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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:miRSM.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings miRSM_2.5.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/miRSM.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 ‘miRSM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRSM’ version ‘2.5.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 31 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: ‘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 ... INFO
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
    libs   2.9Mb
* 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 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 ... OK
* checking R code for possible problems ... NOTE
layout.spencer.circle: no visible global function definition for
  ‘orderCommunities’
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’
s4vd: no visible global function definition for ‘BiclustResult’
ssvd: no visible global function definition for ‘irlba’
ssvd: no visible global function definition for ‘%dopar%’
ssvd: no visible global function definition for ‘foreach’
ssvd: no visible global function definition for ‘thresh’
ssvdBC: no visible global function definition for ‘BiclustResult’
Undefined global functions or variables:
  %dopar% .nodePie BiclustResult LinkDensities foreach
  getCommunityConnectedness getCommunityMatrix irlba numberEdgesIn
  orderCommunities thresh which.communities
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives 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
diff_module 7.597  0.182   7.779
miRSM_SS    6.503  0.010   6.515
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL miRSM
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘miRSM’ ...
** this is package ‘miRSM’ version ‘2.5.4’
** 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   -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   -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   -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   -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   -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   -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   -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   -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   -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   -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   -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   -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 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 -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-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 4.5.1 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.

> 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 
 15.774   0.881  16.646