| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:36 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 1324/2194 | 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/bbs-3.17-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MutationalPatterns_3.11.0.tar.gz |
| StartedAt: 2023-05-09 22:38:26 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 23:03:19 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 1493.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MutationalPatterns.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MutationalPatterns_3.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* 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 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 31.571 0.732 32.322
read_vcfs_as_granges 26.356 2.136 36.920
plot_lesion_segregation 21.473 0.172 21.647
genomic_distribution 16.735 0.352 17.094
get_mut_type 15.752 0.176 15.929
calculate_lesion_segregation 15.013 0.280 15.303
bin_mutation_density 12.477 0.600 13.079
plot_indel_contexts 12.089 0.020 12.109
plot_compare_indels 11.727 0.040 11.768
get_indel_context 9.109 0.472 9.587
fit_to_signatures_bootstrapped 8.218 0.016 8.234
plot_spectrum_region 7.409 0.076 7.486
plot_river 7.235 0.036 7.272
plot_compare_dbs 7.154 0.056 7.211
plot_profile_heatmap 6.758 0.052 6.810
plot_spectrum 6.606 0.072 6.679
mut_matrix_stranded 5.869 0.236 6.106
split_muts_region 5.845 0.212 6.057
plot_dbs_contexts 5.403 0.000 5.403
plot_enrichment_depletion 5.118 0.027 5.145
* 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/bbs-3.17-bioc/R/bin/R CMD INSTALL MutationalPatterns ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/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 Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
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 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: synchronicity] | 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
269.400 11.552 303.678
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
| name | user | system | elapsed | |
| bin_mutation_density | 12.477 | 0.600 | 13.079 | |
| binomial_test | 0.013 | 0.000 | 0.013 | |
| calculate_lesion_segregation | 15.013 | 0.280 | 15.303 | |
| cluster_signatures | 0.071 | 0.004 | 0.076 | |
| context_potential_damage_analysis | 31.571 | 0.732 | 32.322 | |
| convert_sigs_to_ref | 0.061 | 0.000 | 0.063 | |
| cos_sim | 0 | 0 | 0 | |
| cos_sim_matrix | 0.027 | 0.007 | 0.034 | |
| count_dbs_contexts | 0.124 | 0.003 | 0.129 | |
| count_indel_contexts | 0.178 | 0.017 | 0.195 | |
| count_mbs_contexts | 0.111 | 0.000 | 0.111 | |
| determine_regional_similarity | 4.258 | 0.120 | 4.422 | |
| enrichment_depletion_test | 0.207 | 0.000 | 0.208 | |
| extract_signatures | 0.002 | 0.000 | 0.002 | |
| fit_to_signatures | 0.142 | 0.004 | 0.147 | |
| fit_to_signatures_bootstrapped | 8.218 | 0.016 | 8.234 | |
| fit_to_signatures_strict | 4.724 | 0.012 | 4.735 | |
| genomic_distribution | 16.735 | 0.352 | 17.094 | |
| get_dbs_context | 0.380 | 0.008 | 0.389 | |
| get_indel_context | 9.109 | 0.472 | 9.587 | |
| get_known_signatures | 0.334 | 0.208 | 0.548 | |
| get_mut_type | 15.752 | 0.176 | 15.929 | |
| lengthen_mut_matrix | 0.014 | 0.004 | 0.019 | |
| merge_signatures | 1.696 | 0.120 | 1.815 | |
| mut_context | 1.497 | 0.140 | 1.637 | |
| mut_matrix | 2.732 | 0.084 | 2.816 | |
| mut_matrix_stranded | 5.869 | 0.236 | 6.106 | |
| mut_strand | 1.403 | 0.004 | 1.406 | |
| mut_type | 0.035 | 0.004 | 0.039 | |
| mut_type_occurrences | 1.286 | 0.060 | 1.347 | |
| mutations_from_vcf | 0.037 | 0.000 | 0.037 | |
| plot_192_profile | 4.253 | 0.020 | 4.275 | |
| plot_96_profile | 3.588 | 0.000 | 3.589 | |
| plot_bootstrapped_contribution | 2.847 | 0.036 | 2.883 | |
| plot_compare_dbs | 7.154 | 0.056 | 7.211 | |
| plot_compare_indels | 11.727 | 0.040 | 11.768 | |
| plot_compare_mbs | 1.207 | 0.008 | 1.216 | |
| plot_compare_profiles | 2.906 | 0.072 | 2.977 | |
| plot_contribution | 4.117 | 0.004 | 4.123 | |
| plot_contribution_heatmap | 2.325 | 0.016 | 2.342 | |
| plot_correlation_bootstrap | 0.682 | 0.023 | 0.704 | |
| plot_cosine_heatmap | 2.990 | 0.032 | 3.022 | |
| plot_dbs_contexts | 5.403 | 0.000 | 5.403 | |
| plot_enrichment_depletion | 5.118 | 0.027 | 5.145 | |
| plot_indel_contexts | 12.089 | 0.020 | 12.109 | |
| plot_lesion_segregation | 21.473 | 0.172 | 21.647 | |
| plot_main_dbs_contexts | 0.726 | 0.007 | 0.734 | |
| plot_main_indel_contexts | 0.775 | 0.004 | 0.779 | |
| plot_mbs_contexts | 0.790 | 0.016 | 0.807 | |
| plot_original_vs_reconstructed | 0.742 | 0.004 | 0.745 | |
| plot_profile_heatmap | 6.758 | 0.052 | 6.810 | |
| plot_profile_region | 1.469 | 0.004 | 1.473 | |
| plot_rainfall | 2.609 | 0.028 | 2.637 | |
| plot_regional_similarity | 2.065 | 0.008 | 2.074 | |
| plot_river | 7.235 | 0.036 | 7.272 | |
| plot_signature_strand_bias | 1.213 | 0.000 | 1.213 | |
| plot_spectrum | 6.606 | 0.072 | 6.679 | |
| plot_spectrum_region | 7.409 | 0.076 | 7.486 | |
| plot_strand | 0.287 | 0.000 | 0.287 | |
| plot_strand_bias | 1.276 | 0.000 | 1.275 | |
| pool_mut_mat | 0.055 | 0.004 | 0.059 | |
| read_vcfs_as_granges | 26.356 | 2.136 | 36.920 | |
| rename_nmf_signatures | 0.043 | 0.016 | 0.059 | |
| signature_potential_damage_analysis | 0.135 | 0.004 | 0.139 | |
| split_muts_region | 5.845 | 0.212 | 6.057 | |
| strand_bias_test | 0.219 | 0.016 | 0.236 | |
| strand_occurrences | 0.213 | 0.020 | 0.232 | |
| type_context | 1.713 | 0.196 | 1.909 | |