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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SomaticSignatures.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SomaticSignatures_2.45.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SomaticSignatures.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SomaticSignatures/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SomaticSignatures’ version ‘2.45.1’
* 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 ‘SomaticSignatures’ 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.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘NMF’
A package should be listed in only one of these fields.
* 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) decomposition-functions.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition-functions.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition-functions.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition-functions.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition-functions.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition-functions.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) granges-utils.Rd:33-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) granges-utils.Rd:36-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) granges-utils.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mutation-distribution.Rd:40-43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mutation-distribution.Rd:45-46: 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:
  granges-utils.Rd: seqnames, mcols
  number-signatures.Rd: NMF
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... ERROR
Running examples in ‘SomaticSignatures-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mutation-distribution
> ### Title: Distributions of mutational locations.
> ### Aliases: mutationDistance plotRainfall
> 
> ### ** Examples
> 
> 
> library(GenomicRanges)
> library(IRanges)
> 
> set.seed(1)
> chr_len = 100
> gr = GRanges(rep(1:3, each = 10),
+   IRanges(start = sample.int(chr_len, 30, replace = FALSE), width = 1),
+   mutation = sample(c("A", "C", "G", "T"), 30, replace = TRUE))
> seqlengths(gr) = rep(chr_len, 3)
> 
> p = plotRainfall(gr)
Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more information.
ℹ The deprecated feature was likely used in the SomaticSignatures package.
  Please report the issue at <https://support.bioconductor.org>.
Error:
! The `facets` argument of `facet_grid()` was deprecated in ggplot2
  2.2.0 and is now defunct.
ℹ Please use the `rows` argument instead.
Backtrace:
     ▆
  1. └─SomaticSignatures::plotRainfall(gr)
  2.   ├─base::suppressMessages(...)
  3.   │ └─base::withCallingHandlers(...)
  4.   └─ggbio::plotGrandLinear(...)
  5.     ├─BiocGenerics::do.call(autoplot, c(list(aes.res), args.non))
  6.     ├─base::do.call(autoplot, c(list(aes.res), args.non))
  7.     ├─ggplot2 (local) `<stndrdGn>`(...)
  8.     └─ggbio (local) `<stndrdGn>`(...)
  9.       └─ggbio (local) .local(object, ...)
 10.         └─ggbio:::.buildFacetsFromArgs(object, args.facets)
 11.           ├─BiocGenerics::do.call(facet_grid, args.facets)
 12.           ├─base::do.call(facet_grid, args.facets)
 13.           └─ggplot2 (local) `<fn>`(scales = "fixed", facets = ~seqnames)
 14.             └─lifecycle::deprecate_stop("2.2.0", "facet_grid(facets)", "facet_grid(rows)")
 15.               └─lifecycle:::deprecate_stop0(msg)
 16.                 └─rlang::cnd_signal(...)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    6.     ├─base::do.call(autoplot, c(list(aes.res), args.non))
    7.     ├─ggplot2 (local) `<stndrdGn>`(...)
    8.     └─ggbio (local) `<stndrdGn>`(...)
    9.       └─ggbio (local) .local(object, ...)
   10.         └─ggbio:::.buildFacetsFromArgs(object, args.facets)
   11.           ├─BiocGenerics::do.call(facet_grid, args.facets)
   12.           ├─base::do.call(facet_grid, args.facets)
   13.           └─ggplot2 (local) `<fn>`(scales = "fixed", facets = ~seqnames)
   14.             └─lifecycle::deprecate_stop("2.2.0", "facet_grid(facets)", "facet_grid(rows)")
   15.               └─lifecycle:::deprecate_stop0(msg)
   16.                 └─rlang::cnd_signal(...)
  
  [ FAIL 1 | WARN 7 | SKIP 1 | PASS 34 ]
  Error: Test failures
  Execution halted
* 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 ERRORs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/SomaticSignatures.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SomaticSignatures
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SomaticSignatures’ ...
** this is package ‘SomaticSignatures’ version ‘2.45.1’
** 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 (SomaticSignatures)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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(SomaticSignatures)
Loading required package: VariantAnnotation
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: 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: Seqinfo
Loading required package: GenomicRanges
Loading required package: stats4
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: SummarizedExperiment
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: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit


Attaching package: 'VariantAnnotation'

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

    tabulate

Loading required package: NMF
Loading required package: registry
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 2/2
  To enable shared memory capabilities, try: install.extras('
NMF
')

Attaching package: 'NMF'

The following object is masked from 'package:S4Vectors':

    nrun

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

    fit

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

    compare

> 
> test_check("SomaticSignatures")
MutationalSignatures:
  Samples (8): gbm, hnsc, ..., skcm, thca
  Signatures (8): S1, S2, ..., S7, S8
  Motifs (96): CA A.A, CA A.C, ..., TG T.G, TG T.T
[ FAIL 1 | WARN 7 | SKIP 1 | PASS 34 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-SomaticSignatures.R:90:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-SomaticSignatures.R:83:5'): 'plotRainfall' work ────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: The `facets` argument of `facet_grid()` was deprecated in ggplot2 2.2.0
and is now defunct.
ℹ Please use the `rows` argument instead.
Backtrace:
     ▆
  1. └─SomaticSignatures::plotRainfall(granges(vr)) at test-SomaticSignatures.R:83:5
  2.   ├─base::suppressMessages(...)
  3.   │ └─base::withCallingHandlers(...)
  4.   └─ggbio::plotGrandLinear(...)
  5.     ├─BiocGenerics::do.call(autoplot, c(list(aes.res), args.non))
  6.     ├─base::do.call(autoplot, c(list(aes.res), args.non))
  7.     ├─ggplot2 (local) `<stndrdGn>`(...)
  8.     └─ggbio (local) `<stndrdGn>`(...)
  9.       └─ggbio (local) .local(object, ...)
 10.         └─ggbio:::.buildFacetsFromArgs(object, args.facets)
 11.           ├─BiocGenerics::do.call(facet_grid, args.facets)
 12.           ├─base::do.call(facet_grid, args.facets)
 13.           └─ggplot2 (local) `<fn>`(scales = "fixed", facets = ~seqnames)
 14.             └─lifecycle::deprecate_stop("2.2.0", "facet_grid(facets)", "facet_grid(rows)")
 15.               └─lifecycle:::deprecate_stop0(msg)
 16.                 └─rlang::cnd_signal(...)

[ FAIL 1 | WARN 7 | SKIP 1 | PASS 34 ]
Error: Test failures
Execution halted