| Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-03-30 11:00:39 -0400 (Thu, 30 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | R Under development (unstable) (2023-03-17 r83997) -- "Unsuffered Consequences" | 4168 |
| 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: 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 1327/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MutationalPatterns 3.9.1 (landing page) Mark van Roosmalen
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | NA | ||||||||
| Package: MutationalPatterns |
| Version: 3.9.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MutationalPatterns_3.9.1.tar.gz |
| StartedAt: 2023-03-29 15:51:21 -0400 (Wed, 29 Mar 2023) |
| EndedAt: 2023-03-29 16:06:37 -0400 (Wed, 29 Mar 2023) |
| EllapsedTime: 915.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MutationalPatterns.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MutationalPatterns_3.9.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MutationalPatterns.Rcheck’
* using R Under development (unstable) (2023-03-17 r83997)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 13.0.0 (clang-1300.0.29.3)
GNU Fortran (GCC) 12.0.1 20220312 (experimental)
* running under: macOS Monterey 12.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MutationalPatterns/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MutationalPatterns’ version ‘3.9.1’
* 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 37.907 0.586 47.632
read_vcfs_as_granges 23.116 1.278 31.377
genomic_distribution 14.044 3.461 30.125
plot_lesion_segregation 17.035 0.220 22.241
get_mut_type 15.504 0.270 20.579
calculate_lesion_segregation 11.986 0.320 15.032
plot_compare_indels 10.437 0.681 14.921
bin_mutation_density 9.966 0.333 13.583
plot_indel_contexts 9.661 0.312 12.842
get_indel_context 8.501 0.892 11.759
plot_river 7.206 0.208 9.339
mut_matrix_stranded 5.687 1.334 11.246
plot_compare_dbs 6.259 0.607 9.548
fit_to_signatures_bootstrapped 6.054 0.474 9.337
plot_profile_heatmap 5.963 0.225 7.404
plot_spectrum_region 5.720 0.158 6.068
plot_spectrum 5.378 0.259 6.934
split_muts_region 5.038 0.082 6.516
plot_enrichment_depletion 4.855 0.208 6.692
determine_regional_similarity 3.780 0.428 6.084
plot_dbs_contexts 4.081 0.041 5.172
plot_96_profile 3.344 0.497 5.714
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
MutationalPatterns.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MutationalPatterns ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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) (2023-03-17 r83997) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 7/8
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
243.339 17.965 356.745
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
| name | user | system | elapsed | |
| bin_mutation_density | 9.966 | 0.333 | 13.583 | |
| binomial_test | 0.069 | 0.001 | 0.086 | |
| calculate_lesion_segregation | 11.986 | 0.320 | 15.032 | |
| cluster_signatures | 0.051 | 0.004 | 0.057 | |
| context_potential_damage_analysis | 37.907 | 0.586 | 47.632 | |
| convert_sigs_to_ref | 0.046 | 0.005 | 0.070 | |
| cos_sim | 0 | 0 | 0 | |
| cos_sim_matrix | 0.021 | 0.005 | 0.035 | |
| count_dbs_contexts | 0.112 | 0.005 | 0.152 | |
| count_indel_contexts | 0.180 | 0.007 | 0.242 | |
| count_mbs_contexts | 0.123 | 0.003 | 0.168 | |
| determine_regional_similarity | 3.780 | 0.428 | 6.084 | |
| enrichment_depletion_test | 1.257 | 0.018 | 1.716 | |
| extract_signatures | 0.001 | 0.001 | 0.004 | |
| fit_to_signatures | 0.099 | 0.013 | 0.147 | |
| fit_to_signatures_bootstrapped | 6.054 | 0.474 | 9.337 | |
| fit_to_signatures_strict | 3.457 | 0.109 | 4.841 | |
| genomic_distribution | 14.044 | 3.461 | 30.125 | |
| get_dbs_context | 0.353 | 0.027 | 0.478 | |
| get_indel_context | 8.501 | 0.892 | 11.759 | |
| get_known_signatures | 0.278 | 0.374 | 0.728 | |
| get_mut_type | 15.504 | 0.270 | 20.579 | |
| lengthen_mut_matrix | 0.013 | 0.013 | 0.033 | |
| merge_signatures | 1.364 | 0.272 | 2.227 | |
| mut_context | 1.487 | 0.193 | 2.272 | |
| mut_matrix | 2.577 | 0.465 | 4.634 | |
| mut_matrix_stranded | 5.687 | 1.334 | 11.246 | |
| mut_strand | 1.406 | 0.177 | 2.330 | |
| mut_type | 0.035 | 0.006 | 0.053 | |
| mut_type_occurrences | 1.208 | 0.203 | 1.995 | |
| mutations_from_vcf | 0.032 | 0.002 | 0.056 | |
| plot_192_profile | 3.455 | 0.087 | 4.976 | |
| plot_96_profile | 3.344 | 0.497 | 5.714 | |
| plot_bootstrapped_contribution | 2.483 | 0.183 | 3.658 | |
| plot_compare_dbs | 6.259 | 0.607 | 9.548 | |
| plot_compare_indels | 10.437 | 0.681 | 14.921 | |
| plot_compare_mbs | 0.939 | 0.023 | 1.283 | |
| plot_compare_profiles | 2.208 | 0.027 | 2.886 | |
| plot_contribution | 3.056 | 0.049 | 3.944 | |
| plot_contribution_heatmap | 1.785 | 0.040 | 2.315 | |
| plot_correlation_bootstrap | 0.580 | 0.013 | 0.768 | |
| plot_cosine_heatmap | 2.200 | 0.033 | 2.867 | |
| plot_dbs_contexts | 4.081 | 0.041 | 5.172 | |
| plot_enrichment_depletion | 4.855 | 0.208 | 6.692 | |
| plot_indel_contexts | 9.661 | 0.312 | 12.842 | |
| plot_lesion_segregation | 17.035 | 0.220 | 22.241 | |
| plot_main_dbs_contexts | 0.707 | 0.016 | 0.943 | |
| plot_main_indel_contexts | 0.655 | 0.040 | 0.944 | |
| plot_mbs_contexts | 0.640 | 0.037 | 0.915 | |
| plot_original_vs_reconstructed | 0.563 | 0.020 | 0.745 | |
| plot_profile_heatmap | 5.963 | 0.225 | 7.404 | |
| plot_profile_region | 1.270 | 0.015 | 1.638 | |
| plot_rainfall | 2.279 | 0.029 | 2.936 | |
| plot_regional_similarity | 1.861 | 0.025 | 2.417 | |
| plot_river | 7.206 | 0.208 | 9.339 | |
| plot_signature_strand_bias | 1.436 | 0.019 | 1.866 | |
| plot_spectrum | 5.378 | 0.259 | 6.934 | |
| plot_spectrum_region | 5.720 | 0.158 | 6.068 | |
| plot_strand | 0.265 | 0.012 | 0.303 | |
| plot_strand_bias | 0.968 | 0.013 | 1.025 | |
| pool_mut_mat | 0.054 | 0.004 | 0.061 | |
| read_vcfs_as_granges | 23.116 | 1.278 | 31.377 | |
| rename_nmf_signatures | 0.036 | 0.044 | 0.087 | |
| signature_potential_damage_analysis | 0.147 | 0.004 | 0.170 | |
| split_muts_region | 5.038 | 0.082 | 6.516 | |
| strand_bias_test | 0.277 | 0.003 | 0.354 | |
| strand_occurrences | 0.230 | 0.008 | 0.301 | |
| type_context | 1.527 | 0.148 | 2.020 | |