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This page was generated on 2024-02-27 11:36:54 -0500 (Tue, 27 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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 1376/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 3.12.0  (landing page)
Mark van Roosmalen
Snapshot Date: 2024-02-26 14:53:20 -0500 (Mon, 26 Feb 2024)
git_url: https://git.bioconductor.org/packages/MutationalPatterns
git_branch: RELEASE_3_18
git_last_commit: 072c251
git_last_commit_date: 2023-10-24 10:53:35 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 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 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for MutationalPatterns on palomino4


To the developers/maintainers of the MutationalPatterns package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MutationalPatterns.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.

raw results


Summary

Package: MutationalPatterns
Version: 3.12.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings MutationalPatterns_3.12.0.tar.gz
StartedAt: 2024-02-27 06:26:37 -0500 (Tue, 27 Feb 2024)
EndedAt: 2024-02-27 06:36:47 -0500 (Tue, 27 Feb 2024)
EllapsedTime: 609.5 seconds
RetCode: 0
Status:   OK  
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings MutationalPatterns_3.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/MutationalPatterns.Rcheck'
* using R version 4.3.2 (2023-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MutationalPatterns/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MutationalPatterns' version '3.12.0'
* 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 whether package 'MutationalPatterns' 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
context_potential_damage_analysis 23.47   0.47   23.95
read_vcfs_as_granges              18.42   1.53   37.53
plot_lesion_segregation           14.00   0.20   14.46
get_mut_type                      10.81   0.11   10.92
genomic_distribution              10.02   0.87   12.17
calculate_lesion_segregation      10.33   0.39   10.72
bin_mutation_density               9.63   0.45   10.08
plot_indel_contexts                8.28   0.08    8.36
plot_compare_indels                8.14   0.06    8.21
get_indel_context                  6.70   1.06    7.76
fit_to_signatures_bootstrapped     6.21   0.31    6.53
plot_spectrum_region               5.66   0.27    5.93
plot_compare_dbs                   5.47   0.05    5.76
plot_profile_heatmap               5.33   0.05    5.37
plot_river                         5.28   0.05    5.32
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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: OK


Installation output

MutationalPatterns.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL MutationalPatterns
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'MutationalPatterns' ...
** 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 (MutationalPatterns)

Tests output

MutationalPatterns.Rcheck/tests/testthat.Rout


R version 4.3.2 (2023-10-31 ucrt) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(MutationalPatterns)
Loading required package: GenomicRanges
Loading required package: stats4
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: 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

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: NMF
Loading required package: registry
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 2/2

Attaching package: 'NMF'

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

    nrun

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

    compare

> 
> test_check("MutationalPatterns")
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 474 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 474 ]
> 
> proc.time()
   user  system elapsed 
 214.57   15.84  247.15 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density 9.63 0.4510.08
binomial_test000
calculate_lesion_segregation10.33 0.3910.72
cluster_signatures0.050.000.05
context_potential_damage_analysis23.47 0.4723.95
convert_sigs_to_ref0.030.030.07
cos_sim0.000.020.01
cos_sim_matrix0.010.000.02
count_dbs_contexts0.130.010.14
count_indel_contexts0.110.000.11
count_mbs_contexts0.060.000.06
determine_regional_similarity3.170.413.58
enrichment_depletion_test0.140.000.14
extract_signatures000
fit_to_signatures0.100.000.09
fit_to_signatures_bootstrapped6.210.316.53
fit_to_signatures_strict2.610.052.66
genomic_distribution10.02 0.8712.17
get_dbs_context0.250.020.27
get_indel_context6.701.067.76
get_known_signatures0.450.160.62
get_mut_type10.81 0.1110.92
lengthen_mut_matrix0.020.000.02
merge_signatures1.000.091.09
mut_context1.000.361.36
mut_matrix2.530.422.96
mut_matrix_stranded4.250.574.82
mut_strand1.130.061.22
mut_type0.030.000.03
mut_type_occurrences0.990.281.27
mutations_from_vcf0.030.000.03
plot_192_profile4.000.024.05
plot_96_profile3.430.033.59
plot_bootstrapped_contribution2.390.062.46
plot_compare_dbs5.470.055.76
plot_compare_indels8.140.068.21
plot_compare_mbs0.890.010.90
plot_compare_profiles2.510.022.53
plot_contribution1.940.031.99
plot_contribution_heatmap1.550.031.58
plot_correlation_bootstrap0.540.000.54
plot_cosine_heatmap1.820.001.81
plot_dbs_contexts3.640.003.64
plot_enrichment_depletion3.420.003.42
plot_indel_contexts8.280.088.36
plot_lesion_segregation14.00 0.2014.46
plot_main_dbs_contexts0.560.010.57
plot_main_indel_contexts0.530.020.55
plot_mbs_contexts0.550.000.55
plot_original_vs_reconstructed0.480.000.48
plot_profile_heatmap5.330.055.37
plot_profile_region0.950.030.99
plot_rainfall1.750.001.75
plot_regional_similarity1.450.001.46
plot_river5.280.055.32
plot_signature_strand_bias0.850.000.85
plot_spectrum4.480.294.79
plot_spectrum_region5.660.275.93
plot_strand0.300.030.33
plot_strand_bias1.010.001.02
pool_mut_mat0.040.000.03
read_vcfs_as_granges18.42 1.5337.53
rename_nmf_signatures0.010.050.06
signature_potential_damage_analysis0.130.000.13
split_muts_region3.870.093.96
strand_bias_test0.10.00.1
strand_occurrences0.150.030.19
type_context1.160.311.46