Daniel Huebschmann
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/YAPSA |
| Branch: RELEASE_3_8 |
| Last Commit: 402f3f7 |
| Last Changed Date: 2018-10-30 11:42:02 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:52:18 -0400 (Tue, 16 Apr 2019).
| Package 1644/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| YAPSA 1.8.0 Daniel Huebschmann
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: YAPSA |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:YAPSA.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings YAPSA_1.8.0.tar.gz |
| StartedAt: 2019-04-16 03:43:29 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 03:48:55 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 326.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: YAPSA.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:YAPSA.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings YAPSA_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/YAPSA.Rcheck’ * using R version 3.5.3 (2019-03-11) * using platform: x86_64-pc-linux-gnu (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 ‘1.8.0’ * 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL YAPSA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘YAPSA’ ... ** 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 * DONE (YAPSA)
YAPSA.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, 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: 63 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
14.132 0.488 14.641
YAPSA.Rcheck/YAPSA-Ex.timings
| name | user | system | elapsed | |
| LCD | 0.008 | 0.000 | 0.007 | |
| LCD_complex_cutoff | 0 | 0 | 0 | |
| add_annotation | 0 | 0 | 0 | |
| add_as_fist_to_list | 0 | 0 | 0 | |
| aggregate_exposures_by_category | 0 | 0 | 0 | |
| annotate_intermut_dist_PID | 0.284 | 0.004 | 0.287 | |
| annotate_intermut_dist_cohort | 0.028 | 0.000 | 0.026 | |
| annotation_exposures_barplot | 0 | 0 | 0 | |
| annotation_heatmap_exposures | 0 | 0 | 0 | |
| attribute_nucleotide_exchanges | 0.004 | 0.000 | 0.003 | |
| build_gene_list_for_pathway | 0 | 0 | 0 | |
| compare_SMCs | 0 | 0 | 0 | |
| compare_exposures | 0 | 0 | 0 | |
| compare_sets | 0.004 | 0.000 | 0.005 | |
| compare_to_catalogues | 0 | 0 | 0 | |
| complex_heatmap_exposures | 1.776 | 0.000 | 1.779 | |
| compute_comparison_stat_df | 0 | 0 | 0 | |
| cosineDist | 0.004 | 0.000 | 0.000 | |
| create_mutation_catalogue_from_VR | 1.956 | 0.092 | 2.998 | |
| create_mutation_catalogue_from_df | 0.900 | 0.036 | 0.940 | |
| cut_breaks_as_intervals | 0.172 | 0.004 | 0.178 | |
| exampleYAPSA | 0.092 | 0.008 | 0.098 | |
| exposures_barplot | 1.292 | 0.024 | 1.316 | |
| extract_names_from_gene_list | 0 | 0 | 0 | |
| find_affected_PIDs | 0 | 0 | 0 | |
| get_extreme_PIDs | 0.088 | 0.004 | 0.089 | |
| hclust_exposures | 0.008 | 0.000 | 0.007 | |
| makeVRangesFromDataFrame | 0.092 | 0.004 | 0.098 | |
| make_catalogue_strata_df | 0 | 0 | 0 | |
| make_comparison_matrix | 0.092 | 0.000 | 0.090 | |
| make_strata_df | 0 | 0 | 0 | |
| make_subgroups_df | 0.036 | 0.008 | 0.045 | |
| melt_exposures | 0 | 0 | 0 | |
| merge_exposures | 0.000 | 0.000 | 0.001 | |
| normalizeMotifs_otherRownames | 0 | 0 | 0 | |
| normalize_df_per_dim | 0.012 | 0.000 | 0.011 | |
| plotExchangeSpectra | 0 | 0 | 0 | |
| plot_SMC | 0 | 0 | 0 | |
| plot_exposures | 0.668 | 0.000 | 0.671 | |
| plot_strata | 0 | 0 | 0 | |
| repeat_df | 0.004 | 0.000 | 0.003 | |
| run_SMC | 4.788 | 0.100 | 4.894 | |
| run_annotate_vcf_pl | 0 | 0 | 0 | |
| 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 | 0.000 | 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 | 0 | 0 | |
| stderrmean | 0.004 | 0.000 | 0.000 | |
| sum_over_list_of_df | 0.000 | 0.000 | 0.002 | |
| test_exposureAffected | 0 | 0 | 0 | |
| test_gene_list_in_exposures | 0 | 0 | 0 | |
| transform_rownames_R_to_MATLAB | 0 | 0 | 0 | |
| translate_to_hg19 | 0.004 | 0.000 | 0.004 | |
| trellis_rainfall_plot | 3.156 | 0.008 | 3.191 | |