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This page was generated on 2024-05-04 11:36:53 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1393/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 3.14.0  (landing page)
Mark van Roosmalen
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/MutationalPatterns
git_branch: RELEASE_3_19
git_last_commit: 268518e
git_last_commit_date: 2024-04-30 10:54:30 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for MutationalPatterns on nebbiolo1


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: 3.14.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MutationalPatterns_3.14.0.tar.gz
StartedAt: 2024-05-04 01:32:47 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 01:51:34 -0400 (Sat, 04 May 2024)
EllapsedTime: 1127.5 seconds
RetCode: 0
Status:   OK  
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MutationalPatterns_3.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MutationalPatterns.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘MutationalPatterns/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MutationalPatterns’ version ‘3.14.0’
* 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 ‘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 loading without being on the library search path ... 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              20.688  1.605  29.111
context_potential_damage_analysis 21.272  0.568  21.841
plot_lesion_segregation           14.256  0.056  14.313
get_mut_type                      10.700  0.024  10.726
bin_mutation_density              10.064  0.640  10.705
genomic_distribution              10.171  0.267  10.443
calculate_lesion_segregation       9.445  0.344   9.789
plot_indel_contexts                7.659  0.048   7.708
plot_compare_indels                7.302  0.024   7.327
get_indel_context                  6.262  0.900   7.163
fit_to_signatures_bootstrapped     5.244  0.028   5.272
plot_profile_heatmap               5.114  0.064   5.179
plot_river                         5.035  0.024   5.059
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/MutationalPatterns.Rcheck/00check.log’
for details.


Installation output

MutationalPatterns.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL MutationalPatterns
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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
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: bigmemory] | 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("MutationalPatterns")
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 474 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 474 ]
> 
> proc.time()
   user  system elapsed 
190.246   9.750 216.897 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density10.064 0.64010.705
binomial_test0.010.000.01
calculate_lesion_segregation9.4450.3449.789
cluster_signatures0.0440.0000.045
context_potential_damage_analysis21.272 0.56821.841
convert_sigs_to_ref0.0380.0000.039
cos_sim000
cos_sim_matrix0.0140.0070.022
count_dbs_contexts0.0780.0050.082
count_indel_contexts0.0940.0000.094
count_mbs_contexts0.0650.0040.069
determine_regional_similarity2.6990.3923.091
enrichment_depletion_test0.1270.0000.127
extract_signatures0.0020.0000.001
fit_to_signatures0.0830.0080.092
fit_to_signatures_bootstrapped5.2440.0285.272
fit_to_signatures_strict2.9440.0082.953
genomic_distribution10.171 0.26710.443
get_dbs_context0.2450.0060.252
get_indel_context6.2620.9007.163
get_known_signatures0.3100.4320.746
get_mut_type10.700 0.02410.726
lengthen_mut_matrix0.0110.0080.019
merge_signatures1.0420.1641.206
mut_context1.1070.1361.243
mut_matrix1.8390.2842.123
mut_matrix_stranded4.0130.4444.457
mut_strand1.0610.0201.080
mut_type0.0250.0040.028
mut_type_occurrences0.8570.1200.978
mutations_from_vcf0.0260.0000.026
plot_192_profile3.7230.1203.843
plot_96_profile2.2570.0032.260
plot_bootstrapped_contribution1.6650.0041.668
plot_compare_dbs4.5220.0324.555
plot_compare_indels7.3020.0247.327
plot_compare_mbs0.7450.0000.745
plot_compare_profiles1.9470.0121.960
plot_contribution1.5000.0481.548
plot_contribution_heatmap1.3450.0121.356
plot_correlation_bootstrap0.4540.0000.453
plot_cosine_heatmap1.6250.0111.637
plot_dbs_contexts3.490.043.53
plot_enrichment_depletion3.1630.0003.163
plot_indel_contexts7.6590.0487.708
plot_lesion_segregation14.256 0.05614.313
plot_main_dbs_contexts0.5720.0040.577
plot_main_indel_contexts0.5190.0000.519
plot_mbs_contexts0.4890.0040.494
plot_original_vs_reconstructed0.5020.0080.509
plot_profile_heatmap5.1140.0645.179
plot_profile_region1.0730.0001.073
plot_rainfall1.7720.0121.785
plot_regional_similarity1.4510.0321.484
plot_river5.0350.0245.059
plot_signature_strand_bias0.6320.0040.637
plot_spectrum4.1350.3484.483
plot_spectrum_region4.4270.1244.551
plot_strand0.2110.0080.218
plot_strand_bias0.8240.0080.831
pool_mut_mat0.0400.0040.044
read_vcfs_as_granges20.688 1.60529.111
rename_nmf_signatures0.0360.0330.070
signature_potential_damage_analysis0.0950.0120.107
split_muts_region4.4560.2204.676
strand_bias_test0.1140.0080.122
strand_occurrences0.1510.0000.150
type_context1.2630.2281.491