Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:59:54 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE YAPSA PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1900/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
YAPSA 1.14.0 Daniel Huebschmann
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | NA | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK |
Package: YAPSA |
Version: 1.14.0 |
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_1.14.0.tar.gz |
StartedAt: 2020-10-17 06:20:49 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 06:29:40 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 530.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: YAPSA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running 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_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/YAPSA.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-apple-darwin17.0 (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 ‘1.14.0’ * 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 ‘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 23.863 0.289 24.152 create_indel_mutation_catalogue_from_df 15.516 0.311 15.826 run_SMC 5.082 0.214 5.296 build_gene_list_for_pathway 4.772 0.124 19.863 * 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 version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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 17.026 0.754 20.710
YAPSA.Rcheck/YAPSA-Ex.timings
name | user | system | elapsed | |
GenomeOfNl_raw | 0.010 | 0.002 | 0.012 | |
LCD | 0.009 | 0.001 | 0.011 | |
LCD_complex_cutoff | 0 | 0 | 0 | |
MutCat_indel_df | 0.005 | 0.002 | 0.007 | |
SMC | 0 | 0 | 0 | |
SMC_perPID | 0.001 | 0.000 | 0.000 | |
add_annotation | 0 | 0 | 0 | |
add_as_fist_to_list | 0 | 0 | 0 | |
aggregate_exposures_by_category | 0.000 | 0.001 | 0.001 | |
annotate_intermut_dist_PID | 0.783 | 0.003 | 0.787 | |
annotate_intermut_dist_cohort | 0.027 | 0.001 | 0.029 | |
annotation_exposures_barplot | 0 | 0 | 0 | |
annotation_exposures_list_barplot | 0 | 0 | 0 | |
annotation_heatmap_exposures | 0.000 | 0.001 | 0.000 | |
attribute_nucleotide_exchanges | 0.003 | 0.001 | 0.004 | |
attribute_sequence_contex_indel | 0.638 | 0.022 | 0.661 | |
attribution_of_indels | 0.576 | 0.071 | 0.647 | |
build_gene_list_for_pathway | 4.772 | 0.124 | 19.863 | |
classify_indels | 0.001 | 0.000 | 0.000 | |
compare_SMCs | 0.000 | 0.000 | 0.001 | |
compare_exposures | 0.000 | 0.001 | 0.001 | |
compare_expousre_sets | 0.004 | 0.000 | 0.004 | |
compare_sets | 0.004 | 0.000 | 0.005 | |
compare_to_catalogues | 0.000 | 0.001 | 0.000 | |
complex_heatmap_exposures | 0.807 | 0.007 | 0.813 | |
computeLogLik | 0.001 | 0.000 | 0.000 | |
compute_comparison_stat_df | 0 | 0 | 0 | |
confIntExp | 1.520 | 0.088 | 1.609 | |
confidence_indel_calulation | 0.001 | 0.001 | 0.003 | |
confidence_indel_only_calulation | 23.863 | 0.289 | 24.152 | |
correct_rounded | 0.000 | 0.001 | 0.000 | |
cosineDist | 0.000 | 0.000 | 0.001 | |
cosineMatchDist | 0.001 | 0.001 | 0.001 | |
create_indel_mut_cat_from_df | 0.520 | 0.012 | 0.532 | |
create_indel_mutation_catalogue_from_df | 15.516 | 0.311 | 15.826 | |
create_mutation_catalogue_from_VR | 1.513 | 0.079 | 1.593 | |
create_mutation_catalogue_from_df | 1.106 | 0.075 | 1.182 | |
cut_breaks_as_intervals | 0.123 | 0.002 | 0.124 | |
deriveSigInd_df | 0.000 | 0.000 | 0.001 | |
disambiguateVector | 0 | 0 | 0 | |
enrichSigs | 0 | 0 | 0 | |
exampleYAPSA | 0.084 | 0.005 | 0.090 | |
exome_mutCatRaw_df | 0.014 | 0.005 | 0.018 | |
exposures_barplot | 2.917 | 0.016 | 2.934 | |
extract_names_from_gene_list | 0 | 0 | 0 | |
find_affected_PIDs | 0.001 | 0.000 | 0.000 | |
getSequenceContext | 0.229 | 0.039 | 0.269 | |
get_extreme_PIDs | 0.032 | 0.002 | 0.033 | |
hclust_exposures | 0.007 | 0.002 | 0.008 | |
logLikelihood | 1.108 | 0.078 | 1.187 | |
lymphomaNature2013_mutCat_df | 0.006 | 0.002 | 0.009 | |
makeVRangesFromDataFrame | 0.146 | 0.002 | 0.148 | |
make_catalogue_strata_df | 0.001 | 0.000 | 0.000 | |
make_comparison_matrix | 0.109 | 0.008 | 0.117 | |
make_strata_df | 0 | 0 | 0 | |
make_subgroups_df | 0.035 | 0.003 | 0.038 | |
melt_exposures | 0.000 | 0.001 | 0.000 | |
merge_exposures | 0 | 0 | 0 | |
normalizeMotifs_otherRownames | 0 | 0 | 0 | |
normalize_df_per_dim | 0.009 | 0.001 | 0.011 | |
plotExchangeSpectra | 0 | 0 | 0 | |
plotExchangeSpectra_indel | 1.229 | 0.006 | 1.235 | |
plotExposuresConfidence | 0.000 | 0.000 | 0.001 | |
plotExposuresConfidence_indel | 0.001 | 0.000 | 0.000 | |
plot_SMC | 0 | 0 | 0 | |
plot_exposures | 1.320 | 0.006 | 1.327 | |
plot_strata | 0.000 | 0.000 | 0.001 | |
read_entry | 0 | 0 | 0 | |
relateSigs | 0.001 | 0.000 | 0.000 | |
repeat_df | 0.003 | 0.001 | 0.003 | |
round_precision | 0.001 | 0.000 | 0.000 | |
run_SMC | 5.082 | 0.214 | 5.296 | |
run_annotate_vcf_pl | 0 | 0 | 0 | |
run_comparison_catalogues | 0.000 | 0.000 | 0.001 | |
run_comparison_general | 0.000 | 0.001 | 0.000 | |
run_kmer_frequency_correction | 0.001 | 0.000 | 0.000 | |
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 | 0.000 | 0.000 | 0.001 | |
stat_plot_subgroups | 0 | 0 | 0 | |
stat_test_SMC | 0 | 0 | 0 | |
stat_test_subgroups | 0 | 0 | 0 | |
stderrmean | 0.001 | 0.000 | 0.001 | |
sum_over_list_of_df | 0.003 | 0.000 | 0.003 | |
temp_trellis_rainfall_plot | 1.730 | 0.009 | 1.741 | |
testSigs | 0 | 0 | 0 | |
test_exposureAffected | 0.000 | 0.000 | 0.001 | |
test_gene_list_in_exposures | 0.000 | 0.001 | 0.000 | |
transform_rownames_R_to_MATLAB | 0 | 0 | 0 | |
translate_to_hg19 | 0.004 | 0.001 | 0.005 | |
trellis_rainfall_plot | 1.726 | 0.008 | 1.735 | |
trellis_rainfall_plot_old | 1.743 | 0.008 | 1.752 | |
variateExp | 2.770 | 0.105 | 2.877 | |
variateExpSingle | 1.053 | 0.076 | 1.128 | |