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This page was generated on 2023-10-20 09:38:15 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 2223/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
YAPSA 1.26.8  (landing page)
Zuguang Gu
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/YAPSA
git_branch: RELEASE_3_17
git_last_commit: 89c3669
git_last_commit_date: 2023-09-25 09:19:07 -0400 (Mon, 25 Sep 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for YAPSA on kjohnson2


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: 1.26.8
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_1.26.8.tar.gz
StartedAt: 2023-10-19 10:30:58 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 10:50:03 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 1144.7 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_1.26.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/YAPSA.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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 Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘YAPSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘YAPSA’ version ‘1.26.8’
* 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        27.457  7.102  81.724
create_indel_mutation_catalogue_from_df 18.925  1.515  40.307
build_gene_list_for_pathway              7.002  1.769  37.235
run_SMC                                  6.578  0.497  11.941
exposures_barplot                        3.755  0.096   7.091
variateExp                               3.356  0.231   6.268
confIntExp                               2.035  0.683   6.491
* 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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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 
 21.485   1.321  39.558 

Example timings

YAPSA.Rcheck/YAPSA-Ex.timings

nameusersystemelapsed
GenomeOfNl_raw0.0110.0040.044
LCD0.0100.0030.033
LCD_complex_cutoff000
MutCat_indel_df0.0040.0030.015
SMC000
SMC_perPID0.0000.0000.001
add_annotation000
add_as_fist_to_list000
aggregate_exposures_by_category0.0000.0000.001
annotate_intermut_dist_PID0.0240.0050.078
annotate_intermut_dist_cohort0.0290.0060.068
annotation_exposures_barplot000
annotation_exposures_list_barplot000
annotation_heatmap_exposures000
attribute_nucleotide_exchanges0.0030.0020.008
attribute_sequence_contex_indel0.9150.0982.174
attribution_of_indels0.6520.0671.915
build_gene_list_for_pathway 7.002 1.76937.235
classify_indels0.0000.0010.001
compare_SMCs000
compare_exposures000
compare_expousre_sets0.0040.0030.008
compare_sets0.0040.0010.019
compare_to_catalogues000
complex_heatmap_exposures1.2270.3343.579
computeLogLik000
compute_comparison_stat_df0.0010.0000.000
confIntExp2.0350.6836.491
confidence_indel_calulation0.0010.0020.003
confidence_indel_only_calulation27.457 7.10281.724
correct_rounded000
cosineDist0.0000.0000.001
cosineMatchDist0.0020.0010.004
create_indel_mut_cat_from_df0.6480.0551.710
create_indel_mutation_catalogue_from_df18.925 1.51540.307
create_mutation_catalogue_from_VR1.7980.6124.866
create_mutation_catalogue_from_df1.3410.2233.061
cut_breaks_as_intervals0.1780.0200.332
deriveSigInd_df000
disambiguateVector000
enrichSigs000
exampleYAPSA0.0890.0120.194
exome_mutCatRaw_df0.0110.0040.027
exposures_barplot3.7550.0967.091
extract_names_from_gene_list000
find_affected_PIDs0.0000.0000.001
getSequenceContext0.2260.0140.417
get_extreme_PIDs0.0090.0030.022
hclust_exposures0.0070.0030.014
logLikelihood1.3310.3693.534
lymphomaNature2013_mutCat_df0.0060.0030.018
makeVRangesFromDataFrame0.1480.0060.277
make_catalogue_strata_df000
make_comparison_matrix0.0990.0140.197
make_strata_df0.0000.0000.001
make_subgroups_df0.0400.0070.085
melt_exposures000
merge_exposures000
normalizeMotifs_otherRownames000
normalize_df_per_dim0.0120.0020.025
plotExchangeSpectra000
plotExchangeSpectra_indel1.8130.0283.051
plotExposuresConfidence0.0000.0000.001
plotExposuresConfidence_indel0.0000.0000.001
plot_SMC000
plot_exposures0.8140.0201.299
plot_strata000
read_entry0.0000.0000.001
relateSigs000
repeat_df0.0030.0010.004
round_precision0.0010.0000.001
run_SMC 6.578 0.49711.941
run_annotate_vcf_pl000
run_comparison_catalogues000
run_comparison_general000
run_kmer_frequency_correction0.0000.0010.000
run_kmer_frequency_normalization000
run_plot_strata_general000
shapiro_if_possible0.0010.0000.005
split_exposures_by_subgroups000
stat_plot_subgroups0.0000.0000.001
stat_test_SMC000
stat_test_subgroups000
stderrmean0.0000.0010.001
sum_over_list_of_df0.0020.0010.006
testSigs000
test_exposureAffected0.0000.0010.001
test_gene_list_in_exposures0.0010.0000.000
transform_rownames_R_to_MATLAB000
translate_to_hg190.0050.0010.012
trellis_rainfall_plot2.2910.0434.113
variateExp3.3560.2316.268
variateExpSingle1.3680.1592.699