| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:37 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 1328/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MutationalPatterns 3.11.0 (landing page) Mark van Roosmalen
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 2023-06-06 02:54:48 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 03:19:46 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 1498.3 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 (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 32.401 0.598 33.143
read_vcfs_as_granges 28.502 0.594 37.965
plot_lesion_segregation 21.682 0.515 22.235
get_mut_type 16.741 0.064 16.834
genomic_distribution 15.968 0.216 16.218
calculate_lesion_segregation 15.913 0.244 16.184
bin_mutation_density 12.701 0.355 13.082
plot_indel_contexts 12.600 0.423 13.046
plot_compare_indels 12.158 0.084 12.265
get_indel_context 9.566 0.455 10.041
fit_to_signatures_bootstrapped 8.943 0.108 9.067
plot_spectrum_region 8.237 0.211 8.465
plot_river 8.150 0.112 8.277
plot_profile_heatmap 7.694 0.132 7.839
mut_matrix_stranded 7.316 0.188 7.518
plot_compare_dbs 7.402 0.044 7.461
plot_spectrum 7.291 0.099 7.404
plot_dbs_contexts 5.646 0.224 5.882
plot_enrichment_depletion 5.429 0.371 5.810
split_muts_region 5.766 0.032 5.810
* 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: 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
277.676 14.969 316.441
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
| name | user | system | elapsed | |
| bin_mutation_density | 12.701 | 0.355 | 13.082 | |
| binomial_test | 0.013 | 0.000 | 0.013 | |
| calculate_lesion_segregation | 15.913 | 0.244 | 16.184 | |
| cluster_signatures | 0.075 | 0.000 | 0.077 | |
| context_potential_damage_analysis | 32.401 | 0.598 | 33.143 | |
| convert_sigs_to_ref | 0.054 | 0.008 | 0.065 | |
| cos_sim | 0.000 | 0.000 | 0.001 | |
| cos_sim_matrix | 0.032 | 0.000 | 0.033 | |
| count_dbs_contexts | 0.122 | 0.004 | 0.126 | |
| count_indel_contexts | 0.148 | 0.000 | 0.149 | |
| count_mbs_contexts | 0.112 | 0.000 | 0.113 | |
| determine_regional_similarity | 4.466 | 0.164 | 4.638 | |
| enrichment_depletion_test | 0.203 | 0.004 | 0.208 | |
| extract_signatures | 0.002 | 0.000 | 0.002 | |
| fit_to_signatures | 0.137 | 0.000 | 0.139 | |
| fit_to_signatures_bootstrapped | 8.943 | 0.108 | 9.067 | |
| fit_to_signatures_strict | 4.324 | 0.008 | 4.339 | |
| genomic_distribution | 15.968 | 0.216 | 16.218 | |
| get_dbs_context | 0.432 | 0.007 | 0.440 | |
| get_indel_context | 9.566 | 0.455 | 10.041 | |
| get_known_signatures | 0.325 | 0.151 | 0.484 | |
| get_mut_type | 16.741 | 0.064 | 16.834 | |
| lengthen_mut_matrix | 0.016 | 0.000 | 0.017 | |
| merge_signatures | 1.807 | 0.044 | 1.854 | |
| mut_context | 1.622 | 0.088 | 1.713 | |
| mut_matrix | 2.789 | 0.133 | 2.927 | |
| mut_matrix_stranded | 7.316 | 0.188 | 7.518 | |
| mut_strand | 1.415 | 0.000 | 1.417 | |
| mut_type | 0.038 | 0.000 | 0.038 | |
| mut_type_occurrences | 1.340 | 0.063 | 1.407 | |
| mutations_from_vcf | 0.037 | 0.000 | 0.036 | |
| plot_192_profile | 4.321 | 0.036 | 4.368 | |
| plot_96_profile | 3.724 | 0.008 | 3.740 | |
| plot_bootstrapped_contribution | 2.846 | 0.016 | 2.869 | |
| plot_compare_dbs | 7.402 | 0.044 | 7.461 | |
| plot_compare_indels | 12.158 | 0.084 | 12.265 | |
| plot_compare_mbs | 1.191 | 0.000 | 1.193 | |
| plot_compare_profiles | 2.961 | 0.000 | 2.966 | |
| plot_contribution | 4.277 | 0.024 | 4.310 | |
| plot_contribution_heatmap | 2.399 | 0.000 | 2.406 | |
| plot_correlation_bootstrap | 0.719 | 0.000 | 0.721 | |
| plot_cosine_heatmap | 3.007 | 0.004 | 3.016 | |
| plot_dbs_contexts | 5.646 | 0.224 | 5.882 | |
| plot_enrichment_depletion | 5.429 | 0.371 | 5.810 | |
| plot_indel_contexts | 12.600 | 0.423 | 13.046 | |
| plot_lesion_segregation | 21.682 | 0.515 | 22.235 | |
| plot_main_dbs_contexts | 0.902 | 0.008 | 0.912 | |
| plot_main_indel_contexts | 0.861 | 0.012 | 0.874 | |
| plot_mbs_contexts | 0.753 | 0.004 | 0.759 | |
| plot_original_vs_reconstructed | 0.843 | 0.015 | 0.860 | |
| plot_profile_heatmap | 7.694 | 0.132 | 7.839 | |
| plot_profile_region | 1.662 | 0.011 | 1.677 | |
| plot_rainfall | 2.783 | 0.008 | 2.796 | |
| plot_regional_similarity | 2.323 | 0.016 | 2.344 | |
| plot_river | 8.150 | 0.112 | 8.277 | |
| plot_signature_strand_bias | 1.276 | 0.004 | 1.282 | |
| plot_spectrum | 7.291 | 0.099 | 7.404 | |
| plot_spectrum_region | 8.237 | 0.211 | 8.465 | |
| plot_strand | 0.296 | 0.012 | 0.308 | |
| plot_strand_bias | 1.364 | 0.012 | 1.378 | |
| pool_mut_mat | 0.057 | 0.004 | 0.061 | |
| read_vcfs_as_granges | 28.502 | 0.594 | 37.965 | |
| rename_nmf_signatures | 0.038 | 0.012 | 0.051 | |
| signature_potential_damage_analysis | 0.123 | 0.000 | 0.125 | |
| split_muts_region | 5.766 | 0.032 | 5.810 | |
| strand_bias_test | 0.168 | 0.004 | 0.173 | |
| strand_occurrences | 0.216 | 0.004 | 0.220 | |
| type_context | 1.683 | 0.112 | 1.798 | |