Multiple platform build/check report for BioC 3.21 - BUILD results for hummingbird 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"	4742
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4456
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 hummingbird on nebbiolo1

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

Version: 1.17.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data hummingbird

StartedAt: 2024-11-20 17:31:08 -0500 (Wed, 20 Nov 2024)

EndedAt: 2024-11-20 17:31:12 -0500 (Wed, 20 Nov 2024)

EllapsedTime: 4.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data hummingbird
###
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* checking for file ‘hummingbird/DESCRIPTION’ ... OK
* preparing ‘hummingbird’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘hummingbird’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c em.cpp -o em.o
em.cpp: In function ‘SEXPREC* hummingbirdEMinternal(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
em.cpp:30:28: error: ‘asReal’ was not declared in this scope
   30 |                 bin_size = asReal(binSize);
      |                            ^~~~~~
em.cpp:36:31: error: ‘getAttrib’ was not declared in this scope; did you mean ‘Rf_getAttrib’?
   36 |         SEXP S_dim_matrices = getAttrib(normM, R_DimSymbol);
      |                               ^~~~~~~~~
      |                               Rf_getAttrib
em.cpp:146:33: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
  146 |                                 error("Error allocating memory.\n");
      |                                 ^~~~~
      |                                 perror
em.cpp:151:33: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
  151 |                                 error("Error allocating memory.\n");
      |                                 ^~~~~
      |                                 perror
em.cpp:156:33: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
  156 |                                 error("Error allocating memory.\n");
      |                                 ^~~~~
      |                                 perror
em.cpp:161:33: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
  161 |                                 error("Error allocating memory.\n");
      |                                 ^~~~~
      |                                 perror
em.cpp:166:33: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
  166 |                                 error("Error allocating memory.\n");
      |                                 ^~~~~
      |                                 perror
em.cpp:171:33: error: ‘error’ was not declared in this scope; did you mean ‘perror’?
  171 |                                 error("Error allocating memory.\n");
      |                                 ^~~~~
      |                                 perror
In file included from utils.h:2,
                 from em.cpp:1:
em.cpp:799:29: error: ‘allocMatrix’ was not declared in this scope; did you mean ‘Rf_allocMatrix’?
  799 |         SEXP S_em = PROTECT(allocMatrix(INTSXP, full_bins, 4));
      |                             ^~~~~~~~~~~
/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)
      |                                    ^
em.cpp:815:30: error: ‘mkNamed’ was not declared in this scope; did you mean ‘Rf_mkNamed’?
  815 |         SEXP S_res = PROTECT(mkNamed(VECSXP, names));
      |                              ^~~~~~~
/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: em.o] Error 1
ERROR: compilation failed for package ‘hummingbird’
* removing ‘/tmp/RtmpbwKycK/Rinstb9540379e38e8/hummingbird’
      -----------------------------------
ERROR: package installation failed