Daniel Huebschmann
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/YAPSA |
| Branch: master |
| Last Commit: c94eeef |
| Last Changed Date: 2020-01-07 06:55:55 -0500 (Tue, 07 Jan 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:46:00 -0500 (Thu, 16 Jan 2020).
| Package 1813/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| YAPSA 1.13.3 Daniel Huebschmann
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | NA | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: YAPSA |
| Version: 1.13.3 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:YAPSA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings YAPSA_1.13.3.tar.gz |
| StartedAt: 2020-01-16 09:55:52 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 10:05:35 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 582.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: YAPSA.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:YAPSA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings YAPSA_1.13.3.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/YAPSA.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘YAPSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘YAPSA’ version ‘1.13.3’
* 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 ‘YAPSA’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
confidence_indel_only_calulation 28.227 0.564 28.790
create_indel_mutation_catalogue_from_df 17.862 0.341 18.202
run_SMC 6.614 0.460 7.075
build_gene_list_for_pathway 5.493 0.274 22.989
* 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
YAPSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL YAPSA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘YAPSA’ ... ** using staged installation ** R ** data ** 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 (YAPSA)
YAPSA.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.
> Sys.setenv(R_TESTS=" ")
> library(testthat)
> library(YAPSA)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: ggplot2
Loading required package: grid
>
> test_check("YAPSA")
YAPSA:::shapiro_if_possible::error: Non-numeric inputYAPSA:::makeVRangesFromDataFrame::warning:strand information missing, set to "+".
YAPSA:::makeVRangesFromDataFrame::in_PID.field found. Retrieving PID information.
YAPSA:::makeVRangesFromDataFrame::in_subgroup.field found. Retrieving subgroup information.
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 62 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
20.245 1.769 21.984
YAPSA.Rcheck/YAPSA-Ex.timings
| name | user | system | elapsed | |
| GenomeOfNl_raw | 0.012 | 0.003 | 0.016 | |
| LCD | 0.010 | 0.002 | 0.014 | |
| LCD_complex_cutoff | 0 | 0 | 0 | |
| MutCat_indel_df | 0.006 | 0.003 | 0.008 | |
| SMC | 0.001 | 0.001 | 0.000 | |
| SMC_perPID | 0.001 | 0.000 | 0.000 | |
| add_annotation | 0.001 | 0.000 | 0.000 | |
| add_as_fist_to_list | 0.001 | 0.000 | 0.000 | |
| aggregate_exposures_by_category | 0.001 | 0.000 | 0.001 | |
| annotate_intermut_dist_PID | 0.026 | 0.002 | 0.026 | |
| annotate_intermut_dist_cohort | 0.032 | 0.002 | 0.034 | |
| annotation_exposures_barplot | 0.001 | 0.000 | 0.000 | |
| annotation_exposures_list_barplot | 0.001 | 0.000 | 0.000 | |
| annotation_heatmap_exposures | 0.001 | 0.000 | 0.001 | |
| attribute_nucleotide_exchanges | 0.004 | 0.000 | 0.005 | |
| attribute_sequence_contex_indel | 1.714 | 0.027 | 1.742 | |
| attribution_of_indels | 0.809 | 0.142 | 0.950 | |
| build_gene_list_for_pathway | 5.493 | 0.274 | 22.989 | |
| classify_indels | 0 | 0 | 0 | |
| compare_SMCs | 0 | 0 | 0 | |
| compare_exposures | 0.000 | 0.001 | 0.000 | |
| compare_expousre_sets | 0.005 | 0.000 | 0.006 | |
| compare_sets | 0.004 | 0.000 | 0.005 | |
| compare_to_catalogues | 0.000 | 0.000 | 0.001 | |
| complex_heatmap_exposures | 0.987 | 0.012 | 0.998 | |
| computeLogLik | 0 | 0 | 0 | |
| compute_comparison_stat_df | 0.000 | 0.000 | 0.001 | |
| confIntExp | 1.981 | 0.195 | 2.177 | |
| confidence_indel_calulation | 0.001 | 0.002 | 0.004 | |
| confidence_indel_only_calulation | 28.227 | 0.564 | 28.790 | |
| correct_rounded | 0.000 | 0.000 | 0.001 | |
| cosineDist | 0 | 0 | 0 | |
| cosineMatchDist | 0.002 | 0.000 | 0.002 | |
| create_indel_mut_cat_from_df | 0.652 | 0.061 | 0.712 | |
| create_indel_mutation_catalogue_from_df | 17.862 | 0.341 | 18.202 | |
| create_mutation_catalogue_from_VR | 1.877 | 0.155 | 2.033 | |
| create_mutation_catalogue_from_df | 1.383 | 0.169 | 1.552 | |
| cut_breaks_as_intervals | 0.167 | 0.005 | 0.173 | |
| deriveSigInd_df | 0.001 | 0.000 | 0.000 | |
| disambiguateVector | 0.001 | 0.000 | 0.000 | |
| enrichSigs | 0 | 0 | 0 | |
| exampleYAPSA | 0.082 | 0.015 | 0.097 | |
| exposures_barplot | 3.558 | 0.028 | 3.586 | |
| extract_names_from_gene_list | 0 | 0 | 0 | |
| find_affected_PIDs | 0 | 0 | 0 | |
| getSequenceContext | 0.191 | 0.007 | 0.197 | |
| get_extreme_PIDs | 0.035 | 0.002 | 0.038 | |
| hclust_exposures | 0.008 | 0.002 | 0.011 | |
| logLikelihood | 1.413 | 0.169 | 1.582 | |
| lymphomaNature2013_mutCat_df | 0.008 | 0.004 | 0.011 | |
| makeVRangesFromDataFrame | 0.145 | 0.005 | 0.150 | |
| make_catalogue_strata_df | 0.000 | 0.000 | 0.001 | |
| make_comparison_matrix | 0.122 | 0.011 | 0.133 | |
| make_strata_df | 0 | 0 | 0 | |
| make_subgroups_df | 0.035 | 0.007 | 0.042 | |
| melt_exposures | 0.000 | 0.000 | 0.001 | |
| merge_exposures | 0.000 | 0.001 | 0.000 | |
| normalizeMotifs_otherRownames | 0.000 | 0.000 | 0.001 | |
| normalize_df_per_dim | 0.011 | 0.001 | 0.012 | |
| plotExchangeSpectra | 0 | 0 | 0 | |
| plotExchangeSpectra_indel | 1.409 | 0.010 | 1.420 | |
| plotExposuresConfidence | 0.000 | 0.001 | 0.000 | |
| plotExposuresConfidence_indel | 0.000 | 0.000 | 0.001 | |
| plot_SMC | 0 | 0 | 0 | |
| plot_exposures | 0.697 | 0.007 | 0.706 | |
| plot_strata | 0 | 0 | 0 | |
| read_entry | 0 | 0 | 0 | |
| relateSigs | 0 | 0 | 0 | |
| repeat_df | 0.003 | 0.001 | 0.003 | |
| round_precision | 0 | 0 | 0 | |
| run_SMC | 6.614 | 0.460 | 7.075 | |
| run_annotate_vcf_pl | 0.001 | 0.000 | 0.000 | |
| run_comparison_catalogues | 0 | 0 | 0 | |
| run_comparison_general | 0 | 0 | 0 | |
| run_kmer_frequency_correction | 0 | 0 | 0 | |
| run_kmer_frequency_normalization | 0 | 0 | 0 | |
| run_plot_strata_general | 0 | 0 | 0 | |
| shapiro_if_possible | 0.001 | 0.000 | 0.001 | |
| split_exposures_by_subgroups | 0 | 0 | 0 | |
| stat_plot_subgroups | 0 | 0 | 0 | |
| stat_test_SMC | 0 | 0 | 0 | |
| stat_test_subgroups | 0.000 | 0.000 | 0.001 | |
| stderrmean | 0.000 | 0.001 | 0.000 | |
| sum_over_list_of_df | 0.003 | 0.000 | 0.004 | |
| temp_trellis_rainfall_plot | 2.494 | 0.021 | 2.519 | |
| testSigs | 0 | 0 | 0 | |
| test_exposureAffected | 0.000 | 0.000 | 0.001 | |
| test_gene_list_in_exposures | 0 | 0 | 0 | |
| transform_rownames_R_to_MATLAB | 0.000 | 0.000 | 0.001 | |
| translate_to_hg19 | 0.006 | 0.000 | 0.006 | |
| trellis_rainfall_plot | 3.513 | 0.018 | 3.533 | |
| trellis_rainfall_plot_old | 2.407 | 0.013 | 2.421 | |
| variateExp | 3.469 | 0.196 | 3.667 | |
| variateExpSingle | 1.427 | 0.201 | 1.627 | |