Daniel Huebschmann
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/YAPSA |
| Branch: RELEASE_3_7 |
| Last Commit: 2455d27 |
| Last Changed Date: 2018-04-30 10:35:43 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:57:03 -0400 (Wed, 17 Oct 2018).
| Package 1556/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| YAPSA 1.6.0 Daniel Huebschmann
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: YAPSA |
| Version: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2018-10-17 00:41:25 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 00:46:55 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 329.9 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_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/YAPSA.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.6.0’
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
run_SMC 5.119 0.262 5.384
* 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/3.5/Resources/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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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.
> 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
13.858 0.706 15.378
YAPSA.Rcheck/YAPSA-Ex.timings
| name | user | system | elapsed | |
| LCD | 0.010 | 0.001 | 0.014 | |
| LCD_complex_cutoff | 0.001 | 0.000 | 0.001 | |
| add_annotation | 0.001 | 0.000 | 0.000 | |
| add_as_fist_to_list | 0.001 | 0.000 | 0.001 | |
| aggregate_exposures_by_category | 0.001 | 0.000 | 0.001 | |
| annotate_intermut_dist_PID | 0.159 | 0.002 | 0.160 | |
| annotate_intermut_dist_cohort | 0.027 | 0.001 | 0.028 | |
| annotation_exposures_barplot | 0.001 | 0.000 | 0.001 | |
| annotation_heatmap_exposures | 0.000 | 0.000 | 0.001 | |
| attribute_nucleotide_exchanges | 0.004 | 0.001 | 0.004 | |
| build_gene_list_for_pathway | 0.002 | 0.000 | 0.002 | |
| compare_SMCs | 0.001 | 0.000 | 0.001 | |
| compare_exposures | 0.001 | 0.000 | 0.000 | |
| compare_sets | 0.005 | 0.000 | 0.006 | |
| compare_to_catalogues | 0.001 | 0.000 | 0.001 | |
| complex_heatmap_exposures | 1.816 | 0.019 | 1.835 | |
| compute_comparison_stat_df | 0.001 | 0.001 | 0.001 | |
| cosineDist | 0.001 | 0.000 | 0.001 | |
| create_mutation_catalogue_from_VR | 1.869 | 0.142 | 2.010 | |
| create_mutation_catalogue_from_df | 0.927 | 0.102 | 1.029 | |
| cut_breaks_as_intervals | 0.192 | 0.005 | 0.199 | |
| exampleYAPSA | 0.079 | 0.009 | 0.088 | |
| exposures_barplot | 1.317 | 0.008 | 1.327 | |
| extract_names_from_gene_list | 0.001 | 0.000 | 0.001 | |
| find_affected_PIDs | 0 | 0 | 0 | |
| get_extreme_PIDs | 0.030 | 0.001 | 0.031 | |
| hclust_exposures | 0.009 | 0.002 | 0.010 | |
| makeVRangesFromDataFrame | 0.089 | 0.004 | 0.093 | |
| make_catalogue_strata_df | 0.001 | 0.000 | 0.001 | |
| make_comparison_matrix | 0.105 | 0.008 | 0.115 | |
| make_strata_df | 0.001 | 0.000 | 0.000 | |
| make_subgroups_df | 0.040 | 0.005 | 0.045 | |
| melt_exposures | 0.001 | 0.000 | 0.000 | |
| merge_exposures | 0.001 | 0.000 | 0.001 | |
| normalizeMotifs_otherRownames | 0.001 | 0.000 | 0.001 | |
| normalize_df_per_dim | 0.012 | 0.000 | 0.013 | |
| plotExchangeSpectra | 0.000 | 0.000 | 0.001 | |
| plot_SMC | 0.000 | 0.000 | 0.001 | |
| plot_exposures | 0.752 | 0.026 | 0.779 | |
| plot_strata | 0.001 | 0.000 | 0.001 | |
| repeat_df | 0.003 | 0.000 | 0.004 | |
| run_SMC | 5.119 | 0.262 | 5.384 | |
| run_annotate_vcf_pl | 0.001 | 0.000 | 0.001 | |
| run_comparison_catalogues | 0.001 | 0.000 | 0.001 | |
| run_comparison_general | 0.001 | 0.000 | 0.000 | |
| run_kmer_frequency_correction | 0.001 | 0.000 | 0.001 | |
| run_kmer_frequency_normalization | 0.000 | 0.000 | 0.001 | |
| run_plot_strata_general | 0.001 | 0.000 | 0.000 | |
| shapiro_if_possible | 0.002 | 0.000 | 0.002 | |
| split_exposures_by_subgroups | 0.001 | 0.000 | 0.001 | |
| stat_plot_subgroups | 0.001 | 0.000 | 0.000 | |
| stat_test_SMC | 0.001 | 0.000 | 0.001 | |
| stat_test_subgroups | 0.001 | 0.000 | 0.001 | |
| stderrmean | 0.001 | 0.000 | 0.001 | |
| sum_over_list_of_df | 0.003 | 0.000 | 0.004 | |
| test_exposureAffected | 0.001 | 0.000 | 0.001 | |
| test_gene_list_in_exposures | 0.001 | 0.000 | 0.001 | |
| transform_rownames_R_to_MATLAB | 0.001 | 0.000 | 0.000 | |
| translate_to_hg19 | 0.007 | 0.000 | 0.006 | |
| trellis_rainfall_plot | 2.166 | 0.017 | 2.186 | |