Multiple platform build/check report for BioC 3.21 - CHECK results for microRNA on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4661
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4457
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4468
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4421
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4411
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*

CHECK results for microRNA on palomino7

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: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:microRNA.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings microRNA_1.65.0.tar.gz

StartedAt: 2025-01-29 02:35:40 -0500 (Wed, 29 Jan 2025)

EndedAt: 2025-01-29 02:35:46 -0500 (Wed, 29 Jan 2025)

EllapsedTime: 6.0 seconds

RetCode: 1

Status: ERROR

CheckDir: microRNA.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:microRNA.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings microRNA_1.65.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/microRNA.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'microRNA/DESCRIPTION' ... OK
* this is package 'microRNA' version '1.65.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'microRNA' can be installed ... ERROR
Installation failed.
See 'E:/biocbuild/bbs-3.21-bioc/meat/microRNA.Rcheck/00install.out' for details.
* DONE

Status: 1 ERROR
See
  'E:/biocbuild/bbs-3.21-bioc/meat/microRNA.Rcheck/00check.log'
for details.

Installation output

microRNA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL microRNA
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'microRNA' ...
** this is package 'microRNA' version '1.65.0'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -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 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: *** [E:/biocbuild/bbs-3.21-bioc/R/etc/x64/Makeconf:296: longest_common_substring.o] Error 1
ERROR: compilation failed for package 'microRNA'
* removing 'E:/biocbuild/bbs-3.21-bioc/R/library/microRNA'

CHECK results for microRNA on palomino7

Summary

Command output

Installation output

Tests output

Example timings