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This page was generated on 2024-03-28 11:32:35 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4376
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Package 2259/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
YAPSA 1.28.0  (landing page)
Zuguang Gu
Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 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 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for YAPSA on kjohnson1


To the developers/maintainers of the YAPSA package:
- 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: 2024-03-28 06:42:35 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 06:52:46 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 610.9 seconds
RetCode: 0
Status:   OK  
CheckDir: YAPSA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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-mac-arm64/meat/YAPSA.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* 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        20.367  0.333  21.296
create_indel_mutation_catalogue_from_df 14.351  0.787  15.335
run_SMC                                  4.653  0.456   5.173
build_gene_list_for_pathway              4.991  0.097  30.584
* 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-arm64/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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 
 22.591   1.124  24.137 

Example timings

YAPSA.Rcheck/YAPSA-Ex.timings

nameusersystemelapsed
GenomeOfNl_raw0.0130.0040.018
LCD0.0090.0010.010
LCD_complex_cutoff000
MutCat_indel_df0.0040.0030.007
SMC0.0000.0000.001
SMC_perPID0.0000.0010.000
add_annotation000
add_as_fist_to_list0.0010.0000.000
aggregate_exposures_by_category000
annotate_intermut_dist_PID0.0190.0020.020
annotate_intermut_dist_cohort0.0220.0020.025
annotation_exposures_barplot0.0000.0010.000
annotation_exposures_list_barplot0.0000.0000.001
annotation_heatmap_exposures0.0000.0000.001
attribute_nucleotide_exchanges0.0030.0000.004
attribute_sequence_contex_indel0.6330.0380.687
attribution_of_indels0.5400.0680.615
build_gene_list_for_pathway 4.991 0.09730.584
classify_indels0.0000.0000.001
compare_SMCs0.0000.0010.001
compare_exposures000
compare_expousre_sets0.0050.0010.006
compare_sets0.0030.0010.004
compare_to_catalogues0.0000.0010.000
complex_heatmap_exposures1.0530.0271.107
computeLogLik0.0010.0010.000
compute_comparison_stat_df000
confIntExp1.7830.2082.120
confidence_indel_calulation0.0010.0010.002
confidence_indel_only_calulation20.367 0.33321.296
correct_rounded000
cosineDist0.0000.0000.002
cosineMatchDist0.0020.0010.002
create_indel_mut_cat_from_df0.5110.0320.556
create_indel_mutation_catalogue_from_df14.351 0.78715.335
create_mutation_catalogue_from_VR1.5320.2001.773
create_mutation_catalogue_from_df1.1990.1891.484
cut_breaks_as_intervals0.1640.0070.177
deriveSigInd_df000
disambiguateVector0.0000.0000.001
enrichSigs0.0000.0010.000
exampleYAPSA0.1260.0090.140
exome_mutCatRaw_df0.0120.0050.019
exposures_barplot2.9640.0193.090
extract_names_from_gene_list000
find_affected_PIDs000
getSequenceContext0.2450.0150.306
get_extreme_PIDs0.0100.0030.013
hclust_exposures0.0070.0030.014
logLikelihood1.1670.1891.397
lymphomaNature2013_mutCat_df0.0050.0040.009
makeVRangesFromDataFrame0.1480.0040.153
make_catalogue_strata_df000
make_comparison_matrix0.0960.0100.108
make_strata_df000
make_subgroups_df0.0520.0060.058
melt_exposures000
merge_exposures000
normalizeMotifs_otherRownames0.0000.0000.001
normalize_df_per_dim0.0090.0010.011
plotExchangeSpectra000
plotExchangeSpectra_indel1.4590.0131.485
plotExposuresConfidence000
plotExposuresConfidence_indel000
plot_SMC000
plot_exposures0.5840.0100.598
plot_strata000
read_entry000
relateSigs000
repeat_df0.0030.0000.003
round_precision000
run_SMC4.6530.4565.173
run_annotate_vcf_pl0.0010.0000.000
run_comparison_catalogues0.0000.0010.000
run_comparison_general000
run_kmer_frequency_correction000
run_kmer_frequency_normalization000
run_plot_strata_general0.0000.0000.001
shapiro_if_possible0.0010.0010.002
split_exposures_by_subgroups0.0000.0000.001
stat_plot_subgroups0.0000.0010.000
stat_test_SMC0.0010.0000.000
stat_test_subgroups000
stderrmean0.0010.0000.001
sum_over_list_of_df0.0020.0000.003
testSigs0.0000.0000.001
test_exposureAffected000
test_gene_list_in_exposures000
transform_rownames_R_to_MATLAB000
translate_to_hg190.0040.0010.005
trellis_rainfall_plot1.9780.0222.017
variateExp2.3140.1982.534
variateExpSingle1.2160.1961.436