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This page was generated on 2024-05-13 11:32:16 -0400 (Mon, 13 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
| 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 | ||||
| Package 2223/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| YAPSA 1.31.0 (landing page) Zuguang Gu
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | NA | ||||||||
|
To the developers/maintainers of the YAPSA package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: YAPSA |
| Version: 1.31.0 |
| 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_1.31.0.tar.gz |
| StartedAt: 2024-05-13 06:50:02 -0400 (Mon, 13 May 2024) |
| EndedAt: 2024-05-13 06:59:32 -0400 (Mon, 13 May 2024) |
| EllapsedTime: 569.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: YAPSA.Rcheck |
| Warnings: 0 |
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###
### 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_1.31.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/YAPSA.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘YAPSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘YAPSA’ version ‘1.31.0’
* 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 ... OK
* 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 code 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
confidence_indel_only_calulation 19.731 0.303 20.234
create_indel_mutation_catalogue_from_df 14.785 0.800 15.701
build_gene_list_for_pathway 6.581 0.151 32.628
run_SMC 5.158 0.535 5.727
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
YAPSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL YAPSA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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' ** 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' ** 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' ** testing if installed package keeps a record of temporary installation path * DONE (YAPSA)
YAPSA.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
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'
>
> 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
23.878 1.017 24.892
YAPSA.Rcheck/YAPSA-Ex.timings
| name | user | system | elapsed | |
| GenomeOfNl_raw | 0.011 | 0.003 | 0.015 | |
| LCD | 0.009 | 0.001 | 0.010 | |
| LCD_complex_cutoff | 0.001 | 0.000 | 0.000 | |
| MutCat_indel_df | 0.004 | 0.003 | 0.007 | |
| SMC | 0 | 0 | 0 | |
| SMC_perPID | 0.000 | 0.000 | 0.001 | |
| add_annotation | 0 | 0 | 0 | |
| add_as_fist_to_list | 0 | 0 | 0 | |
| aggregate_exposures_by_category | 0 | 0 | 0 | |
| annotate_intermut_dist_PID | 0.019 | 0.002 | 0.023 | |
| annotate_intermut_dist_cohort | 0.024 | 0.002 | 0.025 | |
| annotation_exposures_barplot | 0 | 0 | 0 | |
| annotation_exposures_list_barplot | 0 | 0 | 0 | |
| annotation_heatmap_exposures | 0.000 | 0.001 | 0.000 | |
| attribute_nucleotide_exchanges | 0.003 | 0.000 | 0.003 | |
| attribute_sequence_contex_indel | 0.641 | 0.042 | 0.685 | |
| attribution_of_indels | 0.718 | 0.043 | 0.765 | |
| build_gene_list_for_pathway | 6.581 | 0.151 | 32.628 | |
| classify_indels | 0.000 | 0.001 | 0.000 | |
| compare_SMCs | 0 | 0 | 0 | |
| compare_exposures | 0 | 0 | 0 | |
| compare_expousre_sets | 0.004 | 0.000 | 0.005 | |
| compare_sets | 0.003 | 0.000 | 0.003 | |
| compare_to_catalogues | 0 | 0 | 0 | |
| complex_heatmap_exposures | 1.016 | 0.031 | 1.048 | |
| computeLogLik | 0.000 | 0.001 | 0.000 | |
| compute_comparison_stat_df | 0 | 0 | 0 | |
| confIntExp | 1.614 | 0.204 | 1.827 | |
| confidence_indel_calulation | 0.001 | 0.003 | 0.003 | |
| confidence_indel_only_calulation | 19.731 | 0.303 | 20.234 | |
| correct_rounded | 0.000 | 0.000 | 0.001 | |
| cosineDist | 0.000 | 0.000 | 0.001 | |
| cosineMatchDist | 0.003 | 0.000 | 0.003 | |
| create_indel_mut_cat_from_df | 0.467 | 0.030 | 0.501 | |
| create_indel_mutation_catalogue_from_df | 14.785 | 0.800 | 15.701 | |
| create_mutation_catalogue_from_VR | 1.226 | 0.154 | 1.408 | |
| create_mutation_catalogue_from_df | 1.149 | 0.184 | 1.364 | |
| cut_breaks_as_intervals | 0.159 | 0.005 | 0.164 | |
| deriveSigInd_df | 0.000 | 0.000 | 0.001 | |
| disambiguateVector | 0 | 0 | 0 | |
| enrichSigs | 0 | 0 | 0 | |
| exampleYAPSA | 0.121 | 0.009 | 0.131 | |
| exome_mutCatRaw_df | 0.011 | 0.005 | 0.015 | |
| exposures_barplot | 3.182 | 0.043 | 3.236 | |
| extract_names_from_gene_list | 0 | 0 | 0 | |
| find_affected_PIDs | 0 | 0 | 0 | |
| getSequenceContext | 0.213 | 0.012 | 0.225 | |
| get_extreme_PIDs | 0.010 | 0.003 | 0.012 | |
| hclust_exposures | 0.007 | 0.003 | 0.010 | |
| logLikelihood | 1.165 | 0.192 | 1.362 | |
| lymphomaNature2013_mutCat_df | 0.005 | 0.004 | 0.009 | |
| makeVRangesFromDataFrame | 0.169 | 0.006 | 0.176 | |
| make_catalogue_strata_df | 0 | 0 | 0 | |
| make_comparison_matrix | 0.091 | 0.010 | 0.101 | |
| make_strata_df | 0 | 0 | 0 | |
| make_subgroups_df | 0.047 | 0.007 | 0.055 | |
| melt_exposures | 0 | 0 | 0 | |
| merge_exposures | 0 | 0 | 0 | |
| normalizeMotifs_otherRownames | 0.000 | 0.000 | 0.001 | |
| normalize_df_per_dim | 0.008 | 0.001 | 0.011 | |
| plotExchangeSpectra | 0 | 0 | 0 | |
| plotExchangeSpectra_indel | 1.385 | 0.010 | 1.427 | |
| plotExposuresConfidence | 0 | 0 | 0 | |
| plotExposuresConfidence_indel | 0 | 0 | 0 | |
| plot_SMC | 0.000 | 0.000 | 0.001 | |
| plot_exposures | 0.632 | 0.012 | 0.646 | |
| plot_strata | 0.000 | 0.000 | 0.001 | |
| read_entry | 0.000 | 0.001 | 0.001 | |
| relateSigs | 0.001 | 0.000 | 0.000 | |
| repeat_df | 0.002 | 0.001 | 0.003 | |
| round_precision | 0 | 0 | 0 | |
| run_SMC | 5.158 | 0.535 | 5.727 | |
| 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 | 0.000 | 0.001 | 0.000 | |
| shapiro_if_possible | 0.001 | 0.000 | 0.001 | |
| split_exposures_by_subgroups | 0 | 0 | 0 | |
| stat_plot_subgroups | 0 | 0 | 0 | |
| stat_test_SMC | 0 | 0 | 0 | |
| stat_test_subgroups | 0 | 0 | 0 | |
| stderrmean | 0 | 0 | 0 | |
| sum_over_list_of_df | 0.002 | 0.001 | 0.003 | |
| testSigs | 0.000 | 0.000 | 0.001 | |
| test_exposureAffected | 0.000 | 0.000 | 0.001 | |
| test_gene_list_in_exposures | 0 | 0 | 0 | |
| transform_rownames_R_to_MATLAB | 0.001 | 0.000 | 0.000 | |
| translate_to_hg19 | 0.003 | 0.001 | 0.004 | |
| trellis_rainfall_plot | 1.922 | 0.023 | 1.953 | |
| variateExp | 2.822 | 0.218 | 3.077 | |
| variateExpSingle | 1.142 | 0.188 | 1.341 | |