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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:miRspongeR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings miRspongeR_2.13.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/miRspongeR.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 ‘miRspongeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRspongeR’ version ‘2.13.5’
* 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 ‘miRspongeR’ 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 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
cernia_parallel: no visible binding for global variable ‘i’
hermes_parallel: no visible binding for global variable ‘i’
layout.spencer.circle: no visible global function definition for
  ‘orderCommunities’
miRHomology_parallel: no visible binding for global variable ‘i’
muTaME_parallel: no visible binding for global variable ‘i’
pc_parallel: no visible binding for global variable ‘i’
plotLinkCommGraph: no visible global function definition for
  ‘which.communities’
plotLinkCommGraph: no visible global function definition for
  ‘orderCommunities’
plotLinkCommGraph: no visible global function definition for
  ‘numberEdgesIn’
plotLinkCommGraph: no visible global function definition for ‘.nodePie’
plotLinkCommMembers: no visible global function definition for
  ‘getCommunityMatrix’
plotLinkCommSummComm: no visible global function definition for
  ‘LinkDensities’
plotLinkCommSummComm: no visible global function definition for
  ‘getCommunityConnectedness’
ppc_parallel: no visible binding for global variable ‘i’
sample_cor_network: no visible binding for global variable ‘i’
sponge_parallel: no visible binding for global variable ‘i’
sponge_sample_specific: no visible binding for global variable ‘i’
sppc_parallel: no visible binding for global variable ‘i’
Undefined global functions or variables:
  .nodePie LinkDensities getCommunityConnectedness getCommunityMatrix i
  numberEdgesIn orderCommunities which.communities
* 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 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
moduleDEA              14.178  0.924  18.148
sample_cor_network      4.844  1.428  59.779
sponge_sample_specific  0.765  0.048  23.321
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test_miRspongeR.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-3.22-bioc/meat/miRspongeR.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL miRspongeR
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘miRspongeR’ ...
** this is package ‘miRspongeR’ version ‘2.13.5’
** 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’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c OCG_algorithm.c -o OCG_algorithm.o
OCG_algorithm.c: In function ‘getOCGclusters’:
OCG_algorithm.c:568:2: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  568 |  for(j=0;j<CardMax;j++)
      |  ^~~
OCG_algorithm.c:571:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  571 |   k=0;
      |   ^
OCG_algorithm.c:445:52: warning: variable ‘flag3’ set but not used [-Wunused-but-set-variable]
  445 |   int   NbY, Nl, Long, NewLong, cli, flag1, flag2, flag3;
      |                                                    ^~~~~
OCG_algorithm.c:790:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  790 |     for (j=0; j<i; j++)
      |     ^~~
OCG_algorithm.c:794:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  794 |       for (k=0; k<N; k++) Clas[k]=0;
      |       ^~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c complex.c -o complex.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c edge_duplicates.cpp -o edge_duplicates.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c linkcomm_edgesims.cpp -o linkcomm_edgesims.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c linkcomm_edgesims_all.cpp -o linkcomm_edgesims_all.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c linkcomm_functions.cpp -o linkcomm_functions.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c linkcomm_hclust.cpp -o linkcomm_hclust.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c linkcomm_init.c -o linkcomm_init.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c linkcomm_linkdensities.cpp -o linkcomm_linkdensities.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c linkcommhclust_order.cpp -o linkcommhclust_order.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c read_OCG.cpp -o read_OCG.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o miRspongeR.so OCG_algorithm.o complex.o edge_duplicates.o linkcomm_edgesims.o linkcomm_edgesims_all.o linkcomm_functions.o linkcomm_hclust.o linkcomm_init.o linkcomm_linkdensities.o linkcommhclust_order.o read_OCG.o registerDynamicSymbol.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-miRspongeR/00new/miRspongeR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘biomaRt::select’ by ‘dplyr::select’ when loading ‘SPONGE’
Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ when loading ‘SPONGE’
Warning: replacing previous import ‘cvms::font’ by ‘ggpubr::font’ when loading ‘SPONGE’
Warning: replacing previous import ‘ggplot2::margin’ by ‘randomForest::margin’ when loading ‘SPONGE’
Warning: replacing previous import ‘dplyr::combine’ by ‘randomForest::combine’ when loading ‘SPONGE’
Warning: replacing previous import ‘Biobase::exprs’ by ‘rlang::exprs’ when loading ‘SPONGE’
Warning: replacing previous import ‘rlang::exprs’ by ‘Biobase::exprs’ when loading ‘SPONGE’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘biomaRt::select’ by ‘dplyr::select’ when loading ‘SPONGE’
Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ when loading ‘SPONGE’
Warning: replacing previous import ‘cvms::font’ by ‘ggpubr::font’ when loading ‘SPONGE’
Warning: replacing previous import ‘ggplot2::margin’ by ‘randomForest::margin’ when loading ‘SPONGE’
Warning: replacing previous import ‘dplyr::combine’ by ‘randomForest::combine’ when loading ‘SPONGE’
Warning: replacing previous import ‘Biobase::exprs’ by ‘rlang::exprs’ when loading ‘SPONGE’
Warning: replacing previous import ‘rlang::exprs’ by ‘Biobase::exprs’ when loading ‘SPONGE’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘biomaRt::select’ by ‘dplyr::select’ when loading ‘SPONGE’
Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ when loading ‘SPONGE’
Warning: replacing previous import ‘cvms::font’ by ‘ggpubr::font’ when loading ‘SPONGE’
Warning: replacing previous import ‘ggplot2::margin’ by ‘randomForest::margin’ when loading ‘SPONGE’
Warning: replacing previous import ‘dplyr::combine’ by ‘randomForest::combine’ when loading ‘SPONGE’
Warning: replacing previous import ‘Biobase::exprs’ by ‘rlang::exprs’ when loading ‘SPONGE’
Warning: replacing previous import ‘rlang::exprs’ by ‘Biobase::exprs’ when loading ‘SPONGE’
** testing if installed package keeps a record of temporary installation path
* DONE (miRspongeR)

R version 4.5.1 Patched (2025-08-23 r88802) -- "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(miRspongeR)


Warning messages:
1: replacing previous import 'biomaRt::select' by 'dplyr::select' when loading 'SPONGE' 
2: replacing previous import 'Biobase::combine' by 'dplyr::combine' when loading 'SPONGE' 
3: replacing previous import 'cvms::font' by 'ggpubr::font' when loading 'SPONGE' 
4: replacing previous import 'ggplot2::margin' by 'randomForest::margin' when loading 'SPONGE' 
5: replacing previous import 'dplyr::combine' by 'randomForest::combine' when loading 'SPONGE' 
6: replacing previous import 'Biobase::exprs' by 'rlang::exprs' when loading 'SPONGE' 
7: replacing previous import 'rlang::exprs' by 'Biobase::exprs' when loading 'SPONGE' 
> 
> miR2Target <- system.file("extdata", "miR2Target.csv", package="miRspongeR")
> miRTarget <- read.csv(miR2Target, header=TRUE, sep=",")
> ExpDatacsv <- system.file("extdata", "ExpData.csv", package="miRspongeR")
> ExpData <- read.csv(ExpDatacsv, header=TRUE, sep=",")
> 
> # miRHomology method
> miRHomologyceRInt <- spongeMethod(miRTarget, method = "miRHomology")
> 
> # pc method
> pcceRInt <- spongeMethod(miRTarget, ExpData, method = "pc")
> 
> # sppc method
> sppcceRInt <- spongeMethod(miRTarget, ExpData, senscorcutoff = 0.1, method = "sppc")
> 
> 
> test_that("Test spongeMethod", {
+     expect_equal(spongeMethod(miRTarget, method = "miRHomology"), miRHomologyceRInt)
+     expect_equal(spongeMethod(miRTarget, ExpData, method = "pc"), pcceRInt)
+     expect_equal(spongeMethod(miRTarget, ExpData, senscorcutoff = 0.1, method = "sppc"), sppcceRInt)    
+ })
Test passed 🎉
> 
> proc.time()
   user  system elapsed 
 10.276   0.681  10.951