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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 1357/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 3.15.0  (landing page)
Mark van Roosmalen
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/MutationalPatterns
git_branch: devel
git_last_commit: 3141f44
git_last_commit_date: 2024-04-30 10:54:30 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.6.5 Ventura / arm64  OK    ERROR  skippedskipped
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for MutationalPatterns on palomino6

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: 3.15.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MutationalPatterns_3.15.0.tar.gz
StartedAt: 2024-07-16 02:11:49 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 02:20:50 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 540.8 seconds
RetCode: 0
Status:   OK  
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MutationalPatterns_3.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/MutationalPatterns.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 '3.15.0'
* 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 ... 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 ... 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
read_vcfs_as_granges              21.22   1.52   26.89
context_potential_damage_analysis 18.94   0.52   19.47
plot_lesion_segregation           17.61   0.19   17.83
get_mut_type                       9.61   0.12    9.76
genomic_distribution               8.94   0.73    9.67
bin_mutation_density               9.04   0.56    9.67
calculate_lesion_segregation       8.28   0.30    8.60
plot_river                         8.23   0.16    7.13
plot_indel_contexts                6.98   0.06    7.09
get_indel_context                  5.65   1.03    6.68
plot_compare_indels                6.61   0.02    6.68
plot_profile_heatmap               5.25   0.17    5.43
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/MutationalPatterns.Rcheck/00check.log'
for details.


Installation output

MutationalPatterns.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL MutationalPatterns
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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, 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 
 189.62   22.20  220.60 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density9.040.569.67
binomial_test0.010.000.01
calculate_lesion_segregation8.280.308.60
cluster_signatures0.050.000.04
context_potential_damage_analysis18.94 0.5219.47
convert_sigs_to_ref0.030.010.05
cos_sim000
cos_sim_matrix0.010.020.03
count_dbs_contexts0.070.000.06
count_indel_contexts0.080.000.08
count_mbs_contexts0.060.000.06
determine_regional_similarity2.450.332.79
enrichment_depletion_test0.110.000.11
extract_signatures0.020.000.01
fit_to_signatures0.070.000.08
fit_to_signatures_bootstrapped4.720.254.97
fit_to_signatures_strict2.530.272.81
genomic_distribution8.940.739.67
get_dbs_context0.200.000.21
get_indel_context5.651.036.68
get_known_signatures0.390.210.60
get_mut_type9.610.129.76
lengthen_mut_matrix0.010.000.02
merge_signatures1.130.101.22
mut_context1.030.191.22
mut_matrix2.740.252.98
mut_matrix_stranded3.340.453.78
mut_strand0.810.050.86
mut_type0.030.000.03
mut_type_occurrences0.720.140.86
mutations_from_vcf0.010.000.01
plot_192_profile2.470.062.54
plot_96_profile2.020.032.06
plot_bootstrapped_contribution1.470.051.52
plot_compare_dbs4.390.044.44
plot_compare_indels6.610.026.68
plot_compare_mbs0.700.000.71
plot_compare_profiles1.740.041.78
plot_contribution1.390.021.41
plot_contribution_heatmap1.230.021.25
plot_correlation_bootstrap0.360.000.35
plot_cosine_heatmap1.520.011.54
plot_dbs_contexts3.210.033.26
plot_enrichment_depletion2.750.052.81
plot_indel_contexts6.980.067.09
plot_lesion_segregation17.61 0.1917.83
plot_main_dbs_contexts0.580.030.61
plot_main_indel_contexts0.490.000.49
plot_mbs_contexts0.540.000.54
plot_original_vs_reconstructed0.440.000.44
plot_profile_heatmap5.250.175.43
plot_profile_region0.960.020.99
plot_rainfall1.690.011.70
plot_regional_similarity1.720.021.73
plot_river8.230.167.13
plot_signature_strand_bias0.750.030.76
plot_spectrum4.520.154.74
plot_spectrum_region4.670.184.84
plot_strand0.860.040.97
plot_strand_bias0.720.030.75
pool_mut_mat0.050.000.05
read_vcfs_as_granges21.22 1.5226.89
rename_nmf_signatures0.030.030.06
signature_potential_damage_analysis0.080.000.08
split_muts_region4.540.204.74
strand_bias_test0.100.020.11
strand_occurrences0.170.000.17
type_context1.340.171.51