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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:QUBIC.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings QUBIC_1.37.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/QUBIC.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘QUBIC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QUBIC’ version ‘1.37.0’
* 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 ‘QUBIC’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BCQU-class.Rd: biclust
  QUBIC.Rd: biclust
  qudiscretize.Rd: discretize
  quheatmap.Rd: heatmapBC
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.22-bioc/R/site-library/QUBIC/libs/QUBIC.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/QUBIC.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL QUBIC
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘QUBIC’ ...
** this is package ‘QUBIC’ version ‘1.37.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
   66 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
      |                                                                                                                                                                                                       ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c charset.cc -o charset.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c cluster.cc -o cluster.o
cluster.cc: In function ‘bool internal::check_seed(const Edge*, const std::vector<Block>&, std::size_t)’:
cluster.cc:132:19: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  132 |   return e->score >= b3;
      |          ~~~~~~~~~^~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c discretize.cc -o discretize.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c edge_list.cc -o edge_list.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c fib.c -o fib.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c fopen_matrix.cc -o fopen_matrix.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c qubic.cc -o qubic.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c rcpp_qubic.cpp -o rcpp_qubic.o
In file included from /home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from rcpp_qubic.cpp:18:
/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
   66 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
      |                                                                                                                                                                                                       ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c struct.cc -o struct.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o QUBIC.so RcppExports.o charset.o cluster.o discretize.o edge_list.o fib.o fopen_matrix.o qubic.o rcpp_qubic.o struct.o -fopenmp -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-QUBIC/00new/QUBIC/libs
** R
** 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 (QUBIC)