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CHECK report for YAPSA on merida1

This page was generated on 2019-04-16 11:59:53 -0400 (Tue, 16 Apr 2019).

Package 1644/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
YAPSA 1.8.0
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)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: YAPSA
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2019-04-16 03:25:13 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:30:40 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 327.1 seconds
RetCode: 0
Status:  OK 
CheckDir: YAPSA.Rcheck
Warnings: 0

Command output

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### 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/YAPSA.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.8.0’
* 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
Examples with CPU or elapsed time > 5s
         user system elapsed
run_SMC 5.111  0.306   5.417
* 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


Installation output

YAPSA.Rcheck/00install.out

##############################################################################
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###
### 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)

Tests output

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-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 
 14.103   0.716  14.800 

Example timings

YAPSA.Rcheck/YAPSA-Ex.timings

nameusersystemelapsed
LCD0.0080.0000.009
LCD_complex_cutoff000
add_annotation000
add_as_fist_to_list000
aggregate_exposures_by_category000
annotate_intermut_dist_PID0.2990.0020.301
annotate_intermut_dist_cohort0.0280.0010.028
annotation_exposures_barplot0.0010.0000.001
annotation_heatmap_exposures0.0000.0000.001
attribute_nucleotide_exchanges0.0030.0000.004
build_gene_list_for_pathway0.0000.0010.000
compare_SMCs000
compare_exposures000
compare_sets0.0060.0000.006
compare_to_catalogues000
complex_heatmap_exposures1.8320.0361.868
compute_comparison_stat_df0.0000.0000.001
cosineDist0.0010.0000.000
create_mutation_catalogue_from_VR1.8520.1411.992
create_mutation_catalogue_from_df0.8890.0900.980
cut_breaks_as_intervals0.1850.0090.195
exampleYAPSA0.0970.0130.110
exposures_barplot1.4550.0661.521
extract_names_from_gene_list0.0010.0000.001
find_affected_PIDs0.0000.0000.001
get_extreme_PIDs0.0380.0070.044
hclust_exposures0.0100.0030.012
makeVRangesFromDataFrame0.1540.0080.162
make_catalogue_strata_df000
make_comparison_matrix0.1040.0090.114
make_strata_df000
make_subgroups_df0.0400.0060.047
melt_exposures000
merge_exposures000
normalizeMotifs_otherRownames000
normalize_df_per_dim0.0110.0000.012
plotExchangeSpectra000
plot_SMC000
plot_exposures0.6990.0080.707
plot_strata000
repeat_df0.0020.0000.003
run_SMC5.1110.3065.417
run_annotate_vcf_pl0.0010.0000.000
run_comparison_catalogues000
run_comparison_general000
run_kmer_frequency_correction0.0000.0000.001
run_kmer_frequency_normalization000
run_plot_strata_general000
shapiro_if_possible0.0010.0010.001
split_exposures_by_subgroups000
stat_plot_subgroups000
stat_test_SMC000
stat_test_subgroups0.0010.0000.000
stderrmean0.0010.0000.001
sum_over_list_of_df0.0030.0000.003
test_exposureAffected000
test_gene_list_in_exposures0.0000.0010.001
transform_rownames_R_to_MATLAB0.0000.0000.001
translate_to_hg190.0050.0000.005
trellis_rainfall_plot2.9800.0203.002