Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-08-13 17:41 -0400 (Tue, 13 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4758 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4493 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4471 |
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 2293/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
YAPSA 1.30.0 (landing page) Zuguang Gu
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | NA | |||||||||
To the developers/maintainers of the YAPSA package: - 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 Troubleshooting Build Report for more information. - 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: 1.30.0 |
Command: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:YAPSA.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings YAPSA_1.30.0.tar.gz |
StartedAt: 2024-08-12 06:40:33 -0400 (Mon, 12 Aug 2024) |
EndedAt: 2024-08-12 06:48:58 -0400 (Mon, 12 Aug 2024) |
EllapsedTime: 504.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: YAPSA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:YAPSA.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings YAPSA_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/YAPSA.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'YAPSA/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'YAPSA' version '1.30.0' * 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 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 19.64 0.85 20.71 create_indel_mutation_catalogue_from_df 12.43 0.92 13.38 build_gene_list_for_pathway 5.53 0.19 23.09 * 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: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL YAPSA ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.19-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' ** 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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 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' > > 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 17.00 1.81 19.07
YAPSA.Rcheck/YAPSA-Ex.timings
name | user | system | elapsed | |
GenomeOfNl_raw | 0.02 | 0.01 | 0.04 | |
LCD | 0.01 | 0.04 | 0.06 | |
LCD_complex_cutoff | 0 | 0 | 0 | |
MutCat_indel_df | 0.02 | 0.01 | 0.04 | |
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 | 0.01 | 0.00 | 0.01 | |
annotate_intermut_dist_cohort | 0.02 | 0.00 | 0.02 | |
annotation_exposures_barplot | 0 | 0 | 0 | |
annotation_exposures_list_barplot | 0 | 0 | 0 | |
annotation_heatmap_exposures | 0 | 0 | 0 | |
attribute_nucleotide_exchanges | 0 | 0 | 0 | |
attribute_sequence_contex_indel | 0.53 | 0.03 | 0.56 | |
attribution_of_indels | 0.58 | 0.08 | 0.66 | |
build_gene_list_for_pathway | 5.53 | 0.19 | 23.09 | |
classify_indels | 0 | 0 | 0 | |
compare_SMCs | 0 | 0 | 0 | |
compare_exposures | 0 | 0 | 0 | |
compare_expousre_sets | 0.02 | 0.00 | 0.02 | |
compare_sets | 0 | 0 | 0 | |
compare_to_catalogues | 0 | 0 | 0 | |
complex_heatmap_exposures | 1.09 | 0.39 | 1.16 | |
computeLogLik | 0 | 0 | 0 | |
compute_comparison_stat_df | 0 | 0 | 0 | |
confIntExp | 1.36 | 0.36 | 1.67 | |
confidence_indel_calulation | 0 | 0 | 0 | |
confidence_indel_only_calulation | 19.64 | 0.85 | 20.71 | |
correct_rounded | 0 | 0 | 0 | |
cosineDist | 0 | 0 | 0 | |
cosineMatchDist | 0.02 | 0.00 | 0.01 | |
create_indel_mut_cat_from_df | 0.37 | 0.06 | 0.44 | |
create_indel_mutation_catalogue_from_df | 12.43 | 0.92 | 13.38 | |
create_mutation_catalogue_from_VR | 1.29 | 0.24 | 1.53 | |
create_mutation_catalogue_from_df | 0.97 | 0.15 | 1.13 | |
cut_breaks_as_intervals | 0.09 | 0.03 | 0.12 | |
deriveSigInd_df | 0 | 0 | 0 | |
disambiguateVector | 0 | 0 | 0 | |
enrichSigs | 0 | 0 | 0 | |
exampleYAPSA | 0.06 | 0.03 | 0.10 | |
exome_mutCatRaw_df | 0.02 | 0.00 | 0.01 | |
exposures_barplot | 2.51 | 0.03 | 2.54 | |
extract_names_from_gene_list | 0 | 0 | 0 | |
find_affected_PIDs | 0 | 0 | 0 | |
getSequenceContext | 0.16 | 0.02 | 0.19 | |
get_extreme_PIDs | 0.02 | 0.00 | 0.02 | |
hclust_exposures | 0.01 | 0.00 | 0.01 | |
logLikelihood | 0.92 | 0.20 | 1.14 | |
lymphomaNature2013_mutCat_df | 0.00 | 0.00 | 0.02 | |
makeVRangesFromDataFrame | 0.11 | 0.00 | 0.11 | |
make_catalogue_strata_df | 0 | 0 | 0 | |
make_comparison_matrix | 0.1 | 0.0 | 0.1 | |
make_strata_df | 0.00 | 0.01 | 0.01 | |
make_subgroups_df | 0.03 | 0.00 | 0.03 | |
melt_exposures | 0 | 0 | 0 | |
merge_exposures | 0 | 0 | 0 | |
normalizeMotifs_otherRownames | 0 | 0 | 0 | |
normalize_df_per_dim | 0 | 0 | 0 | |
plotExchangeSpectra | 0 | 0 | 0 | |
plotExchangeSpectra_indel | 1.24 | 0.00 | 1.23 | |
plotExposuresConfidence | 0 | 0 | 0 | |
plotExposuresConfidence_indel | 0 | 0 | 0 | |
plot_SMC | 0 | 0 | 0 | |
plot_exposures | 0.51 | 0.02 | 0.54 | |
plot_strata | 0 | 0 | 0 | |
read_entry | 0 | 0 | 0 | |
relateSigs | 0 | 0 | 0 | |
repeat_df | 0 | 0 | 0 | |
round_precision | 0 | 0 | 0 | |
run_SMC | 4.05 | 0.62 | 4.73 | |
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 | 0 | 0 | |
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 | 0.02 | 0.00 | 0.02 | |
testSigs | 0 | 0 | 0 | |
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 | 0 | 0 | |
trellis_rainfall_plot | 2.04 | 0.03 | 2.12 | |
variateExp | 2.33 | 0.32 | 2.64 | |
variateExpSingle | 0.90 | 0.23 | 1.14 | |