##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:cliqueMS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings cliqueMS_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/cliqueMS.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cliqueMS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cliqueMS’ version ‘1.23.0’
* package encoding: UTF-8
* 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 ‘cliqueMS’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
* 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 ... 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 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
* checking files in ‘vignettes’ ... OK
* checking examples ...

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


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘cliqueMS’ ...
** this is package ‘cliqueMS’ version ‘1.23.0’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fPIC  -g -O2  -Wall -Werror=format-security  -c findAnnotationR.cpp -o findAnnotationR.o
In file included from findAnnotationR.cpp:1:
annotationCliqueMSR.h: In function ‘std::vector<std::pair<double, double> > sortMass(annotData&, int, std::unordered_map<double, std::pair<double, double> >, int)’:
annotationCliqueMSR.h:440:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<double, double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  440 |     if(id < allM.size()) // not add more masses in case that for that feature are less than "n" top masses
      |        ~~~^~~~~~~~~~~~~
annotationCliqueMSR.h: In function ‘std::unordered_set<double> getTopScoringMasses(annotData&, int, rawadList, int, int, double)’:
annotationCliqueMSR.h:476:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<double, double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  476 |     if(id < allM.size()) // not add more masses in case that there are less than "n" top masses
      |        ~~~^~~~~~~~~~~~~
annotationCliqueMSR.h: In function ‘std::vector<int> sortAnnotations(std::unordered_map<int, Annotation>&, int)’:
annotationCliqueMSR.h:725:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<double, int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  725 |     if(id < allAn.size() )
      |        ~~~^~~~~~~~~~~~~~
annotationCliqueMSR.h: In function ‘double computeMaxScore(std::vector<double>&, int, double)’:
annotationCliqueMSR.h:739:24: warning: ‘completeroundscore’ may be used uninitialized [-Wmaybe-uninitialized]
  739 |     completeroundscore += *ritv;
      |     ~~~~~~~~~~~~~~~~~~~^~~~~~~~
annotationCliqueMSR.h:733:10: note: ‘completeroundscore’ was declared here
  733 |   double completeroundscore,remainderroundscore = 0;
      |          ^~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fPIC  -g -O2  -Wall -Werror=format-security  -c findCliquesR.cpp -o findCliquesR.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:24,
                 from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
                 from networkCliqueMSR.h:7,
                 from findCliquesR.cpp:2:
/home/biocbuild/R/R-4.5.0/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.")
      |                                                                                                                                                                                                       ^
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fPIC  -g -O2  -Wall -Werror=format-security  -c findIsotopesR.cpp -o findIsotopesR.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o cliqueMS.so RcppExports.o findAnnotationR.o findCliquesR.o findIsotopesR.o -fopenmp -lopenblas -lgfortran -lm -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-cliqueMS/00new/cliqueMS/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 (cliqueMS)