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This page was generated on 2025-03-14 11:41 -0400 (Fri, 14 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4781
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4537
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4567
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4519
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4451
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 2298/2309HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XNAString 1.15.0  (landing page)
Marianna Plucinska
Snapshot Date: 2025-03-13 13:40 -0400 (Thu, 13 Mar 2025)
git_url: https://git.bioconductor.org/packages/XNAString
git_branch: devel
git_last_commit: 6cd7edb
git_last_commit_date: 2024-10-29 11:00:11 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  ERROR    ERROR  skipped

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: 2025-03-13 15:47:35 -0400 (Thu, 13 Mar 2025)
EndedAt: 2025-03-13 15:47:40 -0400 (Thu, 13 Mar 2025)
EllapsedTime: 5.3 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  -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  -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  -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  -c ViennaRNA/utils/higher_order_functions.c -o ViennaRNA/utils/higher_order_functions.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  -c ViennaRNA/utils/string_utils.c -o ViennaRNA/utils/string_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  -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  -c ViennaRNA/utils/utils.c -o ViennaRNA/utils/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  -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') {
      |                     ^~
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  -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  -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  -c ViennaRNA/constraints/hard.c -o ViennaRNA/constraints/hard.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  -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  -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  -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:201: ViennaRNA/datastructures/lists.o] Error 1
ERROR: compilation failed for package ‘XNAString’
* removing ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/XNAString’