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This page was generated on 2024-05-20 11:32:23 -0400 (Mon, 20 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" | 4381 |
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 2226/2233 | 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 | OK | ![]() | |||||||
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: 2024-05-20 06:33:10 -0400 (Mon, 20 May 2024) |
EndedAt: 2024-05-20 06:42:44 -0400 (Mon, 20 May 2024) |
EllapsedTime: 574.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: YAPSA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * 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 20.911 0.312 21.289 create_indel_mutation_catalogue_from_df 14.919 0.842 15.863 build_gene_list_for_pathway 6.408 0.147 31.863 run_SMC 5.112 0.548 5.715 * 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 23.753 0.968 24.714
YAPSA.Rcheck/YAPSA-Ex.timings
name | user | system | elapsed | |
GenomeOfNl_raw | 0.011 | 0.004 | 0.016 | |
LCD | 0.010 | 0.001 | 0.011 | |
LCD_complex_cutoff | 0 | 0 | 0 | |
MutCat_indel_df | 0.004 | 0.004 | 0.008 | |
SMC | 0 | 0 | 0 | |
SMC_perPID | 0.000 | 0.000 | 0.001 | |
add_annotation | 0.000 | 0.000 | 0.001 | |
add_as_fist_to_list | 0.000 | 0.001 | 0.000 | |
aggregate_exposures_by_category | 0 | 0 | 0 | |
annotate_intermut_dist_PID | 0.018 | 0.002 | 0.019 | |
annotate_intermut_dist_cohort | 0.020 | 0.002 | 0.022 | |
annotation_exposures_barplot | 0 | 0 | 0 | |
annotation_exposures_list_barplot | 0 | 0 | 0 | |
annotation_heatmap_exposures | 0 | 0 | 0 | |
attribute_nucleotide_exchanges | 0.003 | 0.001 | 0.004 | |
attribute_sequence_contex_indel | 0.640 | 0.042 | 0.685 | |
attribution_of_indels | 0.709 | 0.041 | 0.751 | |
build_gene_list_for_pathway | 6.408 | 0.147 | 31.863 | |
classify_indels | 0.000 | 0.000 | 0.001 | |
compare_SMCs | 0 | 0 | 0 | |
compare_exposures | 0 | 0 | 0 | |
compare_expousre_sets | 0.004 | 0.001 | 0.004 | |
compare_sets | 0.003 | 0.000 | 0.004 | |
compare_to_catalogues | 0 | 0 | 0 | |
complex_heatmap_exposures | 1.062 | 0.027 | 1.093 | |
computeLogLik | 0 | 0 | 0 | |
compute_comparison_stat_df | 0.000 | 0.001 | 0.001 | |
confIntExp | 1.858 | 0.220 | 2.088 | |
confidence_indel_calulation | 0.001 | 0.002 | 0.004 | |
confidence_indel_only_calulation | 20.911 | 0.312 | 21.289 | |
correct_rounded | 0 | 0 | 0 | |
cosineDist | 0.000 | 0.001 | 0.000 | |
cosineMatchDist | 0.002 | 0.000 | 0.002 | |
create_indel_mut_cat_from_df | 0.496 | 0.031 | 0.530 | |
create_indel_mutation_catalogue_from_df | 14.919 | 0.842 | 15.863 | |
create_mutation_catalogue_from_VR | 1.529 | 0.199 | 1.740 | |
create_mutation_catalogue_from_df | 1.105 | 0.187 | 1.297 | |
cut_breaks_as_intervals | 0.153 | 0.006 | 0.160 | |
deriveSigInd_df | 0.001 | 0.000 | 0.000 | |
disambiguateVector | 0 | 0 | 0 | |
enrichSigs | 0 | 0 | 0 | |
exampleYAPSA | 0.123 | 0.010 | 0.134 | |
exome_mutCatRaw_df | 0.010 | 0.005 | 0.015 | |
exposures_barplot | 3.293 | 0.046 | 3.419 | |
extract_names_from_gene_list | 0 | 0 | 0 | |
find_affected_PIDs | 0.001 | 0.000 | 0.000 | |
getSequenceContext | 0.221 | 0.016 | 0.248 | |
get_extreme_PIDs | 0.011 | 0.003 | 0.014 | |
hclust_exposures | 0.007 | 0.003 | 0.009 | |
logLikelihood | 1.176 | 0.199 | 1.385 | |
lymphomaNature2013_mutCat_df | 0.005 | 0.003 | 0.009 | |
makeVRangesFromDataFrame | 0.168 | 0.006 | 0.177 | |
make_catalogue_strata_df | 0 | 0 | 0 | |
make_comparison_matrix | 0.093 | 0.010 | 0.104 | |
make_strata_df | 0.000 | 0.000 | 0.001 | |
make_subgroups_df | 0.048 | 0.007 | 0.055 | |
melt_exposures | 0.000 | 0.001 | 0.000 | |
merge_exposures | 0 | 0 | 0 | |
normalizeMotifs_otherRownames | 0 | 0 | 0 | |
normalize_df_per_dim | 0.008 | 0.002 | 0.010 | |
plotExchangeSpectra | 0 | 0 | 0 | |
plotExchangeSpectra_indel | 1.386 | 0.010 | 1.398 | |
plotExposuresConfidence | 0 | 0 | 0 | |
plotExposuresConfidence_indel | 0 | 0 | 0 | |
plot_SMC | 0 | 0 | 0 | |
plot_exposures | 0.620 | 0.014 | 0.637 | |
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 | 0 | 0 | |
run_SMC | 5.112 | 0.548 | 5.715 | |
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 | 0.001 | 0.000 | 0.001 | |
run_plot_strata_general | 0 | 0 | 0 | |
shapiro_if_possible | 0.002 | 0.000 | 0.002 | |
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 | 0.000 | 0.000 | 0.001 | |
sum_over_list_of_df | 0.002 | 0.001 | 0.003 | |
testSigs | 0.000 | 0.000 | 0.001 | |
test_exposureAffected | 0 | 0 | 0 | |
test_gene_list_in_exposures | 0 | 0 | 0 | |
transform_rownames_R_to_MATLAB | 0 | 0 | 0 | |
translate_to_hg19 | 0.003 | 0.001 | 0.005 | |
trellis_rainfall_plot | 1.940 | 0.021 | 1.973 | |
variateExp | 2.757 | 0.224 | 3.003 | |
variateExpSingle | 1.139 | 0.204 | 1.342 | |