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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:microRNA.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings microRNA_1.65.1.tar.gz
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/microRNA.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘microRNA/DESCRIPTION’ ... OK
* this is package ‘microRNA’ version ‘1.65.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘microRNA’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data      5.4Mb
    extdata   2.0Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Fatal error: cannot create 'R_TempDir'

Found the following possibly unsafe calls:
Fatal error: cannot create 'R_TempDir'
* checking Rd files ... WARNING
RNA2DNA.Rd: Sections \title, and \name must exist and be unique in Rd files
get_selfhyb_subseq.Rd: Sections \title, and \name must exist and be unique in Rd files
hsSeqs.Rd: Sections \title, and \name must exist and be unique in Rd files
hsTargets.Rd: Sections \title, and \name must exist and be unique in Rd files
matchSeeds.Rd: Sections \title, and \name must exist and be unique in Rd files
mmSeqs.Rd: Sections \title, and \name must exist and be unique in Rd files
mmTargets.Rd: Sections \title, and \name must exist and be unique in Rd files
s3utr.Rd: Sections \title, and \name must exist and be unique in Rd files
seedRegions.Rd: Sections \title, and \name must exist and be unique in Rd files
problems found in ‘RNA2DNA.Rd’, ‘get_selfhyb_subseq.Rd’, ‘hsSeqs.Rd’, ‘hsTargets.Rd’, ‘matchSeeds.Rd’, ‘mmSeqs.Rd’, ‘mmTargets.Rd’, ‘s3utr.Rd’, ‘seedRegions.Rd’
* checking Rd metadata ... NOTE
Fatal error: cannot create 'R_TempDir'
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/microRNA.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL microRNA
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘microRNA’ ...
** this is package ‘microRNA’ version ‘1.65.1’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -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
      |             ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib -o microRNA.so longest_common_substring.o
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-microRNA/00new/microRNA/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (microRNA)