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This page was generated on 2022-12-06 11:10:42 -0500 (Tue, 06 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4277
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4193
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4236
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 merida1


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 2149/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
YAPSA 1.25.0  (landing page)
Daniel Huebschmann
Snapshot Date: 2022-12-05 14:00:11 -0500 (Mon, 05 Dec 2022)
git_url: https://git.bioconductor.org/packages/YAPSA
git_branch: master
git_last_commit: 68115ee
git_last_commit_date: 2022-11-01 11:14:20 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  NO, package depends on 'SomaticSignatures' which is not available

Summary

Package: YAPSA
Version: 1.25.0
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_1.25.0.tar.gz
StartedAt: 2022-12-06 07:39:46 -0500 (Tue, 06 Dec 2022)
EndedAt: 2022-12-06 07:52:41 -0500 (Tue, 06 Dec 2022)
EllapsedTime: 774.6 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_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/YAPSA.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* 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 ‘1.25.0’
* 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-3.17-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        25.943  0.436  26.383
create_indel_mutation_catalogue_from_df 16.294  0.300  16.619
run_SMC                                  5.929  0.215   6.146
build_gene_list_for_pathway              6.008  0.080  21.483
* 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-3.17-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/4.3/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’
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’
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’
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 Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences"
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, 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 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'
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 1 | SKIP 0 | PASS 62 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 62 ]
> 
> proc.time()
   user  system elapsed 
 20.062   0.895  20.943 

Example timings

YAPSA.Rcheck/YAPSA-Ex.timings

nameusersystemelapsed
GenomeOfNl_raw0.0090.0020.011
LCD0.0080.0010.009
LCD_complex_cutoff000
MutCat_indel_df0.0050.0020.006
SMC000
SMC_perPID000
add_annotation000
add_as_fist_to_list000
aggregate_exposures_by_category0.0010.0000.000
annotate_intermut_dist_PID0.0210.0010.022
annotate_intermut_dist_cohort0.0260.0010.026
annotation_exposures_barplot000
annotation_exposures_list_barplot000
annotation_heatmap_exposures0.0010.0000.000
attribute_nucleotide_exchanges0.0030.0000.003
attribute_sequence_contex_indel0.6540.0460.700
attribution_of_indels0.5800.0730.653
build_gene_list_for_pathway 6.008 0.08021.483
classify_indels0.0010.0000.000
compare_SMCs000
compare_exposures0.0000.0010.000
compare_expousre_sets0.0040.0000.005
compare_sets0.0040.0010.004
compare_to_catalogues000
complex_heatmap_exposures1.1500.0131.162
computeLogLik000
compute_comparison_stat_df0.0000.0010.000
confIntExp1.7040.3532.884
confidence_indel_calulation0.0010.0020.003
confidence_indel_only_calulation25.943 0.43626.383
correct_rounded000
cosineDist000
cosineMatchDist0.0020.0000.001
create_indel_mut_cat_from_df0.5170.0110.528
create_indel_mutation_catalogue_from_df16.294 0.30016.619
create_mutation_catalogue_from_VR1.5220.0761.597
create_mutation_catalogue_from_df1.1220.0711.192
cut_breaks_as_intervals0.1660.0030.169
deriveSigInd_df0.0010.0000.001
disambiguateVector000
enrichSigs000
exampleYAPSA0.0890.0060.094
exome_mutCatRaw_df0.0140.0030.016
exposures_barplot3.5130.0073.521
extract_names_from_gene_list000
find_affected_PIDs000
getSequenceContext0.1880.0070.195
get_extreme_PIDs0.0360.0020.037
hclust_exposures0.0070.0020.009
logLikelihood1.1240.0721.197
lymphomaNature2013_mutCat_df0.0060.0020.008
makeVRangesFromDataFrame0.1390.0030.143
make_catalogue_strata_df000
make_comparison_matrix0.1190.0050.125
make_strata_df000
make_subgroups_df0.0370.0030.039
melt_exposures0.0000.0000.001
merge_exposures000
normalizeMotifs_otherRownames000
normalize_df_per_dim0.0100.0010.011
plotExchangeSpectra000
plotExchangeSpectra_indel1.7280.0051.733
plotExposuresConfidence000
plotExposuresConfidence_indel000
plot_SMC000
plot_exposures0.6720.0050.678
plot_strata000
read_entry0.0000.0000.001
relateSigs000
repeat_df0.0020.0000.003
round_precision000
run_SMC5.9290.2156.146
run_annotate_vcf_pl000
run_comparison_catalogues000
run_comparison_general000
run_kmer_frequency_correction0.0000.0000.001
run_kmer_frequency_normalization0.0010.0000.000
run_plot_strata_general000
shapiro_if_possible0.0010.0000.001
split_exposures_by_subgroups000
stat_plot_subgroups000
stat_test_SMC0.0000.0000.001
stat_test_subgroups000
stderrmean0.0010.0000.000
sum_over_list_of_df0.0030.0010.003
temp_trellis_rainfall_plot2.1930.0132.208
testSigs000
test_exposureAffected000
test_gene_list_in_exposures0.0000.0000.001
transform_rownames_R_to_MATLAB000
translate_to_hg190.0040.0000.005
trellis_rainfall_plot2.2160.0102.228
trellis_rainfall_plot_old2.2100.0092.221
variateExp3.1060.1003.208
variateExpSingle1.1540.0791.233