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This page was generated on 2022-01-17 11:06:42 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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 nebbiolo1


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 2069/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
YAPSA 1.21.1  (landing page)
Daniel Huebschmann
Snapshot Date: 2022-01-16 13:55:18 -0500 (Sun, 16 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: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:YAPSA.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings YAPSA_1.21.1.tar.gz
StartedAt: 2022-01-16 21:33:32 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 21:39:32 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 359.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: YAPSA.Rcheck
Warnings: 1

Command output

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


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/YAPSA.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (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 ‘1.21.1’
* 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 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 ‘/home/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        15.435  0.180  15.617
create_indel_mutation_catalogue_from_df  9.096  0.660   9.756
build_gene_list_for_pathway              3.339  0.103  25.949
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/YAPSA.Rcheck/00check.log’
for details.



Installation output

YAPSA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL YAPSA
###
##############################################################################
##############################################################################


* installing to library ‘/home/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
** 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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 12.154   0.570  12.708 

Example timings

YAPSA.Rcheck/YAPSA-Ex.timings

nameusersystemelapsed
GenomeOfNl_raw0.0030.0040.007
LCD0.0060.0000.006
LCD_complex_cutoff000
MutCat_indel_df0.0030.0000.003
SMC0.0010.0000.000
SMC_perPID0.0000.0000.001
add_annotation000
add_as_fist_to_list000
aggregate_exposures_by_category000
annotate_intermut_dist_PID0.0110.0030.014
annotate_intermut_dist_cohort0.0150.0010.017
annotation_exposures_barplot0.0000.0000.001
annotation_exposures_list_barplot000
annotation_heatmap_exposures000
attribute_nucleotide_exchanges0.0020.0010.002
attribute_sequence_contex_indel1.2100.0251.235
attribution_of_indels0.3120.0780.390
build_gene_list_for_pathway 3.339 0.10325.949
classify_indels0.0010.0000.000
compare_SMCs000
compare_exposures0.0000.0000.001
compare_expousre_sets0.0030.0000.003
compare_sets0.0030.0000.002
compare_to_catalogues000
complex_heatmap_exposures0.6780.0280.707
computeLogLik0.0000.0000.001
compute_comparison_stat_df000
confIntExp1.0530.3481.403
confidence_indel_calulation0.0010.0000.001
confidence_indel_only_calulation15.435 0.18015.617
correct_rounded000
cosineDist0.0010.0000.001
cosineMatchDist0.0020.0000.001
create_indel_mut_cat_from_df0.2850.0280.313
create_indel_mutation_catalogue_from_df9.0960.6609.756
create_mutation_catalogue_from_VR0.8380.1721.009
create_mutation_catalogue_from_df0.5710.1680.739
cut_breaks_as_intervals0.0850.0040.089
deriveSigInd_df0.0010.0000.000
disambiguateVector000
enrichSigs000
exampleYAPSA0.0620.0040.067
exome_mutCatRaw_df0.0050.0040.009
exposures_barplot1.9520.0121.965
extract_names_from_gene_list000
find_affected_PIDs000
getSequenceContext0.0940.0020.095
get_extreme_PIDs0.0190.0000.019
hclust_exposures0.0000.0040.004
logLikelihood0.5980.1480.746
lymphomaNature2013_mutCat_df0.0050.0000.005
makeVRangesFromDataFrame0.0960.0040.100
make_catalogue_strata_df0.0000.0000.001
make_comparison_matrix0.0670.0010.069
make_strata_df0.0000.0010.000
make_subgroups_df0.0250.0030.029
melt_exposures000
merge_exposures000
normalizeMotifs_otherRownames000
normalize_df_per_dim0.0080.0000.008
plotExchangeSpectra000
plotExchangeSpectra_indel0.8210.0000.821
plotExposuresConfidence000
plotExposuresConfidence_indel0.0010.0000.001
plot_SMC000
plot_exposures0.3370.0040.341
plot_strata000
read_entry000
relateSigs000
repeat_df0.0020.0000.002
round_precision000
run_SMC3.1170.3883.506
run_annotate_vcf_pl0.0000.0000.001
run_comparison_catalogues000
run_comparison_general000
run_kmer_frequency_correction000
run_kmer_frequency_normalization000
run_plot_strata_general0.0000.0000.001
shapiro_if_possible0.0010.0000.001
split_exposures_by_subgroups0.0000.0000.001
stat_plot_subgroups000
stat_test_SMC000
stat_test_subgroups000
stderrmean0.0010.0000.000
sum_over_list_of_df0.0020.0000.002
temp_trellis_rainfall_plot1.3170.0001.318
testSigs000
test_exposureAffected0.0000.0000.001
test_gene_list_in_exposures000
transform_rownames_R_to_MATLAB000
translate_to_hg190.0000.0030.004
trellis_rainfall_plot1.2850.0151.300
trellis_rainfall_plot_old1.3050.0041.309
variateExp1.7030.1521.855
variateExpSingle0.6460.1320.779