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This page was generated on 2024-05-04 11:38:10 -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 palomino3


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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings MutationalPatterns_3.14.0.tar.gz
StartedAt: 2024-05-04 05:56:52 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 06:08:39 -0400 (Sat, 04 May 2024)
EllapsedTime: 706.9 seconds
RetCode: 0
Status:   OK  
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings MutationalPatterns_3.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/MutationalPatterns.Rcheck'
* using R version 4.4.0 beta (2024-04-15 r86425 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 '3.14.0'
* 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 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              25.17   2.33   34.06
context_potential_damage_analysis 26.28   0.64   26.93
plot_lesion_segregation           18.98   0.21   19.38
get_mut_type                      14.47   0.09   14.60
genomic_distribution              12.78   1.33   15.69
bin_mutation_density              12.05   0.61   12.67
calculate_lesion_segregation      11.77   0.50   12.27
plot_indel_contexts               10.60   0.04   10.64
get_indel_context                  8.55   1.42    9.97
plot_compare_indels                8.98   0.10    9.08
fit_to_signatures_bootstrapped     6.81   0.27    7.08
plot_profile_heatmap               6.38   0.33    6.70
plot_river                         6.25   0.18    6.43
mut_matrix_stranded                5.09   0.89    6.01
plot_spectrum_region               5.41   0.33    5.75
split_muts_region                  5.58   0.14    5.72
plot_compare_dbs                   5.44   0.06    5.50
* 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
  'F:/biocbuild/bbs-3.19-bioc/meat/MutationalPatterns.Rcheck/00check.log'
for details.


Installation output

MutationalPatterns.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL MutationalPatterns
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup"
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 
 248.71   20.71  287.62 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density12.05 0.6112.67
binomial_test0.020.000.01
calculate_lesion_segregation11.77 0.5012.27
cluster_signatures0.030.030.09
context_potential_damage_analysis26.28 0.6426.93
convert_sigs_to_ref0.060.040.09
cos_sim000
cos_sim_matrix0.050.000.05
count_dbs_contexts0.120.000.12
count_indel_contexts0.130.000.13
count_mbs_contexts0.110.000.11
determine_regional_similarity3.700.454.15
enrichment_depletion_test0.220.000.22
extract_signatures000
fit_to_signatures0.110.060.17
fit_to_signatures_bootstrapped6.810.277.08
fit_to_signatures_strict4.080.174.25
genomic_distribution12.78 1.3315.69
get_dbs_context0.310.010.33
get_indel_context8.551.429.97
get_known_signatures0.400.240.75
get_mut_type14.47 0.0914.60
lengthen_mut_matrix0.020.020.03
merge_signatures1.150.041.20
mut_context1.020.321.33
mut_matrix2.500.392.89
mut_matrix_stranded5.090.896.01
mut_strand1.420.031.48
mut_type0.030.000.03
mut_type_occurrences1.170.251.42
mutations_from_vcf0.020.020.03
plot_192_profile4.950.034.99
plot_96_profile2.480.032.51
plot_bootstrapped_contribution2.140.092.24
plot_compare_dbs5.440.065.50
plot_compare_indels8.980.109.08
plot_compare_mbs1.060.001.06
plot_compare_profiles2.890.032.93
plot_contribution1.470.031.50
plot_contribution_heatmap1.520.021.53
plot_correlation_bootstrap0.580.010.59
plot_cosine_heatmap202
plot_dbs_contexts4.760.104.86
plot_enrichment_depletion3.990.003.99
plot_indel_contexts10.60 0.0410.64
plot_lesion_segregation18.98 0.2119.38
plot_main_dbs_contexts0.630.000.62
plot_main_indel_contexts0.540.010.56
plot_mbs_contexts0.580.030.61
plot_original_vs_reconstructed0.670.000.68
plot_profile_heatmap6.380.336.70
plot_profile_region1.450.021.47
plot_rainfall2.160.002.15
plot_regional_similarity1.860.011.88
plot_river6.250.186.43
plot_signature_strand_bias0.790.020.81
plot_spectrum4.580.224.80
plot_spectrum_region5.410.335.75
plot_strand0.340.030.37
plot_strand_bias0.810.030.84
pool_mut_mat0.050.000.05
read_vcfs_as_granges25.17 2.3334.06
rename_nmf_signatures0.050.030.08
signature_potential_damage_analysis0.110.000.13
split_muts_region5.580.145.72
strand_bias_test0.200.020.21
strand_occurrences0.300.030.33
type_context1.730.322.06