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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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

Package 978/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hummingbird 1.17.0  (landing page)
Eleni Adam
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/hummingbird
git_branch: devel
git_last_commit: 8a0488f
git_last_commit_date: 2024-10-29 10:49:11 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  ERROR    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    ERROR  skipped

BUILD results for hummingbird on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: hummingbird
Version: 1.17.0
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data hummingbird
StartedAt: 2024-12-23 23:48:12 -0000 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 23:48:18 -0000 (Mon, 23 Dec 2024)
EllapsedTime: 6.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data hummingbird
###
##############################################################################
##############################################################################


* 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -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/R/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/R/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
  388 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
make: *** [/home/biocbuild/R/R/etc/Makeconf:204: em.o] Error 1
ERROR: compilation failed for package ‘hummingbird’
* removing ‘/home/biocbuild/tmp/RtmpyA3qpI/Rinst315f8e4c78a762/hummingbird’
      -----------------------------------
ERROR: package installation failed