Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:08:09 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 875/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
hipathia 2.10.0 (landing page) Marta R. Hidalgo
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: 2.10.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hipathia.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hipathia_2.10.0.tar.gz |
StartedAt: 2022-04-12 14:16:33 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 14:39:09 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 1356.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: hipathia.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:hipathia.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings hipathia_2.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/hipathia.Rcheck’ * using R version 4.1.3 (2022-03-10) * 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 ‘2.10.0’ * 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 ‘hipathia’ can be installed ... OK * checking installed package size ... NOTE installed size is 10.4Mb sub-directories of 1Mb or more: data 5.8Mb 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 59.333 1.485 64.008 get_pathways_annotations 41.517 0.860 45.029 create_report 34.711 0.914 38.049 hipathia 33.581 0.476 34.966 visualize_report 32.524 0.527 33.917 node_color 32.438 0.510 33.807 save_results 31.423 0.408 32.861 normalize_paths 30.853 0.357 31.898 get_node_names 30.802 0.392 31.808 pathway_comparison_plot 30.714 0.423 31.911 node_color_per_de 30.591 0.382 31.852 get_path_names 30.429 0.504 31.643 load_pathways 30.171 0.347 32.261 get_pathways_list 30.060 0.344 31.198 get_pathways_summary 29.570 0.365 33.345 normalize_data 20.614 0.414 21.783 translate_data 18.514 0.419 19.786 get_go_names 9.256 0.444 10.466 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.14-bioc/meat/hipathia.Rcheck/00check.log’ for details.
hipathia.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/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 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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 Attaching package: 'BiocGenerics' 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 425.107 8.766 448.314
hipathia.Rcheck/hipathia-Ex.timings
name | user | system | elapsed | |
create_report | 34.711 | 0.914 | 38.049 | |
do_pca | 0.073 | 0.003 | 0.076 | |
do_wilcoxon | 0.111 | 0.006 | 0.118 | |
get_go_names | 9.256 | 0.444 | 10.466 | |
get_node_names | 30.802 | 0.392 | 31.808 | |
get_nodes_data | 0.010 | 0.003 | 0.013 | |
get_path_names | 30.429 | 0.504 | 31.643 | |
get_paths_data | 0.011 | 0.003 | 0.014 | |
get_pathways_annotations | 41.517 | 0.860 | 45.029 | |
get_pathways_list | 30.060 | 0.344 | 31.198 | |
get_pathways_summary | 29.570 | 0.365 | 33.345 | |
heatmap_plot | 0.334 | 0.011 | 0.344 | |
hhead | 0.002 | 0.002 | 0.004 | |
hipathia | 33.581 | 0.476 | 34.966 | |
load_pathways | 30.171 | 0.347 | 32.261 | |
multiple_pca_plot | 0.092 | 0.005 | 0.098 | |
node_color | 32.438 | 0.510 | 33.807 | |
node_color_per_de | 30.591 | 0.382 | 31.852 | |
normalize_data | 20.614 | 0.414 | 21.783 | |
normalize_paths | 30.853 | 0.357 | 31.898 | |
paths_to_go_ancestor | 0.433 | 0.010 | 0.443 | |
pathway_comparison_plot | 30.714 | 0.423 | 31.911 | |
pca_plot | 0.061 | 0.005 | 0.066 | |
quantify_terms | 59.333 | 1.485 | 64.008 | |
save_results | 31.423 | 0.408 | 32.861 | |
top_pathways | 0.010 | 0.003 | 0.014 | |
translate_data | 18.514 | 0.419 | 19.786 | |
visualize_report | 32.524 | 0.527 | 33.917 | |