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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MetNet.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MetNet_1.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MetNet.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MetNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetNet’ version ‘1.25.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘MetNet’ can be installed ... OK
* 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) partialCorrelation.Rd:33: Lost braces; missing escapes or markup?
    33 | The correlation coefficients $r_{ij|S}$ are obtained from `cor2pcor`
       |                                 ^
checkRd: (-1) threshold.Rd:49: Lost braces; missing escapes or markup?
    49 | a^*_{ij} = min(a_ij, a_ji)
       |     ^
checkRd: (-1) threshold.Rd:50: Lost braces; missing escapes or markup?
    50 | a^*_{ij} = max(a_ij, a_ji)}
       |     ^
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
MetNet-package 51.316  0.197  51.515
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/MetNet.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL MetNet
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘MetNet’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MetNet)

R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 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("MetNet")
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: IRanges
Loading required package: GenomeInfoDb
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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians


Attaching package: 'MetNet'

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

    combine

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

    combine, type

> 
> test_check("MetNet")
[1] "clr finished."
[1] "aracne finished."
[1] "pearson finished."
[1] "spearman finished."
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0987 

[1] "ggm finished."
[1] "pearson finished."
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.1038 

[1] "ggm finished."
[1] "clr finished."
[1] "aracne finished."
[1] "pearson finished."
[1] "spearman finished."
[1] "clr finished."
[1] "aracne finished."
[1] "pearson finished."
[1] "spearman finished."
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.3859 

[1] "ggm finished."
[1] "bayes finished."
[1] "clr finished."
[1] "aracne finished."
[1] "pearson finished."
[1] "spearman finished."
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0761 

Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0806 

Estimating optimal shrinkage intensity lambda (correlation matrix): 0.1024 

Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0211 

Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0222 

Estimating optimal shrinkage intensity lambda (correlation matrix): 0.1024 

[1] "randomForest finished."
[1] "clr finished."
[1] "aracne finished."
[1] "pearson finished."
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0761 

[1] "pearson_partial finished."
[1] "spearman finished."
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0806 

[1] "spearman_partial finished."
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.1024 

[1] "ggm finished."
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0761 

Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0806 

Estimating optimal shrinkage intensity lambda (correlation matrix): 0.1024 

[1] "pearson finished."
[1] "spearman finished."
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0987 

[1] "ggm finished."
[1] "randomForest finished."
[1] "clr finished."
[1] "aracne finished."
[1] "pearson finished."
[1] "spearman finished."
[1] "bayes finished."
[1] "pearson finished."
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.1139 

[1] "ggm finished."
[1] "clr finished."
[1] "aracne finished."
[1] "pearson finished."
[1] "spearman finished."
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.0461 

[1] "ggm finished."
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 766 ]
> 
> proc.time()
   user  system elapsed 
113.572  66.932  98.321