| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-23 01:34:14 -0000 (Thu, 23 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4245 |
| 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: - 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1302/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MutationalPatterns 3.9.1 (landing page) Mark van Roosmalen
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: MutationalPatterns |
| Version: 3.9.1 |
| 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/library --timings MutationalPatterns_3.9.1.tar.gz |
| StartedAt: 2023-02-22 08:57:32 -0000 (Wed, 22 Feb 2023) |
| EndedAt: 2023-02-22 09:23:43 -0000 (Wed, 22 Feb 2023) |
| EllapsedTime: 1570.5 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/library --timings MutationalPatterns_3.9.1.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* 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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MutationalPatterns/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MutationalPatterns’ version ‘3.9.1’
* 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 ... 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 46.838 0.644 47.482
read_vcfs_as_granges 27.689 0.495 37.338
plot_lesion_segregation 20.976 0.040 21.016
get_mut_type 17.712 0.056 17.769
genomic_distribution 15.409 0.300 15.717
calculate_lesion_segregation 14.982 0.269 15.259
plot_compare_indels 13.510 0.188 13.700
bin_mutation_density 11.995 0.699 12.696
plot_indel_contexts 12.540 0.036 12.576
get_indel_context 9.776 0.432 10.216
plot_spectrum_region 7.970 0.092 8.063
plot_river 7.881 0.052 7.934
plot_profile_heatmap 7.689 0.160 7.849
fit_to_signatures_bootstrapped 7.825 0.020 7.846
plot_compare_dbs 7.815 0.020 7.839
plot_spectrum 7.294 0.136 7.431
mut_matrix_stranded 6.514 0.252 6.767
split_muts_region 6.279 0.008 6.287
plot_enrichment_depletion 6.058 0.012 6.069
plot_dbs_contexts 5.283 0.048 5.331
* 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/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) (2023-01-14 r83615) -- "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 31/32
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 12 | SKIP 0 | PASS 474 ]
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 474 ]
>
> proc.time()
user system elapsed
295.211 6.275 331.179
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
| name | user | system | elapsed | |
| bin_mutation_density | 11.995 | 0.699 | 12.696 | |
| binomial_test | 0.088 | 0.004 | 0.092 | |
| calculate_lesion_segregation | 14.982 | 0.269 | 15.259 | |
| cluster_signatures | 0.075 | 0.000 | 0.076 | |
| context_potential_damage_analysis | 46.838 | 0.644 | 47.482 | |
| convert_sigs_to_ref | 0.052 | 0.008 | 0.062 | |
| cos_sim | 0 | 0 | 0 | |
| cos_sim_matrix | 0.029 | 0.004 | 0.032 | |
| count_dbs_contexts | 0.176 | 0.008 | 0.184 | |
| count_indel_contexts | 0.178 | 0.000 | 0.180 | |
| count_mbs_contexts | 0.141 | 0.000 | 0.142 | |
| determine_regional_similarity | 4.516 | 0.204 | 4.751 | |
| enrichment_depletion_test | 1.609 | 0.008 | 1.618 | |
| extract_signatures | 0.001 | 0.000 | 0.002 | |
| fit_to_signatures | 0.143 | 0.004 | 0.148 | |
| fit_to_signatures_bootstrapped | 7.825 | 0.020 | 7.846 | |
| fit_to_signatures_strict | 4.399 | 0.004 | 4.402 | |
| genomic_distribution | 15.409 | 0.300 | 15.717 | |
| get_dbs_context | 0.441 | 0.000 | 0.442 | |
| get_indel_context | 9.776 | 0.432 | 10.216 | |
| get_known_signatures | 0.335 | 0.160 | 0.501 | |
| get_mut_type | 17.712 | 0.056 | 17.769 | |
| lengthen_mut_matrix | 0.011 | 0.004 | 0.015 | |
| merge_signatures | 1.915 | 0.036 | 1.950 | |
| mut_context | 1.603 | 0.088 | 1.692 | |
| mut_matrix | 3.026 | 0.160 | 3.186 | |
| mut_matrix_stranded | 6.514 | 0.252 | 6.767 | |
| mut_strand | 1.544 | 0.020 | 1.564 | |
| mut_type | 0.037 | 0.000 | 0.037 | |
| mut_type_occurrences | 1.386 | 0.056 | 1.442 | |
| mutations_from_vcf | 0.04 | 0.00 | 0.04 | |
| plot_192_profile | 4.629 | 0.012 | 4.644 | |
| plot_96_profile | 3.883 | 0.008 | 3.892 | |
| plot_bootstrapped_contribution | 2.952 | 0.008 | 2.961 | |
| plot_compare_dbs | 7.815 | 0.020 | 7.839 | |
| plot_compare_indels | 13.510 | 0.188 | 13.700 | |
| plot_compare_mbs | 1.272 | 0.008 | 1.281 | |
| plot_compare_profiles | 2.915 | 0.000 | 2.915 | |
| plot_contribution | 3.925 | 0.056 | 3.981 | |
| plot_contribution_heatmap | 2.241 | 0.028 | 2.270 | |
| plot_correlation_bootstrap | 0.668 | 0.004 | 0.671 | |
| plot_cosine_heatmap | 2.708 | 0.008 | 2.716 | |
| plot_dbs_contexts | 5.283 | 0.048 | 5.331 | |
| plot_enrichment_depletion | 6.058 | 0.012 | 6.069 | |
| plot_indel_contexts | 12.540 | 0.036 | 12.576 | |
| plot_lesion_segregation | 20.976 | 0.040 | 21.016 | |
| plot_main_dbs_contexts | 0.868 | 0.008 | 0.876 | |
| plot_main_indel_contexts | 0.843 | 0.004 | 0.847 | |
| plot_mbs_contexts | 0.783 | 0.000 | 0.783 | |
| plot_original_vs_reconstructed | 0.731 | 0.000 | 0.731 | |
| plot_profile_heatmap | 7.689 | 0.160 | 7.849 | |
| plot_profile_region | 1.607 | 0.004 | 1.611 | |
| plot_rainfall | 2.610 | 0.008 | 2.618 | |
| plot_regional_similarity | 2.180 | 0.004 | 2.186 | |
| plot_river | 7.881 | 0.052 | 7.934 | |
| plot_signature_strand_bias | 1.883 | 0.000 | 1.883 | |
| plot_spectrum | 7.294 | 0.136 | 7.431 | |
| plot_spectrum_region | 7.970 | 0.092 | 8.063 | |
| plot_strand | 0.260 | 0.007 | 0.267 | |
| plot_strand_bias | 1.402 | 0.004 | 1.405 | |
| pool_mut_mat | 0.083 | 0.000 | 0.083 | |
| read_vcfs_as_granges | 27.689 | 0.495 | 37.338 | |
| rename_nmf_signatures | 0.052 | 0.000 | 0.052 | |
| signature_potential_damage_analysis | 0.176 | 0.000 | 0.177 | |
| split_muts_region | 6.279 | 0.008 | 6.287 | |
| strand_bias_test | 0.362 | 0.000 | 0.362 | |
| strand_occurrences | 0.236 | 0.000 | 0.236 | |
| type_context | 1.755 | 0.172 | 1.927 | |