Multiple platform build/check report for BioC 3.20 - CHECK results for messina on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4481
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4479
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4359
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4539
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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*

CHECK 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: 1.42.0

Command: /home/biocbuild/R/R/bin/R CMD check --install=check:messina.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings messina_1.42.0.tar.gz

StartedAt: 2024-11-20 09:36:23 -0000 (Wed, 20 Nov 2024)

EndedAt: 2024-11-20 09:39:48 -0000 (Wed, 20 Nov 2024)

EllapsedTime: 204.3 seconds

RetCode: 0

Status: WARNINGS

CheckDir: messina.Rcheck

Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:messina.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings messina_1.42.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/messina.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘messina/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘messina’ version ‘1.42.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘messina’ can be installed ... WARNING
Found the following significant warnings:
  crossval.cpp:229:40: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:230:40: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:231:40: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:238:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:239:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:240:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:246:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:247:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:248:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:254:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:255:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:256:32: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:268:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:269:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  crossval.cpp:270:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  messinaExtern.cpp:138:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  messinaExtern.cpp:139:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  messinaExtern.cpp:86:24: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  messinaExtern.cpp:92:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/messina.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
messina: no visible binding for global variable ‘Biobase’
messinaSurv: no visible binding for global variable ‘Biobase’
Undefined global functions or variables:
  Biobase
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                        user system elapsed
plot-MessinaSurvResult-missing-method 69.005  0.368  69.516
messinaSurv                           55.454  0.152  55.732
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/messina.Rcheck/00check.log’
for details.

Installation output

messina.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL messina
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘messina’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Classifier.cpp -o Classifier.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Data.cpp -o Data.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -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)
      |                                            ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c errors.cpp -o errors.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c init.cpp -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -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)
      |                                                   ^
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/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-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/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)

Tests output

Example timings

messina.Rcheck/messina-Ex.timings

name	user	system	elapsed
messina	1.954	0.064	2.032
messinaDE	1.781	0.012	1.797
messinaSurv	55.454	0.152	55.732
messinaTopResults	1.026	0.027	1.056
plot-MessinaClassResult-missing-method	2.910	0.024	2.938
plot-MessinaSurvResult-missing-method	69.005	0.368	69.516