| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:39 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 | ||||
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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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1326/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MutationalPatterns 3.11.0 (landing page) Mark van Roosmalen
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: MutationalPatterns |
| Version: 3.11.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings MutationalPatterns_3.11.0.tar.gz |
| StartedAt: 2023-05-30 13:22:34 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 13:48:16 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 1542.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MutationalPatterns.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings MutationalPatterns_3.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MutationalPatterns.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘MutationalPatterns/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MutationalPatterns’ version ‘3.11.0’
* 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 ... 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 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
context_potential_damage_analysis 33.052 0.688 33.742
read_vcfs_as_granges 25.464 0.496 35.751
plot_lesion_segregation 21.486 0.268 21.754
genomic_distribution 16.882 0.360 17.249
get_mut_type 16.398 0.028 16.428
calculate_lesion_segregation 15.783 0.420 16.204
bin_mutation_density 13.060 0.516 13.579
plot_indel_contexts 12.446 0.316 12.762
plot_compare_indels 11.770 0.124 11.894
get_indel_context 10.708 0.540 11.250
fit_to_signatures_bootstrapped 8.595 0.040 8.635
plot_spectrum 8.172 0.232 8.404
plot_river 7.852 0.008 7.861
plot_profile_heatmap 7.456 0.116 7.575
plot_spectrum_region 7.217 0.132 7.351
plot_compare_dbs 7.173 0.084 7.258
mut_matrix_stranded 6.031 0.412 6.444
split_muts_region 5.782 0.036 5.821
plot_dbs_contexts 5.453 0.060 5.512
plot_enrichment_depletion 5.311 0.048 5.360
* 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 ...
‘Introduction_to_MutationalPatterns.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
MutationalPatterns.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL MutationalPatterns ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/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)
MutationalPatterns.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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
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
274.510 8.556 308.805
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
| name | user | system | elapsed | |
| bin_mutation_density | 13.060 | 0.516 | 13.579 | |
| binomial_test | 0.013 | 0.000 | 0.013 | |
| calculate_lesion_segregation | 15.783 | 0.420 | 16.204 | |
| cluster_signatures | 0.080 | 0.000 | 0.082 | |
| context_potential_damage_analysis | 33.052 | 0.688 | 33.742 | |
| convert_sigs_to_ref | 0.061 | 0.004 | 0.067 | |
| cos_sim | 0 | 0 | 0 | |
| cos_sim_matrix | 0.033 | 0.000 | 0.034 | |
| count_dbs_contexts | 0.135 | 0.004 | 0.139 | |
| count_indel_contexts | 0.160 | 0.004 | 0.165 | |
| count_mbs_contexts | 0.124 | 0.000 | 0.126 | |
| determine_regional_similarity | 4.488 | 0.180 | 4.668 | |
| enrichment_depletion_test | 0.218 | 0.000 | 0.218 | |
| extract_signatures | 0.001 | 0.000 | 0.002 | |
| fit_to_signatures | 0.138 | 0.008 | 0.146 | |
| fit_to_signatures_bootstrapped | 8.595 | 0.040 | 8.635 | |
| fit_to_signatures_strict | 4.830 | 0.012 | 4.842 | |
| genomic_distribution | 16.882 | 0.360 | 17.249 | |
| get_dbs_context | 0.395 | 0.004 | 0.400 | |
| get_indel_context | 10.708 | 0.540 | 11.250 | |
| get_known_signatures | 0.317 | 0.216 | 0.539 | |
| get_mut_type | 16.398 | 0.028 | 16.428 | |
| lengthen_mut_matrix | 0.014 | 0.004 | 0.019 | |
| merge_signatures | 1.834 | 0.056 | 1.891 | |
| mut_context | 1.616 | 0.184 | 1.800 | |
| mut_matrix | 2.929 | 0.292 | 3.221 | |
| mut_matrix_stranded | 6.031 | 0.412 | 6.444 | |
| mut_strand | 1.567 | 0.044 | 1.611 | |
| mut_type | 0.034 | 0.004 | 0.039 | |
| mut_type_occurrences | 1.327 | 0.076 | 1.402 | |
| mutations_from_vcf | 0.037 | 0.000 | 0.038 | |
| plot_192_profile | 4.389 | 0.160 | 4.550 | |
| plot_96_profile | 3.693 | 0.003 | 3.697 | |
| plot_bootstrapped_contribution | 2.862 | 0.020 | 2.883 | |
| plot_compare_dbs | 7.173 | 0.084 | 7.258 | |
| plot_compare_indels | 11.770 | 0.124 | 11.894 | |
| plot_compare_mbs | 1.197 | 0.008 | 1.206 | |
| plot_compare_profiles | 2.815 | 0.008 | 2.823 | |
| plot_contribution | 3.859 | 0.020 | 3.879 | |
| plot_contribution_heatmap | 2.526 | 0.040 | 2.567 | |
| plot_correlation_bootstrap | 0.664 | 0.008 | 0.672 | |
| plot_cosine_heatmap | 2.850 | 0.008 | 2.858 | |
| plot_dbs_contexts | 5.453 | 0.060 | 5.512 | |
| plot_enrichment_depletion | 5.311 | 0.048 | 5.360 | |
| plot_indel_contexts | 12.446 | 0.316 | 12.762 | |
| plot_lesion_segregation | 21.486 | 0.268 | 21.754 | |
| plot_main_dbs_contexts | 0.829 | 0.036 | 0.865 | |
| plot_main_indel_contexts | 0.794 | 0.024 | 0.817 | |
| plot_mbs_contexts | 0.711 | 0.024 | 0.735 | |
| plot_original_vs_reconstructed | 0.792 | 0.000 | 0.792 | |
| plot_profile_heatmap | 7.456 | 0.116 | 7.575 | |
| plot_profile_region | 1.618 | 0.004 | 1.623 | |
| plot_rainfall | 2.737 | 0.004 | 2.740 | |
| plot_regional_similarity | 2.253 | 0.024 | 2.278 | |
| plot_river | 7.852 | 0.008 | 7.861 | |
| plot_signature_strand_bias | 1.234 | 0.004 | 1.238 | |
| plot_spectrum | 8.172 | 0.232 | 8.404 | |
| plot_spectrum_region | 7.217 | 0.132 | 7.351 | |
| plot_strand | 0.252 | 0.008 | 0.259 | |
| plot_strand_bias | 1.191 | 0.004 | 1.195 | |
| pool_mut_mat | 0.053 | 0.004 | 0.058 | |
| read_vcfs_as_granges | 25.464 | 0.496 | 35.751 | |
| rename_nmf_signatures | 0.042 | 0.012 | 0.054 | |
| signature_potential_damage_analysis | 0.119 | 0.004 | 0.124 | |
| split_muts_region | 5.782 | 0.036 | 5.821 | |
| strand_bias_test | 0.164 | 0.004 | 0.168 | |
| strand_occurrences | 0.217 | 0.000 | 0.218 | |
| type_context | 1.632 | 0.104 | 1.736 | |