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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:miRSM.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings miRSM_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/miRSM.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘miRSM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRSM’ version ‘1.17.0’
* 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: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 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: ‘org.Hs.eg.db’
  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 ... WARNING
Killed
Killed
* 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 ... ERROR
Running examples in ‘miRSM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: module_Validate
> ### Title: module_Validate
> ### Aliases: module_Validate
> 
> ### ** Examples
> 
> data(BRCASampleData)
> modulegenes_WGCNA <- module_WGCNA(ceRExp, mRExp)
   Power SFT.R.sq   slope truncated.R.sq mean.k. median.k. max.k.
1      1  0.18600  0.4990         0.3700  312.00   371.000  461.0
2      2  0.00831 -0.0737         0.0731  172.00   208.000  325.0
3      3  0.10800 -0.2470        -0.0678  107.00   124.000  243.0
4      4  0.27600 -0.3840         0.0718   70.50    76.000  187.0
5      5  0.41300 -0.4960         0.3180   48.40    47.900  147.0
6      6  0.60300 -0.5900         0.7090   34.20    30.600  117.0
7      7  0.62000 -0.6640         0.8010   24.70    20.100   94.6
8      8  0.62900 -0.7810         0.8280   18.20    13.600   77.5
9      9  0.69900 -0.8980         0.8580   13.70     9.040   64.1
10    10  0.79000 -0.9640         0.9300   10.40     6.120   53.4
11    12  0.84500 -1.1200         0.9210    6.33     2.910   38.2
12    14  0.88100 -1.1800         0.9390    4.05     1.500   28.4
13    16  0.92800 -1.1600         0.9590    2.71     0.756   21.6
14    18  0.96700 -1.1200         0.9810    1.88     0.399   16.7
15    20  0.98600 -1.0900         0.9850    1.36     0.203   13.1
..connectivity..
..matrix multiplication (system BLAS)..
Killed
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test_miRSM.R’
 ERROR
Running the tests in ‘tests/test_miRSM.R’ failed.
Last 13 lines of output:
  |....................###.....|  #       #     # ######    ###   #     # 
  |....................###.....|                                          
  |............................|                                          
  +----------------------------+                                          
  
  Citation: S. Hochreiter et al.,
  FABIA: Factor Analysis for Bicluster Acquisition,
  Bioinformatics 26(12):1520-1527, 2010.
  BibTex: enter 'toBibtex(citation("fabia"))'
  
  Homepage: http://www.bioinf.jku.at/software/fabia/fabia.html
  
  FABIA Package Version 2.45.0
  
  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘miRSM.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘miRSM.Rmd’ using rmarkdown
Killed

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/miRSM.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL miRSM
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘miRSM’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c complex.c -o complex.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c registerDynamicSymbol.c -o registerDynamicSymbol.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o miRSM.so complex.o registerDynamicSymbol.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-miRSM/00new/miRSM/libs
** R
** data
** 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 (miRSM)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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(GSEABase)
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

The following object is masked from 'package:XML':

    addNode

> library(miRSM)

+----------------------------+                                          
|............................|                                          
|............................|                                          
|..............########......|  #######    #    ######    ###      #    
|..............########......|  #         # #   #     #    #      # #   
|.....####.....########......|  #        #   #  #     #    #     #   #  
|.....####.....########......|  #####   #     # ######     #    #     # 
|.....####...................|  #       ####### #     #    #    ####### 
|.....####...........###.....|  #       #     # #     #    #    #     # 
|....................###.....|  #       #     # ######    ###   #     # 
|....................###.....|                                          
|............................|                                          
+----------------------------+                                          

Citation: S. Hochreiter et al.,
FABIA: Factor Analysis for Bicluster Acquisition,
Bioinformatics 26(12):1520-1527, 2010.
BibTex: enter 'toBibtex(citation("fabia"))'

Homepage: http://www.bioinf.jku.at/software/fabia/fabia.html

FABIA Package Version 2.45.0

Killed