Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:31:35 -0400 (Wed, 17 Oct 2018).
Package 689/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
hipathia 1.0.0 Marta R. Hidalgo
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: hipathia |
Version: 1.0.0 |
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:hipathia.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings hipathia_1.0.0.tar.gz |
StartedAt: 2018-10-16 01:09:27 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 01:16:13 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 406.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: hipathia.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:hipathia.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings hipathia_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/hipathia.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘hipathia/DESCRIPTION’ ... OK * this is package ‘hipathia’ version ‘1.0.0’ * 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 8.5Mb sub-directories of 1Mb or more: data 3.8Mb 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed create_report 13.040 0.408 15.644 hipathia 9.916 0.060 9.986 node_color_per_de 8.856 0.052 8.916 get_pathways_annotations 8.740 0.060 8.820 load_pathways 8.624 0.032 8.678 normalize_paths 8.580 0.056 8.645 get_pathways_summary 8.528 0.036 8.566 quantify_terms 8.480 0.080 8.576 get_path_names 8.512 0.036 8.554 get_pathways_list 8.496 0.036 8.538 save_results 8.508 0.024 8.539 pathway_comparison_plot 8.388 0.056 8.447 visualize_report 8.136 0.064 8.204 normalize_data 6.792 0.036 6.851 translate_data 5.324 0.052 5.380 * 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 ‘/home/biocbuild/bbs-3.7-bioc/meat/hipathia.Rcheck/00check.log’ for details.
hipathia.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL hipathia ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘hipathia’ ... ** 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 * DONE (hipathia)
hipathia.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: MultiAssayExperiment Loading required package: SummarizedExperiment Loading required package: GenomicRanges Loading required package: stats4 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid 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:AnnotationHub': cache Loading required package: DelayedArray Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Loading required package: BiocParallel Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following object is masked from 'package:igraph': simplify The following objects are masked from 'package:base': aperm, apply > > 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) ══ testthat results ═══════════════════════════════════════════════════════════ OK: 118 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 113.320 1.244 116.078
hipathia.Rcheck/hipathia-Ex.timings
name | user | system | elapsed | |
create_report | 13.040 | 0.408 | 15.644 | |
do_pca | 0.004 | 0.004 | 0.009 | |
do_wilcoxon | 0.052 | 0.012 | 0.065 | |
get_path_names | 8.512 | 0.036 | 8.554 | |
get_paths_data | 0.008 | 0.000 | 0.008 | |
get_pathways_annotations | 8.74 | 0.06 | 8.82 | |
get_pathways_list | 8.496 | 0.036 | 8.538 | |
get_pathways_summary | 8.528 | 0.036 | 8.566 | |
heatmap_plot | 0.140 | 0.008 | 0.147 | |
hhead | 0.000 | 0.000 | 0.001 | |
hipathia | 9.916 | 0.060 | 9.986 | |
load_pathways | 8.624 | 0.032 | 8.678 | |
multiple_pca_plot | 0.016 | 0.000 | 0.014 | |
node_color_per_de | 8.856 | 0.052 | 8.916 | |
normalize_data | 6.792 | 0.036 | 6.851 | |
normalize_paths | 8.580 | 0.056 | 8.645 | |
paths_to_go_ancestor | 0.192 | 0.004 | 0.197 | |
pathway_comparison_plot | 8.388 | 0.056 | 8.447 | |
pca_plot | 0.008 | 0.000 | 0.007 | |
quantify_terms | 8.480 | 0.080 | 8.576 | |
save_results | 8.508 | 0.024 | 8.539 | |
translate_data | 5.324 | 0.052 | 5.380 | |
visualize_report | 8.136 | 0.064 | 8.204 | |