Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-27 11:37:30 -0400 (Wed, 27 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4698 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4436 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4461 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4376 |
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 2257/2264 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
YAPSA 1.29.0 (landing page) Zuguang Gu
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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: 1.29.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:YAPSA.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings YAPSA_1.29.0.tar.gz |
StartedAt: 2024-03-27 03:46:54 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 03:59:26 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 752.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: YAPSA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:YAPSA.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings YAPSA_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/YAPSA.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘YAPSA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘YAPSA’ version ‘1.29.0’ * 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 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 ... 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 20.626 0.452 21.078 create_indel_mutation_catalogue_from_df 12.527 0.757 13.283 build_gene_list_for_pathway 5.119 0.267 26.098 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
YAPSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL YAPSA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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' ** 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 Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 17.931 1.046 18.964
YAPSA.Rcheck/YAPSA-Ex.timings
name | user | system | elapsed | |
GenomeOfNl_raw | 0.009 | 0.000 | 0.010 | |
LCD | 0.008 | 0.000 | 0.008 | |
LCD_complex_cutoff | 0.001 | 0.000 | 0.000 | |
MutCat_indel_df | 0.000 | 0.004 | 0.004 | |
SMC | 0 | 0 | 0 | |
SMC_perPID | 0 | 0 | 0 | |
add_annotation | 0 | 0 | 0 | |
add_as_fist_to_list | 0.000 | 0.000 | 0.001 | |
aggregate_exposures_by_category | 0 | 0 | 0 | |
annotate_intermut_dist_PID | 0.173 | 0.004 | 0.177 | |
annotate_intermut_dist_cohort | 0.019 | 0.003 | 0.022 | |
annotation_exposures_barplot | 0.001 | 0.000 | 0.000 | |
annotation_exposures_list_barplot | 0.000 | 0.000 | 0.001 | |
annotation_heatmap_exposures | 0 | 0 | 0 | |
attribute_nucleotide_exchanges | 0.000 | 0.003 | 0.003 | |
attribute_sequence_contex_indel | 0.525 | 0.019 | 0.545 | |
attribution_of_indels | 1.491 | 0.052 | 1.543 | |
build_gene_list_for_pathway | 5.119 | 0.267 | 26.098 | |
classify_indels | 0 | 0 | 0 | |
compare_SMCs | 0.000 | 0.000 | 0.001 | |
compare_exposures | 0 | 0 | 0 | |
compare_expousre_sets | 0.005 | 0.000 | 0.004 | |
compare_sets | 0.003 | 0.000 | 0.004 | |
compare_to_catalogues | 0 | 0 | 0 | |
complex_heatmap_exposures | 0.893 | 0.036 | 0.928 | |
computeLogLik | 0 | 0 | 0 | |
compute_comparison_stat_df | 0 | 0 | 0 | |
confIntExp | 1.302 | 0.379 | 1.699 | |
confidence_indel_calulation | 0.001 | 0.000 | 0.001 | |
confidence_indel_only_calulation | 20.626 | 0.452 | 21.078 | |
correct_rounded | 0 | 0 | 0 | |
cosineDist | 0 | 0 | 0 | |
cosineMatchDist | 0.002 | 0.000 | 0.002 | |
create_indel_mut_cat_from_df | 0.482 | 0.063 | 0.544 | |
create_indel_mutation_catalogue_from_df | 12.527 | 0.757 | 13.283 | |
create_mutation_catalogue_from_VR | 1.215 | 0.136 | 1.351 | |
create_mutation_catalogue_from_df | 0.802 | 0.156 | 0.958 | |
cut_breaks_as_intervals | 0.127 | 0.004 | 0.130 | |
deriveSigInd_df | 0 | 0 | 0 | |
disambiguateVector | 0 | 0 | 0 | |
enrichSigs | 0 | 0 | 0 | |
exampleYAPSA | 0.088 | 0.000 | 0.088 | |
exome_mutCatRaw_df | 0.007 | 0.004 | 0.011 | |
exposures_barplot | 2.597 | 0.024 | 2.621 | |
extract_names_from_gene_list | 0 | 0 | 0 | |
find_affected_PIDs | 0.001 | 0.000 | 0.000 | |
getSequenceContext | 0.120 | 0.009 | 0.130 | |
get_extreme_PIDs | 0.009 | 0.000 | 0.009 | |
hclust_exposures | 0.002 | 0.004 | 0.006 | |
logLikelihood | 0.816 | 0.156 | 0.973 | |
lymphomaNature2013_mutCat_df | 0.006 | 0.000 | 0.005 | |
makeVRangesFromDataFrame | 0.125 | 0.000 | 0.125 | |
make_catalogue_strata_df | 0 | 0 | 0 | |
make_comparison_matrix | 0.077 | 0.008 | 0.084 | |
make_strata_df | 0.000 | 0.000 | 0.001 | |
make_subgroups_df | 0.031 | 0.004 | 0.035 | |
melt_exposures | 0 | 0 | 0 | |
merge_exposures | 0 | 0 | 0 | |
normalizeMotifs_otherRownames | 0.001 | 0.000 | 0.000 | |
normalize_df_per_dim | 0.001 | 0.008 | 0.008 | |
plotExchangeSpectra | 0.000 | 0.000 | 0.001 | |
plotExchangeSpectra_indel | 1.249 | 0.004 | 1.253 | |
plotExposuresConfidence | 0 | 0 | 0 | |
plotExposuresConfidence_indel | 0 | 0 | 0 | |
plot_SMC | 0.000 | 0.000 | 0.001 | |
plot_exposures | 0.519 | 0.018 | 0.536 | |
plot_strata | 0 | 0 | 0 | |
read_entry | 0.000 | 0.000 | 0.001 | |
relateSigs | 0 | 0 | 0 | |
repeat_df | 0.000 | 0.002 | 0.002 | |
round_precision | 0 | 0 | 0 | |
run_SMC | 3.996 | 0.468 | 4.465 | |
run_annotate_vcf_pl | 0.001 | 0.000 | 0.000 | |
run_comparison_catalogues | 0 | 0 | 0 | |
run_comparison_general | 0 | 0 | 0 | |
run_kmer_frequency_correction | 0.001 | 0.000 | 0.000 | |
run_kmer_frequency_normalization | 0 | 0 | 0 | |
run_plot_strata_general | 0 | 0 | 0 | |
shapiro_if_possible | 0.001 | 0.000 | 0.002 | |
split_exposures_by_subgroups | 0 | 0 | 0 | |
stat_plot_subgroups | 0 | 0 | 0 | |
stat_test_SMC | 0.000 | 0.000 | 0.001 | |
stat_test_subgroups | 0 | 0 | 0 | |
stderrmean | 0.001 | 0.000 | 0.000 | |
sum_over_list_of_df | 0.000 | 0.003 | 0.003 | |
testSigs | 0 | 0 | 0 | |
test_exposureAffected | 0 | 0 | 0 | |
test_gene_list_in_exposures | 0.000 | 0.000 | 0.001 | |
transform_rownames_R_to_MATLAB | 0 | 0 | 0 | |
translate_to_hg19 | 0.003 | 0.001 | 0.003 | |
trellis_rainfall_plot | 1.658 | 0.014 | 1.674 | |
variateExp | 2.351 | 0.228 | 2.580 | |
variateExpSingle | 0.813 | 0.128 | 0.941 | |