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This page was generated on 2022-01-17 11:11:36 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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

CHECK results for MutationalPatterns on merida1


To the developers/maintainers of the MutationalPatterns package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1250/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 3.5.1  (landing page)
Mark van Roosmalen
Snapshot Date: 2022-01-16 13:55:18 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/MutationalPatterns
git_branch: master
git_last_commit: e3da76a
git_last_commit_date: 2021-11-03 09:56:47 -0500 (Wed, 03 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MutationalPatterns
Version: 3.5.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MutationalPatterns_3.5.1.tar.gz
StartedAt: 2022-01-17 03:20:10 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 03:37:30 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 1040.1 seconds
RetCode: 0
Status:   OK  
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MutationalPatterns_3.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/MutationalPatterns.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MutationalPatterns/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MutationalPatterns’ version ‘3.5.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 45.096  0.587  45.770
read_vcfs_as_granges              36.766  1.002  49.639
plot_lesion_segregation           31.547  0.126  33.114
get_mut_type                      23.638  0.037  23.699
calculate_lesion_segregation      22.549  0.221  22.814
genomic_distribution              20.152  0.566  20.767
plot_indel_contexts               15.903  0.044  16.489
bin_mutation_density              15.246  0.456  15.737
plot_compare_indels               14.652  0.037  14.716
get_indel_context                 12.854  0.589  13.457
fit_to_signatures_bootstrapped    10.458  0.294  10.763
plot_spectrum_region               9.389  0.122   9.530
mut_matrix_stranded                9.182  0.326   9.575
plot_compare_dbs                   8.900  0.031   8.946
plot_spectrum                      8.705  0.112   8.830
plot_profile_heatmap               8.698  0.108   8.820
plot_river                         8.538  0.053   8.602
split_muts_region                  7.574  0.055   7.638
determine_regional_similarity      6.469  0.254   6.860
plot_dbs_contexts                  6.635  0.016   6.658
plot_enrichment_depletion          6.551  0.017   6.674
fit_to_signatures_strict           5.947  0.145   6.107
plot_192_profile                   5.356  0.016   5.381
plot_contribution                  5.230  0.015   5.253
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/MutationalPatterns.Rcheck/00check.log’
for details.



Installation output

MutationalPatterns.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MutationalPatterns
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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, 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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: NMF
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

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

    new2

Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 23/24
  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("MutationalPatterns")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 470 ]
> 
> proc.time()
   user  system elapsed 
375.858   9.577 401.378 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density15.246 0.45615.737
binomial_test0.0170.0010.018
calculate_lesion_segregation22.549 0.22122.814
cluster_signatures0.1060.0060.113
context_potential_damage_analysis45.096 0.58745.770
convert_sigs_to_ref0.0780.0040.085
cos_sim0.0000.0000.001
cos_sim_matrix0.0380.0050.044
count_dbs_contexts0.1580.0020.160
count_indel_contexts0.1900.0010.192
count_mbs_contexts0.1320.0010.133
determine_regional_similarity6.4690.2546.860
enrichment_depletion_test0.2740.0010.275
extract_signatures0.0020.0000.002
fit_to_signatures0.1880.0180.208
fit_to_signatures_bootstrapped10.458 0.29410.763
fit_to_signatures_strict5.9470.1456.107
genomic_distribution20.152 0.56620.767
get_dbs_context0.5400.0020.543
get_indel_context12.854 0.58913.457
get_known_signatures0.5030.3210.828
get_mut_type23.638 0.03723.699
lengthen_mut_matrix0.0190.0070.025
merge_signatures2.7150.2112.928
mut_context2.0710.1312.204
mut_matrix4.3340.1814.520
mut_matrix_stranded9.1820.3269.575
mut_strand1.9960.0222.020
mut_type0.0520.0020.054
mut_type_occurrences1.9510.1022.056
mutations_from_vcf0.0470.0010.047
plot_192_profile5.3560.0165.381
plot_96_profile4.6610.0124.680
plot_bootstrapped_contribution3.5840.0123.600
plot_compare_dbs8.9000.0318.946
plot_compare_indels14.652 0.03714.716
plot_compare_mbs1.5370.0041.545
plot_compare_profiles3.3810.0093.395
plot_contribution5.2300.0155.253
plot_contribution_heatmap3.0120.0133.030
plot_correlation_bootstrap0.7530.0030.759
plot_cosine_heatmap3.6850.0113.701
plot_dbs_contexts6.6350.0166.658
plot_enrichment_depletion6.5510.0176.674
plot_indel_contexts15.903 0.04416.489
plot_lesion_segregation31.547 0.12633.114
plot_main_dbs_contexts0.9460.0040.951
plot_main_indel_contexts1.0340.0041.042
plot_mbs_contexts0.8630.0040.867
plot_original_vs_reconstructed0.8520.0040.858
plot_profile_heatmap8.6980.1088.820
plot_profile_region1.9610.0101.972
plot_rainfall3.4200.0093.434
plot_regional_similarity2.7570.0092.768
plot_river8.5380.0538.602
plot_signature_strand_bias1.4690.0051.477
plot_spectrum8.7050.1128.830
plot_spectrum_region9.3890.1229.530
plot_strand0.3140.0080.323
plot_strand_bias1.3890.0071.400
pool_mut_mat0.0650.0020.067
read_vcfs_as_granges36.766 1.00249.639
rename_nmf_signatures0.0570.0210.077
signature_potential_damage_analysis0.1740.0020.176
split_muts_region7.5740.0557.638
strand_bias_test0.2220.0010.223
strand_occurrences0.2960.0090.306
type_context2.4850.1382.625