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This page was generated on 2022-08-12 11:08:33 -0400 (Fri, 12 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4375
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4159
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4167
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

CHECK results for YAPSA on lconway


To the developers/maintainers of the YAPSA package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2133/2139HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
YAPSA 1.23.0  (landing page)
Daniel Huebschmann
Snapshot Date: 2022-08-11 14:00:04 -0400 (Thu, 11 Aug 2022)
git_url: https://git.bioconductor.org/packages/YAPSA
git_branch: master
git_last_commit: 68d5478
git_last_commit_date: 2022-04-26 11:35:04 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: YAPSA
Version: 1.23.0
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_1.23.0.tar.gz
StartedAt: 2022-08-11 23:10:07 -0400 (Thu, 11 Aug 2022)
EndedAt: 2022-08-11 23:16:17 -0400 (Thu, 11 Aug 2022)
EllapsedTime: 370.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: YAPSA.Rcheck
Warnings: 1

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_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/YAPSA.Rcheck’
* using R version 4.2.1 Patched (2022-07-09 r82577)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.23.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘GenomicRanges::subtract’ by ‘magrittr::subtract’ when loading ‘YAPSA’
See ‘/Users/biocbuild/bbs-3.16-bioc/meat/YAPSA.Rcheck/00install.out’ for details.
* 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 ... NOTE
read_list: no visible global function definition for 'detectCores'
read_list: no visible global function definition for 'makeCluster'
read_list: no visible global function definition for 'mclapply'
read_list: no visible global function definition for 'stopCluster'
Undefined global functions or variables:
  detectCores makeCluster mclapply stopCluster
* 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 installed files from ‘inst/doc’ ... 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        13.634  0.360  13.999
create_indel_mutation_catalogue_from_df  8.515  0.396   8.922
build_gene_list_for_pathway              2.484  0.024  28.070
* 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/YAPSA.Rcheck/00check.log’
for details.



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/4.2/Resources/library’
* installing *source* package ‘YAPSA’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Warning: replacing previous import ‘GenomicRanges::subtract’ by ‘magrittr::subtract’ when loading ‘YAPSA’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Warning: replacing previous import ‘GenomicRanges::subtract’ by ‘magrittr::subtract’ when loading ‘YAPSA’
** testing if installed package can be loaded from final location
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by ‘Rmpfr’
Warning: replacing previous import ‘GenomicRanges::subtract’ by ‘magrittr::subtract’ when loading ‘YAPSA’
** testing if installed package keeps a record of temporary installation path
* DONE (YAPSA)

Tests output

YAPSA.Rcheck/tests/testthat.Rout


R version 4.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.

> 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, 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 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
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix'
Also defined by 'Rmpfr'
Warning message:
replacing previous import 'GenomicRanges::subtract' by 'magrittr::subtract' when loading 'YAPSA' 
> 
> 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 0 | SKIP 0 | PASS 62 ]
> 
> proc.time()
   user  system elapsed 
 12.294   0.713  13.004 

Example timings

YAPSA.Rcheck/YAPSA-Ex.timings

nameusersystemelapsed
GenomeOfNl_raw0.0050.0010.007
LCD0.0050.0010.006
LCD_complex_cutoff000
MutCat_indel_df0.0020.0010.004
SMC000
SMC_perPID0.0000.0010.000
add_annotation0.0000.0000.001
add_as_fist_to_list000
aggregate_exposures_by_category000
annotate_intermut_dist_PID0.0120.0010.012
annotate_intermut_dist_cohort0.0130.0010.014
annotation_exposures_barplot000
annotation_exposures_list_barplot000
annotation_heatmap_exposures000
attribute_nucleotide_exchanges0.0010.0000.002
attribute_sequence_contex_indel0.3440.0220.370
attribution_of_indels0.3150.0560.372
build_gene_list_for_pathway 2.484 0.02428.070
classify_indels000
compare_SMCs0.0000.0010.000
compare_exposures000
compare_expousre_sets0.0020.0000.003
compare_sets0.0020.0000.002
compare_to_catalogues0.0000.0000.001
complex_heatmap_exposures0.6110.0170.629
computeLogLik0.0000.0000.001
compute_comparison_stat_df000
confIntExp1.0590.3232.303
confidence_indel_calulation0.0000.0010.002
confidence_indel_only_calulation13.634 0.36013.999
correct_rounded000
cosineDist0.0000.0000.001
cosineMatchDist0.0010.0010.002
create_indel_mut_cat_from_df0.2890.0140.303
create_indel_mutation_catalogue_from_df8.5150.3968.922
create_mutation_catalogue_from_VR0.8370.0900.927
create_mutation_catalogue_from_df0.6020.0830.685
cut_breaks_as_intervals0.0800.0020.082
deriveSigInd_df000
disambiguateVector000
enrichSigs000
exampleYAPSA0.0560.0040.059
exome_mutCatRaw_df0.0060.0030.008
exposures_barplot1.7080.0101.719
extract_names_from_gene_list000
find_affected_PIDs0.0000.0000.001
getSequenceContext0.0870.0070.094
get_extreme_PIDs0.0160.0020.018
hclust_exposures0.0030.0010.005
logLikelihood0.6180.0860.704
lymphomaNature2013_mutCat_df0.0030.0020.004
makeVRangesFromDataFrame0.0750.0020.077
make_catalogue_strata_df000
make_comparison_matrix0.0510.0050.056
make_strata_df000
make_subgroups_df0.0240.0020.026
melt_exposures000
merge_exposures000
normalizeMotifs_otherRownames000
normalize_df_per_dim0.0060.0010.006
plotExchangeSpectra000
plotExchangeSpectra_indel0.7070.0040.711
plotExposuresConfidence000
plotExposuresConfidence_indel000
plot_SMC000
plot_exposures0.3330.0040.338
plot_strata0.0000.0000.001
read_entry000
relateSigs0.0010.0000.000
repeat_df0.0010.0000.001
round_precision000
run_SMC2.8990.2493.151
run_annotate_vcf_pl000
run_comparison_catalogues000
run_comparison_general0.0000.0000.001
run_kmer_frequency_correction000
run_kmer_frequency_normalization000
run_plot_strata_general0.0000.0000.001
shapiro_if_possible0.0000.0000.001
split_exposures_by_subgroups000
stat_plot_subgroups000
stat_test_SMC000
stat_test_subgroups000
stderrmean0.0000.0000.001
sum_over_list_of_df0.0020.0010.002
temp_trellis_rainfall_plot1.0980.0141.114
testSigs000
test_exposureAffected000
test_gene_list_in_exposures000
transform_rownames_R_to_MATLAB000
translate_to_hg190.0020.0010.003
trellis_rainfall_plot1.1180.0081.127
trellis_rainfall_plot_old1.1240.0081.133
variateExp1.6110.1101.721
variateExpSingle0.6090.0880.698