Multiple platform build/check report for BioC 3.21 - BUILD results for girafe on kjohnson3

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"	4396
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4110
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*

BUILD results for girafe on kjohnson3

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: 1.59.1

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data girafe

StartedAt: 2024-11-26 16:24:32 -0500 (Tue, 26 Nov 2024)

EndedAt: 2024-11-26 16:24:33 -0500 (Tue, 26 Nov 2024)

EllapsedTime: 1.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data girafe
###
##############################################################################
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* checking for file ‘girafe/DESCRIPTION’ ... OK
* preparing ‘girafe’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘girafe’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c coverage.cpp -o coverage.o
coverage.cpp:2:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
coverage.cpp:44:15: error: use of undeclared identifier 'length'
    int len = length(starts);
              ^
coverage.cpp:104:20: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'?
    PROTECT( res = allocVector( INTSXP, xxit * 2) );
                   ^~~~~~~~~~~
                   Rf_allocVector
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1078:10: note: 'Rf_allocVector' declared here
SEXP     Rf_allocVector(SEXPTYPE, R_xlen_t);
         ^
coverage.cpp:114:20: error: use of undeclared identifier 'allocVector'; did you mean 'Rf_allocVector'?
    PROTECT( dim = allocVector(INTSXP, 2));
                   ^~~~~~~~~~~
                   Rf_allocVector
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:388:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1078:10: note: 'Rf_allocVector' declared here
SEXP     Rf_allocVector(SEXPTYPE, R_xlen_t);
         ^
1 warning and 3 errors generated.
make: *** [coverage.o] Error 1
ERROR: compilation failed for package ‘girafe’
* removing ‘/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpMke4pa/Rinstde6b3c7eb5a6/girafe’
      -----------------------------------
ERROR: package installation failed