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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:cliqueMS.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings cliqueMS_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/cliqueMS.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘cliqueMS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cliqueMS’ version ‘1.22.0’
* 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: ‘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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
createNetwork  7.891  2.772  10.428
anClique-class 6.849  0.990   7.733
computeCliques 4.910  0.644   5.555
anClique       3.815  1.357   5.063
createanClique 3.389  1.224   8.046
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/cliqueMS.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL cliqueMS
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘cliqueMS’ ...
** this is package ‘cliqueMS’ version ‘1.22.0’
** using staged installation
** libs
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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/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;
      |          ^~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/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/bbs-3.21-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/fixprob.h:24,
                 from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include/RcppArmadilloExtensions/sample.h:30,
                 from networkCliqueMSR.h:7,
                 from findCliquesR.cpp:2:
/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp  -fpic  -g -O2  -Wall -Werror=format-security  -c findIsotopesR.cpp -o findIsotopesR.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o cliqueMS.so RcppExports.o findAnnotationR.o findCliquesR.o findIsotopesR.o -fopenmp -llapack -L/home/biocbuild/bbs-3.21-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/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)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(cliqueMS)
> 
> test_check("cliqueMS")
         adduct  log10freq      massdiff nummol charge
1  [M+2H-NH3]2+ -3.5129044 -15.012016600      1      2
2       [Cat]3+ -3.5129044  -0.001645737      1      3
3       [Cat]2+ -3.5129044  -0.001040400      1      2
4     [Cat+H]2+ -3.3368132   1.006178842      1      2
5      [M+2H]2+ -1.8139344   2.014552000      1      2
6    [M+H+Na]2+ -2.6999911  23.996494000      1      2
7   [M+2H+Na]3+ -3.8139344  25.003770000      1      3
8     [M+H+K]2+ -2.2341508  39.970434000      1      2
9     [M+2Na]2+ -2.6678064  45.978436000      1      2
10  [M+H+2Na]3+ -3.5129044  46.985730000      1      3
11    [M+3Na]3+ -3.5129044  68.967654000      1      3
12       [M+H]+ -0.2689987   1.007276000      1      1
13   [M+H-H2O]+ -0.7476085 -17.003277800      1      1
14      [M+Na]+ -0.9632882  22.989218000      1      1
15   [M+H-NH3]+ -1.5886251 -16.019274320      1      1
16   [M-H+2Na]+ -1.8596919  44.971164440      1      1
17       [Cat]+ -1.8948563  -0.000548579      1      1
18  [M-2H+3Na]+ -1.9108444  66.953081400      1      1
19   [M+H+H2O]+ -2.3225727  19.017868210      1      1
20       [M+K]+ -2.4159944  38.963158000      1      1
21     [M+NH4]+ -2.4917151  18.033823000      1      1
22    [M-H+2K]+ -3.1149644  76.919040000      1      1
23   [Cat+H2O]+ -3.2118744  18.010011000      1      1
24    [M+H-OH]+ -3.2118744 -15.995481930      1      1
25   [Cat-H2O]+ -3.5129044 -18.011087900      1      1
26     [Cat-H]+ -3.5129044  -1.008340400      1      1
27  [M+Na-H2O]+ -3.5129044   4.978142219      1      1
28   [M-2H+3K]+ -3.5129044 114.874881400      1      1
29   [M+K-H2O]+ -3.8139344  20.952042220      1      1
30  [M-CO2H+H]+ -4.8139344 -43.989863780      1      1
31  [3M+H-H2O]+ -4.8139344 -17.003277800      3      1
32      [2M+H]+ -1.2239848   1.007276000      2      1
33      [3M+H]+ -2.2698664   1.007276000      3      1
34 [2M+Na-H2O]+ -3.8139344   4.978142219      2      1
35  [2M+K-H2O]+ -3.8139344  20.952042220      2      1
36  [3M+K-H2O]+ -4.8139344  20.952042220      3      1
37     [2M+Na]+ -2.9688364  22.989218000      2      1
38      [2M+K]+ -3.8139344  38.963142220      2      1
39      [3M+K]+ -3.8139344  38.963142220      3      1
 [1] -1.31290442 -1.31290442 -1.31290442 -1.13681316  0.38606558 -0.49999107
 [7] -1.61393442 -0.03415082 -0.46780638 -1.31290442 -1.31290442  1.93100135
[13]  1.45239151  1.23671182  0.61137486  0.34030809  0.30514367  0.28915557
[19] -0.12257272 -0.21599441 -0.29171512 -0.91496441 -1.01187443 -1.01187443
[25] -1.31290442 -1.31290442 -1.31290442 -1.31290442 -1.61393442 -2.61393442
[31] -2.61393442  0.97601518 -0.06986637 -1.61393442 -1.61393442 -2.61393442
[37] -0.76883638 -1.61393442 -1.61393442
Beggining value of logl is -712.347 
Aggregate cliques done, with 144 rounds
Kernighan-Lin done with 2 rounds
Finishing value of logl is -164.568 
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 14 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
 25.662   3.978  29.403