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This page was generated on 2022-01-21 11:08:54 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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 riesling1


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? here 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 2070/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
YAPSA 1.21.1  (landing page)
Daniel Huebschmann
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/YAPSA
git_branch: master
git_last_commit: 2261ecf
git_last_commit_date: 2021-11-13 14:32:49 -0500 (Sat, 13 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
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  UNNEEDED, same version is already published

Summary

Package: YAPSA
Version: 1.21.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:YAPSA.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings YAPSA_1.21.1.tar.gz
StartedAt: 2022-01-20 20:24:54 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 20:30:35 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 340.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: YAPSA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:YAPSA.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings YAPSA_1.21.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/YAPSA.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'YAPSA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'YAPSA' version '1.21.1'
* 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 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 'D:/biocbuild/bbs-3.15-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        16.49   0.04   16.53
create_indel_mutation_catalogue_from_df  8.92   0.38    9.30
build_gene_list_for_pathway              2.96   0.10   20.56
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/YAPSA.Rcheck/00check.log'
for details.



Installation output

YAPSA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL YAPSA
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/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
  converting help for package 'YAPSA'
    finding HTML links ... done
    GenomeOfNl_raw                          html  
    LCD                                     html  
    LCD_SMC                                 html  
    LCD_complex_cutoff                      html  
    MutCat_indel_df                         html  
    SMC                                     html  
    SMC_perPID                              html  
    YAPSA                                   html  
    add_annotation                          html  
    add_as_fist_to_list                     html  
    aggregate_exposures_by_category         html  
    annotate_intermut_dist_PID              html  
    annotate_intermut_dist_cohort           html  
    annotation_exposures_barplot            html  
    annotation_exposures_list_barplot       html  
    annotation_heatmap_exposures            html  
    attribute_nucleotide_exchanges          html  
    attribute_sequence_contex_indel         html  
    attribution_of_indels                   html  
    build_gene_list_for_pathway             html  
    classify_indels                         html  
    compare_SMCs                            html  
    compare_exposures                       html  
    compare_expousre_sets                   html  
    compare_sets                            html  
    compare_to_catalogues                   html  
    complex_heatmap_exposures               html  
    computeLogLik                           html  
    compute_comparison_stat_df              html  
    confIntExp                              html  
    confidence_indel_calulation             html  
    confidence_indel_only_calulation        html  
    correct_rounded                         html  
    cosineDist                              html  
    cosineMatchDist                         html  
    create_indel_mut_cat_from_df            html  
    create_indel_mutation_catalogue_from_df
                                            html  
    create_mutation_catalogue_from_VR       html  
    create_mutation_catalogue_from_df       html  
    finding level-2 HTML links ... done

    cut_breaks_as_intervals                 html  
    cutoffs                                 html  
    cutoffs_pcawg                           html  
    deriveSigInd_df                         html  
    disambiguateVector                      html  
    enrichSigs                              html  
    exampleINDEL_YAPSA                      html  
    exampleYAPSA                            html  
    exchange_colour_vector                  html  
    exome_mutCatRaw_df                      html  
    exposures_barplot                       html  
    extract_names_from_gene_list            html  
    find_affected_PIDs                      html  
    getSequenceContext                      html  
    get_extreme_PIDs                        html  
    hclust_exposures                        html  
    logLikelihood                           html  
    lymphomaNature2013_mutCat_df            html  
    makeVRangesFromDataFrame                html  
    make_catalogue_strata_df                html  
    make_comparison_matrix                  html  
    make_strata_df                          html  
    make_subgroups_df                       html  
    melt_exposures                          html  
    merge_exposures                         html  
    normalizeMotifs_otherRownames           html  
    normalize_df_per_dim                    html  
    plotExchangeSpectra                     html  
    plotExchangeSpectra_indel               html  
    plotExposuresConfidence                 html  
    plotExposuresConfidence_indel           html  
    plot_SMC                                html  
    plot_exposures                          html  
    plot_strata                             html  
    read_entry                              html  
    relateSigs                              html  
    repeat_df                               html  
    round_precision                         html  
    run_SMC                                 html  
    run_annotate_vcf_pl                     html  
    run_comparison_catalogues               html  
    run_comparison_general                  html  
    run_kmer_frequency_correction           html  
    run_kmer_frequency_normalization        html  
    run_plot_strata_general                 html  
    shapiro_if_possible                     html  
    sigs                                    html  
    sigs_pcawg                              html  
    split_exposures_by_subgroups            html  
    stat_plot_subgroups                     html  
    stat_test_SMC                           html  
    stat_test_subgroups                     html  
    stderrmean                              html  
    sum_over_list_of_df                     html  
    targetCapture_cor_factors               html  
    temp_trellis_rainfall_plot              html  
    testSigs                                html  
    test_exposureAffected                   html  
    test_gene_list_in_exposures             html  
    transform_rownames_R_to_MATLAB          html  
    translate_to_hg19                       html  
    trellis_rainfall_plot                   html  
    trellis_rainfall_plot_old               html  
    variateExp                              html  
    variateExpSingle                        html  
** 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)
Making 'packages.html' ... done

Tests output

YAPSA.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

Attaching package: 'IRanges'

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

    windows

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 
  11.78    0.46   12.23 

Example timings

YAPSA.Rcheck/YAPSA-Ex.timings

nameusersystemelapsed
GenomeOfNl_raw0.020.000.02
LCD000
LCD_complex_cutoff000
MutCat_indel_df000
SMC000
SMC_perPID000
add_annotation000
add_as_fist_to_list000
aggregate_exposures_by_category000
annotate_intermut_dist_PID0.020.000.01
annotate_intermut_dist_cohort0.010.000.02
annotation_exposures_barplot000
annotation_exposures_list_barplot000
annotation_heatmap_exposures000
attribute_nucleotide_exchanges0.020.000.01
attribute_sequence_contex_indel1.080.041.13
attribution_of_indels0.320.060.39
build_gene_list_for_pathway 2.96 0.1020.56
classify_indels000
compare_SMCs000
compare_exposures000
compare_expousre_sets000
compare_sets000
compare_to_catalogues000
complex_heatmap_exposures0.680.010.70
computeLogLik000
compute_comparison_stat_df000
confIntExp1.00.11.1
confidence_indel_calulation000
confidence_indel_only_calulation16.49 0.0416.53
correct_rounded000
cosineDist000
cosineMatchDist000
create_indel_mut_cat_from_df0.340.000.34
create_indel_mutation_catalogue_from_df8.920.389.30
create_mutation_catalogue_from_VR0.830.171.00
create_mutation_catalogue_from_df0.650.060.72
cut_breaks_as_intervals0.080.020.10
deriveSigInd_df000
disambiguateVector000
enrichSigs000
exampleYAPSA0.070.000.07
exome_mutCatRaw_df000
exposures_barplot1.920.001.92
extract_names_from_gene_list000
find_affected_PIDs000
getSequenceContext0.100.010.11
get_extreme_PIDs0.010.000.02
hclust_exposures0.020.000.01
logLikelihood0.670.080.75
lymphomaNature2013_mutCat_df0.020.000.02
makeVRangesFromDataFrame0.070.000.08
make_catalogue_strata_df000
make_comparison_matrix0.050.030.08
make_strata_df000
make_subgroups_df0.030.000.03
melt_exposures000
merge_exposures000
normalizeMotifs_otherRownames000
normalize_df_per_dim000
plotExchangeSpectra000
plotExchangeSpectra_indel0.860.000.86
plotExposuresConfidence000
plotExposuresConfidence_indel000
plot_SMC000
plot_exposures0.340.000.35
plot_strata000
read_entry000
relateSigs000
repeat_df000
round_precision000
run_SMC3.150.233.39
run_annotate_vcf_pl000
run_comparison_catalogues000
run_comparison_general000
run_kmer_frequency_correction000
run_kmer_frequency_normalization000
run_plot_strata_general000
shapiro_if_possible000
split_exposures_by_subgroups000
stat_plot_subgroups000
stat_test_SMC000
stat_test_subgroups000
stderrmean000
sum_over_list_of_df000
temp_trellis_rainfall_plot1.420.021.44
testSigs000
test_exposureAffected000
test_gene_list_in_exposures000
transform_rownames_R_to_MATLAB000
translate_to_hg19000
trellis_rainfall_plot1.440.021.45
trellis_rainfall_plot_old1.450.011.47
variateExp1.770.141.91
variateExpSingle0.690.060.75