| Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:08:08 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1262/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MutationalPatterns 3.5.5 (landing page) Mark van Roosmalen
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MutationalPatterns |
| Version: 3.5.5 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MutationalPatterns_3.5.5.tar.gz |
| StartedAt: 2022-03-17 19:42:01 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:51:34 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 572.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MutationalPatterns.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MutationalPatterns_3.5.5.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MutationalPatterns.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MutationalPatterns/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MutationalPatterns' version '3.5.5'
* 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 whether package 'MutationalPatterns' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.0Mb
sub-directories of 1Mb or more:
extdata 2.5Mb
states 1.3Mb
* 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 23.33 0.37 23.70
read_vcfs_as_granges 18.24 1.21 28.40
calculate_lesion_segregation 11.67 0.27 11.95
get_mut_type 11.01 0.02 11.04
genomic_distribution 9.54 0.98 10.55
plot_lesion_segregation 10.44 0.03 10.50
bin_mutation_density 9.53 0.33 9.86
plot_compare_indels 6.33 0.00 6.33
plot_indel_contexts 6.28 0.03 6.31
get_indel_context 5.25 0.72 5.97
fit_to_signatures_bootstrapped 5.17 0.05 5.22
plot_spectrum_region 4.56 0.14 5.18
* 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: 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/MutationalPatterns.Rcheck/00check.log'
for details.
MutationalPatterns.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MutationalPatterns
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MutationalPatterns' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MutationalPatterns'
finding HTML links ... done
MutationalPatterns-defunct html
MutationalPatterns-package html
bin_mutation_density html
binomial_test html
calculate_lesion_segregation html
cluster_signatures html
context_potential_damage_analysis html
convert_sigs_to_ref html
cos_sim html
cos_sim_matrix html
count_dbs_contexts html
count_indel_contexts html
count_mbs_contexts html
determine_regional_similarity html
enrichment_depletion_test html
extract_signatures html
fit_to_signatures html
fit_to_signatures_bootstrapped html
fit_to_signatures_strict html
genomic_distribution html
get_dbs_context html
get_indel_context html
get_known_signatures html
get_mut_type html
get_sim_tb html
lengthen_mut_matrix html
merge_signatures html
mut_192_occurrences html
mut_96_occurrences html
mut_context html
mut_matrix html
mut_matrix_stranded html
mut_strand html
mut_type html
mut_type_occurrences html
mutations_from_vcf html
plot_192_profile html
plot_96_profile html
plot_bootstrapped_contribution html
plot_compare_dbs html
plot_compare_indels html
plot_compare_mbs html
plot_compare_profiles html
plot_contribution html
plot_contribution_heatmap html
plot_correlation_bootstrap html
plot_cosine_heatmap html
plot_dbs_contexts html
plot_enrichment_depletion html
plot_indel_contexts html
plot_lesion_segregation html
plot_main_dbs_contexts html
plot_main_indel_contexts html
plot_mbs_contexts html
plot_original_vs_reconstructed html
plot_profile_heatmap html
plot_profile_region html
plot_rainfall html
plot_regional_similarity html
plot_river html
plot_signature_strand_bias html
plot_spectrum html
plot_spectrum_region html
plot_strand html
plot_strand_bias html
pool_mut_mat html
read_vcfs_as_granges html
region_cossim-class html
rename_nmf_signatures html
show-region_cossim-method html
signature_potential_damage_analysis html
split_muts_region html
strand_bias_test html
strand_occurrences html
type_context html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'epivizrChart' is missing or broken
done
MutationalPatterns.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: NMF
Loading required package: pkgmaker
Loading required package: registry
Attaching package: 'pkgmaker'
The following object is masked from 'package:S4Vectors':
new2
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: windows] | Cores 79/80
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 0 | SKIP 0 | PASS 474 ]
>
> proc.time()
user system elapsed
195.25 12.54 257.78
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
| name | user | system | elapsed | |
| bin_mutation_density | 9.53 | 0.33 | 9.86 | |
| binomial_test | 0 | 0 | 0 | |
| calculate_lesion_segregation | 11.67 | 0.27 | 11.95 | |
| cluster_signatures | 0.04 | 0.00 | 0.05 | |
| context_potential_damage_analysis | 23.33 | 0.37 | 23.70 | |
| convert_sigs_to_ref | 0.03 | 0.02 | 0.05 | |
| cos_sim | 0 | 0 | 0 | |
| cos_sim_matrix | 0.02 | 0.00 | 0.01 | |
| count_dbs_contexts | 0.08 | 0.00 | 0.08 | |
| count_indel_contexts | 0.09 | 0.00 | 0.10 | |
| count_mbs_contexts | 0.05 | 0.01 | 0.06 | |
| determine_regional_similarity | 2.23 | 0.31 | 2.55 | |
| enrichment_depletion_test | 0.11 | 0.00 | 0.11 | |
| extract_signatures | 0 | 0 | 0 | |
| fit_to_signatures | 0.08 | 0.00 | 0.07 | |
| fit_to_signatures_bootstrapped | 5.17 | 0.05 | 5.22 | |
| fit_to_signatures_strict | 2.24 | 0.02 | 2.25 | |
| genomic_distribution | 9.54 | 0.98 | 10.55 | |
| get_dbs_context | 0.21 | 0.00 | 0.20 | |
| get_indel_context | 5.25 | 0.72 | 5.97 | |
| get_known_signatures | 0.42 | 0.12 | 0.55 | |
| get_mut_type | 11.01 | 0.02 | 11.04 | |
| lengthen_mut_matrix | 0.00 | 0.02 | 0.02 | |
| merge_signatures | 1.08 | 0.06 | 1.14 | |
| mut_context | 1.10 | 0.25 | 1.34 | |
| mut_matrix | 1.79 | 0.23 | 2.04 | |
| mut_matrix_stranded | 3.34 | 0.42 | 3.77 | |
| mut_strand | 1.19 | 0.08 | 1.26 | |
| mut_type | 0.01 | 0.00 | 0.02 | |
| mut_type_occurrences | 0.69 | 0.13 | 0.81 | |
| mutations_from_vcf | 0.02 | 0.00 | 0.02 | |
| plot_192_profile | 1.9 | 0.0 | 1.9 | |
| plot_96_profile | 1.68 | 0.01 | 1.69 | |
| plot_bootstrapped_contribution | 1.40 | 0.00 | 1.41 | |
| plot_compare_dbs | 3.64 | 0.00 | 3.64 | |
| plot_compare_indels | 6.33 | 0.00 | 6.33 | |
| plot_compare_mbs | 0.7 | 0.0 | 0.7 | |
| plot_compare_profiles | 1.75 | 0.02 | 1.76 | |
| plot_contribution | 2.56 | 0.00 | 2.56 | |
| plot_contribution_heatmap | 2.02 | 0.03 | 2.05 | |
| plot_correlation_bootstrap | 0.39 | 0.03 | 0.42 | |
| plot_cosine_heatmap | 1.67 | 0.00 | 1.67 | |
| plot_dbs_contexts | 2.70 | 0.00 | 2.71 | |
| plot_enrichment_depletion | 3.25 | 0.00 | 3.28 | |
| plot_indel_contexts | 6.28 | 0.03 | 6.31 | |
| plot_lesion_segregation | 10.44 | 0.03 | 10.50 | |
| plot_main_dbs_contexts | 0.55 | 0.02 | 0.56 | |
| plot_main_indel_contexts | 0.39 | 0.00 | 0.39 | |
| plot_mbs_contexts | 0.36 | 0.00 | 0.36 | |
| plot_original_vs_reconstructed | 0.37 | 0.00 | 0.38 | |
| plot_profile_heatmap | 3.46 | 0.06 | 3.51 | |
| plot_profile_region | 0.76 | 0.00 | 0.77 | |
| plot_rainfall | 1.35 | 0.00 | 1.34 | |
| plot_regional_similarity | 1.11 | 0.02 | 1.13 | |
| plot_river | 4.07 | 0.03 | 4.11 | |
| plot_signature_strand_bias | 0.58 | 0.00 | 0.58 | |
| plot_spectrum | 3.59 | 0.12 | 3.73 | |
| plot_spectrum_region | 4.56 | 0.14 | 5.18 | |
| plot_strand | 0.21 | 0.02 | 0.22 | |
| plot_strand_bias | 0.74 | 0.02 | 0.75 | |
| pool_mut_mat | 0.04 | 0.00 | 0.05 | |
| read_vcfs_as_granges | 18.24 | 1.21 | 28.40 | |
| rename_nmf_signatures | 0.05 | 0.00 | 0.05 | |
| signature_potential_damage_analysis | 0.11 | 0.00 | 0.11 | |
| split_muts_region | 3.72 | 0.05 | 3.76 | |
| strand_bias_test | 0.17 | 0.00 | 0.17 | |
| strand_occurrences | 0.25 | 0.02 | 0.27 | |
| type_context | 1.22 | 0.12 | 1.35 | |