Multiple platform build/check report for BioC 3.21 - INSTALL results for Harman on kunpeng2

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"	4752
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4464
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4415
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4370
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4279
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 Harman on kunpeng2

To the developers/maintainers of the Harman package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/Harman.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: Harman

Version: 1.35.0

Command: /home/biocbuild/R/R/bin/R CMD INSTALL Harman

StartedAt: 2024-12-11 19:32:34 -0000 (Wed, 11 Dec 2024)

EndedAt: 2024-12-11 19:32:54 -0000 (Wed, 11 Dec 2024)

EllapsedTime: 19.6 seconds

RetCode: 1

Status: ERROR

Command output

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###
### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL Harman
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘Harman’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_ARRAYALIGNEMT=4 -D_USE_RCPP=1 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include   `/home/biocbuild/R/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -I.  -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c Harman.cpp -o Harman.o
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/libs/Rcpp.so':
  /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.32' not found (required by /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/libs/Rcpp.so)
Calls: loadNamespace -> library.dynam -> dyn.load
Execution halted
Harman.cpp: In function ‘SEXPREC* HarmanMain(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
Harman.cpp:3008:3: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation]
 3008 |   else
      |   ^~~~
Harman.cpp:3022:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’
 3022 |     std::vector<unsigned int>    tr_std_tmp     = Rcpp::as<std::vector<unsigned int> >(tr) ;
      |     ^~~
In file included from Harman.cpp:182:
CSelectRandom.h: In instantiation of ‘std::vector<unsigned int>* CSelectRandom<T>::ReturnVectOf32bitIntegersInRange_CSTDLIB(size_t, size_t, size_t, size_t) [with T = double; size_t = long unsigned int]’:
Harman.cpp:1764:117:   required from here
CSelectRandom.h:943:20: warning: comparison of integer expressions of different signedness: ‘long long int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  943 |     while (currval < howManyIN)
      |            ~~~~~~~~^~~~~~~~~~~
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/libs/Rcpp.so':
  /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.32' not found (required by /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/libs/Rcpp.so)
Calls: loadNamespace -> library.dynam -> dyn.load
Execution halted
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o Harman.so Harman.o -L/home/biocbuild/R/R/lib -lR
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/libs/Rcpp.so':
  /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.32' not found (required by /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/libs/Rcpp.so)
Calls: loadNamespace -> library.dynam -> dyn.load
Execution halted
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-Harman/00new/Harman/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/libs/Rcpp.so':
  /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.32' not found (required by /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/libs/Rcpp.so)
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘Harman’
* removing ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Harman’
* restoring previous ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Harman’