Multiple platform build/check report for BioC 3.20 - INSTALL results for SCArray on teran2

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4451
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4417
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4456
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4489
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4436
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4435
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 SCArray on teran2

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

Version: 1.13.1

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL SCArray

StartedAt: 2024-09-26 16:52:07 -0400 (Thu, 26 Sep 2024)

EndedAt: 2024-09-26 16:52:08 -0400 (Thu, 26 Sep 2024)

EllapsedTime: 1.0 seconds

RetCode: 1

Status: ERROR

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL SCArray
###
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘SCArray’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c sc_main.cpp -o sc_main.o
In file included from sc_main.h:25,
                 from sc_main.cpp:20:
sc_main.cpp: In constructor ‘SparseMatrix::SparseMatrix(SEXP)’:
sc_main.cpp:37:33: error: ‘mkString’ was not declared in this scope; did you mean ‘Rf_mkString’?
   37 |         SEXP ii = GET_SLOT(mat, mkString("nzcoo"));
      |                                 ^~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:151:46: note: in definition of macro ‘GET_SLOT’
  151 | #define GET_SLOT(x, what)       R_do_slot(x, what)
      |                                              ^~~~
sc_main.cpp: In function ‘void get_mat_size(SEXP, int&, int&)’:
sc_main.cpp:79:41: error: ‘mkString’ was not declared in this scope; did you mean ‘Rf_mkString’?
   79 |                 SEXP dm = GET_SLOT(mat, mkString("dim"));
      |                                         ^~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:151:46: note: in definition of macro ‘GET_SLOT’
  151 | #define GET_SLOT(x, what)       R_do_slot(x, what)
      |                                              ^~~~
make: *** [/home/biocbuild/bbs-3.20-bioc/R/etc/Makeconf:202: sc_main.o] Error 1
ERROR: compilation failed for package ‘SCArray’
* removing ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/SCArray’
* restoring previous ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/SCArray’