Daniel Huebschmann
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/YAPSA |
| git_branch: RELEASE_3_16 |
| git_last_commit: 68d1c9c |
| git_last_commit_date: 2022-11-01 11:14:20 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:23 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
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. |
| Package 2177/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| YAPSA 1.24.0 (landing page) Daniel Huebschmann
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: YAPSA |
| Version: 1.24.0 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:YAPSA.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings YAPSA_1.24.0.tar.gz |
| StartedAt: 2023-04-11 00:53:38 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 01:03:41 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 603.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: YAPSA.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:YAPSA.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings YAPSA_1.24.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/YAPSA.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘YAPSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘YAPSA’ version ‘1.24.0’
* 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 ‘/home/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 loading without being on the library search path ... 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 15.890 0.592 16.482
create_indel_mutation_catalogue_from_df 9.880 0.234 10.114
build_gene_list_for_pathway 4.412 0.102 24.105
* 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 ...
‘YAPSA.Rmd’ using ‘UTF-8’... OK
‘vignette_confidenceIntervals.Rmd’ using ‘UTF-8’... OK
‘vignette_exomes.Rmd’ using ‘UTF-8’... OK
‘vignette_signature_specific_cutoffs.Rmd’ using ‘UTF-8’... OK
‘vignette_stratifiedAnalysis.Rmd’ using ‘UTF-8’... OK
‘vignettes_Indel.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.16-bioc/meat/YAPSA.Rcheck/00check.log’
for details.
YAPSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL YAPSA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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)
YAPSA.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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, 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'
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
13.722 0.764 14.467
YAPSA.Rcheck/YAPSA-Ex.timings
| name | user | system | elapsed | |
| GenomeOfNl_raw | 0.003 | 0.004 | 0.007 | |
| LCD | 0.007 | 0.001 | 0.006 | |
| LCD_complex_cutoff | 0.000 | 0.000 | 0.001 | |
| MutCat_indel_df | 0.003 | 0.000 | 0.003 | |
| SMC | 0 | 0 | 0 | |
| SMC_perPID | 0 | 0 | 0 | |
| add_annotation | 0 | 0 | 0 | |
| add_as_fist_to_list | 0 | 0 | 0 | |
| aggregate_exposures_by_category | 0 | 0 | 0 | |
| annotate_intermut_dist_PID | 0.012 | 0.003 | 0.015 | |
| annotate_intermut_dist_cohort | 0.014 | 0.003 | 0.018 | |
| annotation_exposures_barplot | 0 | 0 | 0 | |
| annotation_exposures_list_barplot | 0 | 0 | 0 | |
| annotation_heatmap_exposures | 0 | 0 | 0 | |
| attribute_nucleotide_exchanges | 0.002 | 0.000 | 0.002 | |
| attribute_sequence_contex_indel | 0.431 | 0.031 | 0.464 | |
| attribution_of_indels | 0.364 | 0.022 | 0.387 | |
| build_gene_list_for_pathway | 4.412 | 0.102 | 24.105 | |
| classify_indels | 0 | 0 | 0 | |
| compare_SMCs | 0 | 0 | 0 | |
| compare_exposures | 0 | 0 | 0 | |
| compare_expousre_sets | 0.001 | 0.002 | 0.003 | |
| compare_sets | 0.001 | 0.001 | 0.002 | |
| compare_to_catalogues | 0 | 0 | 0 | |
| complex_heatmap_exposures | 0.726 | 0.064 | 0.790 | |
| computeLogLik | 0 | 0 | 0 | |
| compute_comparison_stat_df | 0 | 0 | 0 | |
| confIntExp | 1.168 | 0.108 | 1.276 | |
| confidence_indel_calulation | 0.001 | 0.000 | 0.001 | |
| confidence_indel_only_calulation | 15.890 | 0.592 | 16.482 | |
| correct_rounded | 0 | 0 | 0 | |
| cosineDist | 0 | 0 | 0 | |
| cosineMatchDist | 0.000 | 0.001 | 0.001 | |
| create_indel_mut_cat_from_df | 0.316 | 0.011 | 0.326 | |
| create_indel_mutation_catalogue_from_df | 9.880 | 0.234 | 10.114 | |
| create_mutation_catalogue_from_VR | 0.912 | 0.052 | 0.964 | |
| create_mutation_catalogue_from_df | 0.659 | 0.044 | 0.703 | |
| cut_breaks_as_intervals | 0.124 | 0.004 | 0.128 | |
| deriveSigInd_df | 0 | 0 | 0 | |
| disambiguateVector | 0 | 0 | 0 | |
| enrichSigs | 0 | 0 | 0 | |
| exampleYAPSA | 0.061 | 0.004 | 0.066 | |
| exome_mutCatRaw_df | 0.007 | 0.000 | 0.007 | |
| exposures_barplot | 2.008 | 0.048 | 2.056 | |
| extract_names_from_gene_list | 0 | 0 | 0 | |
| find_affected_PIDs | 0 | 0 | 0 | |
| getSequenceContext | 0.102 | 0.000 | 0.101 | |
| get_extreme_PIDs | 0.015 | 0.004 | 0.019 | |
| hclust_exposures | 0.004 | 0.000 | 0.004 | |
| logLikelihood | 0.653 | 0.048 | 0.701 | |
| lymphomaNature2013_mutCat_df | 0.015 | 0.000 | 0.016 | |
| makeVRangesFromDataFrame | 0.09 | 0.00 | 0.09 | |
| make_catalogue_strata_df | 0 | 0 | 0 | |
| make_comparison_matrix | 0.057 | 0.004 | 0.060 | |
| make_strata_df | 0 | 0 | 0 | |
| make_subgroups_df | 0.027 | 0.000 | 0.027 | |
| melt_exposures | 0.001 | 0.000 | 0.000 | |
| merge_exposures | 0 | 0 | 0 | |
| normalizeMotifs_otherRownames | 0 | 0 | 0 | |
| normalize_df_per_dim | 0.003 | 0.002 | 0.007 | |
| plotExchangeSpectra | 0 | 0 | 0 | |
| plotExchangeSpectra_indel | 0.989 | 0.001 | 0.989 | |
| plotExposuresConfidence | 0 | 0 | 0 | |
| plotExposuresConfidence_indel | 0 | 0 | 0 | |
| plot_SMC | 0 | 0 | 0 | |
| plot_exposures | 0.444 | 0.004 | 0.448 | |
| plot_strata | 0 | 0 | 0 | |
| read_entry | 0 | 0 | 0 | |
| relateSigs | 0 | 0 | 0 | |
| repeat_df | 0.002 | 0.000 | 0.002 | |
| round_precision | 0.000 | 0.000 | 0.001 | |
| run_SMC | 3.452 | 0.088 | 3.540 | |
| run_annotate_vcf_pl | 0 | 0 | 0 | |
| run_comparison_catalogues | 0 | 0 | 0 | |
| run_comparison_general | 0 | 0 | 0 | |
| run_kmer_frequency_correction | 0 | 0 | 0 | |
| run_kmer_frequency_normalization | 0 | 0 | 0 | |
| run_plot_strata_general | 0 | 0 | 0 | |
| shapiro_if_possible | 0.001 | 0.000 | 0.001 | |
| split_exposures_by_subgroups | 0 | 0 | 0 | |
| stat_plot_subgroups | 0.000 | 0.000 | 0.001 | |
| stat_test_SMC | 0 | 0 | 0 | |
| stat_test_subgroups | 0 | 0 | 0 | |
| stderrmean | 0.000 | 0.000 | 0.001 | |
| sum_over_list_of_df | 0.001 | 0.000 | 0.001 | |
| temp_trellis_rainfall_plot | 1.323 | 0.012 | 1.336 | |
| testSigs | 0 | 0 | 0 | |
| test_exposureAffected | 0 | 0 | 0 | |
| test_gene_list_in_exposures | 0 | 0 | 0 | |
| transform_rownames_R_to_MATLAB | 0.000 | 0.000 | 0.001 | |
| translate_to_hg19 | 0.003 | 0.000 | 0.003 | |
| trellis_rainfall_plot | 1.386 | 0.024 | 1.411 | |
| trellis_rainfall_plot_old | 1.382 | 0.032 | 1.413 | |
| variateExp | 1.842 | 0.052 | 1.894 | |
| variateExpSingle | 0.652 | 0.033 | 0.685 | |