| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:12 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1960/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SomaticSignatures 2.36.0 (landing page) Julian Gehring
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | ERROR | OK | ||||||||
|
To the developers/maintainers of the SomaticSignatures package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: SomaticSignatures |
| Version: 2.36.0 |
| 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_2.36.0.tar.gz |
| StartedAt: 2023-10-19 02:29:21 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 02:43:13 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 832.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: SomaticSignatures.Rcheck |
| Warnings: NA |
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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_2.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SomaticSignatures.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SomaticSignatures/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SomaticSignatures’ version ‘2.36.0’
* 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
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 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 ... 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 ... OK
* 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
number-signatures 23.066 0.220 39.878
mutational-signatures 3.895 0.046 6.618
* 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:
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test-SomaticSignatures.R:81:1',
'test-SomaticSignatures.R:90:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-SomaticSignatures.R:124:5'): 'motifMatrix' works ─────────────
all(colSums(mm) == 1) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 5 | SKIP 2 | PASS 33 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SomaticSignatures.Rcheck/00check.log’
for details.
SomaticSignatures.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SomaticSignatures ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘SomaticSignatures’ ... ** 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)
SomaticSignatures.Rcheck/tests/testthat.Rout.fail
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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(SomaticSignatures)
Loading required package: VariantAnnotation
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: 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: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4
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: GenomicRanges
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: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 5 | SKIP 2 | PASS 33 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test-SomaticSignatures.R:81:1',
'test-SomaticSignatures.R:90:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-SomaticSignatures.R:124:5'): 'motifMatrix' works ─────────────
all(colSums(mm) == 1) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 5 | SKIP 2 | PASS 33 ]
Error: Test failures
Execution halted
SomaticSignatures.Rcheck/SomaticSignatures-Ex.timings
| name | user | system | elapsed | |
| SomaticSignatures-package | 0.003 | 0.001 | 0.007 | |
| gc | 0.453 | 0.024 | 0.848 | |
| granges-utils | 0.276 | 0.023 | 0.525 | |
| hs-chrs | 0.001 | 0.001 | 0.002 | |
| kmers-data | 0.004 | 0.002 | 0.009 | |
| kmers | 0.968 | 0.116 | 1.925 | |
| motif-functions | 0.027 | 0.008 | 0.054 | |
| mutation-context | 0.349 | 0.005 | 0.643 | |
| mutation-distribution | 0.797 | 0.044 | 1.506 | |
| mutational-signatures | 3.895 | 0.046 | 6.618 | |
| mutect | 0.095 | 0.002 | 0.156 | |
| number-signatures | 23.066 | 0.220 | 39.878 | |
| sca-data | 0.009 | 0.004 | 0.021 | |
| signature-plot-functions | 1.892 | 0.121 | 3.676 | |
| signatures21-data | 0.003 | 0.002 | 0.009 | |