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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4748
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4459
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4349
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 girafe on nebbiolo1

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

Version: 1.59.0

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

StartedAt: 2024-11-24 15:25:04 -0500 (Sun, 24 Nov 2024)

EndedAt: 2024-11-24 15:25:05 -0500 (Sun, 24 Nov 2024)

EllapsedTime: 1.4 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 girafe
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘girafe’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c coverage.cpp -o coverage.o
coverage.cpp: In function ‘SEXPREC* girafe_coverage(SEXP, SEXP, SEXP, SEXP)’:
coverage.cpp:44:15: error: ‘length’ was not declared in this scope
   44 |     int len = length(starts);
      |               ^~~~~~
In file included from /home/biocbuild/bbs-3.21-bioc/R/include/Rdefines.h:41,
                 from coverage.cpp:8:
coverage.cpp:104:20: error: ‘allocVector’ was not declared in this scope; did you mean ‘Rf_allocVector’?
  104 |     PROTECT( res = allocVector( INTSXP, xxit * 2) );
      |                    ^~~~~~~~~~~
/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:202: coverage.o] Error 1
ERROR: compilation failed for package ‘girafe’
* removing ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/girafe’
* restoring previous ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/girafe’