Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-14 11:41 -0400 (Fri, 14 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4781 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4537 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4567 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4519 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R 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 2298/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
XNAString 1.15.0 (landing page) Marianna Plucinska
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | ERROR | skipped | ||||||||||
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. |
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 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL XNAString ### ############################################################################## ############################################################################## * 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’