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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4756
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4475
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4435
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4390
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4383
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 microRNA on nebbiolo1

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

Version: 1.65.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL microRNA

StartedAt: 2025-01-03 15:11:28 -0500 (Fri, 03 Jan 2025)

EndedAt: 2025-01-03 15:11:29 -0500 (Fri, 03 Jan 2025)

EllapsedTime: 1.0 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 microRNA
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘microRNA’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c longest_common_substring.cpp -o longest_common_substring.o
longest_common_substring.cpp: In function ‘SEXPREC* longest_common_substring(SEXP)’:
longest_common_substring.cpp:55:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’} [-Wsign-compare]
   55 |         if (i == len[index] - 1) { // ignore null termination character
      |             ~~^~~~~~~~~~~~~~~~~
longest_common_substring.cpp:87:35: error: ‘mkCharLen’ was not declared in this scope; did you mean ‘Rf_mkCharLen’?
   87 |         SET_STRING_ELT(result, i, mkCharLen(found[i], lcs_len));
      |                                   ^~~~~~~~~
      |                                   Rf_mkCharLen
make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:202: longest_common_substring.o] Error 1
ERROR: compilation failed for package ‘microRNA’
* removing ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/microRNA’
* restoring previous ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/microRNA’