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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:moanin.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings moanin_1.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/moanin.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘moanin/DESCRIPTION’ ... OK
* this is package ‘moanin’ 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 ‘moanin’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 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) DE_timepoints.Rd:129-130: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DE_timepoints.Rd:131-132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DE_timepoints.Rd:133-136: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_log_fold_change.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_log_fold_change.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_log_fold_change.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_log_fold_change.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_log_fold_change.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_log_fold_change.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_log_fold_change.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) splines_kmeans.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) splines_kmeans.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) splines_kmeans.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) splines_kmeans_score_and_label.Rd:69-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) splines_kmeans_score_and_label.Rd:72-73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) splines_kmeans_score_and_label.Rd:74-75: Lost braces in \itemize; \value handles \item{}{} directly
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Moanin-class.Rd: SummarizedExperiment
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Unknown package ‘KEGGprofile’ in Rd xrefs
* 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
get_auc_similarity_scores 16.724  0.715  17.507
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL moanin
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘moanin’ ...
** this is package ‘moanin’ version ‘1.17.0’
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path
* DONE (moanin)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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.

> library(testthat)
> library(moanin)
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: 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

Loading required package: S4Vectors

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: IRanges
Loading required package: Seqinfo
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

Loading required package: topGO
Loading required package: graph
Loading required package: GO.db
Loading required package: AnnotationDbi

Loading required package: SparseM

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

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

    members

> test_check("moanin")
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 64 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test-estimate_lfc.R:6:1', 'test-splines_model.R:18:1'

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 64 ]
> 
> proc.time()
   user  system elapsed 
  6.382   0.307   6.687