Test Builds (Linux only) of a subset of BioC 3.21<BR>using R 4.5 (devel) + _R_USE_STRICT_R_HEADERS_=true + _R_CXX_USE_NO_REMAP_=true<BR>Report updated every 6 hours

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-22 r87265) -- "Unsuffered Consequences"	855
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 teran2

To the developers/maintainers of the microRNA package:
- 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/bioctesting/bbs-3.21-bioc-testing/R/bin/R CMD check --install=check:microRNA.install-out.txt --library=/home/bioctesting/bbs-3.21-bioc-testing/R/site-library --timings microRNA_1.65.0.tar.gz

StartedAt: 2024-11-12 09:02:49 -0500 (Tue, 12 Nov 2024)

EndedAt: 2024-11-12 09:02:56 -0500 (Tue, 12 Nov 2024)

EllapsedTime: 6.3 seconds

RetCode: 1

Status: ERROR

CheckDir: microRNA.Rcheck

Warnings: NA

Command output

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###
### Running command:
###
###   /home/bioctesting/bbs-3.21-bioc-testing/R/bin/R CMD check --install=check:microRNA.install-out.txt --library=/home/bioctesting/bbs-3.21-bioc-testing/R/site-library --timings microRNA_1.65.0.tar.gz
###
##############################################################################
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* using log directory ‘/media/volume/teran2_disk/bioctesting/bbs-3.21-bioc-testing/meat/microRNA.Rcheck’
* using R Under development (unstable) (2024-10-22 r87265)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘microRNA/DESCRIPTION’ ... OK
* this is package ‘microRNA’ version ‘1.65.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘microRNA’ can be installed ... ERROR
Installation failed.
See ‘/media/volume/teran2_disk/bioctesting/bbs-3.21-bioc-testing/meat/microRNA.Rcheck/00install.out’ for details.
* DONE

Status: 1 ERROR
See
  ‘/media/volume/teran2_disk/bioctesting/bbs-3.21-bioc-testing/meat/microRNA.Rcheck/00check.log’
for details.

Installation output

microRNA.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/bioctesting/bbs-3.21-bioc-testing/R/bin/R CMD INSTALL microRNA
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/bioctesting/bbs-3.21-bioc-testing/R/site-library’
* installing *source* package ‘microRNA’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
g++ -std=gnu++17 -I"/home/bioctesting/bbs-3.21-bioc-testing/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/bioctesting/bbs-3.21-bioc-testing/R/etc/Makeconf:202: longest_common_substring.o] Error 1
ERROR: compilation failed for package ‘microRNA’
* removing ‘/media/volume/teran2_disk/bioctesting/bbs-3.21-bioc-testing/R/site-library/microRNA’
* restoring previous ‘/media/volume/teran2_disk/bioctesting/bbs-3.21-bioc-testing/R/site-library/microRNA’

CHECK results for microRNA on teran2

Summary

Command output

Installation output

Tests output

Example timings