used [-Wunused-variable]
   60 | PRIVATE char  scale2[]  = "....,....5....,....6....,....7....,....8";
      |               ^~~~~~
ViennaRNA/utils/utils.c:59:15: warning: ‘scale1’ defined but not used [-Wunused-variable]
   59 | PRIVATE char  scale1[]  = "....,....1....,....2....,....3....,....4";
      |               ^~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ViennaRNA/constraints/SHAPE.c -o ViennaRNA/constraints/SHAPE.o
ViennaRNA/constraints/SHAPE.c: In function ‘vrna_constraints_add_SHAPE’:
ViennaRNA/constraints/SHAPE.c:202:10: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  202 |   method = shape_method;
      |          ^
ViennaRNA/constraints/SHAPE.c:206:51: warning: comparison between pointer and integer
  206 |   vrna_file_SHAPE_read(shape_file, length, method == 'W' ? 0 : -1, sequence, values);
      |                                                   ^~
ViennaRNA/constraints/SHAPE.c:208:14: warning: comparison between pointer and integer
  208 |   if (method == 'D') {
      |              ^~
ViennaRNA/constraints/SHAPE.c:210:21: warning: comparison between pointer and integer
  210 |   } else if (method == 'Z') {
      |                     ^~
ViennaRNA/constraints/SHAPE.c: In function ‘sc_parse_parameters’:
ViennaRNA/constraints/SHAPE.c:612:15: warning: unused variable ‘warning’ [-Wunused-variable]
  612 |   const char  warning[] = "SHAPE method parameters not recognized! Using default parameters!";
      |               ^~~~~~~
ViennaRNA/constraints/SHAPE.c: In function ‘vrna_constraints_add_SHAPE’:
ViennaRNA/constraints/SHAPE.c:209:11: warning: ‘p2’ may be used uninitialized [-Wmaybe-uninitialized]
  209 |     (void)vrna_sc_add_SHAPE_deigan(vc, (const double *)values, p1, p2, constraint_type);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ViennaRNA/constraints/SHAPE.c:196:15: note: ‘p2’ was declared here
  196 |   float   p1, p2;
      |               ^~
ViennaRNA/constraints/SHAPE.c:209:11: warning: ‘p1’ may be used uninitialized [-Wmaybe-uninitialized]
  209 |     (void)vrna_sc_add_SHAPE_deigan(vc, (const double *)values, p1, p2, constraint_type);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ViennaRNA/constraints/SHAPE.c:196:11: note: ‘p1’ was declared here
  196 |   float   p1, p2;
      |           ^~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ViennaRNA/constraints/constraints.c -o ViennaRNA/constraints/constraints.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ViennaRNA/constraints/soft.c -o ViennaRNA/constraints/soft.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ViennaRNA/constraints/hard.c -o ViennaRNA/constraints/hard.o
In file included from ViennaRNA/constraints/hard.c:37:
ViennaRNA/constraints/hc_depot.inc: In function ‘hc_depot_store_bp’:
ViennaRNA/constraints/hc_depot.inc:229:38: warning: unused variable ‘entry’ [-Wunused-variable]
  229 |   size_t    k, old_size, next_entry, entry;
      |                                      ^~~~~
ViennaRNA/constraints/hc_depot.inc:229:16: warning: unused variable ‘old_size’ [-Wunused-variable]
  229 |   size_t    k, old_size, next_entry, entry;
      |                ^~~~~~~~
ViennaRNA/constraints/hc_depot.inc:229:13: warning: unused variable ‘k’ [-Wunused-variable]
  229 |   size_t    k, old_size, next_entry, entry;
      |             ^
ViennaRNA/constraints/hc_depot.inc: In function ‘hc_depot_free’:
ViennaRNA/constraints/hc_depot.inc:263:25: warning: unused variable ‘n’ [-Wunused-variable]
  263 |   unsigned int    s, i, n;
      |                         ^
ViennaRNA/constraints/hard.c: In function ‘vrna_hc_update’:
ViennaRNA/constraints/hard.c:211:20: warning: variable ‘maxdist’ set but not used [-Wunused-but-set-variable]
  211 |   unsigned int  n, maxdist;
      |                    ^~~~~~~
ViennaRNA/constraints/hard.c: In function ‘vrna_hc_add_up_strand_batch’:
ViennaRNA/constraints/hard.c:386:46: warning: variable ‘sn’ set but not used [-Wunused-but-set-variable]
  386 |   unsigned int  i, strand, pos, n_pos, *ss, *sn;
      |                                              ^~
ViennaRNA/constraints/hard.c:386:41: warning: variable ‘ss’ set but not used [-Wunused-but-set-variable]
  386 |   unsigned int  i, strand, pos, n_pos, *ss, *sn;
      |                                         ^~
ViennaRNA/constraints/hard.c: In function ‘vrna_hc_add_bp_nonspecific’:
ViennaRNA/constraints/hard.c:437:17: warning: unused variable ‘p’ [-Wunused-variable]
  437 |   int           p;
      |                 ^
ViennaRNA/constraints/hard.c:436:49: warning: variable ‘se’ set but not used [-Wunused-but-set-variable]
  436 |   unsigned int  n, strand, actual_i, *sn, *ss, *se;
      |                                                 ^~
ViennaRNA/constraints/hard.c:436:17: warning: variable ‘n’ set but not used [-Wunused-but-set-variable]
  436 |   unsigned int  n, strand, actual_i, *sn, *ss, *se;
      |                 ^
ViennaRNA/constraints/hard.c: In function ‘vrna_hc_add_bp_strand’:
ViennaRNA/constraints/hard.c:476:48: warning: unused variable ‘l’ [-Wunused-variable]
  476 |   unsigned int  n, *sn, *se, *ss, n_i, n_j, k, l;
      |                                                ^
ViennaRNA/constraints/hard.c:476:45: warning: unused variable ‘k’ [-Wunused-variable]
  476 |   unsigned int  n, *sn, *se, *ss, n_i, n_j, k, l;
      |                                             ^
ViennaRNA/constraints/hard.c:476:31: warning: variable ‘ss’ set but not used [-Wunused-but-set-variable]
  476 |   unsigned int  n, *sn, *se, *ss, n_i, n_j, k, l;
      |                               ^~
ViennaRNA/constraints/hard.c:476:26: warning: variable ‘se’ set but not used [-Wunused-but-set-variable]
  476 |   unsigned int  n, *sn, *se, *ss, n_i, n_j, k, l;
      |                          ^~
ViennaRNA/constraints/hard.c:476:21: warning: variable ‘sn’ set but not used [-Wunused-but-set-variable]
  476 |   unsigned int  n, *sn, *se, *ss, n_i, n_j, k, l;
      |                     ^~
ViennaRNA/constraints/hard.c:476:17: warning: unused variable ‘n’ [-Wunused-variable]
  476 |   unsigned int  n, *sn, *se, *ss, n_i, n_j, k, l;
      |                 ^
ViennaRNA/constraints/hard.c: In function ‘vrna_hc_add_bp’:
ViennaRNA/constraints/hard.c:533:20: warning: unused variable ‘l’ [-Wunused-variable]
  533 |   int           k, l, ret;
      |                    ^
ViennaRNA/constraints/hard.c:533:17: warning: unused variable ‘k’ [-Wunused-variable]
  533 |   int           k, l, ret;
      |                 ^
ViennaRNA/constraints/hard.c:532:26: warning: variable ‘se’ set but not used [-Wunused-but-set-variable]
  532 |   unsigned int  n, *sn, *se, *ss, strand_i, strand_j, actual_i, actual_j;
      |                          ^~
ViennaRNA/constraints/hard.c:532:17: warning: variable ‘n’ set but not used [-Wunused-but-set-variable]
  532 |   unsigned int  n, *sn, *se, *ss, strand_i, strand_j, actual_i, actual_j;
      |                 ^
ViennaRNA/constraints/hard.c: In function ‘vrna_hc_free’:
ViennaRNA/constraints/hard.c:588:20: warning: unused variable ‘i’ [-Wunused-variable]
  588 |       unsigned int i;
      |                    ^
ViennaRNA/constraints/hard.c: In function ‘default_hc_up’:
ViennaRNA/constraints/hard.c:841:20: warning: unused variable ‘depot’ [-Wunused-variable]
  841 |   vrna_hc_depot_t *depot;
      |                    ^~~~~
ViennaRNA/constraints/hard.c: In function ‘prepare_hc_bp’:
ViennaRNA/constraints/hard.c:1011:25: warning: unused variable ‘ij’ [-Wunused-variable]
 1011 |   int             *idx, ij;
      |                         ^~
ViennaRNA/constraints/hard.c:1010:109: warning: variable ‘se’ set but not used [-Wunused-but-set-variable]
 1010 |   unsigned int    i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
      |                                                                                                             ^~
ViennaRNA/constraints/hard.c:1010:99: warning: variable ‘sn’ set but not used [-Wunused-but-set-variable]
 1010 |   unsigned int    i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
      |                                                                                                   ^~
ViennaRNA/constraints/hard.c:1010:88: warning: unused variable ‘t_end’ [-Wunused-variable]
 1010 |   unsigned int    i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
      |                                                                                        ^~~~~
ViennaRNA/constraints/hard.c:1010:79: warning: unused variable ‘t_start’ [-Wunused-variable]
 1010 |   unsigned int    i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
      |                                                                               ^~~~~~~
ViennaRNA/constraints/hard.c:1010:74: warning: unused variable ‘end’ [-Wunused-variable]
 1010 |   unsigned int    i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
      |                                                                          ^~~
ViennaRNA/constraints/hard.c:1010:67: warning: unused variable ‘start’ [-Wunused-variable]
 1010 |   unsigned int    i, j, k, p, q, n, actual_i, actual_j, strand_j, start, end, t_start, t_end, s, *sn, *ss, *se;
      |                                                                   ^~~~~
ViennaRNA/constraints/hard.c:1009:27: warning: unused variable ‘type’ [-Wunused-variable]
 1009 |   unsigned char   option, type;
      |                           ^~~~
ViennaRNA/constraints/hard.c: In function ‘populate_hc_bp’:
ViennaRNA/constraints/hard.c:1122:39: warning: unused variable ‘t2’ [-Wunused-variable]
 1122 |   unsigned char constraint, type, t1, t2;
      |                                       ^~
ViennaRNA/constraints/hard.c:1122:35: warning: unused variable ‘t1’ [-Wunused-variable]
 1122 |   unsigned char constraint, type, t1, t2;
      |                                   ^~
ViennaRNA/constraints/hard.c: In function ‘hc_update_up’:
ViennaRNA/constraints/hard.c:1887:23: warning: unused variable ‘u’ [-Wunused-variable]
 1887 |   unsigned int  i, n, u;
      |                       ^
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ViennaRNA/constraints/ligand.c -o ViennaRNA/constraints/ligand.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ViennaRNA/datastructures/basic_datastructures.c -o ViennaRNA/datastructures/basic_datastructures.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -Dlibcaf_core_shared_EXPORTS -I../src -I../src -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c ViennaRNA/datastructures/lists.c -o ViennaRNA/datastructures/lists.o
ViennaRNA/datastructures/lists.c:97:1: error: conflicting types for ‘lst_kill’; have ‘void(LIST *, void (*)(void *))’
   97 | lst_kill (LIST * l, void (*freeNode) (void *node))
      | ^~~~~~~~
In file included from ViennaRNA/datastructures/lists.c:33:
../src/ViennaRNA/datastructures/lists.h:58:6: note: previous declaration of ‘lst_kill’ with type ‘void(LIST *, void (*)(void))’
   58 | void lst_kill (LIST * l, void (*freeNode) ());
      |      ^~~~~~~~
ViennaRNA/datastructures/lists.c:284:1: error: conflicting types for ‘lst_mergesort’; have ‘void(LIST *, int (*)(void *, void *))’
  284 | lst_mergesort (LIST * l, int (*cmp_func) (void *, void *))
      | ^~~~~~~~~~~~~
../src/ViennaRNA/datastructures/lists.h:63:6: note: previous declaration of ‘lst_mergesort’ with type ‘void(LIST *, int (*)(void))’
   63 | void lst_mergesort (LIST * l, int (*cmp_func) ());
      |      ^~~~~~~~~~~~~
make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:202: ViennaRNA/datastructures/lists.o] Error 1
ERROR: compilation failed for package ‘XNAString’
* removing ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/XNAString’