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

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"	4658
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4455
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4408
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 eiR on nebbiolo1

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

Version: 1.47.0

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

StartedAt: 2025-01-24 15:57:52 -0500 (Fri, 24 Jan 2025)

EndedAt: 2025-01-24 15:57:53 -0500 (Fri, 24 Jan 2025)

EllapsedTime: 1.1 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 eiR
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘eiR’ ...
** this is package ‘eiR’ version ‘1.47.0’
** 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    -fpic  -g -O2  -DR_NO_REMAP -c optimFunctions.cc -o optimFunctions.o
optimFunctions.cc: In function ‘SEXPREC* calcF(SEXP, SEXP, SEXP)’:
optimFunctions.cc:40:17: error: ‘length’ was not declared in this scope
   40 |         int k = length(xS); //length of result vector
      |                 ^~~~~~
In file included from optimFunctions.cc:2:
optimFunctions.cc:91:31: error: ‘allocVector’ was not declared in this scope; did you mean ‘Rf_allocVector’?
   91 |         SEXP result = PROTECT(allocVector(REALSXP, 1));
      |                               ^~~~~~~~~~~
/home/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
optimFunctions.cc: In function ‘SEXPREC* calcG(SEXP, SEXP, SEXP)’:
optimFunctions.cc:99:17: error: ‘length’ was not declared in this scope
   99 |         int k = length(xS); //length of result vector
      |                 ^~~~~~
optimFunctions.cc:102:31: error: ‘allocVector’ was not declared in this scope; did you mean ‘Rf_allocVector’?
  102 |         SEXP result = PROTECT(allocVector(REALSXP, k));
      |                               ^~~~~~~~~~~
/home/biocbuild/bbs-3.21-bioc/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:200: optimFunctions.o] Error 1
ERROR: compilation failed for package ‘eiR’
* removing ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/eiR’