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This page was generated on 2023-11-02 11:40:35 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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 513/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decompTumor2Sig 2.18.0  (landing page)
Rosario M. Piro
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/decompTumor2Sig
git_branch: RELEASE_3_18
git_last_commit: d01f0b5
git_last_commit_date: 2023-10-24 11:09:45 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for decompTumor2Sig on kunpeng2


To the developers/maintainers of the decompTumor2Sig package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decompTumor2Sig.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: decompTumor2Sig
Version: 2.18.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings decompTumor2Sig_2.18.0.tar.gz
StartedAt: 2023-11-02 09:49:51 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 09:57:16 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 444.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: decompTumor2Sig.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings decompTumor2Sig_2.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/decompTumor2Sig.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decompTumor2Sig/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decompTumor2Sig’ version ‘2.18.0’
* 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 ‘decompTumor2Sig’ 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 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘decompTumor2Sig-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convertGenomesFromVRanges
> ### Title: Convert genomes from a 'VRanges' object
> ### Aliases: convertGenomesFromVRanges
> 
> ### ** Examples
> 
> 
> ### load the reference genome and the transcript annotation database
> refGenome <- BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19
> transcriptAnno <-
+   TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene
> 
> ### take the breast cancer genomes from Nik-Zainal et al (PMID: 22608084) 
> gfile <- system.file("extdata",
+          "Nik-Zainal_PMID_22608084-VCF-convertedfromMPF.vcf.gz", 
+          package="decompTumor2Sig")
> 
> ### get the corresponding VRanges object (using the VariantAnnotation
> ### package)
> library(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

> vr <- readVcfAsVRanges(gfile, genome="hg19")
> 
> ### convert the VRanges object to the decompTumor2Sig format
> genomes <- convertGenomesFromVRanges(vr, numBases=5, type="Shiraishi",
+          trDir=TRUE, enforceUniqueTrDir=TRUE, refGenome=refGenome, 
+          transcriptAnno=transcriptAnno, verbose=FALSE)
* 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
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/decompTumor2Sig.Rcheck/00check.log’
for details.


Installation output

decompTumor2Sig.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL decompTumor2Sig
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘decompTumor2Sig’ ...
** using staged installation
** R
** 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 (decompTumor2Sig)

Tests output


Example timings

decompTumor2Sig.Rcheck/decompTumor2Sig-Ex.timings

nameusersystemelapsed
adjustSignaturesForRegionSet3.0121.0839.138
composeGenomesFromExposures0.2810.0121.999
computeExplainedVariance0.2600.0244.269
convertAlexandrov2Shiraishi0.1120.6963.667