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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cliqueMS.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings cliqueMS_1.9.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/cliqueMS.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cliqueMS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cliqueMS' version '1.9.0'
* 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 whether package 'cliqueMS' can be installed ... OK
* 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 R 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'MSnbase'
  All declared Imports should be used.
* 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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/cliqueMS/libs/x64/cliqueMS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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. 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
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
createNetwork  4.44   0.07   27.95
anClique-class 2.50   0.08   12.78
createanClique 2.50   0.00   28.47
computeCliques 2.13   0.05   12.31
anClique       1.69   0.05   12.28
getCliques     1.45   0.02   12.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/cliqueMS.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL cliqueMS
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'cliqueMS' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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 long unsigned int'} [-Wsign-compare]
     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 long unsigned int'} [-Wsign-compare]
     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 long unsigned int'} [-Wsign-compare]
     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 in this function [-Wmaybe-uninitialized]
     completeroundscore += *ritv;
     ~~~~~~~~~~~~~~~~~~~^~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c findCliquesR.cpp -o findCliquesR.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c findIsotopesR.cpp -o findIsotopesR.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o cliqueMS.dll tmp.def RcppExports.o findAnnotationR.o findCliquesR.o findIsotopesR.o -fopenmp -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-cliqueMS/00new/cliqueMS/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cliqueMS'
    finding HTML links ... done
    anClique-class                          html  
    anClique                                html  
    cliqueMS                                html  
    computeCliques                          html  
    createNetwork                           html  
    createanClique                          html  
    ex.cliqueGroups                         html  
    getAnnotation                           html  
    getCliques                              html  
    getIsotopes                             html  
    negative.adinfo                         html  
    positive.adinfo                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cliqueMS)
Making 'packages.html' ... done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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 -722.284 
Aggregate cliques done, with 164 rounds
Kernighan-Lin done with 2 rounds
Finishing value of logl is -161.574 
[ FAIL 0 | WARN 38 | SKIP 0 | PASS 14 ]

[ FAIL 0 | WARN 38 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
  14.95    1.09   38.06