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###
### 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_2.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/miRSM.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘miRSM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRSM’ version ‘2.0.0’
* 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 ‘miRSM’ can be installed ... OK
* 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 ... OK
* checking R code for possible problems ... OK
* 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
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
diff_module          12.663  0.216  19.372
miRSM_SS             10.246  0.110  15.529
module_GFA            4.658  0.174   6.459
module_group_sim      4.418  0.105   7.100
module_Validate       4.188  0.088   6.239
share_miRs            4.180  0.081   6.704
module_miRdistribute  4.174  0.081   6.326
module_CEA            4.107  0.076   5.842
module_miRtarget      4.092  0.090   5.946
module_miRsponge      4.094  0.085   5.420
module_Coexpress      4.073  0.075   6.056
module_NMF            3.552  0.106   5.002
module_WGCNA          3.352  0.043   5.121
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/miRSM.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL miRSM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘miRSM’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -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 -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 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o miRSM.so complex.o registerDynamicSymbol.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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 
 19.103   1.279  31.022