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This page was generated on 2024-03-04 11:38:01 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2259/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
YAPSA 1.28.0  (landing page)
Zuguang Gu
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/YAPSA
git_branch: RELEASE_3_18
git_last_commit: 257bdf9
git_last_commit_date: 2023-10-24 10:52:21 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for YAPSA on lconway


To the developers/maintainers of the YAPSA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/YAPSA.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: YAPSA
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:YAPSA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings YAPSA_1.28.0.tar.gz
StartedAt: 2024-03-04 00:14:02 -0500 (Mon, 04 Mar 2024)
EndedAt: 2024-03-04 00:21:07 -0500 (Mon, 04 Mar 2024)
EllapsedTime: 424.5 seconds
RetCode: 0
Status:   OK  
CheckDir: YAPSA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:YAPSA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings YAPSA_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/YAPSA.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘YAPSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘YAPSA’ version ‘1.28.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                          user system elapsed
confidence_indel_only_calulation        14.266  0.253  14.519
create_indel_mutation_catalogue_from_df  8.995  0.410   9.405
build_gene_list_for_pathway              3.063  0.038  22.502
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL YAPSA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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)

Tests output

YAPSA.Rcheck/tests/testthat.Rout


R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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

Attaching package: 'BiocGenerics'

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, aperm, 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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

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.
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 62 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 62 ]
> 
> proc.time()
   user  system elapsed 
 13.130   0.827  13.958 

Example timings

YAPSA.Rcheck/YAPSA-Ex.timings

nameusersystemelapsed
GenomeOfNl_raw0.0060.0020.007
LCD0.0050.0010.006
LCD_complex_cutoff000
MutCat_indel_df0.0030.0010.005
SMC000
SMC_perPID000
add_annotation000
add_as_fist_to_list000
aggregate_exposures_by_category000
annotate_intermut_dist_PID0.0110.0010.012
annotate_intermut_dist_cohort0.0140.0020.016
annotation_exposures_barplot000
annotation_exposures_list_barplot000
annotation_heatmap_exposures000
attribute_nucleotide_exchanges0.0010.0010.002
attribute_sequence_contex_indel0.3640.0180.383
attribution_of_indels0.3280.0450.373
build_gene_list_for_pathway 3.063 0.03822.502
classify_indels000
compare_SMCs0.0010.0000.000
compare_exposures000
compare_expousre_sets0.0030.0000.002
compare_sets0.0020.0010.002
compare_to_catalogues000
complex_heatmap_exposures0.6250.0160.642
computeLogLik000
compute_comparison_stat_df0.0000.0000.001
confIntExp0.9320.1021.034
confidence_indel_calulation0.0010.0010.002
confidence_indel_only_calulation14.266 0.25314.519
correct_rounded000
cosineDist000
cosineMatchDist0.0010.0010.001
create_indel_mut_cat_from_df0.3130.0150.328
create_indel_mutation_catalogue_from_df8.9950.4109.405
create_mutation_catalogue_from_VR0.8680.0940.964
create_mutation_catalogue_from_df0.6390.0930.732
cut_breaks_as_intervals0.0880.0020.091
deriveSigInd_df000
disambiguateVector0.0000.0000.001
enrichSigs000
exampleYAPSA0.0570.0040.060
exome_mutCatRaw_df0.0060.0020.009
exposures_barplot1.8360.0091.846
extract_names_from_gene_list000
find_affected_PIDs0.0000.0000.001
getSequenceContext0.1120.0090.122
get_extreme_PIDs0.0050.0020.007
hclust_exposures0.0040.0010.005
logLikelihood0.6430.0940.737
lymphomaNature2013_mutCat_df0.0030.0020.006
makeVRangesFromDataFrame0.0800.0020.083
make_catalogue_strata_df000
make_comparison_matrix0.0570.0060.063
make_strata_df000
make_subgroups_df0.0240.0020.027
melt_exposures000
merge_exposures000
normalizeMotifs_otherRownames000
normalize_df_per_dim0.0060.0010.007
plotExchangeSpectra000
plotExchangeSpectra_indel0.9200.0070.927
plotExposuresConfidence000
plotExposuresConfidence_indel000
plot_SMC000
plot_exposures0.3560.0040.361
plot_strata0.0000.0000.001
read_entry000
relateSigs000
repeat_df0.0020.0000.002
round_precision000
run_SMC3.0130.2583.273
run_annotate_vcf_pl0.0000.0010.001
run_comparison_catalogues000
run_comparison_general000
run_kmer_frequency_correction0.0010.0000.000
run_kmer_frequency_normalization000
run_plot_strata_general000
shapiro_if_possible0.0000.0000.001
split_exposures_by_subgroups000
stat_plot_subgroups0.0000.0000.001
stat_test_SMC000
stat_test_subgroups0.0010.0000.000
stderrmean0.0000.0000.001
sum_over_list_of_df0.0020.0010.002
testSigs000
test_exposureAffected0.0010.0000.000
test_gene_list_in_exposures0.0000.0010.000
transform_rownames_R_to_MATLAB000
translate_to_hg190.0030.0000.003
trellis_rainfall_plot1.1270.0091.138
variateExp1.7340.1241.858
variateExpSingle0.6540.0980.753