Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:38 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the hipathia package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hipathia.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 865/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
hipathia 2.8.0 (landing page) Marta R. Hidalgo
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: hipathia |
Version: 2.8.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:hipathia.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings hipathia_2.8.0.tar.gz |
StartedAt: 2021-10-14 20:00:53 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 20:20:19 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 1166.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: hipathia.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:hipathia.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings hipathia_2.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/hipathia.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘hipathia/DESCRIPTION’ ... OK * this is package ‘hipathia’ version ‘2.8.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘hipathia’ can be installed ... OK * checking installed package size ... NOTE installed size is 9.6Mb sub-directories of 1Mb or more: data 4.9Mb extdata 4.3Mb * 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 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed quantify_terms 48.894 1.157 52.632 get_pathways_annotations 34.815 0.799 37.182 hipathia 28.673 0.500 29.947 create_report 28.127 0.744 30.051 visualize_report 27.902 0.357 28.855 node_color 27.769 0.468 29.053 get_path_names 26.755 0.445 27.940 save_results 26.812 0.325 27.766 node_color_per_de 26.668 0.336 27.784 load_pathways 25.903 0.310 26.945 pathway_comparison_plot 25.695 0.392 26.741 get_pathways_list 25.441 0.328 26.282 get_node_names 24.561 0.414 25.688 normalize_paths 24.520 0.434 25.818 get_pathways_summary 24.376 0.313 25.389 normalize_data 16.111 0.318 17.060 translate_data 15.247 0.315 16.258 get_go_names 7.210 0.483 8.408 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/hipathia.Rcheck/00check.log’ for details.
hipathia.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL hipathia ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘hipathia’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (hipathia)
hipathia.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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. > library(testthat) > library(hipathia) Loading required package: igraph Attaching package: 'igraph' The following object is masked from 'package:testthat': compare The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union Loading required package: AnnotationHub Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:igraph': normalize, path, union 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, 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: BiocFileCache Loading required package: dbplyr Loading required package: MultiAssayExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 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: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians The following object is masked from 'package:AnnotationHub': cache > > test_check("hipathia") HiPathia processing... hsa03320 - PPAR signaling pathway hsa04012 - ErbB signaling pathway HiPathia processing... hsa03320 - PPAR signaling pathway hsa04012 - ErbB signaling pathway translated ids = 3184 (1) untranslated ids = 3 (0.00094) multihit ids = 0 (0) [ FAIL 0 | WARN 0 | SKIP 0 | PASS 119 ] > > proc.time() user system elapsed 358.203 7.178 379.062
hipathia.Rcheck/hipathia-Ex.timings
name | user | system | elapsed | |
create_report | 28.127 | 0.744 | 30.051 | |
do_pca | 0.085 | 0.006 | 0.091 | |
do_wilcoxon | 0.134 | 0.012 | 0.146 | |
get_go_names | 7.210 | 0.483 | 8.408 | |
get_node_names | 24.561 | 0.414 | 25.688 | |
get_nodes_data | 0.007 | 0.002 | 0.009 | |
get_path_names | 26.755 | 0.445 | 27.940 | |
get_paths_data | 0.007 | 0.001 | 0.008 | |
get_pathways_annotations | 34.815 | 0.799 | 37.182 | |
get_pathways_list | 25.441 | 0.328 | 26.282 | |
get_pathways_summary | 24.376 | 0.313 | 25.389 | |
heatmap_plot | 0.268 | 0.009 | 0.277 | |
hhead | 0.002 | 0.003 | 0.004 | |
hipathia | 28.673 | 0.500 | 29.947 | |
load_pathways | 25.903 | 0.310 | 26.945 | |
multiple_pca_plot | 0.074 | 0.005 | 0.079 | |
node_color | 27.769 | 0.468 | 29.053 | |
node_color_per_de | 26.668 | 0.336 | 27.784 | |
normalize_data | 16.111 | 0.318 | 17.060 | |
normalize_paths | 24.520 | 0.434 | 25.818 | |
paths_to_go_ancestor | 0.285 | 0.008 | 0.293 | |
pathway_comparison_plot | 25.695 | 0.392 | 26.741 | |
pca_plot | 0.195 | 0.005 | 0.202 | |
quantify_terms | 48.894 | 1.157 | 52.632 | |
save_results | 26.812 | 0.325 | 27.766 | |
top_pathways | 0.013 | 0.002 | 0.015 | |
translate_data | 15.247 | 0.315 | 16.258 | |
visualize_report | 27.902 | 0.357 | 28.855 | |