Multiple platform build/check report for BioC 3.21 - INSTALL results for messina 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"	4754
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4472
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4426
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4381
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R 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*

INSTALL results for messina on kunpeng2

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

Version: 1.43.0

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

StartedAt: 2024-12-23 20:15:32 -0000 (Mon, 23 Dec 2024)

EndedAt: 2024-12-23 20:16:03 -0000 (Mon, 23 Dec 2024)

EllapsedTime: 30.9 seconds

RetCode: 0

Status: OK

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL messina
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘messina’ ...
** 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 Classifier.cpp -o Classifier.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 Data.cpp -o Data.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 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 crossval.cpp -o crossval.o
crossval.cpp: In function ‘STATUS CrossVal::cv(int32_t, uint16_t, Classifier&, Result*, bool, bool)’:
crossval.cpp:229:40: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  229 |                                 delete train_indices;
      |                                        ^~~~~~~~~~~~~
crossval.cpp:184:52: note: returned from ‘void* operator new [](std::size_t)’
  184 |         if ((train_indices = new int32_t[train_size]) == NULL)
      |                                                    ^
crossval.cpp:230:40: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  230 |                                 delete test_indices;
      |                                        ^~~~~~~~~~~~
crossval.cpp:187:50: note: returned from ‘void* operator new [](std::size_t)’
  187 |         if ((test_indices = new int32_t[test_size]) == NULL)
      |                                                  ^
crossval.cpp:231:40: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  231 |                                 delete in_test_set;
      |                                        ^~~~~~~~~~~
crossval.cpp:193:44: note: returned from ‘void* operator new [](std::size_t)’
  193 |         if ((in_test_set = new bool[n_samps]) == NULL)
      |                                            ^
crossval.cpp:238:32: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  238 |                         delete train_indices;
      |                                ^~~~~~~~~~~~~
crossval.cpp:184:52: note: returned from ‘void* operator new [](std::size_t)’
  184 |         if ((train_indices = new int32_t[train_size]) == NULL)
      |                                                    ^
crossval.cpp:239:32: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  239 |                         delete test_indices;
      |                                ^~~~~~~~~~~~
crossval.cpp:187:50: note: returned from ‘void* operator new [](std::size_t)’
  187 |         if ((test_indices = new int32_t[test_size]) == NULL)
      |                                                  ^
crossval.cpp:240:32: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  240 |                         delete in_test_set;
      |                                ^~~~~~~~~~~
crossval.cpp:193:44: note: returned from ‘void* operator new [](std::size_t)’
  193 |         if ((in_test_set = new bool[n_samps]) == NULL)
      |                                            ^
crossval.cpp:246:32: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  246 |                         delete train_indices;
      |                                ^~~~~~~~~~~~~
crossval.cpp:184:52: note: returned from ‘void* operator new [](std::size_t)’
  184 |         if ((train_indices = new int32_t[train_size]) == NULL)
      |                                                    ^
crossval.cpp:247:32: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  247 |                         delete test_indices;
      |                                ^~~~~~~~~~~~
crossval.cpp:187:50: note: returned from ‘void* operator new [](std::size_t)’
  187 |         if ((test_indices = new int32_t[test_size]) == NULL)
      |                                                  ^
crossval.cpp:248:32: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  248 |                         delete in_test_set;
      |                                ^~~~~~~~~~~
crossval.cpp:193:44: note: returned from ‘void* operator new [](std::size_t)’
  193 |         if ((in_test_set = new bool[n_samps]) == NULL)
      |                                            ^
crossval.cpp:254:32: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  254 |                         delete train_indices;
      |                                ^~~~~~~~~~~~~
crossval.cpp:184:52: note: returned from ‘void* operator new [](std::size_t)’
  184 |         if ((train_indices = new int32_t[train_size]) == NULL)
      |                                                    ^
crossval.cpp:255:32: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  255 |                         delete test_indices;
      |                                ^~~~~~~~~~~~
crossval.cpp:187:50: note: returned from ‘void* operator new [](std::size_t)’
  187 |         if ((test_indices = new int32_t[test_size]) == NULL)
      |                                                  ^
crossval.cpp:256:32: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  256 |                         delete in_test_set;
      |                                ^~~~~~~~~~~
crossval.cpp:193:44: note: returned from ‘void* operator new [](std::size_t)’
  193 |         if ((in_test_set = new bool[n_samps]) == NULL)
      |                                            ^
crossval.cpp:268:16: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  268 |         delete train_indices;
      |                ^~~~~~~~~~~~~
crossval.cpp:184:52: note: returned from ‘void* operator new [](std::size_t)’
  184 |         if ((train_indices = new int32_t[train_size]) == NULL)
      |                                                    ^
crossval.cpp:269:16: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  269 |         delete test_indices;
      |                ^~~~~~~~~~~~
crossval.cpp:187:50: note: returned from ‘void* operator new [](std::size_t)’
  187 |         if ((test_indices = new int32_t[test_size]) == NULL)
      |                                                  ^
crossval.cpp:270:16: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  270 |         delete in_test_set;
      |                ^~~~~~~~~~~
crossval.cpp:193:44: note: returned from ‘void* operator new [](std::size_t)’
  193 |         if ((in_test_set = new bool[n_samps]) == NULL)
      |                                            ^
/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 errors.cpp -o errors.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 init.cpp -o init.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 messinaExtern.cpp -o messinaExtern.o
messinaExtern.cpp: In function ‘STATUS convertRMatrix2Data(Rcpp::NumericMatrix&, Rcpp::LogicalVector&, Data&)’:
messinaExtern.cpp:138:16: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  138 |         delete exprs_array;
      |                ^~~~~~~~~~~
messinaExtern.cpp:115:61: note: returned from ‘void* operator new [](std::size_t)’
  115 |         if ((exprs_array = new uint16_t[n_probes * n_samples]) == NULL)
      |                                                             ^
messinaExtern.cpp:139:16: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  139 |         delete class_array;
      |                ^~~~~~~~~~~
messinaExtern.cpp:119:46: note: returned from ‘void* operator new [](std::size_t)’
  119 |         if ((class_array = new bool[n_samples]) == NULL)
      |                                              ^
messinaExtern.cpp: In function ‘Rcpp::List messinaC(Rcpp::NumericMatrix, Rcpp::LogicalVector, uint32_t, uint32_t, float, float, bool, bool)’:
messinaExtern.cpp:86:24: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
   86 |                 delete results;
      |                        ^~~~~~~
messinaExtern.cpp:78:51: note: returned from ‘void* operator new [](std::size_t)’
   78 |         if ((results = new Result[data.getNGenes()]) == NULL)
      |                                                   ^
messinaExtern.cpp:92:16: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
   92 |         delete results;
      |                ^~~~~~~
messinaExtern.cpp:78:51: note: returned from ‘void* operator new [](std::size_t)’
   78 |         if ((results = new Result[data.getNGenes()]) == NULL)
      |                                                   ^
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o messina.so Classifier.o Data.o RcppExports.o crossval.o errors.o init.o messinaExtern.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-messina/00new/messina/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (messina)