##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:miRSM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings miRSM_2.5.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/miRSM.Rcheck’
* using R version 4.5.0 Patched (2025-04-21 r88169)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘miRSM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRSM’ version ‘2.5.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 32 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘miRSM’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function calls without 'PACKAGE' argument:
  .C("edgeDuplicates", ...)
  .C("getEdgeSimilarities", ...)
  .C("getEdgeSimilarities_all", ...)
  .C("getEdgeSimilarities", ...)
  .C("getEdgeSimilarities_all", ...)
  .C("hclustLinkComm", ...)
  .C("hclustPlotOrder", ...)
  .C("getLinkDensities", ...)
  .C("getNumClusters", ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
layout.spencer.circle: no visible global function definition for
  ‘orderCommunities’
plotLinkCommDend: no visible global function definition for
  ‘colorRampPalette’
plotLinkCommGraph: no visible global function definition for
  ‘which.communities’
plotLinkCommGraph: no visible global function definition for
  ‘colorRampPalette’
plotLinkCommGraph: no visible global function definition for
  ‘orderCommunities’
plotLinkCommGraph: no visible global function definition for ‘dev.hold’
plotLinkCommGraph: no visible global function definition for
  ‘dev.flush’
plotLinkCommGraph: no visible global function definition for
  ‘numberEdgesIn’
plotLinkCommGraph: no visible global function definition for ‘.nodePie’
plotLinkCommMembers: no visible global function definition for
  ‘getCommunityMatrix’
plotLinkCommMembers: no visible global function definition for
  ‘colorRampPalette’
plotLinkCommSumm: no visible global function definition for
  ‘colorRampPalette’
plotLinkCommSummComm: no visible global function definition for
  ‘colorRampPalette’
plotLinkCommSummComm: no visible global function definition for
  ‘LinkDensities’
plotLinkCommSummComm: no visible global function definition for
  ‘getCommunityConnectedness’
Undefined global functions or variables:
  .nodePie LinkDensities colorRampPalette dev.flush dev.hold
  getCommunityConnectedness getCommunityMatrix numberEdgesIn
  orderCommunities which.communities
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.flush", "dev.hold")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) module_GFA.Rd:47: Lost braces
    47 | Bunte K, Lepp\'{a}aho E, Saarinen I, Kaski S. 
       |                ^
checkRd: (-1) module_GFA.Rd:50: Lost braces
    50 | Lepp\'{a}aho E, Ammad-ud-din M, Kaski S. GFA: 
       |       ^
checkRd: (-1) module_biclust.Rd:54: Lost braces
    54 | Preli\'{c} A, Bleuler S, Zimmermann P, Wille A, 
       |        ^
checkRd: (-1) module_biclust.Rd:55: Lost braces
    55 | B\'{u}hlmann P, Gruissem W, Hennig L, Thiele L, Zitzler E. 
       |    ^
checkRd: (-1) module_biclust.Rd:80: Lost braces
    80 | Talloen W, Bijnens L, G\'{o}hlmann HW, Shkedy Z, Clevert DA. 
       |                          ^
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test_miRSM.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/miRSM.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL miRSM
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘miRSM’ ...
** this is package ‘miRSM’ version ‘2.5.2’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c OCG_algorithm.c -o OCG_algorithm.o
OCG_algorithm.c:445:52: warning: variable 'flag3' set but not used [-Wunused-but-set-variable]
  int   NbY, Nl, Long, NewLong, cli, flag1, flag2, flag3;
                                                   ^
OCG_algorithm.c:435:26: warning: variable 'Somcard' set but not used [-Wunused-but-set-variable]
  int Adj, NbAdj, mis=0, Somcard=0;
                         ^
OCG_algorithm.c:879:15: warning: variable 'NbElEl' set but not used [-Wunused-but-set-variable]
  int           ncard, NbElEl=0;
                       ^
3 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c complex.c -o complex.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c edge_duplicates.cpp -o edge_duplicates.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c linkcomm_edgesims.cpp -o linkcomm_edgesims.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c linkcomm_edgesims_all.cpp -o linkcomm_edgesims_all.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c linkcomm_functions.cpp -o linkcomm_functions.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c linkcomm_hclust.cpp -o linkcomm_hclust.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c linkcomm_init.c -o linkcomm_init.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c linkcomm_linkdensities.cpp -o linkcomm_linkdensities.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c linkcommhclust_order.cpp -o linkcommhclust_order.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c read_OCG.cpp -o read_OCG.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o miRSM.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 -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-miRSM/00new/miRSM/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 (miRSM)

R version 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> suppressPackageStartupMessages(library(testthat))
> suppressPackageStartupMessages(library(GSEABase))
> suppressPackageStartupMessages(library(miRSM))
> 
> # Load datasets
> data(BRCASampleData)
> 
> # Identify gene co-expression modules using igraph method
> modulegenes_igraph <- module_igraph(ceRExp[, seq_len(10)], 
+     mRExp[, seq_len(10)])
> 
> 
> test_that("Test miRSM", {
+     expect_equal(geneIds(module_igraph(ceRExp[, seq_len(10)], 
+         mRExp[, seq_len(10)])), geneIds(modulegenes_igraph))
+ })
Test passed 🎉
> 
> proc.time()
   user  system elapsed 
  5.771   0.289   6.092